diff --git a/.github/actions/build-app-runner/action.yml b/.github/actions/build-app-runner/action.yml
index 48c11978..66519602 100644
--- a/.github/actions/build-app-runner/action.yml
+++ b/.github/actions/build-app-runner/action.yml
@@ -8,7 +8,7 @@ inputs:
   source-path:
     description: 'Path to app runner source code'
     required: false
-    default: 'app_runner'
+    default: 'bfabric_app_runner'
 outputs:
   artifact-name:
     description: 'Name of the uploaded artifact'
diff --git a/.github/workflows/build_app_runner.yml b/.github/workflows/build_app_runner.yml
index b843c06c..feea5ebe 100644
--- a/.github/workflows/build_app_runner.yml
+++ b/.github/workflows/build_app_runner.yml
@@ -41,7 +41,7 @@ jobs:
         id: build
         with:
           output-path: build-output
-          source-path: app_runner
+          source-path: bfabric_app_runner
       - name: Comment PR
         if: github.event_name == 'pull_request'
         uses: actions/github-script@v7
diff --git a/.github/workflows/complete_release.yml b/.github/workflows/complete_release.yml
deleted file mode 100644
index 0a0b30e3..00000000
--- a/.github/workflows/complete_release.yml
+++ /dev/null
@@ -1,51 +0,0 @@
-name: Complete Release
-on:
-  push:
-    branches: [stable]
-  # TODO remove after testing
-  workflow_dispatch:
-jobs:
-  create_tag:
-    name: Create Tag
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - name: Set up Python
-        uses: actions/setup-python@v5
-        with:
-          python-version: 3.12
-      - name: Git Config
-        run: |
-          git config --global user.name "bfabricPy Bot"
-          git config --global user.email "bfabricpy-bot-noreply@fgcz.ethz.ch"
-      - name: Create tag (with Python)
-        run: |
-          set -euxo pipefail
-          # Find the version
-          VERSION=$(python3 -c "import tomllib; from pathlib import Path; print(tomllib.loads(Path('pyproject.toml').read_text())['project']['version'], end='')")
-          # Check if tag exists
-          if git rev-parse $VERSION >/dev/null 2>&1; then
-              echo "Tag $VERSION already exists"
-              exit 1
-          fi
-          # Create tag
-          git tag -a $VERSION -m "Release $VERSION"
-          # Push tag
-          git push origin $VERSION
-  publish_documentation:
-    name: Publish Docs
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: 3.12
-      - name: Install nox
-        run: pip install nox uv
-      - name: Publish documentation
-        run: |
-          set -euxo pipefail
-          git fetch --unshallow origin gh-pages
-          git checkout gh-pages && git pull && git checkout -
-          nox -s docs
-          nox -s publish_docs
diff --git a/.github/workflows/publish_release.yml b/.github/workflows/publish_release.yml
index 655dc762..b6654e36 100644
--- a/.github/workflows/publish_release.yml
+++ b/.github/workflows/publish_release.yml
@@ -4,7 +4,7 @@ on:
     branches:
       - release_bfabric
       - release_bfabric_scripts
-      - release_app_runner
+      - release_bfabric_app_runner
   workflow_dispatch:
     inputs:
       package:
@@ -13,7 +13,7 @@ on:
         options:
           - bfabric
           - bfabric_scripts
-          - app_runner
+          - bfabric_app_runner
         default: bfabric
       environment:
         description: 'Target PyPI'
@@ -28,6 +28,7 @@ jobs:
     runs-on: ubuntu-latest
     permissions:
       id-token: write
+      contents: write # permission to create tags
     steps:
       - uses: actions/checkout@v4
       # Step: Determine the package that is being built
@@ -62,6 +63,13 @@ jobs:
           python-version: '3.11'
       - name: Install hatch
         run: pip install hatch
+      - name: Get package version
+        id: get-version
+        run: |
+          cd ${{ env.PACKAGE }}
+          VERSION=$(hatch version)
+          echo "VERSION=$VERSION" >> $GITHUB_ENV
+          echo "Package version: $VERSION"
       - name: Build package
         run: |
           cd ${{ env.PACKAGE }}
@@ -71,11 +79,20 @@ jobs:
         with:
           repository-url: ${{ env.PYPI_REPOSITORY_URL }}
           packages-dir: ${{ env.PACKAGE }}/dist
+      - name: Create and push tag
+        run: |
+          git config --global user.email "github-actions[bot]@users.noreply.github.com"
+          git config --global user.name "github-actions[bot]"
+          TAG_NAME="${{ env.PACKAGE }}/${{ env.VERSION }}"
+          git tag -a "$TAG_NAME" -m "Release ${{ env.PACKAGE }} version ${{ env.VERSION }}"
+          git push origin "$TAG_NAME"
       - name: Debug package info
         run: |
           echo "Built and published package: ${{ env.PACKAGE }}"
+          echo "Created tag: ${{ env.PACKAGE }}/${{ env.VERSION }}"
           if [ "${{ env.PYPI_REPOSITORY_URL }}" == "https://pypi.org/legacy/" ]; then
             echo "Check it at: https://pypi.org/project/${{ env.PACKAGE }}/"
           else
             echo "Check it at: https://test.pypi.org/project/${{ env.PACKAGE }}/"
           fi
+        if: always()
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index e58c0afb..204b3ce1 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -3,7 +3,7 @@ ci:
   autofix_commit_msg: "style: pre-commit fixes"
 repos:
   - repo: https://github.com/psf/black
-    rev: "24.8.0"
+    rev: "25.1.0"
     hooks:
       - id: black
   - repo: https://github.com/adamchainz/blacken-docs
diff --git a/app_runner/docs/index.md b/app_runner/docs/index.md
deleted file mode 100644
index 3b48680c..00000000
--- a/app_runner/docs/index.md
+++ /dev/null
@@ -1,18 +0,0 @@
-## Install App Runner
-
-```bash
-uv tool install app_runner@git+https://github.com/fgcz/bfabricPy.git@main#egg=app_runner&subdirectory=app_runner
-```
-
-## Contents
-
-```{toctree}
-:glob:
-workunit_definition
-architecture/overview
-specs/input_specification
-specs/output_specification
-specs/app_specification
-changelog
-*
-```
diff --git a/bfabric/pyproject.toml b/bfabric/pyproject.toml
index 9757557f..7d346c25 100644
--- a/bfabric/pyproject.toml
+++ b/bfabric/pyproject.toml
@@ -5,7 +5,7 @@ build-backend = "hatchling.build"
 [project]
 name = "bfabric"
 description = "Python client for the B-Fabric API"
-version = "1.13.18"
+version = "1.13.19"
 license = { text = "GPL-3.0" }
 authors = [
     { name = "Christian Panse", email = "cp@fgcz.ethz.ch" },
@@ -53,7 +53,7 @@ Repository = "https://github.com/fgcz/bfabricPy"
 
 
 [tool.uv]
-reinstall-package = ["bfabric", "bfabric_scripts", "app_runner"]
+reinstall-package = ["bfabric", "bfabric_scripts", "bfabric_app_runner"]
 
 [tool.black]
 line-length = 120
diff --git a/bfabric/src/bfabric/bfabric.py b/bfabric/src/bfabric/bfabric.py
index c0d84dc1..1ec4974d 100644
--- a/bfabric/src/bfabric/bfabric.py
+++ b/bfabric/src/bfabric/bfabric.py
@@ -95,9 +95,7 @@ def from_config(
             If it is set to None, no authentication will be used.
         :param engine: Engine to use for the API. Default is SUDS.
         """
-        config, auth_config = get_system_auth(
-            config_env=config_env, config_path=config_path
-        )
+        config, auth_config = get_system_auth(config_env=config_env, config_path=config_path)
         auth_used: BfabricAuth | None = auth_config if auth == "config" else auth
         return cls(config, auth_used, engine=engine)
 
@@ -195,9 +193,7 @@ def read(
             response_items += results[page_offset:]
             page_offset = 0
 
-        result = ResultContainer(
-            response_items, total_pages_api=n_available_pages, errors=errors
-        )
+        result = ResultContainer(response_items, total_pages_api=n_available_pages, errors=errors)
         if check:
             result.assert_success()
         return result.get_first_n_results(max_results)
@@ -217,16 +213,12 @@ def save(
             appropriate to be used instead.
         :return a ResultContainer describing the saved object if successful
         """
-        results = self._engine.save(
-            endpoint=endpoint, obj=obj, auth=self.auth, method=method
-        )
+        results = self._engine.save(endpoint=endpoint, obj=obj, auth=self.auth, method=method)
         if check:
             results.assert_success()
         return results
 
-    def delete(
-        self, endpoint: str, id: int | list[int], check: bool = True
-    ) -> ResultContainer:
+    def delete(self, endpoint: str, id: int | list[int], check: bool = True) -> ResultContainer:
         """Deletes the object with the specified ID from the specified endpoint.
         :param endpoint: the endpoint to delete from, e.g. "sample"
         :param id: the ID of the object to delete
@@ -353,19 +345,11 @@ def get_system_auth(
     if not resolved_path.is_file():
         if config_path:
             # NOTE: If user explicitly specifies a path to a wrong config file, this has to be an exception
-            raise OSError(
-                f"Explicitly specified config file does not exist: {resolved_path}"
-            )
+            raise OSError(f"Explicitly specified config file does not exist: {resolved_path}")
         # TODO: Convert to log
-        print(
-            f"Warning: could not find the config file in the default location: {resolved_path}"
-        )
+        print(f"Warning: could not find the config file in the default location: {resolved_path}")
         config = BfabricClientConfig(base_url=base_url)
-        auth = (
-            None
-            if login is None or password is None
-            else BfabricAuth(login=login, password=password)
-        )
+        auth = None if login is None or password is None else BfabricAuth(login=login, password=password)
 
     # Load config from file, override some of the fields with the provided ones
     else:
diff --git a/bfabric/src/bfabric/bfabric2.py b/bfabric/src/bfabric/bfabric2.py
index 82dde5e2..ac138da5 100755
--- a/bfabric/src/bfabric/bfabric2.py
+++ b/bfabric/src/bfabric/bfabric2.py
@@ -1,7 +1,5 @@
 #!/usr/bin/env python3
 import warnings
 
-warnings.warn(
-    "bfabric.bfabric2 module is deprecated, use bfabric instead", DeprecationWarning
-)
+warnings.warn("bfabric.bfabric2 module is deprecated, use bfabric instead", DeprecationWarning)
 # TODO deprecated - import from bfabric instead
diff --git a/bfabric/src/bfabric/bfabric_config.py b/bfabric/src/bfabric/bfabric_config.py
index ee484101..cf4ca7e9 100644
--- a/bfabric/src/bfabric/bfabric_config.py
+++ b/bfabric/src/bfabric/bfabric_config.py
@@ -31,8 +31,6 @@ def read_config(
         - If not, finally, the parser will select the default_config specified in [GENERAL] of the .bfabricpy.yml file
     """
     logger.debug(f"Reading configuration from: {config_path}")
-    config_file = ConfigFile.model_validate(
-        yaml.safe_load(Path(config_path).read_text())
-    )
+    config_file = ConfigFile.model_validate(yaml.safe_load(Path(config_path).read_text()))
     env_config = config_file.get_selected_config(explicit_config_env=config_env)
     return env_config.config, env_config.auth
diff --git a/bfabric/src/bfabric/cli_formatting.py b/bfabric/src/bfabric/cli_formatting.py
index 78c287b8..d9ef6be1 100644
--- a/bfabric/src/bfabric/cli_formatting.py
+++ b/bfabric/src/bfabric/cli_formatting.py
@@ -22,12 +22,10 @@ def setup_script_logging(debug: bool = False) -> None:
     if os.environ.get(setup_flag_key, "0") == "1":
         return
     logger.remove()
-    packages = ["bfabric", "bfabric_scripts", "app_runner", "__main__"]
+    packages = ["bfabric", "bfabric_scripts", "bfabric_app_runner", "__main__"]
     if not (debug or os.environ.get("BFABRICPY_DEBUG")):
         for package in packages:
-            logger.add(
-                sys.stderr, filter=package, level="INFO", format="{level} {message}"
-            )
+            logger.add(sys.stderr, filter=package, level="INFO", format="{level} {message}")
     else:
         for package in packages:
             logger.add(sys.stderr, filter=package, level="DEBUG")
diff --git a/bfabric/src/bfabric/config/bfabric_client_config.py b/bfabric/src/bfabric/config/bfabric_client_config.py
index 7d0819ba..e7bfe72b 100644
--- a/bfabric/src/bfabric/config/bfabric_client_config.py
+++ b/bfabric/src/bfabric/config/bfabric_client_config.py
@@ -27,9 +27,7 @@ class BfabricClientConfig(BaseModel):
 
     def __init__(self, **kwargs: Any) -> None:
         # TODO remove this custom constructor (note that this is currently used in some places when "None" is passed)
-        super().__init__(
-            **{key: value for key, value in kwargs.items() if value is not None}
-        )
+        super().__init__(**{key: value for key, value in kwargs.items() if value is not None})
 
     def copy_with(
         self,
@@ -39,9 +37,7 @@ def copy_with(
         """Returns a copy of the configuration with new values applied, if they are not None."""
         return BfabricClientConfig(
             base_url=base_url if base_url is not None else self.base_url,
-            application_ids=(
-                application_ids if application_ids is not None else self.application_ids
-            ),
+            application_ids=(application_ids if application_ids is not None else self.application_ids),
             job_notification_emails=self.job_notification_emails,
         )
 
diff --git a/bfabric/src/bfabric/config/config_file.py b/bfabric/src/bfabric/config/config_file.py
index 4cb6faa8..b7a1485c 100644
--- a/bfabric/src/bfabric/config/config_file.py
+++ b/bfabric/src/bfabric/config/config_file.py
@@ -25,11 +25,7 @@ def gather_config(cls, values: dict[str, Any]) -> dict[str, Any]:
         """Gathers all configs into the config field."""
         if not isinstance(values, dict):
             return values
-        values["config"] = {
-            key: value
-            for key, value in values.items()
-            if key not in ["login", "password"]
-        }
+        values["config"] = {key: value for key, value in values.items() if key not in ["login", "password"]}
         return values
 
     @model_validator(mode="before")
@@ -78,21 +74,13 @@ def get_selected_config_env(self, explicit_config_env: str | None) -> str:
         if explicit_config_env:
             return explicit_config_env
         elif "BFABRICPY_CONFIG_ENV" in os.environ:
-            logger.debug(
-                f"found BFABRICPY_CONFIG_ENV = {os.environ['BFABRICPY_CONFIG_ENV']}"
-            )
+            logger.debug(f"found BFABRICPY_CONFIG_ENV = {os.environ['BFABRICPY_CONFIG_ENV']}")
             return os.environ["BFABRICPY_CONFIG_ENV"]
         else:
-            logger.debug(
-                f"BFABRICPY_CONFIG_ENV not found, using default environment {self.general.default_config}"
-            )
+            logger.debug(f"BFABRICPY_CONFIG_ENV not found, using default environment {self.general.default_config}")
             return self.general.default_config
 
-    def get_selected_config(
-        self, explicit_config_env: str | None = None
-    ) -> EnvironmentConfig:
+    def get_selected_config(self, explicit_config_env: str | None = None) -> EnvironmentConfig:
         """Returns the selected configuration, by checking the hierarchy of config_env definitions.
         See selected_config_env for details."""
-        return self.environments[
-            self.get_selected_config_env(explicit_config_env=explicit_config_env)
-        ]
+        return self.environments[self.get_selected_config_env(explicit_config_env=explicit_config_env)]
diff --git a/bfabric/src/bfabric/engine/engine_suds.py b/bfabric/src/bfabric/engine/engine_suds.py
index 5888298c..592d7c6f 100644
--- a/bfabric/src/bfabric/engine/engine_suds.py
+++ b/bfabric/src/bfabric/engine/engine_suds.py
@@ -57,9 +57,7 @@ def read(
         response = service.read(full_query)
         return self._convert_results(response=response, endpoint=endpoint)
 
-    def save(
-        self, endpoint: str, obj: dict, auth: BfabricAuth, method: str = "save"
-    ) -> ResultContainer:
+    def save(self, endpoint: str, obj: dict, auth: BfabricAuth, method: str = "save") -> ResultContainer:
         """Saves the provided object to the specified endpoint.
         :param endpoint: the endpoint to save to, e.g. "sample"
         :param obj: the object to save
@@ -72,14 +70,10 @@ def save(
         try:
             response = getattr(service, method)(query)
         except MethodNotFound as e:
-            raise BfabricRequestError(
-                f"SUDS failed to find save method for the {endpoint} endpoint."
-            ) from e
+            raise BfabricRequestError(f"SUDS failed to find save method for the {endpoint} endpoint.") from e
         return self._convert_results(response=response, endpoint=endpoint)
 
-    def delete(
-        self, endpoint: str, id: int | list[int], auth: BfabricAuth
-    ) -> ResultContainer:
+    def delete(self, endpoint: str, id: int | list[int], auth: BfabricAuth) -> ResultContainer:
         """Deletes the object with the specified ID from the specified endpoint.
         :param endpoint: the endpoint to delete from, e.g. "sample"
         :param id: the ID of the object to delete
@@ -99,9 +93,7 @@ def _get_suds_service(self, endpoint: str) -> ServiceProxy:
         """Returns a SUDS service for the given endpoint. Reuses existing instances when possible."""
         if endpoint not in self._cl:
             try:
-                self._cl[endpoint] = Client(
-                    f"{self._base_url}/{endpoint}?wsdl", cache=None
-                )
+                self._cl[endpoint] = Client(f"{self._base_url}/{endpoint}?wsdl", cache=None)
             except suds.transport.TransportError as error:
                 if error.httpcode == 404:
                     msg = f"Non-existent endpoint {repr(endpoint)} or the configured B-Fabric instance was not found."
@@ -127,6 +119,4 @@ def _convert_results(self, response: Any, endpoint: str) -> ResultContainer:
                 sort_keys=True,
             )
             results += [result_parsed]
-        return ResultContainer(
-            results=results, total_pages_api=n_available_pages, errors=errors
-        )
+        return ResultContainer(results=results, total_pages_api=n_available_pages, errors=errors)
diff --git a/bfabric/src/bfabric/engine/engine_zeep.py b/bfabric/src/bfabric/engine/engine_zeep.py
index 32aa8b60..75f883ef 100644
--- a/bfabric/src/bfabric/engine/engine_zeep.py
+++ b/bfabric/src/bfabric/engine/engine_zeep.py
@@ -65,15 +65,11 @@ def read(
         )
 
         client = self._get_client(endpoint)
-        with client.settings(
-            strict=False, xml_huge_tree=True, xsd_ignore_sequence_order=True
-        ):
+        with client.settings(strict=False, xml_huge_tree=True, xsd_ignore_sequence_order=True):
             response = client.service.read(full_query)
         return self._convert_results(response=response, endpoint=endpoint)
 
-    def save(
-        self, endpoint: str, obj: dict, auth: BfabricAuth, method: str = "save"
-    ) -> ResultContainer:
+    def save(self, endpoint: str, obj: dict, auth: BfabricAuth, method: str = "save") -> ResultContainer:
         """Saves the provided object to the specified endpoint.
         :param endpoint: the endpoint to save to, e.g. "sample"
         :param obj: the object to save
@@ -97,15 +93,11 @@ def save(
                 response = getattr(client.service, method)(full_query)
         except AttributeError as e:
             if e.args[0] == "Service has no operation 'save'":
-                raise BfabricRequestError(
-                    f"ZEEP failed to find save method for the {endpoint} endpoint."
-                ) from e
+                raise BfabricRequestError(f"ZEEP failed to find save method for the {endpoint} endpoint.") from e
             raise e
         return self._convert_results(response=response, endpoint=endpoint)
 
-    def delete(
-        self, endpoint: str, id: int | list[int], auth: BfabricAuth
-    ) -> ResultContainer:
+    def delete(self, endpoint: str, id: int | list[int], auth: BfabricAuth) -> ResultContainer:
         """Deletes the object with the specified ID from the specified endpoint.
         :param endpoint: the endpoint to delete from, e.g. "sample"
         :param id: the ID of the object to delete
@@ -151,9 +143,7 @@ def _convert_results(self, response: Any, endpoint: str) -> ResultContainer:
                 sort_keys=True,
             )
             results += [results_parsed]
-        return ResultContainer(
-            results=results, total_pages_api=n_available_pages, errors=errors
-        )
+        return ResultContainer(results=results, total_pages_api=n_available_pages, errors=errors)
 
 
 # TODO: The reason why Zeep requires to explicitly skip certain values remains unclear
@@ -161,9 +151,7 @@ def _convert_results(self, response: Any, endpoint: str) -> ResultContainer:
 #      formatting they appear to zeep as compulsory. The current solution is envisioned by developers of Zeep, but
 #      it is a hack, and should ideally be handled internally by Zeep.
 #    If developers of Zeep ever resume its maintenance, it would make sense to revisit
-def _zeep_query_append_skipped(
-    query: dict, skipped_keys: list, inplace: bool = False, overwrite: bool = False
-) -> dict:
+def _zeep_query_append_skipped(query: dict, skipped_keys: list, inplace: bool = False, overwrite: bool = False) -> dict:
     """
     This function is used to fix a buggy behaviour of Zeep/BFabric. Specifically, Zeep does not return correct
     query results if some of the optional parameters are not mentioned in the query.
diff --git a/bfabric/src/bfabric/engine/response_format_suds.py b/bfabric/src/bfabric/engine/response_format_suds.py
index 20a1f579..eda2988b 100644
--- a/bfabric/src/bfabric/engine/response_format_suds.py
+++ b/bfabric/src/bfabric/engine/response_format_suds.py
@@ -37,9 +37,7 @@ def suds_asdict_recursive(d: Any, convert_types: bool = False) -> dict[str, Valu
             items: list[Value] = []
             for item in v:
                 if hasattr(item, "__keylist__"):
-                    items.append(
-                        suds_asdict_recursive(item, convert_types=convert_types)
-                    )
+                    items.append(suds_asdict_recursive(item, convert_types=convert_types))
                 else:
                     items.append(convert_suds_type(item) if convert_types else item)
             out[k] = items
diff --git a/bfabric/src/bfabric/entities/core/entity.py b/bfabric/src/bfabric/entities/core/entity.py
index b5bd2242..78ac0806 100644
--- a/bfabric/src/bfabric/entities/core/entity.py
+++ b/bfabric/src/bfabric/entities/core/entity.py
@@ -76,9 +76,7 @@ def find_all(cls, ids: list[int], client: Bfabric) -> dict[int, Self]:
         return cls.__ensure_results_order(ids_requested, results_cached, results_fresh)
 
     @classmethod
-    def find_by(
-        cls, obj: dict[str, Any], client: Bfabric, max_results: int | None = 100
-    ) -> dict[int, Self]:
+    def find_by(cls, obj: dict[str, Any], client: Bfabric, max_results: int | None = 100) -> dict[int, Self]:
         """Returns a dictionary of entities that match the given query."""
         result = client.read(cls.ENDPOINT, obj=obj, max_results=max_results)
         return {x["id"]: cls(x, client=client) for x in result}
@@ -113,9 +111,7 @@ def __check_ids_list(cls, ids: list[int]) -> list[int]:
         there are duplicates."""
         ids_requested = [int(id) for id in ids]
         if len(ids_requested) != len(set(ids_requested)):
-            duplicates = [
-                item for item in set(ids_requested) if ids_requested.count(item) > 1
-            ]
+            duplicates = [item for item in set(ids_requested) if ids_requested.count(item) > 1]
             raise ValueError(f"Duplicate IDs are not allowed, duplicates: {duplicates}")
         return ids_requested
 
@@ -143,11 +139,7 @@ def __ensure_results_order(
     ) -> dict[int, Self]:
         """Ensures the results are in the same order as requested and prints a warning if some results are missing."""
         results = {**results_cached, **results_fresh}
-        results = {
-            entity_id: results[entity_id]
-            for entity_id in ids_requested
-            if entity_id in results
-        }
+        results = {entity_id: results[entity_id] for entity_id in ids_requested if entity_id in results}
         if len(results) != len(ids_requested):
             logger.warning(f"Only found {len(results)} out of {len(ids_requested)}.")
         return results
diff --git a/bfabric/src/bfabric/entities/core/has_container_mixin.py b/bfabric/src/bfabric/entities/core/has_container_mixin.py
index 108c23bc..4f54081b 100644
--- a/bfabric/src/bfabric/entities/core/has_container_mixin.py
+++ b/bfabric/src/bfabric/entities/core/has_container_mixin.py
@@ -29,21 +29,13 @@ def container(self: EntityProtocol) -> Project | Order:
 
         result: Project | Order | None
         if self.data_dict["container"]["classname"] == Project.ENDPOINT:
-            result = Project.find(
-                id=self.data_dict["container"]["id"], client=self._client
-            )
+            result = Project.find(id=self.data_dict["container"]["id"], client=self._client)
         elif self.data_dict["container"]["classname"] == Order.ENDPOINT:
-            result = Order.find(
-                id=self.data_dict["container"]["id"], client=self._client
-            )
+            result = Order.find(id=self.data_dict["container"]["id"], client=self._client)
         else:
-            raise ValueError(
-                f"Unknown container classname: {self.data_dict['container']['classname']}"
-            )
+            raise ValueError(f"Unknown container classname: {self.data_dict['container']['classname']}")
 
         if result is None:
-            raise ValueError(
-                f"Could not find container with ID {self.data_dict['container']['id']}"
-            )
+            raise ValueError(f"Could not find container with ID {self.data_dict['container']['id']}")
 
         return result
diff --git a/bfabric/src/bfabric/entities/core/has_many.py b/bfabric/src/bfabric/entities/core/has_many.py
index 51748dc4..04af9947 100644
--- a/bfabric/src/bfabric/entities/core/has_many.py
+++ b/bfabric/src/bfabric/entities/core/has_many.py
@@ -48,9 +48,7 @@ def __get__(self, obj: T | None, objtype: type[T] | None = None) -> _HasManyProx
     def _get_ids(self, obj: T) -> list[int]:
         if self._bfabric_field is not None:
             if self._ids_property is not None:
-                raise ValueError(
-                    "Exactly one of bfabric_field and ids_property must be set, but both are set"
-                )
+                raise ValueError("Exactly one of bfabric_field and ids_property must be set, but both are set")
             if self._optional and self._bfabric_field not in obj.data_dict:
                 return []
             return [x["id"] for x in obj.data_dict[self._bfabric_field]]
@@ -59,9 +57,7 @@ def _get_ids(self, obj: T) -> list[int]:
                 return []
             return getattr(obj, self._ids_property)
         else:
-            raise ValueError(
-                "Exactly one of bfabric_field and ids_property must be set, but neither is set"
-            )
+            raise ValueError("Exactly one of bfabric_field and ids_property must be set, but neither is set")
 
 
 class _HasManyProxy(Generic[E]):
diff --git a/bfabric/src/bfabric/entities/core/has_one.py b/bfabric/src/bfabric/entities/core/has_one.py
index dbbeb7d0..2fdc13ee 100644
--- a/bfabric/src/bfabric/entities/core/has_one.py
+++ b/bfabric/src/bfabric/entities/core/has_one.py
@@ -13,9 +13,7 @@
 
 
 class HasOne(Relationship[E]):
-    def __init__(
-        self, entity: str, *, bfabric_field: str, optional: bool = False
-    ) -> None:
+    def __init__(self, entity: str, *, bfabric_field: str, optional: bool = False) -> None:
         super().__init__(entity)
         self._bfabric_field = bfabric_field
         self._optional = optional
diff --git a/bfabric/src/bfabric/entities/core/relationship.py b/bfabric/src/bfabric/entities/core/relationship.py
index e7662f9c..f543e63c 100644
--- a/bfabric/src/bfabric/entities/core/relationship.py
+++ b/bfabric/src/bfabric/entities/core/relationship.py
@@ -17,6 +17,6 @@ def __init__(self, entity: str) -> None:
 
     @cached_property
     def _entity_type(self) -> type[E]:
-        return importlib.import_module(
-            f"bfabric.entities.{self._entity_type_name.lower()}"
-        ).__dict__[self._entity_type_name]
+        return importlib.import_module(f"bfabric.entities.{self._entity_type_name.lower()}").__dict__[
+            self._entity_type_name
+        ]
diff --git a/bfabric/src/bfabric/entities/dataset.py b/bfabric/src/bfabric/entities/dataset.py
index a563a47f..4ec1ef10 100644
--- a/bfabric/src/bfabric/entities/dataset.py
+++ b/bfabric/src/bfabric/entities/dataset.py
@@ -19,9 +19,7 @@ class Dataset(Entity):
 
     ENDPOINT: str = "dataset"
 
-    def __init__(
-        self, data_dict: dict[str, Any], client: Bfabric | None = None
-    ) -> None:
+    def __init__(self, data_dict: dict[str, Any], client: Bfabric | None = None) -> None:
         super().__init__(data_dict=data_dict, client=client)
 
     def to_polars(self) -> DataFrame:
diff --git a/bfabric/src/bfabric/entities/executable.py b/bfabric/src/bfabric/entities/executable.py
index f9e263ce..728acebb 100644
--- a/bfabric/src/bfabric/entities/executable.py
+++ b/bfabric/src/bfabric/entities/executable.py
@@ -16,9 +16,7 @@ class Executable(Entity):
 
     storage = HasOne(entity="Storage", bfabric_field="storage", optional=True)
 
-    def __init__(
-        self, data_dict: dict[str, Any], client: Bfabric | None = None
-    ) -> None:
+    def __init__(self, data_dict: dict[str, Any], client: Bfabric | None = None) -> None:
         super().__init__(data_dict=data_dict, client=client)
 
     @cached_property
diff --git a/bfabric/src/bfabric/entities/externaljob.py b/bfabric/src/bfabric/entities/externaljob.py
index 8779b93b..146d9dae 100644
--- a/bfabric/src/bfabric/entities/externaljob.py
+++ b/bfabric/src/bfabric/entities/externaljob.py
@@ -18,9 +18,7 @@ class ExternalJob(Entity):
     def __init__(self, data_dict: dict[str, Any], client: Bfabric | None) -> None:
         super().__init__(data_dict=data_dict, client=client)
 
-    executable: HasOne[Executable] = HasOne(
-        entity="Executable", bfabric_field="executable"
-    )
+    executable: HasOne[Executable] = HasOne(entity="Executable", bfabric_field="executable")
 
     @cached_property
     def workunit(self) -> Workunit | None:
@@ -30,8 +28,6 @@ def workunit(self) -> Workunit | None:
             if self._client is None:
                 raise ValueError("Client must be set to resolve Workunit")
 
-            return Workunit.find(
-                id=self.data_dict["cliententityid"], client=self._client
-            )
+            return Workunit.find(id=self.data_dict["cliententityid"], client=self._client)
         else:
             return None
diff --git a/bfabric/src/bfabric/entities/multiplexkit.py b/bfabric/src/bfabric/entities/multiplexkit.py
index a18847f6..6f78de8f 100644
--- a/bfabric/src/bfabric/entities/multiplexkit.py
+++ b/bfabric/src/bfabric/entities/multiplexkit.py
@@ -18,9 +18,7 @@ class MultiplexKit(Entity):
     def __init__(self, data_dict: dict[str, Any], client: Bfabric | None) -> None:
         super().__init__(data_dict=data_dict, client=client)
 
-    multiplex_ids: HasMany[MultiplexId] = HasMany(
-        "MultiplexId", bfabric_field="multiplexid"
-    )
+    multiplex_ids: HasMany[MultiplexId] = HasMany("MultiplexId", bfabric_field="multiplexid")
 
     @cached_property
     def ids(self) -> pl.DataFrame:
diff --git a/bfabric/src/bfabric/entities/resource.py b/bfabric/src/bfabric/entities/resource.py
index 74cb6032..144356d8 100644
--- a/bfabric/src/bfabric/entities/resource.py
+++ b/bfabric/src/bfabric/entities/resource.py
@@ -15,9 +15,7 @@
 class Resource(Entity):
     ENDPOINT = "resource"
 
-    def __init__(
-        self, data_dict: dict[str, Any], client: Bfabric | None = None
-    ) -> None:
+    def __init__(self, data_dict: dict[str, Any], client: Bfabric | None = None) -> None:
         super().__init__(data_dict=data_dict, client=client)
 
     storage: HasOne[Storage] = HasOne("Storage", bfabric_field="storage")
diff --git a/bfabric/src/bfabric/entities/sample.py b/bfabric/src/bfabric/entities/sample.py
index 3b7abdbb..40bf80aa 100644
--- a/bfabric/src/bfabric/entities/sample.py
+++ b/bfabric/src/bfabric/entities/sample.py
@@ -12,7 +12,5 @@
 class Sample(Entity, HasContainerMixin):
     ENDPOINT = "sample"
 
-    def __init__(
-        self, data_dict: dict[str, Any], client: Bfabric | None = None
-    ) -> None:
+    def __init__(self, data_dict: dict[str, Any], client: Bfabric | None = None) -> None:
         super().__init__(data_dict=data_dict, client=client)
diff --git a/bfabric/src/bfabric/entities/storage.py b/bfabric/src/bfabric/entities/storage.py
index daf967cb..4d73c5a8 100644
--- a/bfabric/src/bfabric/entities/storage.py
+++ b/bfabric/src/bfabric/entities/storage.py
@@ -22,8 +22,4 @@ def __init__(self, data_dict: dict[str, Any], client: Bfabric | None) -> None:
     def scp_prefix(self) -> str | None:
         """SCP prefix with storage base path included."""
         protocol = self.data_dict["protocol"]
-        return (
-            f"{self.data_dict['host']}:{self.data_dict['basepath']}"
-            if protocol == "scp"
-            else None
-        )
+        return f"{self.data_dict['host']}:{self.data_dict['basepath']}" if protocol == "scp" else None
diff --git a/bfabric/src/bfabric/entities/workunit.py b/bfabric/src/bfabric/entities/workunit.py
index 717ef1cc..5214c19b 100644
--- a/bfabric/src/bfabric/entities/workunit.py
+++ b/bfabric/src/bfabric/entities/workunit.py
@@ -27,29 +27,15 @@ class Workunit(Entity, HasContainerMixin):
 
     ENDPOINT = "workunit"
 
-    def __init__(
-        self, data_dict: dict[str, Any], client: Bfabric | None = None
-    ) -> None:
+    def __init__(self, data_dict: dict[str, Any], client: Bfabric | None = None) -> None:
         super().__init__(data_dict=data_dict, client=client)
 
-    application: HasOne[Application] = HasOne(
-        entity="Application", bfabric_field="application"
-    )
-    parameters: HasMany[Parameter] = HasMany(
-        entity="Parameter", bfabric_field="parameter", optional=True
-    )
-    resources: HasMany[Resource] = HasMany(
-        entity="Resource", bfabric_field="resource", optional=True
-    )
-    input_resources: HasMany[Resource] = HasMany(
-        entity="Resource", bfabric_field="inputresource", optional=True
-    )
-    input_dataset: HasOne[Dataset] = HasOne(
-        entity="Dataset", bfabric_field="inputdataset", optional=True
-    )
-    external_jobs: HasMany[ExternalJob] = HasMany(
-        entity="ExternalJob", bfabric_field="externaljob", optional=True
-    )
+    application: HasOne[Application] = HasOne(entity="Application", bfabric_field="application")
+    parameters: HasMany[Parameter] = HasMany(entity="Parameter", bfabric_field="parameter", optional=True)
+    resources: HasMany[Resource] = HasMany(entity="Resource", bfabric_field="resource", optional=True)
+    input_resources: HasMany[Resource] = HasMany(entity="Resource", bfabric_field="inputresource", optional=True)
+    input_dataset: HasOne[Dataset] = HasOne(entity="Dataset", bfabric_field="inputdataset", optional=True)
+    external_jobs: HasMany[ExternalJob] = HasMany(entity="ExternalJob", bfabric_field="externaljob", optional=True)
 
     @cached_property
     def parameter_values(self) -> dict[str, Any]:
@@ -59,13 +45,9 @@ def parameter_values(self) -> dict[str, Any]:
     def store_output_folder(self) -> Path:
         """Relative path in the storage for the workunit output."""
         if self.application is None:
-            raise ValueError(
-                "Cannot determine the storage path without an application."
-            )
+            raise ValueError("Cannot determine the storage path without an application.")
         if self.application.storage is None:
-            raise ValueError(
-                "Cannot determine the storage path without an application storage configuration."
-            )
+            raise ValueError("Cannot determine the storage path without an application storage configuration.")
         date = dateutil.parser.parse(self.data_dict["created"])
         return Path(
             f"{self.application.storage['projectfolderprefix']}{self.container.id}",
diff --git a/bfabric/src/bfabric/errors.py b/bfabric/src/bfabric/errors.py
index 501d1c58..a8d2a634 100644
--- a/bfabric/src/bfabric/errors.py
+++ b/bfabric/src/bfabric/errors.py
@@ -30,10 +30,6 @@ def get_response_errors(response: Any, endpoint: str) -> list[BfabricRequestErro
     if getattr(response, "errorreport", None):
         return [BfabricRequestError(response.errorreport)]
     elif endpoint in response:
-        return [
-            BfabricRequestError(r.errorreport)
-            for r in response[endpoint]
-            if getattr(r, "errorreport", None)
-        ]
+        return [BfabricRequestError(r.errorreport) for r in response[endpoint] if getattr(r, "errorreport", None)]
     else:
         return []
diff --git a/bfabric/src/bfabric/examples/compare_zeep_suds_pagination.py b/bfabric/src/bfabric/examples/compare_zeep_suds_pagination.py
index cf9b7baa..04f621d8 100644
--- a/bfabric/src/bfabric/examples/compare_zeep_suds_pagination.py
+++ b/bfabric/src/bfabric/examples/compare_zeep_suds_pagination.py
@@ -37,9 +37,7 @@ def _calc_query(config, auth, engine, endpoint):
         return_id_only=False,
         includedeletableupdateable=True,
     )
-    response_dict = response_class.to_list_dict(
-        drop_empty=True, have_sort_responses=True
-    )
+    response_dict = response_class.to_list_dict(drop_empty=True, have_sort_responses=True)
     return list_dict_to_df(response_dict)
 
 
@@ -58,9 +56,7 @@ def _set_partition_test(a, b) -> bool:
     return (len(unique1) == 0) and (len(unique2) == 0)
 
 
-def dataframe_pagination_test(
-    config, auth, endpoint, use_cached: bool = False, store_cached: bool = True
-):
+def dataframe_pagination_test(config, auth, endpoint, use_cached: bool = False, store_cached: bool = True):
     pwd_zeep = "tmp_zeep_" + endpoint + ".csv"
     pwd_suds = "tmp_suds_" + endpoint + ".csv"
 
@@ -101,7 +97,5 @@ def dataframe_pagination_test(
 
 config, auth = get_system_auth(config_env="TEST")
 
-result = dataframe_pagination_test(
-    config, auth, "user", use_cached=False, store_cached=True
-)
+result = dataframe_pagination_test(config, auth, "user", use_cached=False, store_cached=True)
 report_test_result(result, "pagination")
diff --git a/bfabric/src/bfabric/examples/compare_zeep_suds_query.py b/bfabric/src/bfabric/examples/compare_zeep_suds_query.py
index 26b902d8..04e00f75 100644
--- a/bfabric/src/bfabric/examples/compare_zeep_suds_query.py
+++ b/bfabric/src/bfabric/examples/compare_zeep_suds_query.py
@@ -48,9 +48,7 @@ def read_suds(wsdl, fullQuery, raw=True):
         return suds_asdict_recursive(ret, convert_types=True)
 
 
-def full_query(
-    auth: BfabricAuth, query: dict, includedeletableupdateable: bool = False
-) -> dict:
+def full_query(auth: BfabricAuth, query: dict, includedeletableupdateable: bool = False) -> dict:
     thisQuery = deepcopy(query)
     thisQuery["includedeletableupdateable"] = includedeletableupdateable
 
@@ -142,15 +140,11 @@ def recursive_comparison(generic_container1, generic_container2, prefix: list) -
                 print(prefix, "Not in 2: ", k, "=", generic_container1[k])
                 matched = False
             else:
-                matched_recursive = recursive_comparison(
-                    generic_container1[k], generic_container2[k], prefix + [k]
-                )
+                matched_recursive = recursive_comparison(generic_container1[k], generic_container2[k], prefix + [k])
                 matched = matched and matched_recursive
     elif isinstance(generic_container1, list):
         if len(generic_container1) != len(generic_container2):
-            print(
-                prefix, "length", len(generic_container1), "!=", len(generic_container2)
-            )
+            print(prefix, "length", len(generic_container1), "!=", len(generic_container2))
             matched = False
         else:
             for i, (el1, el2) in enumerate(zip(generic_container1, generic_container2)):
diff --git a/bfabric/src/bfabric/examples/zeep_debug.py b/bfabric/src/bfabric/examples/zeep_debug.py
index 56dda1b4..15c7e287 100644
--- a/bfabric/src/bfabric/examples/zeep_debug.py
+++ b/bfabric/src/bfabric/examples/zeep_debug.py
@@ -18,9 +18,7 @@
 """
 
 
-def full_query(
-    auth: BfabricAuth, query: dict, includedeletableupdateable: bool = False
-) -> dict:
+def full_query(auth: BfabricAuth, query: dict, includedeletableupdateable: bool = False) -> dict:
     thisQuery = deepcopy(query)
     thisQuery["includedeletableupdateable"] = includedeletableupdateable
 
diff --git a/bfabric/src/bfabric/experimental/entity_lookup_cache.py b/bfabric/src/bfabric/experimental/entity_lookup_cache.py
index ffbeb41c..24c13c17 100644
--- a/bfabric/src/bfabric/experimental/entity_lookup_cache.py
+++ b/bfabric/src/bfabric/experimental/entity_lookup_cache.py
@@ -51,9 +51,7 @@ class EntityLookupCache:
     __class_instance = None
 
     def __init__(self, max_size: int = 0) -> None:
-        self._caches: dict[type[Entity], Cache[Entity | None]] = defaultdict(
-            lambda: Cache(max_size=max_size)
-        )
+        self._caches: dict[type[Entity], Cache[Entity | None]] = defaultdict(lambda: Cache(max_size=max_size))
 
     def contains(self, entity_type: type[Entity], entity_id: int) -> bool:
         """Returns whether the cache contains an entity with the given type and ID."""
@@ -68,24 +66,14 @@ def get(self, entity_type: type[E], entity_id: int) -> E | None:
             logger.debug(f"Cache miss for entity {entity_type} with ID {entity_id}")
             return None
 
-    def get_all(
-        self, entity_type: type[Entity], entity_ids: list[int]
-    ) -> dict[int, Entity]:
+    def get_all(self, entity_type: type[Entity], entity_ids: list[int]) -> dict[int, Entity]:
         """Returns a dictionary of entities with the given type and IDs,
         containing only the entities that exist in the cache.
         """
-        results = {
-            entity_id: self.get(entity_type, entity_id) for entity_id in entity_ids
-        }
-        return {
-            entity_id: result
-            for entity_id, result in results.items()
-            if result is not None
-        }
-
-    def put(
-        self, entity_type: type[Entity], entity_id: int, entity: Entity | None
-    ) -> None:
+        results = {entity_id: self.get(entity_type, entity_id) for entity_id in entity_ids}
+        return {entity_id: result for entity_id, result in results.items() if result is not None}
+
+    def put(self, entity_type: type[Entity], entity_id: int, entity: Entity | None) -> None:
         """Puts an entity with the given type and ID into the cache."""
         logger.debug(f"Caching entity {entity_type} with ID {entity_id}")
         self._caches[entity_type].put(entity_id, entity)
diff --git a/bfabric/src/bfabric/experimental/multi_query.py b/bfabric/src/bfabric/experimental/multi_query.py
index 29934017..22ad5253 100644
--- a/bfabric/src/bfabric/experimental/multi_query.py
+++ b/bfabric/src/bfabric/experimental/multi_query.py
@@ -42,9 +42,7 @@ def read_multi(
         """
         # TODO add `check` parameter
         response_tot = ResultContainer([], total_pages_api=0)
-        obj_extended = deepcopy(
-            obj
-        )  # Make a copy of the query, not to make edits to the argument
+        obj_extended = deepcopy(obj)  # Make a copy of the query, not to make edits to the argument
 
         # Iterate over request chunks that fit into a single API page
         for page_vals in page_iter(multi_query_vals):
@@ -59,9 +57,7 @@ def read_multi(
             #   exceptions to this? -> yes, when not reading by id but for instance matching a pattern, one might not
             #   be aware that they might accidentally pull the whole db, so it's better to have max_results here as well
             #   but it is not completely trivial to implement
-            response_this = self._client.read(
-                endpoint, obj_extended, max_results=None, return_id_only=return_id_only
-            )
+            response_this = self._client.read(endpoint, obj_extended, max_results=None, return_id_only=return_id_only)
             response_tot.extend(response_this, reset_total_pages_api=True)
 
         return response_tot
@@ -96,9 +92,7 @@ def delete_multi(self, endpoint: str, id_list: list[int]) -> ResultContainer:
 
         return response_tot
 
-    def exists_multi(
-        self, endpoint: str, key: str, value: list[int | str] | int | str
-    ) -> bool | list[bool]:
+    def exists_multi(self, endpoint: str, key: str, value: list[int | str] | int | str) -> bool | list[bool]:
         """
         :param endpoint:  endpoint
         :param key:       A key for the query (e.g. id or name)
@@ -108,9 +102,7 @@ def exists_multi(
         """
         is_scalar = isinstance(value, (int, str))
         if is_scalar:
-            return self._client.exists(
-                endpoint=endpoint, key=key, value=value, check=True
-            )
+            return self._client.exists(endpoint=endpoint, key=key, value=value, check=True)
         elif not isinstance(value, list):
             raise ValueError("Unexpected data type", type(value))
 
diff --git a/bfabric/src/bfabric/experimental/upload_dataset.py b/bfabric/src/bfabric/experimental/upload_dataset.py
index e5598c81..f10c451f 100644
--- a/bfabric/src/bfabric/experimental/upload_dataset.py
+++ b/bfabric/src/bfabric/experimental/upload_dataset.py
@@ -35,10 +35,7 @@ def polars_to_bfabric_dataset(
     ]
     items = [
         {
-            "field": [
-                {"attributeposition": i_field + 1, "value": value}
-                for i_field, value in enumerate(row)
-            ],
+            "field": [{"attributeposition": i_field + 1, "value": value} for i_field, value in enumerate(row)],
             "position": i_row + 1,
         }
         for i_row, row in enumerate(data.iter_rows())
@@ -57,9 +54,7 @@ def bfabric_save_csv2dataset(
     invalid_characters: str,
 ) -> None:
     """Creates a dataset in B-Fabric from a csv file."""
-    data = pl.read_csv(
-        csv_file, separator=sep, has_header=has_header, infer_schema_length=None
-    )
+    data = pl.read_csv(csv_file, separator=sep, has_header=has_header, infer_schema_length=None)
     check_for_invalid_characters(data=data, invalid_characters=invalid_characters)
     obj = polars_to_bfabric_dataset(data)
     obj["name"] = dataset_name
@@ -75,9 +70,7 @@ def check_for_invalid_characters(data: pl.DataFrame, invalid_characters: str) ->
     """Raises a RuntimeError if any cell in the DataFrame contains an invalid character."""
     if not invalid_characters:
         return
-    invalid_columns_df = data.select(
-        pl.col(pl.String).str.contains_any(list(invalid_characters)).any()
-    )
+    invalid_columns_df = data.select(pl.col(pl.String).str.contains_any(list(invalid_characters)).any())
     if invalid_columns_df.is_empty():
         return
     invalid_columns = (
diff --git a/bfabric/src/bfabric/experimental/workunit_definition.py b/bfabric/src/bfabric/experimental/workunit_definition.py
index d2a67628..369150ce 100644
--- a/bfabric/src/bfabric/experimental/workunit_definition.py
+++ b/bfabric/src/bfabric/experimental/workunit_definition.py
@@ -78,9 +78,7 @@ class WorkunitDefinition(BaseModel):
     registration: WorkunitRegistrationDefinition | None
 
     @classmethod
-    def from_ref(
-        cls, workunit: Path | int, client: Bfabric, cache_file: Path | None = None
-    ) -> WorkunitDefinition:
+    def from_ref(cls, workunit: Path | int, client: Bfabric, cache_file: Path | None = None) -> WorkunitDefinition:
         """Loads the workunit definition from the provided reference, which can be a path to a YAML file,
         or a workunit ID.
 
diff --git a/bfabric/src/bfabric/results/response_format_dict.py b/bfabric/src/bfabric/results/response_format_dict.py
index b4587c80..dc5daeab 100644
--- a/bfabric/src/bfabric/results/response_format_dict.py
+++ b/bfabric/src/bfabric/results/response_format_dict.py
@@ -24,9 +24,7 @@ def _recursive_drop_empty(response_elem: list | dict) -> None:
         for el in response_elem:
             _recursive_drop_empty(el)
     elif isinstance(response_elem, dict):
-        keys_to_delete = (
-            []
-        )  # NOTE: Avoid deleting keys inside iterator, may break iterator
+        keys_to_delete = []  # NOTE: Avoid deleting keys inside iterator, may break iterator
         for k, v in response_elem.items():
             if (v is None) or (isinstance(v, list) and len(v) == 0):
                 keys_to_delete += [k]
@@ -37,9 +35,7 @@ def _recursive_drop_empty(response_elem: list | dict) -> None:
 
 
 @overload
-def drop_empty_elements(
-    response: list[dict[str, Any]], inplace: bool
-) -> list[dict[str, Any]]: ...
+def drop_empty_elements(response: list[dict[str, Any]], inplace: bool) -> list[dict[str, Any]]: ...
 
 
 @overload
@@ -72,9 +68,7 @@ def _recursive_map_keys(response_elem: list | dict, keymap: dict) -> None:
         for el in response_elem:
             _recursive_map_keys(el, keymap)
     elif isinstance(response_elem, dict):
-        keys_to_delete = (
-            []
-        )  # NOTE: Avoid deleting keys inside iterator, may break iterator
+        keys_to_delete = []  # NOTE: Avoid deleting keys inside iterator, may break iterator
         for k, v in response_elem.items():
             _recursive_map_keys(v, keymap)
             if k in keymap:
@@ -85,9 +79,7 @@ def _recursive_map_keys(response_elem: list | dict, keymap: dict) -> None:
             del response_elem[k]  # Delete old key
 
 
-def map_element_keys(
-    response: list | dict, keymap: dict, inplace: bool = True
-) -> list | dict:
+def map_element_keys(response: list | dict, keymap: dict, inplace: bool = True) -> list | dict:
     """
     Iterates over all nested lists, dictionaries and basic values. Whenever a dictionary key is found for which
        the mapping is requested, that the key is renamed to the corresponding mapped one
@@ -121,9 +113,7 @@ def _recursive_sort_dicts_by_key(response_elem: list | dict) -> None:
             _recursive_sort_dicts_by_key(v)
 
 
-def sort_dicts_by_key(
-    response: list | dict, inplace: bool = True
-) -> list | dict | None:
+def sort_dicts_by_key(response: list | dict, inplace: bool = True) -> list | dict | None:
     """
     Iterates over all nested lists, dictionaries and basic values. Whenever a nested dictionary is found, it is sorted
        by key by converting into OrderedDict and back
@@ -137,9 +127,7 @@ def sort_dicts_by_key(
     return response_filtered
 
 
-def clean_result(
-    result: dict, drop_underscores_suds: bool = True, sort_keys: bool = False
-) -> dict:
+def clean_result(result: dict, drop_underscores_suds: bool = True, sort_keys: bool = False) -> dict:
     """
     :param result: the response dictionary to clean
     :param drop_underscores_suds: if True, the keys of the dictionaries in the response will have leading
diff --git a/bfabric/src/bfabric/results/result_container.py b/bfabric/src/bfabric/results/result_container.py
index 11696202..e7edf66e 100644
--- a/bfabric/src/bfabric/results/result_container.py
+++ b/bfabric/src/bfabric/results/result_container.py
@@ -79,9 +79,7 @@ def errors(self) -> list[BfabricRequestError]:
         """List of errors that occurred during the query. An empty list indicates success."""
         return self._errors
 
-    def extend(
-        self, other: ResultContainer, reset_total_pages_api: bool = False
-    ) -> None:
+    def extend(self, other: ResultContainer, reset_total_pages_api: bool = False) -> None:
         """Merges the results of `other` into this container.
         :param other: The container whose elements to append to the end of this container
         :param reset_total_pages_api: If True, the total_pages_api attribute will be reset to None
diff --git a/bfabric/src/bfabric/utils/paginator.py b/bfabric/src/bfabric/utils/paginator.py
index 9d575e63..d4004982 100644
--- a/bfabric/src/bfabric/utils/paginator.py
+++ b/bfabric/src/bfabric/utils/paginator.py
@@ -10,9 +10,7 @@
 BFABRIC_QUERY_LIMIT = 100
 
 
-def page_iter(
-    objs: list, page_size: int = BFABRIC_QUERY_LIMIT
-) -> Generator[list, None, None]:
+def page_iter(objs: list, page_size: int = BFABRIC_QUERY_LIMIT) -> Generator[list, None, None]:
     """
     :param objs:       A list of objects to provide to bfabric as part of a query
     :param page_size:  Number of objects per page
@@ -48,12 +46,7 @@ def compute_requested_pages(
 
     # Determine the page indices to request
     idx_max_return = math.ceil((n_item_return_max + n_item_offset) / n_item_per_page)
-    idx_arr = [
-        idx + index_start
-        for idx in range(
-            n_item_offset // n_item_per_page, min(n_page_total, idx_max_return)
-        )
-    ]
+    idx_arr = [idx + index_start for idx in range(n_item_offset // n_item_per_page, min(n_page_total, idx_max_return))]
 
     # Determine the initial offset on the first page
     initial_offset = min(n_item_offset, n_item_return_max) % n_item_per_page
diff --git a/bfabric/src/bfabric/utils/polars_utils.py b/bfabric/src/bfabric/utils/polars_utils.py
index 8bbe2e6c..ac384242 100644
--- a/bfabric/src/bfabric/utils/polars_utils.py
+++ b/bfabric/src/bfabric/utils/polars_utils.py
@@ -9,11 +9,6 @@ def flatten_relations(df: pl.DataFrame) -> pl.DataFrame:
     All non-struct fields will be kept as is.
     If there are conflicts this raises an error.
     """
-    struct_cols = [
-        col for col, dtype in zip(df.columns, df.dtypes) if isinstance(dtype, pl.Struct)
-    ]
+    struct_cols = [col for col, dtype in zip(df.columns, df.dtypes) if isinstance(dtype, pl.Struct)]
     flat_cols = [col for col in df.columns if col not in struct_cols]
-    return df.select(
-        flat_cols
-        + [pl.col(col).struct.unnest().name.prefix(f"{col}_") for col in struct_cols]
-    )
+    return df.select(flat_cols + [pl.col(col).struct.unnest().name.prefix(f"{col}_") for col in struct_cols])
diff --git a/bfabric/src/bfabric/wrapper_creator/bfabric_external_job.py b/bfabric/src/bfabric/wrapper_creator/bfabric_external_job.py
index da25abab..424dd6f0 100644
--- a/bfabric/src/bfabric/wrapper_creator/bfabric_external_job.py
+++ b/bfabric/src/bfabric/wrapper_creator/bfabric_external_job.py
@@ -27,9 +27,7 @@ def __init__(self, login=None, password=None, externaljobid=None):
 
     def logger(self, msg):
         if self.externaljobid:
-            super().save_object(
-                "externaljob", {"id": self.externaljobid, "logthis": str(msg)}
-            )
+            super().save_object("externaljob", {"id": self.externaljobid, "logthis": str(msg)})
         else:
             print(str(msg))
 
@@ -40,12 +38,8 @@ def save_object(self, endpoint, obj, debug=None):
         return res
 
     def get_workunitid_of_externaljob(self):
-        print(
-            f"DEBUG get_workunitid_of_externaljob self.externaljobid={self.externaljobid}"
-        )
-        res = self.read_object(endpoint="externaljob", obj={"id": self.externaljobid})[
-            0
-        ]
+        print(f"DEBUG get_workunitid_of_externaljob self.externaljobid={self.externaljobid}")
+        res = self.read_object(endpoint="externaljob", obj={"id": self.externaljobid})[0]
         print(res)
         print("DEBUG END")
         workunit_id = None
@@ -62,13 +56,9 @@ def get_application_name(self):
             raise ValueError("no workunit available for the given externaljobid.")
         workunit = self.read_object(endpoint="workunit", obj={"id": workunitid})[0]
         if workunit is None:
-            raise ValueError(
-                "ERROR: no workunit available for the given externaljobid."
-            )
+            raise ValueError("ERROR: no workunit available for the given externaljobid.")
         assert isinstance(workunit._id, int)
-        application = self.read_object(
-            "application", obj={"id": workunit.application._id}
-        )[0]
+        application = self.read_object("application", obj={"id": workunit.application._id})[0]
         return application.name.replace(" ", "_")
 
     def get_executable_of_externaljobid(self):
@@ -85,9 +75,7 @@ def get_executable_of_externaljobid(self):
             return None
 
         executables = list()
-        for executable in self.read_object(
-            endpoint="executable", obj={"workunitid": workunitid}
-        ):
+        for executable in self.read_object(endpoint="executable", obj={"workunitid": workunitid}):
             if hasattr(executable, "base64"):
                 executables.append(executable)
 
diff --git a/bfabric/src/bfabric/wrapper_creator/bfabric_submitter.py b/bfabric/src/bfabric/wrapper_creator/bfabric_submitter.py
index d6b1079f..b510c178 100644
--- a/bfabric/src/bfabric/wrapper_creator/bfabric_submitter.py
+++ b/bfabric/src/bfabric/wrapper_creator/bfabric_submitter.py
@@ -75,9 +75,7 @@ def __init__(
         self.application = self.workunit.application
 
         default_config = self.slurm_dict.get(self.application["name"], {})
-        self.partition = self.parameters.get(
-            "partition", default_config.get("partition")
-        )
+        self.partition = self.parameters.get("partition", default_config.get("partition"))
         self.nodelist = self.parameters.get("nodelist", default_config.get("nodelist"))
         self.memory = self.parameters.get("memory", default_config.get("memory"))
 
@@ -93,9 +91,7 @@ def submit_slurm(self, script: str = "/tmp/runme.bash") -> None:
         res_slurm_batch = slurm.sbatch(script=script)
         logger.debug(f"{res_slurm_batch}")
 
-    def compose_bash_script(
-        self, configuration=None, configuration_parser=lambda x: yaml.safe_load(x)
-    ) -> str:
+    def compose_bash_script(self, configuration=None, configuration_parser=lambda x: yaml.safe_load(x)) -> str:
         """
         composes the bash script which is executed by the submitter (sun grid engine).
         as an argument it takes a configuration file, e.g., yaml, xml, json, or whatsoever, and a parser function.
@@ -242,9 +238,7 @@ def submitter_yaml(self) -> None:
 
         return None
         """
-        executables = Executable.find_by(
-            {"workunitid": self.workunit.id}, client=self._client
-        ).values()
+        executables = Executable.find_by({"workunitid": self.workunit.id}, client=self._client).values()
         for executable in executables:
             if not executable["base64"]:
                 continue
diff --git a/bfabric/src/bfabric/wrapper_creator/bfabric_wrapper_creator.py b/bfabric/src/bfabric/wrapper_creator/bfabric_wrapper_creator.py
index 78d0b17e..8b7753a5 100644
--- a/bfabric/src/bfabric/wrapper_creator/bfabric_wrapper_creator.py
+++ b/bfabric/src/bfabric/wrapper_creator/bfabric_wrapper_creator.py
@@ -64,21 +64,15 @@ def create_output_resource(self) -> Resource:
 
         # Determine the correct path
         output_folder = self._workunit.store_output_folder
-        output_filename = (
-            f"{resource_id}.{self._application.data_dict['outputfileformat']}"
-        )
+        output_filename = f"{resource_id}.{self._application.data_dict['outputfileformat']}"
         relative_path = str(output_folder / output_filename)
 
         # Save the path
         logger.info("Saving correct path")
-        result = self._client.save(
-            "resource", {"id": resource_id, "relativepath": relative_path}
-        )
+        result = self._client.save("resource", {"id": resource_id, "relativepath": relative_path})
         return Resource(result[0])
 
-    def create_log_resource(
-        self, variant: Literal["out", "err"], output_resource: Resource
-    ) -> Resource:
+    def create_log_resource(self, variant: Literal["out", "err"], output_resource: Resource) -> Resource:
         logger.info("Creating log resource")
         result = self._client.save(
             "resource",
@@ -95,9 +89,7 @@ def get_application_section(self, output_resource: Resource) -> dict[str, Any]:
         logger.info("Creating application section")
         output_url = f"bfabric@{self._application.storage.data_dict['host']}:{self._application.storage.data_dict['basepath']}{output_resource.data_dict['relativepath']}"
         inputs = defaultdict(list)
-        for resource in Resource.find_all(
-            self.workunit_definition.execution.resources, client=self._client
-        ).values():
+        for resource in Resource.find_all(self.workunit_definition.execution.resources, client=self._client).values():
             inputs[resource.workunit.application["name"]].append(
                 f"bfabric@{resource.storage.scp_prefix}{resource.data_dict['relativepath']}"
             )
@@ -133,13 +125,9 @@ def get_job_configuration_section(
             }
 
         inputs = defaultdict(list)
-        for resource in Resource.find_all(
-            self.workunit_definition.execution.resources, client=self._client
-        ).values():
+        for resource in Resource.find_all(self.workunit_definition.execution.resources, client=self._client).values():
             web_url = Resource({"id": resource.id}, client=self._client).web_url
-            inputs[resource.workunit.application["name"]].append(
-                {"resource_id": resource.id, "resource_url": web_url}
-            )
+            inputs[resource.workunit.application["name"]].append({"resource_id": resource.id, "resource_url": web_url})
 
         return {
             "executable": str(self._workunit.application.executable["program"]),
@@ -163,35 +151,20 @@ def get_job_configuration_section(
 
     @cached_property
     def _order(self) -> Order | None:
-        return (
-            self._workunit.container
-            if isinstance(self._workunit.container, Order)
-            else None
-        )
+        return self._workunit.container if isinstance(self._workunit.container, Order) else None
 
     @cached_property
     def _project(self) -> Project | None:
-        return (
-            self._workunit.container
-            if isinstance(self._workunit.container, Project)
-            else self._order.project
-        )
+        return self._workunit.container if isinstance(self._workunit.container, Project) else self._order.project
 
     @cached_property
     def _fasta_sequence(self) -> str:
         if self._order is not None and "fastasequence" in self._order.data_dict:
-            return "\n".join(
-                [
-                    x.strip()
-                    for x in str(self._order.data_dict["fastasequence"]).split("\r")
-                ]
-            )
+            return "\n".join([x.strip() for x in str(self._order.data_dict["fastasequence"]).split("\r")])
         else:
             return ""
 
-    def write_results(
-        self, config_serialized: str
-    ) -> tuple[dict[str, Any], dict[str, Any]]:
+    def write_results(self, config_serialized: str) -> tuple[dict[str, Any], dict[str, Any]]:
         logger.info("Saving executable")
         yaml_workunit_executable = self._client.save(
             "executable",
@@ -221,26 +194,18 @@ def write_results(
 
         logger.info(yaml_workunit_externaljob)
         logger.info("Setting external job status to 'done'")
-        self._client.save(
-            "externaljob", {"id": self._external_job_id, "status": "done"}
-        )
+        self._client.save("externaljob", {"id": self._external_job_id, "status": "done"})
 
         return yaml_workunit_executable, yaml_workunit_externaljob
 
     def create(self) -> tuple[dict[str, Any], dict[str, Any], dict[str, Any]]:
         """Creates the YAML file external job and resources, and registers everything in B-Fabric."""
         output_resource = self.create_output_resource()
-        stdout_resource = self.create_log_resource(
-            variant="out", output_resource=output_resource
-        )
-        stderr_resource = self.create_log_resource(
-            variant="err", output_resource=output_resource
-        )
+        stdout_resource = self.create_log_resource(variant="out", output_resource=output_resource)
+        stderr_resource = self.create_log_resource(variant="err", output_resource=output_resource)
 
         config_dict = {
-            "application": self.get_application_section(
-                output_resource=output_resource
-            ),
+            "application": self.get_application_section(output_resource=output_resource),
             "job_configuration": self.get_job_configuration_section(
                 output_resource=output_resource,
                 stdout_resource=stdout_resource,
@@ -248,7 +213,5 @@ def create(self) -> tuple[dict[str, Any], dict[str, Any], dict[str, Any]]:
             ),
         }
         config_serialized = yaml.safe_dump(config_dict)
-        yaml_workunit_executable, yaml_workunit_externaljob = self.write_results(
-            config_serialized=config_serialized
-        )
+        yaml_workunit_executable, yaml_workunit_externaljob = self.write_results(config_serialized=config_serialized)
         return config_dict, yaml_workunit_executable, yaml_workunit_externaljob
diff --git a/bfabric/src/bfabric/wrapper_creator/gridengine.py b/bfabric/src/bfabric/wrapper_creator/gridengine.py
index bc10ddf9..22dd6e92 100755
--- a/bfabric/src/bfabric/wrapper_creator/gridengine.py
+++ b/bfabric/src/bfabric/wrapper_creator/gridengine.py
@@ -85,9 +85,7 @@ def qsub(self, script, arguments=""):
             return
 
         try:
-            qsub_process = subprocess.Popen(
-                qsub_cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=False
-            )
+            qsub_process = subprocess.Popen(qsub_cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=False)
             stdout, stderr = qsub_process.communicate()
 
             return stdout
diff --git a/app_runner/.gitignore b/bfabric_app_runner/.gitignore
similarity index 100%
rename from app_runner/.gitignore
rename to bfabric_app_runner/.gitignore
diff --git a/app_runner/README.md b/bfabric_app_runner/README.md
similarity index 100%
rename from app_runner/README.md
rename to bfabric_app_runner/README.md
diff --git a/app_runner/deploy/build.sh b/bfabric_app_runner/deploy/build.sh
similarity index 100%
rename from app_runner/deploy/build.sh
rename to bfabric_app_runner/deploy/build.sh
diff --git a/app_runner/deploy/build_steps.sh b/bfabric_app_runner/deploy/build_steps.sh
similarity index 84%
rename from app_runner/deploy/build_steps.sh
rename to bfabric_app_runner/deploy/build_steps.sh
index 56b7dd04..150fa39d 100644
--- a/app_runner/deploy/build_steps.sh
+++ b/bfabric_app_runner/deploy/build_steps.sh
@@ -7,5 +7,5 @@ python -m venv /work/venv
 source /work/venv/bin/activate
 uv pip install .
 uv pip install pyinstaller
-pyinstaller -y --onedir --name "${TARGET_NAME}" --distpath "${TARGET_DIR}" src/app_runner/cli/__main__.py
+pyinstaller -y --onedir --name "${TARGET_NAME}" --distpath "${TARGET_DIR}" src/bfabric_app_runner/cli/__main__.py
 deactivate
diff --git a/app_runner/deploy/builder/Dockerfile b/bfabric_app_runner/deploy/builder/Dockerfile
similarity index 100%
rename from app_runner/deploy/builder/Dockerfile
rename to bfabric_app_runner/deploy/builder/Dockerfile
diff --git a/app_runner/docs/Makefile b/bfabric_app_runner/docs/Makefile
similarity index 100%
rename from app_runner/docs/Makefile
rename to bfabric_app_runner/docs/Makefile
diff --git a/app_runner/docs/_design_notes/_app_definition.md b/bfabric_app_runner/docs/_design_notes/_app_definition.md
similarity index 100%
rename from app_runner/docs/_design_notes/_app_definition.md
rename to bfabric_app_runner/docs/_design_notes/_app_definition.md
diff --git a/app_runner/docs/_design_notes/_scheduling.md b/bfabric_app_runner/docs/_design_notes/_scheduling.md
similarity index 100%
rename from app_runner/docs/_design_notes/_scheduling.md
rename to bfabric_app_runner/docs/_design_notes/_scheduling.md
diff --git a/app_runner/docs/architecture/overview.md b/bfabric_app_runner/docs/architecture/overview.md
similarity index 100%
rename from app_runner/docs/architecture/overview.md
rename to bfabric_app_runner/docs/architecture/overview.md
diff --git a/app_runner/docs/architecture/uml/app_model.plantuml b/bfabric_app_runner/docs/architecture/uml/app_model.plantuml
similarity index 100%
rename from app_runner/docs/architecture/uml/app_model.plantuml
rename to bfabric_app_runner/docs/architecture/uml/app_model.plantuml
diff --git a/app_runner/docs/architecture/uml/app_runner_activity.plantuml b/bfabric_app_runner/docs/architecture/uml/app_runner_activity.plantuml
similarity index 100%
rename from app_runner/docs/architecture/uml/app_runner_activity.plantuml
rename to bfabric_app_runner/docs/architecture/uml/app_runner_activity.plantuml
diff --git a/app_runner/docs/changelog.md b/bfabric_app_runner/docs/changelog.md
similarity index 87%
rename from app_runner/docs/changelog.md
rename to bfabric_app_runner/docs/changelog.md
index 2be94f9c..34e265c0 100644
--- a/app_runner/docs/changelog.md
+++ b/bfabric_app_runner/docs/changelog.md
@@ -4,9 +4,31 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/).
 
 ## \[Unreleased\]
 
+## \[0.0.15\] - 2025-02-06
+
+### Added
+
+- New input type `file` which replaces `file_scp` and preserves timestamps whenever possible and allows to create
+    symlinks instead of copying the file, as needed.
+- `BfabricOrderFastaSpec.required` which allows specifying whether the order fasta is required or not
+
+### Changed
+
+- Better error when app version is not found.
+
+### Fixed
+
+- Config: Log messages are shown by default again.
+
+## \[0.0.14\] - 2025-01-30
+
+### Fixed
+
+- Correctly consume bfabricPy from PyPI.
+
 ## \[0.0.13\] - 2025-01-28
 
-## Added
+### Added
 
 - `WorkunitDefinition.registration.workunit_name` field.
 
diff --git a/app_runner/docs/conf.py b/bfabric_app_runner/docs/conf.py
similarity index 100%
rename from app_runner/docs/conf.py
rename to bfabric_app_runner/docs/conf.py
diff --git a/bfabric_app_runner/docs/index.md b/bfabric_app_runner/docs/index.md
new file mode 100644
index 00000000..6820f22f
--- /dev/null
+++ b/bfabric_app_runner/docs/index.md
@@ -0,0 +1,26 @@
+## Install App Runner
+
+To install the most recent released version:
+
+```bash
+uv tool install bfabric_app_runner
+```
+
+To install a development version:
+
+```bash
+uv tool install bfabric_app_runner@git+https://github.com/fgcz/bfabricPy.git@main#egg=bfabric_app_runner&subdirectory=bfabric_app_runner
+```
+
+## Contents
+
+```{toctree}
+:glob:
+workunit_definition
+architecture/overview
+specs/input_specification
+specs/output_specification
+specs/app_specification
+changelog
+*
+```
diff --git a/app_runner/docs/make.bat b/bfabric_app_runner/docs/make.bat
similarity index 100%
rename from app_runner/docs/make.bat
rename to bfabric_app_runner/docs/make.bat
diff --git a/app_runner/docs/plantuml_wrapper.sh b/bfabric_app_runner/docs/plantuml_wrapper.sh
similarity index 100%
rename from app_runner/docs/plantuml_wrapper.sh
rename to bfabric_app_runner/docs/plantuml_wrapper.sh
diff --git a/app_runner/docs/specs/app_specification.md b/bfabric_app_runner/docs/specs/app_specification.md
similarity index 100%
rename from app_runner/docs/specs/app_specification.md
rename to bfabric_app_runner/docs/specs/app_specification.md
diff --git a/app_runner/docs/specs/input_specification.md b/bfabric_app_runner/docs/specs/input_specification.md
similarity index 100%
rename from app_runner/docs/specs/input_specification.md
rename to bfabric_app_runner/docs/specs/input_specification.md
diff --git a/app_runner/docs/specs/output_specification.md b/bfabric_app_runner/docs/specs/output_specification.md
similarity index 100%
rename from app_runner/docs/specs/output_specification.md
rename to bfabric_app_runner/docs/specs/output_specification.md
diff --git a/app_runner/docs/workunit_definition.md b/bfabric_app_runner/docs/workunit_definition.md
similarity index 100%
rename from app_runner/docs/workunit_definition.md
rename to bfabric_app_runner/docs/workunit_definition.md
diff --git a/app_runner/pyproject.toml b/bfabric_app_runner/pyproject.toml
similarity index 77%
rename from app_runner/pyproject.toml
rename to bfabric_app_runner/pyproject.toml
index 85ee4fbe..a084ce5d 100644
--- a/app_runner/pyproject.toml
+++ b/bfabric_app_runner/pyproject.toml
@@ -3,23 +3,23 @@ requires = ["hatchling"]
 build-backend = "hatchling.build"
 
 [project]
-name = "app_runner"
+name = "bfabric_app_runner"
 description = "Application runner for B-Fabric apps"
-version = "0.0.13"
+version = "0.0.15"
 license = { text = "GPL-3.0" }
 authors = [
     {name = "Leonardo Schwarz", email = "leonardo.schwarz@fgcz.ethz.ch"},
 ]
 requires-python = ">=3.12"
 dependencies = [
-    "bfabric",
+    "bfabric>=1.13.19",
     "pydantic",
     "glom",
     "mako",
 ]
 
 [project.scripts]
-"bfabric-app-runner"="app_runner.cli.__main__:app"
+"bfabric-app-runner"="bfabric_app_runner.cli.__main__:app"
 
 [project.optional-dependencies]
 doc = [
@@ -39,14 +39,16 @@ dev = [
 test = ["pytest", "pytest-mock", "logot"]
 
 [tool.uv]
-reinstall-package = ["bfabric", "bfabric_scripts", "app_runner"]
+reinstall-package = ["bfabric", "bfabric_scripts", "bfabric_app_runner"]
 
 [tool.black]
 line-length = 120
+target-version = ["py311"]
 
 [tool.ruff]
 line-length = 120
 indent-width = 4
+target-version = "py311"
 
 [tool.ruff.lint]
 select = ["ANN", "BLE", "D103", "E", "EXE", "F", "N", "PLW", "PTH", "SIM", "TCH", "UP", "W191"]
@@ -60,4 +62,4 @@ classmethod-decorators = [
 
 [tool.ruff.lint.per-file-ignores]
 # This is needed because of false positives in cyclopts code
-"**/app_runner/cli/**" = ["TCH001", "TCH002", "TCH003"]
+"**/bfabric_app_runner/cli/**" = ["TCH001", "TCH002", "TCH003"]
diff --git a/app_runner/src/app_runner/__init__.py b/bfabric_app_runner/src/bfabric_app_runner/__init__.py
similarity index 100%
rename from app_runner/src/app_runner/__init__.py
rename to bfabric_app_runner/src/bfabric_app_runner/__init__.py
diff --git a/app_runner/src/app_runner/app_runner/__init__.py b/bfabric_app_runner/src/bfabric_app_runner/app_runner/__init__.py
similarity index 100%
rename from app_runner/src/app_runner/app_runner/__init__.py
rename to bfabric_app_runner/src/bfabric_app_runner/app_runner/__init__.py
diff --git a/app_runner/src/app_runner/app_runner/resolve_app.py b/bfabric_app_runner/src/bfabric_app_runner/app_runner/resolve_app.py
similarity index 86%
rename from app_runner/src/app_runner/app_runner/resolve_app.py
rename to bfabric_app_runner/src/bfabric_app_runner/app_runner/resolve_app.py
index 1e389a7e..41ba3ae9 100644
--- a/app_runner/src/app_runner/app_runner/resolve_app.py
+++ b/bfabric_app_runner/src/bfabric_app_runner/app_runner/resolve_app.py
@@ -5,8 +5,8 @@
 import yaml
 from pydantic import ValidationError
 
-from app_runner.specs.app.app_spec import AppSpec
-from app_runner.specs.app.app_version import AppVersion
+from bfabric_app_runner.specs.app.app_spec import AppSpec
+from bfabric_app_runner.specs.app.app_version import AppVersion
 from bfabric.experimental.workunit_definition import WorkunitDefinition
 
 if TYPE_CHECKING:
@@ -22,6 +22,14 @@ def resolve_app(versions: AppSpec, workunit_definition: WorkunitDefinition) -> A
         raise ValueError("The workunit definition does not contain an application version.")
     app_version = workunit_definition.execution.raw_parameters["application_version"]
     # TODO graceful handling of invalid versions
+    if app_version in versions and versions[app_version] is not None:
+        return versions[app_version]
+    else:
+        msg = (
+            f"application_version '{app_version}' is not defined in the app spec,\n"
+            f" available versions: {sorted(versions.available_versions)}"
+        )
+        raise ValueError(msg)
     return versions[app_version]
 
 
diff --git a/app_runner/src/app_runner/app_runner/runner.py b/bfabric_app_runner/src/bfabric_app_runner/app_runner/runner.py
similarity index 94%
rename from app_runner/src/app_runner/app_runner/runner.py
rename to bfabric_app_runner/src/bfabric_app_runner/app_runner/runner.py
index f97554d6..e6c43cda 100644
--- a/app_runner/src/app_runner/app_runner/runner.py
+++ b/bfabric_app_runner/src/bfabric_app_runner/app_runner/runner.py
@@ -9,12 +9,12 @@
 from loguru import logger
 from pydantic import BaseModel
 
-from app_runner.input_preparation import prepare_folder
-from app_runner.output_registration import register_outputs
+from bfabric_app_runner.input_preparation import prepare_folder
+from bfabric_app_runner.output_registration import register_outputs
 from bfabric.experimental.workunit_definition import WorkunitDefinition
 
 if TYPE_CHECKING:
-    from app_runner.specs.app.app_version import AppVersion
+    from bfabric_app_runner.specs.app.app_version import AppVersion
     from bfabric import Bfabric
 
 
diff --git a/app_runner/src/app_runner/cli/__init__.py b/bfabric_app_runner/src/bfabric_app_runner/cli/__init__.py
similarity index 100%
rename from app_runner/src/app_runner/cli/__init__.py
rename to bfabric_app_runner/src/bfabric_app_runner/cli/__init__.py
diff --git a/app_runner/src/app_runner/cli/__main__.py b/bfabric_app_runner/src/bfabric_app_runner/cli/__main__.py
similarity index 54%
rename from app_runner/src/app_runner/cli/__main__.py
rename to bfabric_app_runner/src/bfabric_app_runner/cli/__main__.py
index b5fc0756..0545aa83 100644
--- a/app_runner/src/app_runner/cli/__main__.py
+++ b/bfabric_app_runner/src/bfabric_app_runner/cli/__main__.py
@@ -4,13 +4,13 @@
 
 import cyclopts
 
-from app_runner.cli.app import app_app
-from app_runner.cli.chunk import app_chunk
-from app_runner.cli.inputs import app_inputs
-from app_runner.cli.outputs import app_outputs
-from app_runner.cli.validate import app_validate
+from bfabric_app_runner.cli.app import app_app
+from bfabric_app_runner.cli.chunk import app_chunk
+from bfabric_app_runner.cli.inputs import app_inputs
+from bfabric_app_runner.cli.outputs import app_outputs
+from bfabric_app_runner.cli.validate import app_validate
 
-package_version = importlib.metadata.version("app_runner")
+package_version = importlib.metadata.version("bfabric_app_runner")
 
 app = cyclopts.App(
     help="Provides an entrypoint to app execution.\n\nFunctionality/API under active development!",
diff --git a/app_runner/src/app_runner/cli/app.py b/bfabric_app_runner/src/bfabric_app_runner/cli/app.py
similarity index 92%
rename from app_runner/src/app_runner/cli/app.py
rename to bfabric_app_runner/src/bfabric_app_runner/cli/app.py
index b131a97e..399fce09 100644
--- a/app_runner/src/app_runner/cli/app.py
+++ b/bfabric_app_runner/src/bfabric_app_runner/cli/app.py
@@ -4,8 +4,8 @@
 
 import cyclopts
 
-from app_runner.app_runner.resolve_app import load_workunit_information
-from app_runner.app_runner.runner import run_app, Runner
+from bfabric_app_runner.app_runner.resolve_app import load_workunit_information
+from bfabric_app_runner.app_runner.runner import run_app, Runner
 from bfabric import Bfabric
 from bfabric.cli_formatting import setup_script_logging
 from bfabric.experimental.entity_lookup_cache import EntityLookupCache
diff --git a/app_runner/src/app_runner/cli/chunk.py b/bfabric_app_runner/src/bfabric_app_runner/cli/chunk.py
similarity index 94%
rename from app_runner/src/app_runner/cli/chunk.py
rename to bfabric_app_runner/src/bfabric_app_runner/cli/chunk.py
index 49bd4c9f..26516f3d 100644
--- a/app_runner/src/app_runner/cli/chunk.py
+++ b/bfabric_app_runner/src/bfabric_app_runner/cli/chunk.py
@@ -4,9 +4,9 @@
 
 import cyclopts
 
-from app_runner.app_runner.resolve_app import load_workunit_information
-from app_runner.app_runner.runner import run_app, Runner
-from app_runner.output_registration import register_outputs
+from bfabric_app_runner.app_runner.resolve_app import load_workunit_information
+from bfabric_app_runner.app_runner.runner import run_app, Runner
+from bfabric_app_runner.output_registration import register_outputs
 from bfabric import Bfabric
 from bfabric.cli_formatting import setup_script_logging
 from bfabric.experimental.entity_lookup_cache import EntityLookupCache
diff --git a/app_runner/src/app_runner/cli/inputs.py b/bfabric_app_runner/src/bfabric_app_runner/cli/inputs.py
similarity index 93%
rename from app_runner/src/app_runner/cli/inputs.py
rename to bfabric_app_runner/src/bfabric_app_runner/cli/inputs.py
index 1dd79901..0253b036 100644
--- a/app_runner/src/app_runner/cli/inputs.py
+++ b/bfabric_app_runner/src/bfabric_app_runner/cli/inputs.py
@@ -4,14 +4,14 @@
 
 import cyclopts
 
-from app_runner.input_preparation import prepare_folder
-from app_runner.input_preparation.integrity import IntegrityState
-from app_runner.input_preparation.list_inputs import (
+from bfabric_app_runner.input_preparation import prepare_folder
+from bfabric_app_runner.input_preparation.integrity import IntegrityState
+from bfabric_app_runner.input_preparation.list_inputs import (
     list_input_states,
     print_input_states,
     FileState,
 )
-from app_runner.specs.inputs_spec import InputsSpec
+from bfabric_app_runner.specs.inputs_spec import InputsSpec
 from bfabric import Bfabric
 from bfabric.cli_formatting import setup_script_logging
 
diff --git a/app_runner/src/app_runner/cli/outputs.py b/bfabric_app_runner/src/bfabric_app_runner/cli/outputs.py
similarity index 93%
rename from app_runner/src/app_runner/cli/outputs.py
rename to bfabric_app_runner/src/bfabric_app_runner/cli/outputs.py
index d81f13b6..d12bc411 100644
--- a/app_runner/src/app_runner/cli/outputs.py
+++ b/bfabric_app_runner/src/bfabric_app_runner/cli/outputs.py
@@ -5,8 +5,8 @@
 import cyclopts
 from rich.pretty import pprint
 
-from app_runner.output_registration.register import register_all
-from app_runner.specs.outputs_spec import OutputsSpec, CopyResourceSpec, UpdateExisting
+from bfabric_app_runner.output_registration.register import register_all
+from bfabric_app_runner.specs.outputs_spec import OutputsSpec, CopyResourceSpec, UpdateExisting
 from bfabric import Bfabric
 from bfabric.cli_formatting import setup_script_logging
 from bfabric.experimental.workunit_definition import WorkunitDefinition
diff --git a/app_runner/src/app_runner/cli/validate.py b/bfabric_app_runner/src/bfabric_app_runner/cli/validate.py
similarity index 85%
rename from app_runner/src/app_runner/cli/validate.py
rename to bfabric_app_runner/src/bfabric_app_runner/cli/validate.py
index 3f855fda..76406a5d 100644
--- a/app_runner/src/app_runner/cli/validate.py
+++ b/bfabric_app_runner/src/bfabric_app_runner/cli/validate.py
@@ -6,9 +6,9 @@
 import yaml
 from rich.pretty import pprint
 
-from app_runner.specs.app.app_spec import AppSpecTemplate, AppSpec
-from app_runner.specs.inputs_spec import InputsSpec
-from app_runner.specs.outputs_spec import OutputsSpec
+from bfabric_app_runner.specs.app.app_spec import AppSpecTemplate, AppSpec
+from bfabric_app_runner.specs.inputs_spec import InputsSpec
+from bfabric_app_runner.specs.outputs_spec import OutputsSpec
 
 app_validate = cyclopts.App("validate", help="Validate yaml files.")
 
diff --git a/app_runner/src/app_runner/dispatch/__init__.py b/bfabric_app_runner/src/bfabric_app_runner/dispatch/__init__.py
similarity index 100%
rename from app_runner/src/app_runner/dispatch/__init__.py
rename to bfabric_app_runner/src/bfabric_app_runner/dispatch/__init__.py
diff --git a/app_runner/src/app_runner/dispatch/dispatch_individual_resources.py b/bfabric_app_runner/src/bfabric_app_runner/dispatch/dispatch_individual_resources.py
similarity index 96%
rename from app_runner/src/app_runner/dispatch/dispatch_individual_resources.py
rename to bfabric_app_runner/src/bfabric_app_runner/dispatch/dispatch_individual_resources.py
index 4e29f50c..ba219817 100644
--- a/app_runner/src/app_runner/dispatch/dispatch_individual_resources.py
+++ b/bfabric_app_runner/src/bfabric_app_runner/dispatch/dispatch_individual_resources.py
@@ -4,8 +4,8 @@
 
 from pydantic import BaseModel, ConfigDict, model_validator
 
-from app_runner.dispatch.generic import write_workunit_definition_file, write_chunks_file
-from app_runner.dispatch.resource_flow import get_resource_flow_input_resources
+from bfabric_app_runner.dispatch.generic import write_workunit_definition_file, write_chunks_file
+from bfabric_app_runner.dispatch.resource_flow import get_resource_flow_input_resources
 from bfabric.entities import Resource, Dataset
 
 if TYPE_CHECKING:
diff --git a/app_runner/src/app_runner/dispatch/dispatch_single_dataset_flow.py b/bfabric_app_runner/src/bfabric_app_runner/dispatch/dispatch_single_dataset_flow.py
similarity index 90%
rename from app_runner/src/app_runner/dispatch/dispatch_single_dataset_flow.py
rename to bfabric_app_runner/src/bfabric_app_runner/dispatch/dispatch_single_dataset_flow.py
index f1bd481a..016eb3ea 100644
--- a/app_runner/src/app_runner/dispatch/dispatch_single_dataset_flow.py
+++ b/bfabric_app_runner/src/bfabric_app_runner/dispatch/dispatch_single_dataset_flow.py
@@ -2,7 +2,7 @@
 
 from loguru import logger
 
-from app_runner.dispatch.generic import write_workunit_definition_file, write_chunks_file
+from bfabric_app_runner.dispatch.generic import write_workunit_definition_file, write_chunks_file
 from bfabric import Bfabric
 from bfabric.entities import Dataset
 from bfabric.experimental.workunit_definition import WorkunitDefinition
diff --git a/app_runner/src/app_runner/dispatch/dispatch_single_resource_flow.py b/bfabric_app_runner/src/bfabric_app_runner/dispatch/dispatch_single_resource_flow.py
similarity index 91%
rename from app_runner/src/app_runner/dispatch/dispatch_single_resource_flow.py
rename to bfabric_app_runner/src/bfabric_app_runner/dispatch/dispatch_single_resource_flow.py
index 308a2ff6..408856c8 100644
--- a/app_runner/src/app_runner/dispatch/dispatch_single_resource_flow.py
+++ b/bfabric_app_runner/src/bfabric_app_runner/dispatch/dispatch_single_resource_flow.py
@@ -5,11 +5,11 @@
 from pathlib import Path
 from pydantic import BaseModel, ConfigDict
 
-from app_runner.dispatch.generic import (
+from bfabric_app_runner.dispatch.generic import (
     write_chunks_file,
     write_workunit_definition_file,
 )
-from app_runner.dispatch.resource_flow import get_resource_flow_input_resources
+from bfabric_app_runner.dispatch.resource_flow import get_resource_flow_input_resources
 
 
 class ConfigDispatchSingleResourceFlow(BaseModel):
diff --git a/app_runner/src/app_runner/dispatch/generic.py b/bfabric_app_runner/src/bfabric_app_runner/dispatch/generic.py
similarity index 100%
rename from app_runner/src/app_runner/dispatch/generic.py
rename to bfabric_app_runner/src/bfabric_app_runner/dispatch/generic.py
diff --git a/app_runner/src/app_runner/dispatch/resource_flow.py b/bfabric_app_runner/src/bfabric_app_runner/dispatch/resource_flow.py
similarity index 100%
rename from app_runner/src/app_runner/dispatch/resource_flow.py
rename to bfabric_app_runner/src/bfabric_app_runner/dispatch/resource_flow.py
diff --git a/app_runner/src/app_runner/input_preparation/__init__.py b/bfabric_app_runner/src/bfabric_app_runner/input_preparation/__init__.py
similarity index 100%
rename from app_runner/src/app_runner/input_preparation/__init__.py
rename to bfabric_app_runner/src/bfabric_app_runner/input_preparation/__init__.py
diff --git a/app_runner/src/app_runner/input_preparation/collect_annotation.py b/bfabric_app_runner/src/bfabric_app_runner/input_preparation/collect_annotation.py
similarity index 91%
rename from app_runner/src/app_runner/input_preparation/collect_annotation.py
rename to bfabric_app_runner/src/bfabric_app_runner/input_preparation/collect_annotation.py
index d4df3b28..1d19d1df 100644
--- a/app_runner/src/app_runner/input_preparation/collect_annotation.py
+++ b/bfabric_app_runner/src/bfabric_app_runner/input_preparation/collect_annotation.py
@@ -5,7 +5,10 @@
 from bfabric.entities import Resource
 from bfabric.utils.polars_utils import flatten_relations
 
-from app_runner.specs.inputs.bfabric_annotation_spec import BfabricAnnotationResourceSampleSpec, BfabricAnnotationSpec
+from bfabric_app_runner.specs.inputs.bfabric_annotation_spec import (
+    BfabricAnnotationResourceSampleSpec,
+    BfabricAnnotationSpec,
+)
 
 
 def collect_resource_sample_annotation(spec: BfabricAnnotationResourceSampleSpec, client: Bfabric, path: Path) -> None:
diff --git a/app_runner/src/app_runner/input_preparation/integrity.py b/bfabric_app_runner/src/bfabric_app_runner/input_preparation/integrity.py
similarity index 71%
rename from app_runner/src/app_runner/input_preparation/integrity.py
rename to bfabric_app_runner/src/bfabric_app_runner/input_preparation/integrity.py
index 533de22a..c9883569 100644
--- a/app_runner/src/app_runner/input_preparation/integrity.py
+++ b/bfabric_app_runner/src/bfabric_app_runner/input_preparation/integrity.py
@@ -2,18 +2,19 @@
 
 from enum import Enum
 
-from app_runner.specs.inputs.bfabric_order_fasta_spec import BfabricOrderFastaSpec
-from app_runner.specs.inputs.file_scp_spec import FileScpSpec
+from bfabric_app_runner.specs.inputs.bfabric_order_fasta_spec import BfabricOrderFastaSpec
+from bfabric_app_runner.specs.inputs.file_copy_spec import FileSpec
+from bfabric_app_runner.specs.inputs.file_scp_spec import FileScpSpec
 from bfabric.entities import Resource, Dataset
-from app_runner.specs.inputs.bfabric_dataset_spec import BfabricDatasetSpec  # noqa: TC001
-from app_runner.specs.inputs.bfabric_resource_spec import BfabricResourceSpec  # noqa: TC001
-from app_runner.util.checksums import md5sum
+from bfabric_app_runner.specs.inputs.bfabric_dataset_spec import BfabricDatasetSpec  # noqa: TC001
+from bfabric_app_runner.specs.inputs.bfabric_resource_spec import BfabricResourceSpec  # noqa: TC001
+from bfabric_app_runner.util.checksums import md5sum
 from typing import TYPE_CHECKING
 
 if TYPE_CHECKING:
     from pathlib import Path
     from bfabric.bfabric import Bfabric
-    from app_runner.specs.inputs_spec import InputSpecType
+    from bfabric_app_runner.specs.inputs_spec import InputSpecType
 
 
 class IntegrityState(Enum):
@@ -39,7 +40,11 @@ def check_integrity(spec: InputSpecType, local_path: Path, client: Bfabric) -> I
         return _check_resource_spec(spec, local_path, client)
     elif isinstance(spec, BfabricDatasetSpec):
         return _check_dataset_spec(spec, local_path, client)
-    elif isinstance(spec, FileScpSpec) or spec.type == "bfabric_annotation" or isinstance(spec, BfabricOrderFastaSpec):
+    elif (
+        isinstance(spec, FileSpec | FileScpSpec)
+        or spec.type == "bfabric_annotation"
+        or isinstance(spec, BfabricOrderFastaSpec)
+    ):
         return IntegrityState.NotChecked
     else:
         raise ValueError(f"Unsupported spec type: {type(spec)}")
diff --git a/app_runner/src/app_runner/input_preparation/list_inputs.py b/bfabric_app_runner/src/bfabric_app_runner/input_preparation/list_inputs.py
similarity index 91%
rename from app_runner/src/app_runner/input_preparation/list_inputs.py
rename to bfabric_app_runner/src/bfabric_app_runner/input_preparation/list_inputs.py
index 68cb81d1..f0193bf7 100644
--- a/app_runner/src/app_runner/input_preparation/list_inputs.py
+++ b/bfabric_app_runner/src/bfabric_app_runner/input_preparation/list_inputs.py
@@ -5,11 +5,11 @@
 from rich.console import Console
 from rich.table import Table, Column
 
-from app_runner.input_preparation.integrity import check_integrity, IntegrityState
+from bfabric_app_runner.input_preparation.integrity import check_integrity, IntegrityState
 from typing import TYPE_CHECKING
 
 if TYPE_CHECKING:
-    from app_runner.specs.inputs_spec import InputSpecType
+    from bfabric_app_runner.specs.inputs_spec import InputSpecType
     from pathlib import Path
     from bfabric.bfabric import Bfabric
 
diff --git a/app_runner/src/app_runner/input_preparation/prepare.py b/bfabric_app_runner/src/bfabric_app_runner/input_preparation/prepare.py
similarity index 80%
rename from app_runner/src/app_runner/input_preparation/prepare.py
rename to bfabric_app_runner/src/bfabric_app_runner/input_preparation/prepare.py
index 4e55caad..98c3a07b 100644
--- a/app_runner/src/app_runner/input_preparation/prepare.py
+++ b/bfabric_app_runner/src/bfabric_app_runner/input_preparation/prepare.py
@@ -4,19 +4,21 @@
 
 from loguru import logger
 
-from app_runner.input_preparation.collect_annotation import prepare_annotation
-from app_runner.input_preparation.integrity import IntegrityState
-from app_runner.input_preparation.list_inputs import list_input_states
-from app_runner.specs.inputs.bfabric_dataset_spec import BfabricDatasetSpec
-from app_runner.specs.inputs.bfabric_order_fasta_spec import BfabricOrderFastaSpec
-from app_runner.specs.inputs.bfabric_resource_spec import BfabricResourceSpec
-from app_runner.specs.inputs.file_scp_spec import FileScpSpec
-from app_runner.specs.inputs_spec import (
+from bfabric_app_runner.input_preparation.collect_annotation import prepare_annotation
+from bfabric_app_runner.input_preparation.integrity import IntegrityState
+from bfabric_app_runner.input_preparation.list_inputs import list_input_states
+from bfabric_app_runner.input_preparation.prepare_file_spec import prepare_file_spec
+from bfabric_app_runner.specs.inputs.bfabric_dataset_spec import BfabricDatasetSpec
+from bfabric_app_runner.specs.inputs.bfabric_order_fasta_spec import BfabricOrderFastaSpec
+from bfabric_app_runner.specs.inputs.bfabric_resource_spec import BfabricResourceSpec
+from bfabric_app_runner.specs.inputs.file_copy_spec import FileSpec
+from bfabric_app_runner.specs.inputs.file_scp_spec import FileScpSpec
+from bfabric_app_runner.specs.inputs_spec import (
     InputSpecType,
     InputsSpec,
 )
-from app_runner.util.checksums import md5sum
-from app_runner.util.scp import scp
+from bfabric_app_runner.util.checksums import md5sum
+from bfabric_app_runner.util.scp import scp
 from bfabric.entities import Resource, Dataset, Workunit, Order
 
 if TYPE_CHECKING:
@@ -40,6 +42,8 @@ def prepare_all(self, specs: list[InputSpecType]) -> None:
                 logger.debug(f"Skipping {spec} as it already exists and passed integrity check")
             elif isinstance(spec, BfabricResourceSpec):
                 self.prepare_resource(spec)
+            elif isinstance(spec, FileSpec):
+                self.prepare_file_spec(spec)
             elif isinstance(spec, FileScpSpec):
                 self.prepare_file_scp(spec)
             elif isinstance(spec, BfabricDatasetSpec):
@@ -87,6 +91,9 @@ def prepare_resource(self, spec: BfabricResourceSpec) -> None:
             if actual_checksum != resource["filechecksum"]:
                 raise ValueError(f"Checksum mismatch: expected {resource['filechecksum']}, got {actual_checksum}")
 
+    def prepare_file_spec(self, spec: FileSpec) -> None:
+        return prepare_file_spec(spec=spec, client=self._client, working_dir=self._working_dir, ssh_user=self._ssh_user)
+
     def prepare_file_scp(self, spec: FileScpSpec) -> None:
         scp_uri = f"{spec.host}:{spec.absolute_path}"
         result_name = spec.resolve_filename(client=self._client)
@@ -102,12 +109,22 @@ def prepare_dataset(self, spec: BfabricDatasetSpec) -> None:
         dataset.write_csv(path=target_path, separator=spec.separator)
 
     def prepare_order_fasta(self, spec: BfabricOrderFastaSpec) -> None:
+        # Determine the result file.
+        result_name = self._working_dir / spec.filename
+        result_name.parent.mkdir(exist_ok=True, parents=True)
+
         # Find the order.
         match spec.entity:
             case "workunit":
                 workunit = Workunit.find(id=spec.id, client=self._client)
                 if not isinstance(workunit.container, Order):
-                    raise ValueError(f"Workunit {workunit.id} is not associated with an order")
+                    msg = f"Workunit {workunit.id} is not associated with an order"
+                    if spec.required:
+                        raise ValueError(msg)
+                    else:
+                        logger.warning(msg)
+                        result_name.write_text("")
+                        return
                 order = workunit.container
             case "order":
                 order = Order.find(id=spec.id, client=self._client)
@@ -115,8 +132,6 @@ def prepare_order_fasta(self, spec: BfabricOrderFastaSpec) -> None:
                 assert_never(spec.entity)
 
         # Write the result into the file
-        result_name = self._working_dir / spec.filename
-        result_name.parent.mkdir(exist_ok=True, parents=True)
         fasta_content = order.data_dict.get("fastasequence", "")
         if fasta_content and fasta_content[-1] != "\n":
             fasta_content += "\n"
diff --git a/bfabric_app_runner/src/bfabric_app_runner/input_preparation/prepare_file_spec.py b/bfabric_app_runner/src/bfabric_app_runner/input_preparation/prepare_file_spec.py
new file mode 100644
index 00000000..27dd7584
--- /dev/null
+++ b/bfabric_app_runner/src/bfabric_app_runner/input_preparation/prepare_file_spec.py
@@ -0,0 +1,97 @@
+import shlex
+import shutil
+import subprocess
+from pathlib import Path
+from shutil import SameFileError
+from subprocess import CalledProcessError
+from typing import assert_never
+
+from loguru import logger
+
+from bfabric import Bfabric
+from bfabric_app_runner.specs.inputs.file_copy_spec import (
+    FileSpec,
+    FileSourceSsh,
+    FileSourceLocal,
+    FileSourceSshValue,
+)
+from bfabric_app_runner.util.scp import scp
+
+
+def prepare_file_spec(spec: FileSpec, client: Bfabric, working_dir: Path, ssh_user: str | None) -> None:
+    """Prepares the file specified by the spec."""
+    output_path = working_dir / spec.resolve_filename(client=client)
+    output_path.parent.mkdir(exist_ok=True, parents=True)
+
+    if not spec.link:
+        success = _operation_copy_rsync(spec, output_path, ssh_user)
+        if not success:
+            success = _operation_copy(spec, output_path, ssh_user)
+    else:
+        success = _operation_link_symbolic(spec, output_path)
+    if not success:
+        raise RuntimeError(f"Failed to copy file: {spec}")
+
+
+def _operation_copy_rsync(spec: FileSpec, output_path: Path, ssh_user: str | None) -> bool:
+    match spec.source:
+        case FileSourceLocal(local=local):
+            source_str = str(Path(local).resolve())
+        case FileSourceSsh(ssh=FileSourceSshValue(host=host, path=path)):
+            source_str = f"{ssh_user}@{host}:{path}" if ssh_user else f"{host}:{path}"
+        case _:
+            assert_never(spec.source)
+    cmd = ["rsync", "-Pav", source_str, str(output_path)]
+    logger.info(shlex.join(cmd))
+    result = subprocess.run(cmd, check=False)
+    return result.returncode == 0
+
+
+def _operation_copy(spec: FileSpec, output_path: Path, ssh_user: str | None) -> bool:
+    match spec.source:
+        case FileSourceLocal():
+            return _operation_copy_cp(spec, output_path)
+        case FileSourceSsh():
+            return _operation_copy_scp(spec, output_path, ssh_user)
+        case _:
+            assert_never(spec.source)
+
+
+def _operation_copy_scp(spec: FileSpec, output_path: Path, ssh_user: str | None) -> bool:
+    try:
+        source_str = f"{spec.source.ssh.host}:{spec.source.ssh.path}"
+        scp(source=source_str, target=output_path, user=ssh_user)
+    except CalledProcessError:
+        return False
+    return True
+
+
+def _operation_copy_cp(spec: FileSpec, output_path: Path) -> bool:
+    cmd = [str(Path(spec.source.local).resolve()), str(output_path)]
+    logger.info(shlex.join(["cp", *cmd]))
+    try:
+        shutil.copyfile(*cmd)
+    except (OSError, SameFileError):
+        return False
+    return True
+
+
+def _operation_link_symbolic(spec: FileSpec, output_path: Path) -> bool:
+    # the link is created relative to the output file, so it should be more portable across apptainer images etc
+    source_path = Path(spec.source.local).resolve().relative_to(output_path.resolve().parent, walk_up=True)
+
+    # if the file exists, and only if it is a link as well
+    if output_path.is_symlink():
+        # check if it points to the same file, in which case we don't need to do anything
+        if output_path.resolve() == source_path.resolve():
+            logger.info("Link already exists and points to the correct file")
+            return True
+        else:
+            logger.info(f"rm {output_path}")
+            output_path.unlink()
+    elif output_path.exists():
+        raise RuntimeError(f"Output path already exists and is not a symlink: {output_path}")
+    cmd = ["ln", "-s", str(source_path), str(output_path)]
+    logger.info(shlex.join(cmd))
+    result = subprocess.run(cmd, check=False)
+    return result.returncode == 0
diff --git a/app_runner/src/app_runner/output_registration/__init__.py b/bfabric_app_runner/src/bfabric_app_runner/output_registration/__init__.py
similarity index 100%
rename from app_runner/src/app_runner/output_registration/__init__.py
rename to bfabric_app_runner/src/bfabric_app_runner/output_registration/__init__.py
diff --git a/app_runner/src/app_runner/output_registration/register.py b/bfabric_app_runner/src/bfabric_app_runner/output_registration/register.py
similarity index 80%
rename from app_runner/src/app_runner/output_registration/register.py
rename to bfabric_app_runner/src/bfabric_app_runner/output_registration/register.py
index 978b7e08..8e78c390 100644
--- a/app_runner/src/app_runner/output_registration/register.py
+++ b/bfabric_app_runner/src/bfabric_app_runner/output_registration/register.py
@@ -4,15 +4,15 @@
 
 from loguru import logger
 
-from app_runner.specs.outputs_spec import (
+from bfabric_app_runner.specs.outputs_spec import (
     CopyResourceSpec,
     UpdateExisting,
     OutputsSpec,
     SpecType,
     SaveDatasetSpec,
 )
-from app_runner.util.checksums import md5sum
-from app_runner.util.scp import scp
+from bfabric_app_runner.util.checksums import md5sum
+from bfabric_app_runner.util.scp import scp
 from bfabric.entities import Resource
 from bfabric.entities import Storage, Workunit
 from bfabric.experimental.upload_dataset import bfabric_save_csv2dataset
@@ -23,9 +23,7 @@
     from bfabric.experimental.workunit_definition import WorkunitDefinition
 
 
-def _get_output_folder(
-    spec: CopyResourceSpec, workunit_definition: WorkunitDefinition
-) -> Path:
+def _get_output_folder(spec: CopyResourceSpec, workunit_definition: WorkunitDefinition) -> Path:
     if not spec.store_folder_path:
         return workunit_definition.registration.storage_output_folder
     else:
@@ -40,14 +38,8 @@ def register_file_in_workunit(
 ) -> None:
     """Registers a file in the workunit."""
     existing_id = _identify_existing_resource_id(client, spec, workunit_definition)
-    if (
-        resource_id is not None
-        and existing_id is not None
-        and resource_id != existing_id
-    ):
-        raise ValueError(
-            f"Resource id {resource_id} does not match existing resource id {existing_id}"
-        )
+    if resource_id is not None and existing_id is not None and resource_id != existing_id:
+        raise ValueError(f"Resource id {resource_id} does not match existing resource id {existing_id}")
 
     checksum = md5sum(spec.local_path)
     output_folder = _get_output_folder(spec, workunit_definition=workunit_definition)
@@ -85,9 +77,7 @@ def _identify_existing_resource_id(
         if resources:
             return list(resources)[0].id
         elif spec.update_existing == UpdateExisting.REQUIRED:
-            raise ValueError(
-                f"Resource {spec.store_entry_path.name} not found in workunit {workunit_definition.id}"
-            )
+            raise ValueError(f"Resource {spec.store_entry_path.name} not found in workunit {workunit_definition.id}")
     return None
 
 
@@ -104,9 +94,7 @@ def copy_file_to_storage(
     scp(spec.local_path, output_uri, user=ssh_user)
 
 
-def _save_dataset(
-    spec: SaveDatasetSpec, client: Bfabric, workunit_definition: WorkunitDefinition
-) -> None:
+def _save_dataset(spec: SaveDatasetSpec, client: Bfabric, workunit_definition: WorkunitDefinition) -> None:
     """Saves a dataset to the bfabric."""
     # TODO should not print to stdout in the future
     # TODO also it should not be imported from bfabric_scripts, but rather the generic functionality should be available
@@ -123,17 +111,11 @@ def _save_dataset(
     )
 
 
-def find_default_resource_id(
-    workunit_definition: WorkunitDefinition, client: Bfabric
-) -> int | None:
+def find_default_resource_id(workunit_definition: WorkunitDefinition, client: Bfabric) -> int | None:
     """Finds the default resource's id for the workunit. Maybe in the future, this will be always `None`."""
-    workunit = Workunit.find(
-        id=workunit_definition.registration.workunit_id, client=client
-    )
+    workunit = Workunit.find(id=workunit_definition.registration.workunit_id, client=client)
     candidate_resources = [
-        resource
-        for resource in workunit.resources
-        if resource["name"] not in ["slurm_stdout", "slurm_stderr"]
+        resource for resource in workunit.resources if resource["name"] not in ["slurm_stdout", "slurm_stderr"]
     ]
     # We also check that the resource is pending, as else we might re-use a resource that was created by the app...
     if len(candidate_resources) == 1 and candidate_resources[0]["status"] == "pending":
@@ -153,9 +135,7 @@ def register_all(
     for spec in specs_list:
         logger.debug(f"Registering {spec}")
         if isinstance(spec, CopyResourceSpec):
-            storage = Storage.find(
-                workunit_definition.registration.storage_id, client=client
-            )
+            storage = Storage.find(workunit_definition.registration.storage_id, client=client)
             copy_file_to_storage(
                 spec,
                 workunit_definition=workunit_definition,
@@ -163,9 +143,7 @@ def register_all(
                 ssh_user=ssh_user,
             )
             if not default_resource_was_reused:
-                resource_id = find_default_resource_id(
-                    workunit_definition=workunit_definition, client=client
-                )
+                resource_id = find_default_resource_id(workunit_definition=workunit_definition, client=client)
                 default_resource_was_reused = True
             else:
                 resource_id = None
diff --git a/app_runner/src/app_runner/py.typed b/bfabric_app_runner/src/bfabric_app_runner/py.typed
similarity index 100%
rename from app_runner/src/app_runner/py.typed
rename to bfabric_app_runner/src/bfabric_app_runner/py.typed
diff --git a/app_runner/src/app_runner/specs/__init__.py b/bfabric_app_runner/src/bfabric_app_runner/specs/__init__.py
similarity index 100%
rename from app_runner/src/app_runner/specs/__init__.py
rename to bfabric_app_runner/src/bfabric_app_runner/specs/__init__.py
diff --git a/app_runner/src/app_runner/specs/app/__init__.py b/bfabric_app_runner/src/bfabric_app_runner/specs/app/__init__.py
similarity index 100%
rename from app_runner/src/app_runner/specs/app/__init__.py
rename to bfabric_app_runner/src/bfabric_app_runner/specs/app/__init__.py
diff --git a/app_runner/src/app_runner/specs/app/app_spec.py b/bfabric_app_runner/src/bfabric_app_runner/specs/app/app_spec.py
similarity index 90%
rename from app_runner/src/app_runner/specs/app/app_spec.py
rename to bfabric_app_runner/src/bfabric_app_runner/specs/app/app_spec.py
index b7573db6..0644bb6b 100644
--- a/app_runner/src/app_runner/specs/app/app_spec.py
+++ b/bfabric_app_runner/src/bfabric_app_runner/specs/app/app_spec.py
@@ -5,7 +5,7 @@
 import yaml
 from pydantic import BaseModel
 
-from app_runner.specs.app.app_version import AppVersion, AppVersionMultiTemplate  # noqa: TCH001
+from bfabric_app_runner.specs.app.app_version import AppVersion, AppVersionMultiTemplate  # noqa: TCH001
 
 if TYPE_CHECKING:
     from pathlib import Path
@@ -46,6 +46,9 @@ def available_versions(self) -> set[str]:
         """The available versions of the app."""
         return {version.version for version in self.versions}
 
+    def __contains__(self, version: str) -> bool:
+        return version in self.available_versions
+
     def __getitem__(self, version: str) -> AppVersion | None:
         """Returns the app version with the provided version number or None if it does not exist."""
         for app_version in self.versions:
diff --git a/app_runner/src/app_runner/specs/app/app_version.py b/bfabric_app_runner/src/bfabric_app_runner/specs/app/app_version.py
similarity index 87%
rename from app_runner/src/app_runner/specs/app/app_version.py
rename to bfabric_app_runner/src/bfabric_app_runner/specs/app/app_version.py
index 2535faf8..373185f9 100644
--- a/app_runner/src/app_runner/specs/app/app_version.py
+++ b/bfabric_app_runner/src/bfabric_app_runner/specs/app/app_version.py
@@ -4,10 +4,10 @@
 
 from pydantic import BaseModel, field_validator
 
-from app_runner.specs import config_interpolation
-from app_runner.specs.app.commands_spec import CommandsSpec  # noqa: TCH001
-from app_runner.specs.config_interpolation import interpolate_config_strings
-from app_runner.specs.submitter_ref import SubmitterRef  # noqa: TCH001
+from bfabric_app_runner.specs import config_interpolation
+from bfabric_app_runner.specs.app.commands_spec import CommandsSpec  # noqa: TCH001
+from bfabric_app_runner.specs.config_interpolation import interpolate_config_strings
+from bfabric_app_runner.specs.submitter_ref import SubmitterRef  # noqa: TCH001
 
 
 class AppVersion(BaseModel):
diff --git a/app_runner/src/app_runner/specs/app/commands_spec.py b/bfabric_app_runner/src/bfabric_app_runner/specs/app/commands_spec.py
similarity index 100%
rename from app_runner/src/app_runner/specs/app/commands_spec.py
rename to bfabric_app_runner/src/bfabric_app_runner/specs/app/commands_spec.py
diff --git a/app_runner/src/app_runner/specs/common_types.py b/bfabric_app_runner/src/bfabric_app_runner/specs/common_types.py
similarity index 66%
rename from app_runner/src/app_runner/specs/common_types.py
rename to bfabric_app_runner/src/bfabric_app_runner/specs/common_types.py
index cb9d7a82..59e7c7e3 100644
--- a/app_runner/src/app_runner/specs/common_types.py
+++ b/bfabric_app_runner/src/bfabric_app_runner/specs/common_types.py
@@ -4,5 +4,8 @@
 
 from pydantic import Field
 
+AbsoluteFilePath = Annotated[str, Field(pattern=r"^/[^:]*$")]
+"""Absolute file path, excluding ":" characters."""
+
 RelativeFilePath = Annotated[str, Field(pattern=r"^[^/][^:]*$")]
 """Relative file path, excluding absolute paths and ":" characters."""
diff --git a/app_runner/src/app_runner/specs/config_interpolation.py b/bfabric_app_runner/src/bfabric_app_runner/specs/config_interpolation.py
similarity index 100%
rename from app_runner/src/app_runner/specs/config_interpolation.py
rename to bfabric_app_runner/src/bfabric_app_runner/specs/config_interpolation.py
diff --git a/app_runner/src/app_runner/specs/inputs/__init__.py b/bfabric_app_runner/src/bfabric_app_runner/specs/inputs/__init__.py
similarity index 100%
rename from app_runner/src/app_runner/specs/inputs/__init__.py
rename to bfabric_app_runner/src/bfabric_app_runner/specs/inputs/__init__.py
diff --git a/app_runner/src/app_runner/specs/inputs/bfabric_annotation_spec.py b/bfabric_app_runner/src/bfabric_app_runner/specs/inputs/bfabric_annotation_spec.py
similarity index 89%
rename from app_runner/src/app_runner/specs/inputs/bfabric_annotation_spec.py
rename to bfabric_app_runner/src/bfabric_app_runner/specs/inputs/bfabric_annotation_spec.py
index 4e36a975..bba9ae08 100644
--- a/app_runner/src/app_runner/specs/inputs/bfabric_annotation_spec.py
+++ b/bfabric_app_runner/src/bfabric_app_runner/specs/inputs/bfabric_annotation_spec.py
@@ -4,7 +4,7 @@
 
 from pydantic import BaseModel, Field
 
-from app_runner.specs.common_types import RelativeFilePath  # noqa: TC001
+from bfabric_app_runner.specs.common_types import RelativeFilePath  # noqa: TC001
 
 if TYPE_CHECKING:
     from bfabric import Bfabric
diff --git a/app_runner/src/app_runner/specs/inputs/bfabric_dataset_spec.py b/bfabric_app_runner/src/bfabric_app_runner/specs/inputs/bfabric_dataset_spec.py
similarity index 88%
rename from app_runner/src/app_runner/specs/inputs/bfabric_dataset_spec.py
rename to bfabric_app_runner/src/bfabric_app_runner/specs/inputs/bfabric_dataset_spec.py
index 48b91440..4d0dbeb3 100644
--- a/app_runner/src/app_runner/specs/inputs/bfabric_dataset_spec.py
+++ b/bfabric_app_runner/src/bfabric_app_runner/specs/inputs/bfabric_dataset_spec.py
@@ -4,7 +4,7 @@
 
 from pydantic import BaseModel, ConfigDict
 
-from app_runner.specs.common_types import RelativeFilePath  # noqa: TC001
+from bfabric_app_runner.specs.common_types import RelativeFilePath  # noqa: TC001
 
 if TYPE_CHECKING:
     from bfabric import Bfabric
diff --git a/app_runner/src/app_runner/specs/inputs/bfabric_order_fasta_spec.py b/bfabric_app_runner/src/bfabric_app_runner/specs/inputs/bfabric_order_fasta_spec.py
similarity index 82%
rename from app_runner/src/app_runner/specs/inputs/bfabric_order_fasta_spec.py
rename to bfabric_app_runner/src/bfabric_app_runner/specs/inputs/bfabric_order_fasta_spec.py
index 4e741cc4..82ea5762 100644
--- a/app_runner/src/app_runner/specs/inputs/bfabric_order_fasta_spec.py
+++ b/bfabric_app_runner/src/bfabric_app_runner/specs/inputs/bfabric_order_fasta_spec.py
@@ -3,7 +3,7 @@
 
 from pydantic import BaseModel, ConfigDict
 
-from app_runner.specs.common_types import RelativeFilePath  # noqa: TC001
+from bfabric_app_runner.specs.common_types import RelativeFilePath  # noqa: TC001
 
 if TYPE_CHECKING:
     from bfabric import Bfabric
@@ -16,6 +16,7 @@ class BfabricOrderFastaSpec(BaseModel):
     id: int
     entity: Literal["workunit", "order"]
     filename: RelativeFilePath
+    required: bool = False
 
     def resolve_filename(self, client: Bfabric) -> str:
         return self.filename
diff --git a/app_runner/src/app_runner/specs/inputs/bfabric_resource_spec.py b/bfabric_app_runner/src/bfabric_app_runner/specs/inputs/bfabric_resource_spec.py
similarity index 90%
rename from app_runner/src/app_runner/specs/inputs/bfabric_resource_spec.py
rename to bfabric_app_runner/src/bfabric_app_runner/specs/inputs/bfabric_resource_spec.py
index 05257121..5910326c 100644
--- a/app_runner/src/app_runner/specs/inputs/bfabric_resource_spec.py
+++ b/bfabric_app_runner/src/bfabric_app_runner/specs/inputs/bfabric_resource_spec.py
@@ -4,7 +4,7 @@
 
 from pydantic import BaseModel, ConfigDict
 
-from app_runner.specs.common_types import RelativeFilePath  # noqa: TC001
+from bfabric_app_runner.specs.common_types import RelativeFilePath  # noqa: TC001
 from bfabric.entities import Resource
 
 if TYPE_CHECKING:
diff --git a/bfabric_app_runner/src/bfabric_app_runner/specs/inputs/file_copy_spec.py b/bfabric_app_runner/src/bfabric_app_runner/specs/inputs/file_copy_spec.py
new file mode 100644
index 00000000..50da2caa
--- /dev/null
+++ b/bfabric_app_runner/src/bfabric_app_runner/specs/inputs/file_copy_spec.py
@@ -0,0 +1,45 @@
+from __future__ import annotations
+
+from typing import Literal, TYPE_CHECKING, Self
+
+from pydantic import BaseModel, model_validator
+
+from bfabric_app_runner.specs.common_types import RelativeFilePath, AbsoluteFilePath  # noqa: TC001
+
+if TYPE_CHECKING:
+    from bfabric import Bfabric
+
+
+class FileSourceLocal(BaseModel):
+    local: AbsoluteFilePath
+
+    def get_filename(self) -> str:
+        return self.local.split("/")[-1]
+
+
+class FileSourceSshValue(BaseModel):
+    host: str
+    path: AbsoluteFilePath
+
+
+class FileSourceSsh(BaseModel):
+    ssh: FileSourceSshValue
+
+    def get_filename(self) -> str:
+        return self.ssh.path.split("/")[-1]
+
+
+class FileSpec(BaseModel):
+    type: Literal["file"] = "file"
+    source: FileSourceSsh | FileSourceLocal
+    filename: RelativeFilePath | None = None
+    link: bool = False
+
+    @model_validator(mode="after")
+    def validate_no_link_ssh(self) -> Self:
+        if isinstance(self.source, FileSourceSsh) and self.link:
+            raise ValueError("Cannot link to a remote file.")
+        return self
+
+    def resolve_filename(self, client: Bfabric) -> str:
+        return self.filename if self.filename else self.source.get_filename()
diff --git a/app_runner/src/app_runner/specs/inputs/file_scp_spec.py b/bfabric_app_runner/src/bfabric_app_runner/specs/inputs/file_scp_spec.py
similarity index 82%
rename from app_runner/src/app_runner/specs/inputs/file_scp_spec.py
rename to bfabric_app_runner/src/bfabric_app_runner/specs/inputs/file_scp_spec.py
index 212fa927..c77f7ed6 100644
--- a/app_runner/src/app_runner/specs/inputs/file_scp_spec.py
+++ b/bfabric_app_runner/src/bfabric_app_runner/specs/inputs/file_scp_spec.py
@@ -4,12 +4,13 @@
 
 from pydantic import BaseModel, ConfigDict
 
-from app_runner.specs.common_types import RelativeFilePath  # noqa: TC001
+from bfabric_app_runner.specs.common_types import RelativeFilePath  # noqa: TC001
 
 if TYPE_CHECKING:
     from bfabric import Bfabric
 
 
+# TODO(leo): deprecate later
 class FileScpSpec(BaseModel):
     model_config = ConfigDict(extra="forbid")
     type: Literal["file_scp"] = "file_scp"
diff --git a/app_runner/src/app_runner/specs/inputs_spec.py b/bfabric_app_runner/src/bfabric_app_runner/specs/inputs_spec.py
similarity index 66%
rename from app_runner/src/app_runner/specs/inputs_spec.py
rename to bfabric_app_runner/src/bfabric_app_runner/specs/inputs_spec.py
index eca38e24..9b23fe4b 100644
--- a/app_runner/src/app_runner/specs/inputs_spec.py
+++ b/bfabric_app_runner/src/bfabric_app_runner/specs/inputs_spec.py
@@ -5,18 +5,19 @@
 import yaml
 from pydantic import BaseModel, ConfigDict, Field
 
-from app_runner.specs.inputs.bfabric_annotation_spec import BfabricAnnotationSpec
-from app_runner.specs.inputs.bfabric_dataset_spec import BfabricDatasetSpec
-from app_runner.specs.inputs.bfabric_order_fasta_spec import BfabricOrderFastaSpec
-from app_runner.specs.inputs.bfabric_resource_spec import BfabricResourceSpec
-from app_runner.specs.inputs.file_scp_spec import FileScpSpec
+from bfabric_app_runner.specs.inputs.bfabric_annotation_spec import BfabricAnnotationSpec
+from bfabric_app_runner.specs.inputs.bfabric_dataset_spec import BfabricDatasetSpec
+from bfabric_app_runner.specs.inputs.bfabric_order_fasta_spec import BfabricOrderFastaSpec
+from bfabric_app_runner.specs.inputs.bfabric_resource_spec import BfabricResourceSpec
+from bfabric_app_runner.specs.inputs.file_copy_spec import FileSpec
+from bfabric_app_runner.specs.inputs.file_scp_spec import FileScpSpec
 
 if TYPE_CHECKING:
     from pathlib import Path
     from bfabric import Bfabric
 
 InputSpecType = Annotated[
-    BfabricResourceSpec | FileScpSpec | BfabricDatasetSpec | BfabricOrderFastaSpec | BfabricAnnotationSpec,
+    BfabricResourceSpec | FileSpec | FileScpSpec | BfabricDatasetSpec | BfabricOrderFastaSpec | BfabricAnnotationSpec,
     Field(discriminator="type"),
 ]
 
diff --git a/app_runner/src/app_runner/specs/outputs_spec.py b/bfabric_app_runner/src/bfabric_app_runner/specs/outputs_spec.py
similarity index 100%
rename from app_runner/src/app_runner/specs/outputs_spec.py
rename to bfabric_app_runner/src/bfabric_app_runner/specs/outputs_spec.py
diff --git a/app_runner/src/app_runner/specs/submitter_ref.py b/bfabric_app_runner/src/bfabric_app_runner/specs/submitter_ref.py
similarity index 100%
rename from app_runner/src/app_runner/specs/submitter_ref.py
rename to bfabric_app_runner/src/bfabric_app_runner/specs/submitter_ref.py
diff --git a/app_runner/src/app_runner/util/__init__.py b/bfabric_app_runner/src/bfabric_app_runner/util/__init__.py
similarity index 100%
rename from app_runner/src/app_runner/util/__init__.py
rename to bfabric_app_runner/src/bfabric_app_runner/util/__init__.py
diff --git a/app_runner/src/app_runner/util/checksums.py b/bfabric_app_runner/src/bfabric_app_runner/util/checksums.py
similarity index 100%
rename from app_runner/src/app_runner/util/checksums.py
rename to bfabric_app_runner/src/bfabric_app_runner/util/checksums.py
diff --git a/app_runner/src/app_runner/util/scp.py b/bfabric_app_runner/src/bfabric_app_runner/util/scp.py
similarity index 93%
rename from app_runner/src/app_runner/util/scp.py
rename to bfabric_app_runner/src/bfabric_app_runner/util/scp.py
index 117d8a5d..547bba54 100644
--- a/app_runner/src/app_runner/util/scp.py
+++ b/bfabric_app_runner/src/bfabric_app_runner/util/scp.py
@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import shlex
 import subprocess
 from pathlib import Path
 
@@ -38,8 +39,9 @@ def scp(source: str | Path, target: str | Path, *, user: str | None = None, mkdi
             parent_path = Path(target).parent
             parent_path.mkdir(parents=True, exist_ok=True)
 
-    logger.info(f"scp {source} {target}")
-    subprocess.run(["scp", source, target], check=True)
+    cmd = ["scp", source, target]
+    logger.info(shlex.join(cmd))
+    subprocess.run(cmd, check=True)
 
 
 def _is_remote(path: str | Path) -> bool:
diff --git a/bfabric_scripts/doc/changelog.md b/bfabric_scripts/doc/changelog.md
new file mode 100644
index 00000000..495358b8
--- /dev/null
+++ b/bfabric_scripts/doc/changelog.md
@@ -0,0 +1,21 @@
+# Changelog
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/).
+
+Versioning currently follows `X.Y.Z` where
+
+- `X` is used for major changes, that contain breaking changes
+- `Y` should be the current bfabric release
+- `Z` is increased for feature releases, that should not break the API
+
+## \[Unreleased\]
+
+### Added
+
+- `bfabric-cli workunit not-available`:
+    - allows sorting by arbitrary fields, e.g. application id
+    - allows filtering inclusive or exclusive by user
+
+## \[1.13.19\] - 2025-01-29
+
+Initial release of standalone bfabric_scripts package.
diff --git a/bfabric_scripts/pyproject.toml b/bfabric_scripts/pyproject.toml
index e3ce2da9..d509c541 100644
--- a/bfabric_scripts/pyproject.toml
+++ b/bfabric_scripts/pyproject.toml
@@ -5,7 +5,7 @@ build-backend = "hatchling.build"
 [project]
 name = "bfabric_scripts"
 description = "Python command line scripts for the B-Fabric API"
-version = "1.13.18"
+version = "1.13.19"
 
 dependencies = [
     "bfabric"
diff --git a/bfabric_scripts/src/bfabric_scripts/bfabric_feeder_mascot.py b/bfabric_scripts/src/bfabric_scripts/bfabric_feeder_mascot.py
index bc00d664..7ef5ba7a 100755
--- a/bfabric_scripts/src/bfabric_scripts/bfabric_feeder_mascot.py
+++ b/bfabric_scripts/src/bfabric_scripts/bfabric_feeder_mascot.py
@@ -50,8 +50,7 @@
         "Read {len} data items from {name} using {size:.1f} GBytes.".format(
             len=len(DB),
             name=DBfilename,
-            size=sum(map(lambda x: int(x["resource"]["size"]), DB.values()))
-            / (1024 * 1024 * 1024),
+            size=sum(map(lambda x: int(x["resource"]["size"]), DB.values())) / (1024 * 1024 * 1024),
         )
     )
 except OSError:
@@ -67,9 +66,7 @@ def query_mascot_result(file_path: str) -> bool:
         print("\thit")
         wu = DB[file_path]
         if "workunitid" in wu:
-            print(
-                f"\tdat file {file_path} already registered as workunit id {wu['workunitid']}. continue ..."
-            )
+            print(f"\tdat file {file_path} already registered as workunit id {wu['workunitid']}. continue ...")
             return
         else:
             print("\tno workunitid found")
@@ -82,9 +79,7 @@ def query_mascot_result(file_path: str) -> bool:
 
     if len(wu["inputresource"]) > 0:
         if re.search("autoQC4L", wu["name"]) or re.search("autoQC01", wu["name"]):
-            print(
-                f"WARNING This script ignores autoQC based mascot dat file {file_path}."
-            )
+            print(f"WARNING This script ignores autoQC based mascot dat file {file_path}.")
             return
 
         print("\tquerying bfabric ...")
@@ -186,9 +181,7 @@ def parse_mascot_result_file(file_path: str) -> dict[str, Any]:
         "^(FILE|COM|release|USERNAME|USERID|TOL|TOLU|ITOL|ITOLU|MODS|IT_MODS|CHARGE|INSTRUMENT|QUANTITATION|DECOY)=(.+)$"
     )
 
-    control_chars = "".join(
-        map(chr, itertools.chain(range(0x00, 0x20), range(0x7F, 0xA0)))
-    )
+    control_chars = "".join(map(chr, itertools.chain(range(0x00, 0x20), range(0x7F, 0xA0))))
     control_char_re = re.compile(f"[{re.escape(control_chars)}]")
 
     line_count = 0
@@ -209,16 +202,10 @@ def parse_mascot_result_file(file_path: str) -> dict[str, Any]:
             md5.update(line.encode())
             # check if the first character of the line is a 't' for title to save regex time
             if line[0] == "t":
-                result = regex0.match(
-                    urllib.parse.unquote(line.strip())
-                    .replace("\\", "/")
-                    .replace("//", "/")
-                )
+                result = regex0.match(urllib.parse.unquote(line.strip()).replace("\\", "/").replace("//", "/"))
                 if result and result.group(1) not in inputresourceHitHash:
                     inputresourceHitHash[result.group(1)] = result.group(2)
-                    inputresourceList.append(
-                        dict(storageid=2, relativepath=result.group(1))
-                    )
+                    inputresourceList.append(dict(storageid=2, relativepath=result.group(1)))
                     project = result.group(2)
                 else:
                     # nothing as do be done since the input_resource is already recorded
@@ -232,11 +219,7 @@ def parse_mascot_result_file(file_path: str) -> dict[str, Any]:
                     meta_data_dict[result.group(1)] = result.group(2)
 
     desc = desc.encode("ascii", errors="ignore")
-    name = (
-        f"{meta_data_dict['COM']}; {os.path.basename(meta_data_dict['relativepath'])}"[
-            :255
-        ]
-    )
+    name = f"{meta_data_dict['COM']}; {os.path.basename(meta_data_dict['relativepath'])}"[:255]
     rv = dict(
         applicationid=19,
         containerid=project,
@@ -276,8 +259,7 @@ def print_statistics() -> None:
     print_project_frequency(map(lambda x: x["containerid"], DB.values()))
     print(
         "file size\t=\t{} GBytes".format(
-            sum(map(lambda x: int(x["resource"]["size"]), DB.values()))
-            / (1024 * 1024 * 1024)
+            sum(map(lambda x: int(x["resource"]["size"]), DB.values())) / (1024 * 1024 * 1024)
         )
     )
 
@@ -286,9 +268,7 @@ def main() -> None:
     """Parses the CLI arguments and calls the appropriate functions."""
     parser = argparse.ArgumentParser()
     group = parser.add_mutually_exclusive_group(required=True)
-    group.add_argument(
-        "--stdin", action="store_true", help="read file names from stdin"
-    )
+    group.add_argument("--stdin", action="store_true", help="read file names from stdin")
     group.add_argument("--file", type=str, help="processes the provided file")
     parser.add_argument("--statistics", action="store_true", help="print statistics")
 
diff --git a/bfabric_scripts/src/bfabric_scripts/bfabric_feeder_resource_autoQC.py b/bfabric_scripts/src/bfabric_scripts/bfabric_feeder_resource_autoQC.py
index 77522a3b..3945bc39 100755
--- a/bfabric_scripts/src/bfabric_scripts/bfabric_feeder_resource_autoQC.py
+++ b/bfabric_scripts/src/bfabric_scripts/bfabric_feeder_resource_autoQC.py
@@ -46,9 +46,7 @@ def sample_check(self, projectid: int, name: str):
         :return: SID
         """
         try:
-            res = self.client.read(
-                endpoint="sample", obj={"containerid": projectid, "name": name}
-            ).to_list_dict()
+            res = self.client.read(endpoint="sample", obj={"containerid": projectid, "name": name}).to_list_dict()
         except Exception:
             print(res)
             raise
@@ -88,17 +86,11 @@ def sample_check(self, projectid: int, name: str):
 
         if not res:
             if name == "autoQC4L":
-                res = self.client.save(
-                    endpoint="sample", obj=query_autoQC4L
-                ).to_list_dict()
+                res = self.client.save(endpoint="sample", obj=query_autoQC4L).to_list_dict()
             elif name == "autoQC01":
-                res = self.client.save(
-                    endpoint="sample", obj=query_autoQC01
-                ).to_list_dict()
+                res = self.client.save(endpoint="sample", obj=query_autoQC01).to_list_dict()
             elif name == "lipidQC01":
-                res = self.client.save(
-                    endpoint="sample", obj=query_lipidQC01
-                ).to_list_dict()
+                res = self.client.save(endpoint="sample", obj=query_lipidQC01).to_list_dict()
 
         print(res)
         print(res[0])
@@ -241,9 +233,7 @@ def feed(self, line) -> None:
             sampleid = self.sample_check(projectid, name=autoQCType)
             sys.exit(0)
             # print sampleid
-            workunitid = self.workunit_check(
-                projectid, name=autoQCType, applicationid=applicationid
-            )
+            workunitid = self.workunit_check(projectid, name=autoQCType, applicationid=applicationid)
             # print "WUID={}".format(workunitid)
 
             resourceid = self.resource_check(
@@ -258,9 +248,7 @@ def feed(self, line) -> None:
             )
 
             # sampleid=0
-            print(
-                f"p{projectid}\tA{applicationid}\t{filename}\tS{sampleid}\tWU{workunitid}\tR{resourceid}"
-            )
+            print(f"p{projectid}\tA{applicationid}\t{filename}\tS{sampleid}\tWU{workunitid}\tR{resourceid}")
         except Exception as err:
             print(f"# Failed to register to bfabric: {err}")
 
diff --git a/bfabric_scripts/src/bfabric_scripts/bfabric_flask.py b/bfabric_scripts/src/bfabric_scripts/bfabric_flask.py
index 5608ec38..ea1c988b 100755
--- a/bfabric_scripts/src/bfabric_scripts/bfabric_flask.py
+++ b/bfabric_scripts/src/bfabric_scripts/bfabric_flask.py
@@ -85,9 +85,7 @@ def handle_invalid_request_content(e: InvalidRequestContent) -> Response:
     return jsonify({"error": f"invalid request content: {e}"})
 
 
-def get_fields(
-    required_fields: list[str], optional_fields: dict[str, Any]
-) -> dict[str, Any]:
+def get_fields(required_fields: list[str], optional_fields: dict[str, Any]) -> dict[str, Any]:
     """Extracts fields from a JSON request body. All `required_fields` must be present, or an error will be raised
     indicating the missing fields. The optional fields are filled with the default values if not present.
     :param required_fields: list of required fields
@@ -100,10 +98,7 @@ def get_fields(
         raise InvalidRequestContent(sorted(missing_fields))
     else:
         required_values = {field: request.json[field] for field in required_fields}
-        optional_values = {
-            field: request.json.get(field, default)
-            for field, default in optional_fields.items()
-        }
+        optional_values = {field: request.json.get(field, default) for field, default in optional_fields.items()}
         return {**required_values, **optional_values}
 
 
diff --git a/bfabric_scripts/src/bfabric_scripts/bfabric_list_not_available_proteomics_workunits.py b/bfabric_scripts/src/bfabric_scripts/bfabric_list_not_available_proteomics_workunits.py
index 1e45bd9d..48d4a15d 100755
--- a/bfabric_scripts/src/bfabric_scripts/bfabric_list_not_available_proteomics_workunits.py
+++ b/bfabric_scripts/src/bfabric_scripts/bfabric_list_not_available_proteomics_workunits.py
@@ -23,12 +23,8 @@
 def main() -> None:
     """Parses the command line arguments and calls `list_not_available_proteomics_workunits`."""
     setup_script_logging()
-    parser = ArgumentParser(
-        description="Lists proteomics work units that are not available on bfabric."
-    )
-    parser.add_argument(
-        "--max-age", type=int, help="Max age of work units in days", default=14
-    )
+    parser = ArgumentParser(description="Lists proteomics work units that are not available on bfabric.")
+    parser.add_argument("--max-age", type=int, help="Max age of work units in days", default=14)
     args = parser.parse_args()
     list_not_available_proteomics_workunits(max_age=args.max_age)
 
diff --git a/bfabric_scripts/src/bfabric_scripts/bfabric_list_not_existing_storage_directories.py b/bfabric_scripts/src/bfabric_scripts/bfabric_list_not_existing_storage_directories.py
index b4a6f00d..0dcf6a11 100755
--- a/bfabric_scripts/src/bfabric_scripts/bfabric_list_not_existing_storage_directories.py
+++ b/bfabric_scripts/src/bfabric_scripts/bfabric_list_not_existing_storage_directories.py
@@ -68,9 +68,7 @@ def update(self, client: Bfabric) -> None:
         # add some buffer to deal e.g. with miss-configured clocks
         timestamp = (self._data.checked_at - datetime.timedelta(days=1)).isoformat()
         max_results = 300 if "BFABRICPY_DEBUG" in os.environ else None
-        logger.debug(
-            f"Checking for new container ids since {timestamp} with limit {max_results}"
-        )
+        logger.debug(f"Checking for new container ids since {timestamp} with limit {max_results}")
         result = client.read(
             endpoint="container",
             obj={**self._data.query, "createdafter": timestamp},
@@ -83,9 +81,7 @@ def update(self, client: Bfabric) -> None:
         self._data.checked_at = now
 
 
-def list_not_existing_storage_dirs(
-    client: Bfabric, root_dir: Path, cache_path: Path
-) -> None:
+def list_not_existing_storage_dirs(client: Bfabric, root_dir: Path, cache_path: Path) -> None:
     """Lists not existing storage directories for a given technology id."""
     cache = Cache.load(path=cache_path)
     cache.update(client=client)
@@ -101,9 +97,7 @@ def main() -> None:
     client = Bfabric.from_config()
     root_dir = Path("/srv/www/htdocs/")
     cache_path = Path("cache.json")
-    list_not_existing_storage_dirs(
-        client=client, root_dir=root_dir, cache_path=cache_path
-    )
+    list_not_existing_storage_dirs(client=client, root_dir=root_dir, cache_path=cache_path)
 
 
 if __name__ == "__main__":
diff --git a/bfabric_scripts/src/bfabric_scripts/bfabric_list_workunit_parameters.py b/bfabric_scripts/src/bfabric_scripts/bfabric_list_workunit_parameters.py
index 84fe8b96..3ccf8354 100644
--- a/bfabric_scripts/src/bfabric_scripts/bfabric_list_workunit_parameters.py
+++ b/bfabric_scripts/src/bfabric_scripts/bfabric_list_workunit_parameters.py
@@ -9,18 +9,14 @@
 from bfabric.experimental import MultiQuery
 
 
-def bfabric_list_workunit_parameters(
-    client: Bfabric, application_id: int, max_workunits: int, format: str
-) -> None:
+def bfabric_list_workunit_parameters(client: Bfabric, application_id: int, max_workunits: int, format: str) -> None:
     """Lists the workunit parameters of the provided application.
     :param client: The Bfabric client to use.
     :param application_id: The application ID to list the workunit parameters for.
     :param max_workunits: The maximum number of workunits to fetch.
     :param format: The output format to use.
     """
-    workunits_table_full = get_workunits_table_full(
-        application_id, client, max_workunits
-    )
+    workunits_table_full = get_workunits_table_full(application_id, client, max_workunits)
     workunits_table_explode = workunits_table_full.explode("parameter").with_columns(
         parameter_id=pl.col("parameter").struct[1]
     )
@@ -41,15 +37,11 @@ def bfabric_list_workunit_parameters(
     print_results(format, merged_result)
 
 
-def get_workunits_table_full(
-    application_id: int, client: Bfabric, max_workunits: int
-) -> pl.DataFrame:
+def get_workunits_table_full(application_id: int, client: Bfabric, max_workunits: int) -> pl.DataFrame:
     """Returns a table with the workunits for the specified application."""
     # read the workunit data
     workunits_table_full = (
-        client.read(
-            "workunit", {"applicationid": application_id}, max_results=max_workunits
-        )
+        client.read("workunit", {"applicationid": application_id}, max_results=max_workunits)
         .to_polars()
         .rename({"id": "workunit_id"})
     )
@@ -65,9 +57,7 @@ def get_workunits_table_full(
             inputdataset_id=pl.col("inputdataset").struct[1],
         )
     else:
-        workunits_table_full = workunits_table_full.with_columns(
-            inputdataset_id=pl.lit(None)
-        )
+        workunits_table_full = workunits_table_full.with_columns(inputdataset_id=pl.lit(None))
     return workunits_table_full
 
 
@@ -90,9 +80,7 @@ def print_results(format: str, merged_result: pl.DataFrame) -> None:
         raise ValueError("Unsupported format")
 
 
-def get_parameter_table(
-    client: Bfabric, workunits_table_explode: pl.DataFrame
-) -> pl.DataFrame:
+def get_parameter_table(client: Bfabric, workunits_table_explode: pl.DataFrame) -> pl.DataFrame:
     """Returns a wide format table for the specified parameters, with the key `workunit_id` indicating the source."""
     # load the parameters table
     collect = MultiQuery(client=client).read_multi(
@@ -101,9 +89,7 @@ def get_parameter_table(
         multi_query_key="id",
         multi_query_vals=workunits_table_explode["parameter_id"].to_list(),
     )
-    parameter_table_full = collect.to_polars().rename({"id": "parameter_id"})[
-        ["parameter_id", "key", "value"]
-    ]
+    parameter_table_full = collect.to_polars().rename({"id": "parameter_id"})[["parameter_id", "key", "value"]]
     # add workunit id to parameter table
     parameter_table_full = parameter_table_full.join(
         workunits_table_explode[["workunit_id", "parameter_id"]],
@@ -111,9 +97,7 @@ def get_parameter_table(
         how="left",
     )
     # convert to wide format
-    return parameter_table_full.pivot(
-        values="value", index="workunit_id", columns="key"
-    )
+    return parameter_table_full.pivot(values="value", index="workunit_id", columns="key")
 
 
 def main() -> None:
diff --git a/bfabric_scripts/src/bfabric_scripts/bfabric_read.py b/bfabric_scripts/src/bfabric_scripts/bfabric_read.py
index 986d3f4c..4299332e 100755
--- a/bfabric_scripts/src/bfabric_scripts/bfabric_read.py
+++ b/bfabric_scripts/src/bfabric_scripts/bfabric_read.py
@@ -55,9 +55,7 @@ def bfabric_read(
         possible_attributes = sorted(set(res[0].keys()))
         logger.info(f"possible attributes = {possible_attributes}")
 
-    output_format = _determine_output_format(
-        console_out=console_out, output_format=output_format, n_results=len(res)
-    )
+    output_format = _determine_output_format(console_out=console_out, output_format=output_format, n_results=len(res))
     logger.info(f"output format = {output_format}")
 
     if output_format == "json":
@@ -111,9 +109,7 @@ def _print_table_tsv(res: list[dict[str, Any]]) -> None:
         )
 
 
-def _determine_output_format(
-    console_out: Console, output_format: str, n_results: int
-) -> str:
+def _determine_output_format(console_out: Console, output_format: str, n_results: int) -> str:
     """Returns the format to use, based on the number of results, and whether the output is an interactive console.
     If the format is already set to a concrete value instead of "auto", it will be returned unchanged.
     """
diff --git a/bfabric_scripts/src/bfabric_scripts/bfabric_read_samples_from_dataset.py b/bfabric_scripts/src/bfabric_scripts/bfabric_read_samples_from_dataset.py
index 87d3e5a7..246649fe 100755
--- a/bfabric_scripts/src/bfabric_scripts/bfabric_read_samples_from_dataset.py
+++ b/bfabric_scripts/src/bfabric_scripts/bfabric_read_samples_from_dataset.py
@@ -19,16 +19,10 @@
 from bfabric import Bfabric
 
 
-def get_table_row(
-    client: Bfabric, relative_path: str
-) -> tuple[str, int, str, str, str]:
+def get_table_row(client: Bfabric, relative_path: str) -> tuple[str, int, str, str, str]:
     """Returns the row of the table with the information of the resource with the given relative path."""
-    resource = client.read(
-        endpoint="resource", obj={"relativepath": relative_path}
-    ).to_list_dict()[0]
-    sample = client.read(
-        endpoint="sample", obj={"id": resource["sample"]["id"]}
-    ).to_list_dict()[0]
+    resource = client.read(endpoint="resource", obj={"relativepath": relative_path}).to_list_dict()[0]
+    sample = client.read(endpoint="sample", obj={"id": resource["sample"]["id"]}).to_list_dict()[0]
     groupingvar = (sample.get("groupingvar") or {}).get("name") or ""
     return (
         resource["workunit"]["id"],
@@ -45,13 +39,9 @@ def bfabric_read_samples_from_dataset(dataset_id: int) -> None:
     client = Bfabric.from_config()
     dataset = client.read(endpoint="dataset", obj={"id": dataset_id}).to_list_dict()[0]
 
-    positions = [
-        a["position"] for a in dataset["attribute"] if a["name"] == "Relative Path"
-    ]
+    positions = [a["position"] for a in dataset["attribute"] if a["name"] == "Relative Path"]
     if not positions:
-        raise ValueError(
-            f"No 'Relative Path' attribute found in the dataset {dataset_id}"
-        )
+        raise ValueError(f"No 'Relative Path' attribute found in the dataset {dataset_id}")
     relative_path_position = positions[0]
 
     print(
@@ -67,16 +57,10 @@ def bfabric_read_samples_from_dataset(dataset_id: int) -> None:
     )
     for item in dataset["item"]:
         relative_path = [
-            field["value"]
-            for field in item["field"]
-            if field["attributeposition"] == relative_path_position
+            field["value"] for field in item["field"] if field["attributeposition"] == relative_path_position
         ][0]
-        workunitid, resourceid, resourcename, samplename, groupingvar = get_table_row(
-            client, relative_path
-        )
-        print(
-            f"{workunitid}\t{resourceid}\t{resourcename}\t{samplename}\t{groupingvar}"
-        )
+        workunitid, resourceid, resourcename, samplename, groupingvar = get_table_row(client, relative_path)
+        print(f"{workunitid}\t{resourceid}\t{resourcename}\t{samplename}\t{groupingvar}")
 
 
 def main() -> None:
diff --git a/bfabric_scripts/src/bfabric_scripts/bfabric_read_samples_of_workunit.py b/bfabric_scripts/src/bfabric_scripts/bfabric_read_samples_of_workunit.py
index ffb82e64..2893b521 100755
--- a/bfabric_scripts/src/bfabric_scripts/bfabric_read_samples_of_workunit.py
+++ b/bfabric_scripts/src/bfabric_scripts/bfabric_read_samples_of_workunit.py
@@ -27,22 +27,13 @@ def bfabric_read_samples_of_workunit(workunit_id: int) -> None:
     client = Bfabric.from_config()
 
     start_time = time.time()
-    res_workunit = client.read(
-        endpoint="workunit", obj={"id": workunit_id}
-    ).to_list_dict()[0]
+    res_workunit = client.read(endpoint="workunit", obj={"id": workunit_id}).to_list_dict()[0]
     input_resource_ids = [x["id"] for x in res_workunit.get("inputresource", [])]
-    input_resources = client.read(
-        endpoint="resource", obj={"id": input_resource_ids}
-    ).to_list_dict()
+    input_resources = client.read(endpoint="resource", obj={"id": input_resource_ids}).to_list_dict()
     input_resources_name = [(r["id"], r["name"]) for r in input_resources]
 
-    samples = client.read(
-        endpoint="sample", obj={"id": [x["sample"]["id"] for x in input_resources]}
-    ).to_list_dict()
-    groupingvars = [
-        (s["id"], s["name"], (s.get("groupingvar") or {}).get("name", "NA"))
-        for s in samples
-    ]
+    samples = client.read(endpoint="sample", obj={"id": [x["sample"]["id"] for x in input_resources]}).to_list_dict()
+    groupingvars = [(s["id"], s["name"], (s.get("groupingvar") or {}).get("name", "NA")) for s in samples]
 
     print(
         "\t".join(
diff --git a/bfabric_scripts/src/bfabric_scripts/bfabric_save_dataset2csv.py b/bfabric_scripts/src/bfabric_scripts/bfabric_save_dataset2csv.py
index 226d7495..0d329c3f 100755
--- a/bfabric_scripts/src/bfabric_scripts/bfabric_save_dataset2csv.py
+++ b/bfabric_scripts/src/bfabric_scripts/bfabric_save_dataset2csv.py
@@ -24,9 +24,7 @@
 from bfabric_scripts.cli.base import use_client
 
 
-def bfabric_save_dataset2csv(
-    client: Bfabric, dataset_id: int, out_dir: Path, out_filename: Path, sep: str
-) -> None:
+def bfabric_save_dataset2csv(client: Bfabric, dataset_id: int, out_dir: Path, out_filename: Path, sep: str) -> None:
     """Saves the dataset with id `dataset_id` to a csv file at `out_dir/out_filename` or `out_filename` if it's an
     absolute path.
     """
@@ -44,12 +42,8 @@ def bfabric_save_dataset2csv(
 @use_client
 def main(*, client: Bfabric) -> None:
     """Parses arguments and calls `bfabric_save_dataset2csv`."""
-    parser = argparse.ArgumentParser(
-        description="Save a B-Fabric dataset to a csv file"
-    )
-    parser.add_argument(
-        "--id", metavar="int", required=True, help="dataset id", type=int
-    )
+    parser = argparse.ArgumentParser(description="Save a B-Fabric dataset to a csv file")
+    parser.add_argument("--id", metavar="int", required=True, help="dataset id", type=int)
     parser.add_argument(
         "--dir",
         type=Path,
diff --git a/bfabric_scripts/src/bfabric_scripts/bfabric_save_fasta.py b/bfabric_scripts/src/bfabric_scripts/bfabric_save_fasta.py
index 20d963a6..76a614dd 100755
--- a/bfabric_scripts/src/bfabric_scripts/bfabric_save_fasta.py
+++ b/bfabric_scripts/src/bfabric_scripts/bfabric_save_fasta.py
@@ -25,9 +25,7 @@ def save_fasta(container_id: int, fasta_file: Path) -> None:
     with fasta_file.open("rb") as f:
         md5 = hashlib.md5(f.read()).hexdigest()
 
-    resources = client.read(
-        endpoint="resource", obj={"filechecksum": md5}
-    ).to_list_dict()
+    resources = client.read(endpoint="resource", obj={"filechecksum": md5}).to_list_dict()
     if resources:
         print("resource(s) already exist.")
         # TODO this logic was mostly carried over from before, does it still make sense?
@@ -66,9 +64,7 @@ def save_fasta(container_id: int, fasta_file: Path) -> None:
     resource = client.save(endpoint="resource", obj=obj).to_list_dict()
     print(json.dumps(resource, indent=2))
 
-    workunit = client.save(
-        endpoint="workunit", obj={"id": workunit[0]["id"], "status": "available"}
-    ).to_list_dict()
+    workunit = client.save(endpoint="workunit", obj={"id": workunit[0]["id"], "status": "available"}).to_list_dict()
     print(json.dumps(workunit, indent=2))
 
 
diff --git a/bfabric_scripts/src/bfabric_scripts/bfabric_save_importresource_sample.py b/bfabric_scripts/src/bfabric_scripts/bfabric_save_importresource_sample.py
index 57ee3608..773dbd27 100755
--- a/bfabric_scripts/src/bfabric_scripts/bfabric_save_importresource_sample.py
+++ b/bfabric_scripts/src/bfabric_scripts/bfabric_save_importresource_sample.py
@@ -66,9 +66,7 @@ def create_importresource_dict(
     file_date = time.strftime("%Y-%m-%d %H:%M:%S", time.gmtime(file_unix_timestamp))
     bfabric_application_ids = config.application_ids
     if not bfabric_application_ids:
-        raise RuntimeError(
-            "No bfabric_application_ids configured. check '~/.bfabricpy.yml' file!"
-        )
+        raise RuntimeError("No bfabric_application_ids configured. check '~/.bfabricpy.yml' file!")
     bfabric_application_id, bfabric_projectid = get_bfabric_application_and_project_id(
         bfabric_application_ids, file_path
     )
@@ -99,9 +97,7 @@ def get_sample_id_from_path(file_path: str) -> int | None:
         return int(match.group(3))
 
 
-def get_bfabric_application_and_project_id(
-    bfabric_application_ids: dict[str, int], file_path: str
-) -> tuple[int, int]:
+def get_bfabric_application_and_project_id(bfabric_application_ids: dict[str, int], file_path: str) -> tuple[int, int]:
     """Returns the bfabric application id and project id for a given file path."""
     # linear search through dictionary. first hit counts!
     bfabric_applicationid = -1
diff --git a/bfabric_scripts/src/bfabric_scripts/bfabric_save_workflowstep.py b/bfabric_scripts/src/bfabric_scripts/bfabric_save_workflowstep.py
index f91ca833..910df0d9 100755
--- a/bfabric_scripts/src/bfabric_scripts/bfabric_save_workflowstep.py
+++ b/bfabric_scripts/src/bfabric_scripts/bfabric_save_workflowstep.py
@@ -45,22 +45,14 @@ def save_workflowstep(workunit_id: int | None = None) -> None:
     application_id = workunit["application"]["id"]
     container_id = workunit["container"]["id"]
 
-    if (
-        application_id in workflowtemplatestep_ids
-        and application_id in workflowtemplate_ids
-    ):
-        workflows = client.read(
-            "workflow", obj={"containerid": container_id}
-        ).to_list_dict()
+    if application_id in workflowtemplatestep_ids and application_id in workflowtemplate_ids:
+        workflows = client.read("workflow", obj={"containerid": container_id}).to_list_dict()
         # if workflows is None, no workflow is available - > create a new one
         daw_id = -1
         if workflows:
             # check if the corresponding workflow exists (template id 59)
             for item in workflows:
-                if (
-                    item["workflowtemplate"]["id"]
-                    == workflowtemplate_ids[application_id]
-                ):
+                if item["workflowtemplate"]["id"] == workflowtemplate_ids[application_id]:
                     daw_id = item["id"]
                     break
         # case when no workflows are available (workflows == None)
@@ -88,9 +80,7 @@ def save_workflowstep(workunit_id: int | None = None) -> None:
 def main() -> None:
     """Parses command line args and calls `save_workflowstep`."""
     parser = argparse.ArgumentParser(description="Create an analysis workflow step")
-    parser.add_argument(
-        "workunitid", metavar="workunitid", type=int, help="workunit id"
-    )
+    parser.add_argument("workunitid", metavar="workunitid", type=int, help="workunit id")
     args = parser.parse_args()
     save_workflowstep(workunit_id=args.workunitid)
 
diff --git a/bfabric_scripts/src/bfabric_scripts/bfabric_save_workunit_attribute.py b/bfabric_scripts/src/bfabric_scripts/bfabric_save_workunit_attribute.py
index 21806372..1de1462a 100755
--- a/bfabric_scripts/src/bfabric_scripts/bfabric_save_workunit_attribute.py
+++ b/bfabric_scripts/src/bfabric_scripts/bfabric_save_workunit_attribute.py
@@ -17,14 +17,10 @@
 from bfabric import Bfabric
 
 
-def bfabric_save_workunit_attribute(
-    workunit_id: int, attribute: str, value: str
-) -> None:
+def bfabric_save_workunit_attribute(workunit_id: int, attribute: str, value: str) -> None:
     """Sets the specified attribute to the specified value for the specified workunit."""
     client = Bfabric.from_config()
-    result = client.save(
-        endpoint="workunit", obj={"id": workunit_id, attribute: value}
-    ).to_list_dict()
+    result = client.save(endpoint="workunit", obj={"id": workunit_id, attribute: value}).to_list_dict()
     print(json.dumps(result[0], indent=2))
 
 
diff --git a/bfabric_scripts/src/bfabric_scripts/bfabric_setExternalJobStatus_done.py b/bfabric_scripts/src/bfabric_scripts/bfabric_setExternalJobStatus_done.py
index 29f10207..5eb80b1e 100755
--- a/bfabric_scripts/src/bfabric_scripts/bfabric_setExternalJobStatus_done.py
+++ b/bfabric_scripts/src/bfabric_scripts/bfabric_setExternalJobStatus_done.py
@@ -24,9 +24,7 @@ def set_external_job_status_done(client: Bfabric, external_job_id: list[int]) ->
     """Sets the status of the specified external jobs to 'done'."""
     for job_id in external_job_id:
         try:
-            res = client.save(
-                "externaljob", {"id": job_id, "status": "done"}
-            ).to_list_dict()
+            res = client.save("externaljob", {"id": job_id, "status": "done"}).to_list_dict()
             print(res)
         except Exception:
             print(f"failed to set externaljob with id={job_id} 'available'.")
diff --git a/bfabric_scripts/src/bfabric_scripts/bfabric_setWorkunitStatus.py b/bfabric_scripts/src/bfabric_scripts/bfabric_setWorkunitStatus.py
index 2cd8bb65..e120a3ec 100755
--- a/bfabric_scripts/src/bfabric_scripts/bfabric_setWorkunitStatus.py
+++ b/bfabric_scripts/src/bfabric_scripts/bfabric_setWorkunitStatus.py
@@ -17,9 +17,7 @@
 
 def main_generic(result_status: str) -> None:
     """Main function for setting workunit status to `result_status`."""
-    parser = argparse.ArgumentParser(
-        description=f"Sets workunit status to '{result_status}'"
-    )
+    parser = argparse.ArgumentParser(description=f"Sets workunit status to '{result_status}'")
     parser.add_argument("workunit_id", type=int, help="workunit id")
     args = parser.parse_args()
     client = Bfabric.from_config()
diff --git a/bfabric_scripts/src/bfabric_scripts/bfabric_slurm_queue_status.py b/bfabric_scripts/src/bfabric_scripts/bfabric_slurm_queue_status.py
index ad27e769..21d4fa3e 100644
--- a/bfabric_scripts/src/bfabric_scripts/bfabric_slurm_queue_status.py
+++ b/bfabric_scripts/src/bfabric_scripts/bfabric_slurm_queue_status.py
@@ -12,6 +12,7 @@
 
 from bfabric import Bfabric
 from bfabric.entities import Workunit, Application
+from bfabric_scripts.cli.base import use_client
 
 
 def get_slurm_jobs(partition: str, ssh_host: str | None) -> pl.DataFrame:
@@ -25,24 +26,19 @@ def get_slurm_jobs(partition: str, ssh_host: str | None) -> pl.DataFrame:
         command = [
             "ssh",
             ssh_host,
-            "bash -l -c "
-            + shlex.quote(" ".join(shlex.quote(arg) for arg in target_command)),
+            "bash -l -c " + shlex.quote(" ".join(shlex.quote(arg) for arg in target_command)),
         ]
 
-    logger.info(f"Running command: {' '.join(command)}")
+    logger.info(f"Running command: {shlex.join(command)}")
     output = subprocess.run(command, stdout=subprocess.PIPE, text=True, check=True)
     stringio = io.StringIO(output.stdout)
     df = pl.read_csv(stringio, separator="\t")
     df = df.rename({"JOBID": "job_id", "NAME": "name", "NODELIST": "node_list"})
     string_id_expr = pl.col("name").str.extract(r"WU(\d+)")
-    return df.with_columns(
-        workunit_id=pl.when(string_id_expr.is_not_null()).then(string_id_expr.cast(int))
-    )
+    return df.with_columns(workunit_id=pl.when(string_id_expr.is_not_null()).then(string_id_expr.cast(int)))
 
 
-def get_workunit_infos(
-    client: Bfabric, workunit_ids: list[int]
-) -> list[dict[str, str]]:
+def get_workunit_infos(client: Bfabric, workunit_ids: list[int]) -> list[dict[str, str]]:
     """Retrieves information about the workunits with the specified ids.
     If a workunit was deleted, but it is in the slurm queue, it will be considered a zombie.
     """
@@ -57,22 +53,14 @@ def get_workunit_infos(
     return [
         {
             "workunit_id": id,
-            "status": (
-                workunits[id].data_dict["status"] if id in workunits else "ZOMBIE"
-            ),
-            "application_name": (
-                app_names[workunits[id]["application"]["id"]]
-                if id in workunits
-                else "N/A"
-            ),
+            "status": (workunits[id].data_dict["status"] if id in workunits else "ZOMBIE"),
+            "application_name": (app_names[workunits[id]["application"]["id"]] if id in workunits else "N/A"),
         }
         for id in workunit_ids
     ]
 
 
-def find_zombie_jobs(
-    client: Bfabric, partition: str, ssh_host: str | None
-) -> pl.DataFrame:
+def find_zombie_jobs(client: Bfabric, partition: str, ssh_host: str | None) -> pl.DataFrame:
     """Checks the status of the slurm jobs in the specified partition, and returns the ones that are zombies."""
     slurm_jobs = get_slurm_jobs(partition=partition, ssh_host=ssh_host)
     if slurm_jobs.is_empty():
@@ -84,27 +72,19 @@ def find_zombie_jobs(
         )
     )
     pl.Config.set_tbl_rows(100)
-    logger.info(
-        slurm_jobs.join(workunit_info_table, on="workunit_id", how="left").sort(
-            "workunit_id"
-        )
-    )
+    logger.info(slurm_jobs.join(workunit_info_table, on="workunit_id", how="left").sort("workunit_id"))
     logger.info(f"Active jobs: {workunit_info_table.height}")
-    logger.info(
-        f"Found {workunit_info_table.filter(pl.col('status') == 'ZOMBIE').height} zombie jobs."
-    )
+    logger.info(f"Found {workunit_info_table.filter(pl.col('status') == 'ZOMBIE').height} zombie jobs.")
     return workunit_info_table.filter(pl.col("status") == "ZOMBIE")
 
 
-def main() -> None:
+@use_client
+def main(*, client: Bfabric) -> None:
     """Checks the status of the slurm jobs in the specified partition, and reports if there are any zombies."""
     parser = argparse.ArgumentParser()
     parser.add_argument("--partition", type=str, default="prx")
-    parser.add_argument(
-        "--ssh", type=str, default=None, help="SSH into the given node to obtain list."
-    )
+    parser.add_argument("--ssh", type=str, default=None, help="SSH into the given node to obtain list.")
     args = parser.parse_args()
-    client = Bfabric.from_config()
     zombie_jobs = find_zombie_jobs(client, partition=args.partition, ssh_host=args.ssh)
     if zombie_jobs.is_empty():
         print(json.dumps([]))
diff --git a/bfabric_scripts/src/bfabric_scripts/bfabric_upload_resource.py b/bfabric_scripts/src/bfabric_scripts/bfabric_upload_resource.py
index e518fc05..0e9a8937 100755
--- a/bfabric_scripts/src/bfabric_scripts/bfabric_upload_resource.py
+++ b/bfabric_scripts/src/bfabric_scripts/bfabric_upload_resource.py
@@ -36,9 +36,7 @@ def main(*, client: Bfabric) -> None:
     parser.add_argument("filename", help="filename", type=Path)
     parser.add_argument("workunitid", help="workunitid", type=int)
     args = parser.parse_args()
-    bfabric_upload_resource(
-        client=client, filename=args.filename, workunit_id=args.workunitid
-    )
+    bfabric_upload_resource(client=client, filename=args.filename, workunit_id=args.workunitid)
 
 
 if __name__ == "__main__":
diff --git a/bfabric_scripts/src/bfabric_scripts/bfabric_upload_submitter_executable.py b/bfabric_scripts/src/bfabric_scripts/bfabric_upload_submitter_executable.py
index efd35531..26895781 100755
--- a/bfabric_scripts/src/bfabric_scripts/bfabric_upload_submitter_executable.py
+++ b/bfabric_scripts/src/bfabric_scripts/bfabric_upload_submitter_executable.py
@@ -56,9 +56,7 @@ def main() -> None:
         choices=["slurm"],
         help="Valid engines for job handling are: slurm, gridengine",
     )
-    parser.add_argument(
-        "--name", type=str, help="Name of the submitter", required=False
-    )
+    parser.add_argument("--name", type=str, help="Name of the submitter", required=False)
     parser.add_argument(
         "--description",
         type=str,
diff --git a/bfabric_scripts/src/bfabric_scripts/cli/api/cli_api_log.py b/bfabric_scripts/src/bfabric_scripts/cli/api/cli_api_log.py
index 865d0840..f1ef6b71 100644
--- a/bfabric_scripts/src/bfabric_scripts/cli/api/cli_api_log.py
+++ b/bfabric_scripts/src/bfabric_scripts/cli/api/cli_api_log.py
@@ -48,9 +48,7 @@ def write_workunit(client: Bfabric, workunit_id: int, message: str) -> None:
             f"Expected exactly one external job for workunit {workunit_id}, but found {len(external_jobs)}"
         )
     else:
-        write_externaljob(
-            client=client, externaljob_id=external_jobs[0]["id"], message=message
-        )
+        write_externaljob(client=client, externaljob_id=external_jobs[0]["id"], message=message)
 
 
 def write_externaljob(client: Bfabric, externaljob_id: int, message: str) -> None:
diff --git a/bfabric_scripts/src/bfabric_scripts/cli/api/cli_api_read.py b/bfabric_scripts/src/bfabric_scripts/cli/api/cli_api_read.py
index 4eaa969f..6c9b8b20 100644
--- a/bfabric_scripts/src/bfabric_scripts/cli/api/cli_api_read.py
+++ b/bfabric_scripts/src/bfabric_scripts/cli/api/cli_api_read.py
@@ -87,9 +87,7 @@ def bfabric_read(
             console=console_out,
         )
         # _print_query_rich(console_out, query)
-        _print_table_rich(
-            client.config, console_out, endpoint, results, output_columns=output_columns
-        )
+        _print_table_rich(client.config, console_out, endpoint, results, output_columns=output_columns)
     else:
         raise ValueError(f"output format {output_format} not supported")
 
@@ -111,9 +109,7 @@ def _determine_output_columns(
     return columns
 
 
-def _get_results(
-    client: Bfabric, endpoint: str, query: dict[str, str], limit: int
-) -> list[dict[str, Any]]:
+def _get_results(client: Bfabric, endpoint: str, query: dict[str, str], limit: int) -> list[dict[str, Any]]:
     start_time = time.time()
     results = client.read(endpoint=endpoint, obj=query, max_results=limit)
     end_time = time.time()
@@ -160,9 +156,7 @@ def _print_table_rich(
     console_out.print(table)
 
 
-def _determine_output_format(
-    console_out: Console, output_format: OutputFormat, n_results: int
-) -> OutputFormat:
+def _determine_output_format(console_out: Console, output_format: OutputFormat, n_results: int) -> OutputFormat:
     """Returns the format to use, based on the number of results, and whether the output is an interactive console.
     If the format is already set to a concrete value instead of "auto", it will be returned unchanged.
     """
diff --git a/bfabric_scripts/src/bfabric_scripts/cli/cli_external_job.py b/bfabric_scripts/src/bfabric_scripts/cli/cli_external_job.py
index 7122c339..f4a4b4af 100644
--- a/bfabric_scripts/src/bfabric_scripts/cli/cli_external_job.py
+++ b/bfabric_scripts/src/bfabric_scripts/cli/cli_external_job.py
@@ -29,9 +29,7 @@ def find_slurm_root() -> str:
 
 @app.command
 @use_client
-def submitter(
-    external_job_id: int, scheduler: Literal["Slurm"] = "Slurm", *, client: Bfabric
-) -> None:
+def submitter(external_job_id: int, scheduler: Literal["Slurm"] = "Slurm", *, client: Bfabric) -> None:
     if scheduler != "Slurm":
         raise NotImplementedError(f"Unsupported scheduler: {scheduler}")
     slurm_root = find_slurm_root()
diff --git a/bfabric_scripts/src/bfabric_scripts/cli/executable/inspect.py b/bfabric_scripts/src/bfabric_scripts/cli/executable/inspect.py
index d16ae6af..713c9276 100644
--- a/bfabric_scripts/src/bfabric_scripts/cli/executable/inspect.py
+++ b/bfabric_scripts/src/bfabric_scripts/cli/executable/inspect.py
@@ -7,9 +7,7 @@
 from bfabric_scripts.cli.base import use_client
 
 
-def get_storage_info(
-    storage_id: int | None, client: Bfabric
-) -> dict[str, str | int] | None:
+def get_storage_info(storage_id: int | None, client: Bfabric) -> dict[str, str | int] | None:
     if storage_id is None:
         return None
     storage_info = Storage.find(storage_id, client=client)
@@ -20,13 +18,8 @@ def get_storage_info(
 def inspect_executable(executable_id: int, *, client: Bfabric) -> None:
     console = Console()
     executable = Executable.find(executable_id, client=client)
-    metadata = {
-        key: executable.get(key)
-        for key in ("id", "name", "description", "relativepath", "context", "program")
-    }
-    metadata["storage"] = get_storage_info(
-        executable.storage.id if executable.storage else None, client
-    )
+    metadata = {key: executable.get(key) for key in ("id", "name", "description", "relativepath", "context", "program")}
+    metadata["storage"] = get_storage_info(executable.storage.id if executable.storage else None, client)
 
     console.print(Panel("Executable Metadata"))
     pprint(metadata)
diff --git a/bfabric_scripts/src/bfabric_scripts/cli/executable/upload.py b/bfabric_scripts/src/bfabric_scripts/cli/executable/upload.py
index 10054128..3869ac5b 100644
--- a/bfabric_scripts/src/bfabric_scripts/cli/executable/upload.py
+++ b/bfabric_scripts/src/bfabric_scripts/cli/executable/upload.py
@@ -10,9 +10,7 @@
 
 
 @use_client
-def upload_executable(
-    executable_yaml: Path, *, upload: Path | None = None, client: Bfabric
-) -> None:
+def upload_executable(executable_yaml: Path, *, upload: Path | None = None, client: Bfabric) -> None:
     """Uploads an executable defined in the specified YAML to bfabric.
 
     :param executable_yaml: Path to the YAML file containing the executable data.
@@ -28,9 +26,7 @@ def upload_executable(
         raise ValueError(msg)
     executable_data = executable_data["executable"]
     if upload is not None:
-        executable_data["base64"] = base64.encodebytes(upload.read_bytes()).decode(
-            "utf-8"
-        )
+        executable_data["base64"] = base64.encodebytes(upload.read_bytes()).decode("utf-8")
 
     # Ensure id is not set
     if "id" in executable_data:
@@ -46,6 +42,4 @@ def upload_executable(
 
     console.print("Executable uploaded successfully.")
     console.print("Executable ID:", executable_id)
-    console.print(
-        "Executable URL:", Executable({"id": executable_id}, client=client).web_url
-    )
+    console.print("Executable URL:", Executable({"id": executable_id}, client=client).web_url)
diff --git a/bfabric_scripts/src/bfabric_scripts/cli/external_job/upload_submitter_executable.py b/bfabric_scripts/src/bfabric_scripts/cli/external_job/upload_submitter_executable.py
index 1848c5f4..cf1c216a 100644
--- a/bfabric_scripts/src/bfabric_scripts/cli/external_job/upload_submitter_executable.py
+++ b/bfabric_scripts/src/bfabric_scripts/cli/external_job/upload_submitter_executable.py
@@ -9,9 +9,7 @@
 
 
 def slurm_parameters() -> list[dict[str, str]]:
-    parameters = [
-        {"modifiable": "true", "required": "true", "type": "STRING"} for _ in range(3)
-    ]
+    parameters = [{"modifiable": "true", "required": "true", "type": "STRING"} for _ in range(3)]
     parameters[0]["description"] = "Which Slurm partition should be used."
     parameters[0]["enumeration"] = ["prx", "mascot"]
     parameters[0]["key"] = "partition"
@@ -58,10 +56,7 @@ def upload_submitter_executable(
 
     if engine == "slurm":
         name = name or "yaml / Slurm executable"
-        description = (
-            description
-            or "Submitter executable for the bfabric functional test using Slurm."
-        )
+        description = description or "Submitter executable for the bfabric functional test using Slurm."
         attr["version"] = "1.03"
         attr["parameter"] = slurm_parameters()
     else:
diff --git a/bfabric_scripts/src/bfabric_scripts/cli/workunit/export_definition.py b/bfabric_scripts/src/bfabric_scripts/cli/workunit/export_definition.py
index af435489..230ef8d7 100644
--- a/bfabric_scripts/src/bfabric_scripts/cli/workunit/export_definition.py
+++ b/bfabric_scripts/src/bfabric_scripts/cli/workunit/export_definition.py
@@ -8,17 +8,13 @@
 
 
 @use_client
-def export_definition(
-    workunit_id: int, target_path: Path | None = None, *, client: Bfabric
-) -> None:
+def export_definition(workunit_id: int, target_path: Path | None = None, *, client: Bfabric) -> None:
     """Exports a workunit_definition.yml file for the specified workunit.
 
     :param workunit_id: the workunit ID
     :param target_path: the target path for the workunit_definition.yml file (default: workunit_definition.yml)
     """
-    target_path = (
-        target_path if target_path is not None else Path("workunit_definition.yml")
-    )
+    target_path = target_path if target_path is not None else Path("workunit_definition.yml")
     workunit_definition = WorkunitDefinition.from_ref(workunit_id, client=client)
     target_path.parent.mkdir(parents=True, exist_ok=True)
     data = workunit_definition.model_dump(mode="json")
diff --git a/bfabric_scripts/src/bfabric_scripts/cli/workunit/not_available.py b/bfabric_scripts/src/bfabric_scripts/cli/workunit/not_available.py
index 7cd026de..1e58db45 100644
--- a/bfabric_scripts/src/bfabric_scripts/cli/workunit/not_available.py
+++ b/bfabric_scripts/src/bfabric_scripts/cli/workunit/not_available.py
@@ -1,4 +1,6 @@
+from __future__ import annotations
 from datetime import datetime, timedelta
+from typing import Iterable
 
 from loguru import logger
 from rich.console import Console
@@ -9,9 +11,7 @@
 from bfabric_scripts.cli.base import use_client
 
 
-def render_output(
-    workunits_by_status: dict[str, list[Workunit]], client: Bfabric
-) -> None:
+def render_output(workunits: list[Workunit], client: Bfabric) -> None:
     """Renders the output as a table."""
     table = Table(
         Column("Application", no_wrap=False),
@@ -23,55 +23,75 @@ def render_output(
         Column("Nodelist", no_wrap=False),
     )
 
-    workunit_ids = [wu.id for wu_list in workunits_by_status.values() for wu in wu_list]
-    app_ids = {
-        wu["application"]["id"]
-        for wu_list in workunits_by_status.values()
-        for wu in wu_list
-    }
+    workunit_ids = [wu.id for wu in workunits]
+    app_ids = {wu["application"]["id"] for wu in workunits}
 
-    nodelist_params = Parameter.find_by(
-        {"workunitid": workunit_ids, "key": "nodelist"}, client
-    )
-    nodelist_values = {
-        param["workunit"]["id"]: param.value for param in nodelist_params.values()
-    }
+    nodelist_params = Parameter.find_by({"workunitid": workunit_ids, "key": "nodelist"}, client)
+    nodelist_values = {param["workunit"]["id"]: param.value for param in nodelist_params.values()}
     application_values = Application.find_all(ids=sorted(app_ids), client=client)
 
-    for status, workunits_all in workunits_by_status.items():
-        workunits = [
-            x for x in workunits_all if x["createdby"] not in ["gfeeder", "itfeeder"]
-        ]
-        status_color = {
-            "Pending": "yellow",
-            "Processing": "blue",
-            "Failed": "red",
-        }.get(status, "black")
-
-        for wu in workunits:
-            app = application_values[wu["application"]["id"]]
-            table.add_row(
-                f"[link={app.web_url}]A{wu['application']['id']:3} {app['name']}[/link]",
-                f"[link={wu.web_url}&tab=details]WU{wu['id']}[/link]",
-                wu["created"],
-                f"[{status_color}]{status}[/{status_color}]",
-                wu["createdby"],
-                wu["name"],
-                nodelist_values.get(wu.id, "N/A"),
-            )
+    status_colors = {
+        "PENDING": "yellow",
+        "PROCESSING": "blue",
+        "FAILED": "red",
+    }
+
+    for wu in workunits:
+        status_color = status_colors.get(wu["status"], "black")
+        app = application_values[wu["application"]["id"]]
+        table.add_row(
+            f"[link={app.web_url}]A{wu['application']['id']:3} {app['name']}[/link]",
+            f"[link={wu.web_url}&tab=details]WU{wu['id']}[/link]",
+            wu["created"],
+            f"[{status_color}]{wu['status']}[/{status_color}]",
+            wu["createdby"],
+            wu["name"],
+            nodelist_values.get(wu.id, "N/A"),
+        )
 
     console = Console()
     console.print(table)
 
 
+def sort_workunits_by(workunits: Iterable[Workunit], key: str) -> list[Workunit]:
+    if key == "status":
+        order = ["PENDING", "PROCESSING", "FAILED"]
+        return sorted(workunits, key=lambda wu: order.index(wu["status"]))
+    elif key in ("application", "app"):
+        return sorted(workunits, key=lambda wu: wu["application"]["id"])
+    else:
+        workunits_list = list(workunits)
+        if workunits_list and key in workunits_list[0]:
+            return sorted(workunits_list, key=lambda wu: wu[key])
+        logger.warning(f"Unknown sort key: {key}")
+        return list(workunits)
+
+
+def filter_workunits_by_user(workunits: list[Workunit], exclude_user: list[str] | None) -> list[Workunit]:
+    if exclude_user:
+        return [wu for wu in workunits if wu["createdby"] not in exclude_user]
+    return workunits
+
+
 @use_client
 def list_not_available_proteomics_workunits(
-    *, client: Bfabric, max_age: float = 14.0
+    *,
+    client: Bfabric,
+    max_age: float = 14.0,
+    sort_by: str = "status",
+    exclude_user: list[str] | None = None,
+    include_user: list[str] | None = None,
 ) -> None:
     """Lists not available analysis work units.
 
     :param max_age: The maximum age of work units in days.
+    :param sort_by: The field to sort the output by.
+    :param exclude_user: List of users to exclude from the output (implicit default: gfeeder, itfeeder)
+    :param include_user: List of users to include in the output
     """
+    if exclude_user and include_user:
+        raise ValueError("Cannot provide both include and exclude users")
+
     date_cutoff = datetime.today() - timedelta(days=max_age)
     console = Console()
     with console.capture() as capture:
@@ -82,10 +102,19 @@ def list_not_available_proteomics_workunits(
         )
     logger.info(capture.get())
 
-    workunits_by_status = {}
-    for status in ["Pending", "Processing", "Failed"]:
-        workunits_by_status[status] = Workunit.find_by(
-            {"status": status, "createdafter": date_cutoff.isoformat()}, client=client
-        ).values()
-
-    render_output(workunits_by_status, client=client)
+    extra_query = {}
+    if include_user:
+        extra_query["createdby"] = include_user
+    workunits = Workunit.find_by(
+        {
+            "status": ["Pending", "Processing", "Failed"],
+            "createdafter": date_cutoff.isoformat(),
+            **extra_query,
+        },
+        client=client,
+    ).values()
+    workunits = sort_workunits_by(workunits, sort_by)
+    if not include_user and not exclude_user:
+        exclude_user = ["gfeeder", "itfeeder"]
+    workunits = filter_workunits_by_user(workunits, exclude_user)
+    render_output(workunits, client=client)
diff --git a/bfabric_scripts/src/bfabric_scripts/fgcz_maxquant_scaffold-wrapper.py b/bfabric_scripts/src/bfabric_scripts/fgcz_maxquant_scaffold-wrapper.py
index d9286dfe..fa8f461f 100755
--- a/bfabric_scripts/src/bfabric_scripts/fgcz_maxquant_scaffold-wrapper.py
+++ b/bfabric_scripts/src/bfabric_scripts/fgcz_maxquant_scaffold-wrapper.py
@@ -46,18 +46,12 @@ def __init__(self, yamlfilename=None, zipfilename=None) -> None:
 
         try:
             self.fasta = os.path.basename(
-                self.config["application"]["parameters"][
-                    "/fastaFiles/FastaFileInfo/fastaFilePath"
-                ]
+                self.config["application"]["parameters"]["/fastaFiles/FastaFileInfo/fastaFilePath"]
             )
         except:
             raise
 
-        L = [
-            value
-            for values in self.config["application"]["input"].values()
-            for value in values
-        ]
+        L = [value for values in self.config["application"]["input"].values() for value in values]
 
         self.samples = list(map(lambda x: os.path.basename(x).replace(".raw", ""), L))
 
@@ -129,9 +123,7 @@ def run(self) -> None:
         eFastaDatabase.attrib["path"] = f"{os.getcwd()}/{self.fasta}"
 
         for s in self.samples:
-            eExperiment.extend(
-                self.getBiologicalSample(category=s, InputFile=self.zipfilename)
-            )
+            eExperiment.extend(self.getBiologicalSample(category=s, InputFile=self.zipfilename))
 
         xml.write(
             "/dev/stdout",
@@ -169,7 +161,5 @@ def run(self) -> None:
     )
 
     (options, args) = parser.parse_args()
-    driver = FgczMaxQuantScaffold(
-        yamlfilename=options.yaml_filename, zipfilename=options.zip_filename
-    )
+    driver = FgczMaxQuantScaffold(yamlfilename=options.yaml_filename, zipfilename=options.zip_filename)
     driver.run()
diff --git a/bfabric_scripts/src/bfabric_scripts/fgcz_maxquant_wrapper.py b/bfabric_scripts/src/bfabric_scripts/fgcz_maxquant_wrapper.py
index 2318db1d..f0b4d230 100755
--- a/bfabric_scripts/src/bfabric_scripts/fgcz_maxquant_wrapper.py
+++ b/bfabric_scripts/src/bfabric_scripts/fgcz_maxquant_wrapper.py
@@ -41,9 +41,7 @@ class FgczMaxQuantConfig:
     def __init__(self, config=None, scratch="/scratch/MAXQUANT/") -> None:
         if config:
             self.config = config
-            self.scratchdir = Path(
-                f"{scratch}/WU{self.config['job_configuration']['workunit_id']}"
-            )
+            self.scratchdir = Path(f"{scratch}/WU{self.config['job_configuration']['workunit_id']}")
 
             if not os.path.isdir(self.scratchdir):
                 print(f"no scratch dir '{self.scratchdir}'.")
@@ -99,9 +97,7 @@ def generate_mqpar(self, xml_filename, xml_template) -> None:
                     raise TypeError
 
                 estring = etree.Element("string")
-                estring.text = (
-                    f"{os.path.basename(input).replace('.raw', '').replace('.RAW', '')}"
-                )
+                estring.text = f"{os.path.basename(input).replace('.raw', '').replace('.RAW', '')}"
                 ecount += 1
                 element.extend(estring)
 
@@ -479,9 +475,7 @@ def run(self) -> None:
 """
 
 if __name__ == "__main__":
-    parser = OptionParser(
-        usage="usage: %prog -y <yaml formated config file>", version="%prog 1.0"
-    )
+    parser = OptionParser(usage="usage: %prog -y <yaml formated config file>", version="%prog 1.0")
 
     parser.add_option(
         "-y",
diff --git a/docs/changelog.md b/docs/changelog.md
index fd516535..ace55085 100644
--- a/docs/changelog.md
+++ b/docs/changelog.md
@@ -10,6 +10,12 @@ Versioning currently follows `X.Y.Z` where
 
 ## \[Unreleased\]
 
+## \[1.13.19\] - 2025-02-06
+
+### Fixed
+
+- Config: Log messages of app runner are shown by default again.
+
 ## \[1.13.18\] - 2025-01-28
 
 ### Changed
diff --git a/docs/index.md b/docs/index.md
index 8340e54d..bf3c8723 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -7,40 +7,60 @@ Several pieces of functionality are available:
     - General client for all B-Fabric web service operations (CRUD) and configuration management.
     - A relational API for low-boilerplate read access to the B-Fabric system.
 - Scripts: Several scripts we use more or less frequently to interact with the system.
-- A REST API: A REST API to interact with the B-Fabric system. This allows us to interact with B-Fabric from R using [bfabricShiny](https://github.com/cpanse/bfabricShiny).
+- A REST API: A REST API to interact with the B-Fabric system. This allows us to interact with B-Fabric from R
+    using [bfabricShiny](https://github.com/cpanse/bfabricShiny).
 
 Please see below for how to install bfabricPy.
 
 ## Installation
 
-The package is not available on PyPI as of now, but can be installed directly from GitHub and a `stable` branch is available for your convenience.
+The [bfabric](https://pypi.org/project/bfabric/) and [bfabric-scripts](https://pypi.org/project/bfabric-scripts/)
+packages are available on PyPI.
+If you want to use the API in your code the `bfabric` package already provides all relevant functionality, whereas
+`bfabric-scripts` will provide several command line tools to interact with the B-Fabric system.
 
-If you are only interested in running the command line scripts, installation with `uv tool` is recommended as it will create a separate virtual environment for bfabricPy and make it possible to upgrade your installation later easily.
+### Installing the tool
+
+If you are only interested in running the command line scripts, installation with `uv tool` is recommended as it will
+create a separate virtual environment for bfabric-scripts and make it possible to upgrade your installation later
+easily.
+
+```bash
+uv tool install -p 3.13 bfabric-scripts
+```
+
+You can upgrade this installation to the most recent version later with:
 
 ```bash
-uv tool install -p 3.13 "git+https://github.com/fgcz/bfabricPy.git@stable"
+uv tool upgrade bfabric-scripts
 ```
 
-If you want to add it to a `pyproject.toml` the syntax for specifying a git dependency is as follows:
+### Declaring a package dependency
+
+If you want to add it to a `pyproject.toml`, simply add bfabric to your dependencies:
 
 ```toml
 [project]
 dependencies = [
-    "bfabric @ git+https://github.com/fgcz/bfabricPy.git@stable"
+    "bfabric==x.y.z"
 ]
 ```
 
-## Updating
+where you replace `x.y.z` with the version you want to use.
 
-If you installed with `uv`, you can update the package to the most recent release with the following command:
+If you instead want to install a development version, you can specify the git repository and branch to use:
 
-```bash
-uv tool upgrade bfabric
+```toml
+[project]
+dependencies = [
+    "bfabric @ git+https://github.com/fgcz/bfabricPy.git@stable&subdirectory=bfabric#egg=bfabric",
+]
 ```
 
 ## Configuration
 
-Create a file as follows: (note: the password is not your login password, but the web service password available on your profile page)
+Create a file as follows: (note: the password is not your login password, but the web service password available on your
+profile page)
 
 ```yaml
 # ~/.bfabricpy.yml
@@ -54,7 +74,8 @@ PRODUCTION:
   base_url: https://fgcz-bfabric.uzh.ch/bfabric
 ```
 
-You can also append an additional config section for the TEST instance which will be used for instance when running the integration tests:
+You can also append an additional config section for the TEST instance which will be used for instance when running the
+integration tests:
 
 ```yaml
 TEST:
@@ -63,6 +84,9 @@ TEST:
   base_url: https://fgcz-bfabric-test.uzh.ch/bfabric
 ```
 
-When you run an application using bfabricPy, and it does not explicitly set the config when calling `Bfabric.from_config`, you can adjust the
-environment that is used by setting the environemnt variable `BFABRICPY_CONFIG_ENV` to the name of the config section you want to use.
-Command line scripts will log the user and base URL that is used, so you can verify that you are indeed using the correct environment.
+When you run an application using bfabricPy, and it does not explicitly set the config when calling
+`Bfabric.from_config`, you can adjust the
+environment that is used by setting the environemnt variable `BFABRICPY_CONFIG_ENV` to the name of the config section
+you want to use.
+Command line scripts will log the user and base URL that is used, so you can verify that you are indeed using the
+correct environment.
diff --git a/noxfile.py b/noxfile.py
index 54aaa48f..2941c8a0 100644
--- a/noxfile.py
+++ b/noxfile.py
@@ -23,12 +23,10 @@ def tests(session):
 
 @nox.session(python=["3.13"])
 def test_app_runner(session):
-    # TODO this one has a problem that bfabric gets installed from `@main` (so it could break CI)
-    session.install("./bfabric")
-    session.install("./app_runner[test]")
-    session.install("--upgrade", "./bfabric")
+    session.install("-e", "./bfabric")
+    session.install("./bfabric_app_runner[test]")
     session.run("uv", "pip", "list")
-    session.run("pytest", "--durations=50", "tests/app_runner")
+    session.run("pytest", "--durations=50", "tests/bfabric_app_runner")
 
 
 @nox.session
@@ -53,12 +51,12 @@ def docs(session):
         session.install("./bfabric[doc]")
         session.run("mkdocs", "build", "-d", Path(tmpdir) / "build_bfabricpy")
 
-        session.install("./app_runner[doc]")
+        session.install("./bfabric_app_runner[doc]")
         session.run(
             "sphinx-build",
             "-M",
             "html",
-            "app_runner/docs",
+            "bfabric_app_runner/docs",
             Path(tmpdir) / "build_app_runner",
         )
 
@@ -67,9 +65,7 @@ def docs(session):
             shutil.rmtree(target_dir)
 
         shutil.copytree(Path(tmpdir) / "build_bfabricpy", target_dir)
-        shutil.copytree(
-            Path(tmpdir) / "build_app_runner" / "html", target_dir / "app_runner"
-        )
+        shutil.copytree(Path(tmpdir) / "build_app_runner" / "html", target_dir / "app_runner")
 
 
 @nox.session(default=False)
diff --git a/pyproject.toml b/pyproject.toml
index 43300ffe..5a8eb33c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -7,3 +7,12 @@ logot_capturer = "logot.loguru.LoguruCapturer"
 "**/examples/**" = ["ALL"]
 "**/tests/**" = ["ALL"]
 "noxfile.py" = ["ALL"]
+
+[tool.black]
+line-length = 120
+target-version = ["py311"]
+
+[tool.ruff]
+line-length = 120
+indent-width = 4
+target-version = "py39"
diff --git a/tests/bfabric/config/test_bfabric_auth.py b/tests/bfabric/config/test_bfabric_auth.py
index f2624851..8cbeadca 100644
--- a/tests/bfabric/config/test_bfabric_auth.py
+++ b/tests/bfabric/config/test_bfabric_auth.py
@@ -11,17 +11,11 @@ def example_config_path() -> Path:
 
 
 def test_bfabric_auth_repr() -> None:
-    assert (
-        repr(BfabricAuth(login="login", password="x" * 32))
-        == "BfabricAuth(login='login', password=...)"
-    )
+    assert repr(BfabricAuth(login="login", password="x" * 32)) == "BfabricAuth(login='login', password=...)"
 
 
 def test_bfabric_auth_str() -> None:
-    assert (
-        str(BfabricAuth(login="login", password="x" * 32))
-        == "BfabricAuth(login='login', password=...)"
-    )
+    assert str(BfabricAuth(login="login", password="x" * 32)) == "BfabricAuth(login='login', password=...)"
 
 
 if __name__ == "__main__":
diff --git a/tests/bfabric/config/test_bfabric_client_config.py b/tests/bfabric/config/test_bfabric_client_config.py
index 682f408d..c156efc9 100644
--- a/tests/bfabric/config/test_bfabric_client_config.py
+++ b/tests/bfabric/config/test_bfabric_client_config.py
@@ -30,9 +30,7 @@ def test_bfabric_config_default_params_when_omitted() -> None:
 
 
 def test_bfabric_config_default_params_when_specified() -> None:
-    config = BfabricClientConfig(
-        base_url=None, application_ids=None, job_notification_emails=None
-    )
+    config = BfabricClientConfig(base_url=None, application_ids=None, job_notification_emails=None)
     assert config.base_url == "https://fgcz-bfabric.uzh.ch/bfabric"
     assert config.application_ids == {}
     assert config.job_notification_emails == ""
@@ -66,9 +64,7 @@ def test_bfabric_config_copy_with_replaced_when_invalid(
         mock_config.copy_with(base_url="not a url")
 
 
-def test_bfabric_config_read_yml_bypath_default(
-    mocker: MockerFixture, example_config_path: Path, logot: Logot
-) -> None:
+def test_bfabric_config_read_yml_bypath_default(mocker: MockerFixture, example_config_path: Path, logot: Logot) -> None:
     # Ensure environment variable is not available, and the default is environment is loaded
     mocker.patch.dict(os.environ, {}, clear=True)
 
@@ -77,16 +73,8 @@ def test_bfabric_config_read_yml_bypath_default(
     assert auth.password == "01234567890123456789012345678901"
     assert config.base_url == "https://mega-production-server.uzh.ch/myprod"
 
-    logot.assert_logged(
-        logged.debug(
-            f"Reading configuration from: {str(example_config_path.absolute())}"
-        )
-    )
-    logot.assert_logged(
-        logged.debug(
-            "BFABRICPY_CONFIG_ENV not found, using default environment PRODUCTION"
-        )
-    )
+    logot.assert_logged(logged.debug(f"Reading configuration from: {str(example_config_path.absolute())}"))
+    logot.assert_logged(logged.debug("BFABRICPY_CONFIG_ENV not found, using default environment PRODUCTION"))
 
 
 def test_bfabric_config_read_yml_bypath_environment_variable(
@@ -100,11 +88,7 @@ def test_bfabric_config_read_yml_bypath_environment_variable(
     assert auth.password == "012345678901234567890123456789ff"
     assert config.base_url == "https://mega-test-server.uzh.ch/mytest"
 
-    logot.assert_logged(
-        logged.debug(
-            f"Reading configuration from: {str(example_config_path.absolute())}"
-        )
-    )
+    logot.assert_logged(logged.debug(f"Reading configuration from: {str(example_config_path.absolute())}"))
     logot.assert_logged(logged.debug("found BFABRICPY_CONFIG_ENV = TEST"))
 
 
diff --git a/tests/bfabric/config/test_config_file.py b/tests/bfabric/config/test_config_file.py
index a2ec11ec..cab1129d 100644
--- a/tests/bfabric/config/test_config_file.py
+++ b/tests/bfabric/config/test_config_file.py
@@ -69,10 +69,7 @@ def test_config_file_when_auth(data_with_auth):
     assert len(config.environments) == 1
     assert config.environments["PRODUCTION"].config.base_url == "https://example.com/"
     assert config.environments["PRODUCTION"].auth.login == "test-dummy"
-    assert (
-        config.environments["PRODUCTION"].auth.password
-        == "00000000001111111111222222222233"
-    )
+    assert config.environments["PRODUCTION"].auth.password == "00000000001111111111222222222233"
 
 
 def test_config_file_when_no_auth(data_no_auth):
@@ -91,9 +88,7 @@ def test_config_file_when_multiple(data_multiple):
     assert config.environments["PRODUCTION"].auth is None
     assert config.environments["TEST"].config.base_url == "https://test.example.com/"
     assert config.environments["TEST"].auth.login == "test-dummy"
-    assert (
-        config.environments["TEST"].auth.password == "00000000001111111111222222222233"
-    )
+    assert config.environments["TEST"].auth.password == "00000000001111111111222222222233"
 
 
 def test_config_file_when_non_existent_default(data_no_auth):
@@ -117,13 +112,8 @@ def test_get_selected_config_env_when_default(config_with_auth, monkeypatch):
 
 
 def test_get_selected_config(config_with_auth, mocker):
-    mock_get_config_env = mocker.patch.object(
-        ConfigFile, "get_selected_config_env", return_value="PRODUCTION"
-    )
-    assert (
-        config_with_auth.get_selected_config()
-        == config_with_auth.environments["PRODUCTION"]
-    )
+    mock_get_config_env = mocker.patch.object(ConfigFile, "get_selected_config_env", return_value="PRODUCTION")
+    assert config_with_auth.get_selected_config() == config_with_auth.environments["PRODUCTION"]
     mock_get_config_env.assert_called_once_with(explicit_config_env=None)
 
 
diff --git a/tests/bfabric/engine/test_engine_suds.py b/tests/bfabric/engine/test_engine_suds.py
index 3bd54548..99631b3d 100644
--- a/tests/bfabric/engine/test_engine_suds.py
+++ b/tests/bfabric/engine/test_engine_suds.py
@@ -32,9 +32,7 @@ def mock_client(mock_suds_service):
 
 
 def test_read(engine_suds, mock_auth, mock_suds_service, mocker):
-    mocker.patch.object(
-        engine_suds, "_get_suds_service", return_value=mock_suds_service
-    )
+    mocker.patch.object(engine_suds, "_get_suds_service", return_value=mock_suds_service)
     mock_convert = mocker.patch.object(engine_suds, "_convert_results")
 
     obj = {"field1": "value1"}
@@ -52,9 +50,7 @@ def test_read(engine_suds, mock_auth, mock_suds_service, mocker):
 
 
 def test_save(engine_suds, mock_auth, mock_suds_service, mocker):
-    mocker.patch.object(
-        engine_suds, "_get_suds_service", return_value=mock_suds_service
-    )
+    mocker.patch.object(engine_suds, "_get_suds_service", return_value=mock_suds_service)
     mock_convert = mocker.patch.object(engine_suds, "_convert_results")
 
     obj = {"field1": "value1"}
@@ -70,9 +66,7 @@ def test_save(engine_suds, mock_auth, mock_suds_service, mocker):
 
 
 def test_save_method_not_found(engine_suds, mock_auth, mock_suds_service, mocker):
-    mocker.patch.object(
-        engine_suds, "_get_suds_service", return_value=mock_suds_service
-    )
+    mocker.patch.object(engine_suds, "_get_suds_service", return_value=mock_suds_service)
     mock_suds_service.save.side_effect = MethodNotFound("save")
 
     with pytest.raises(
@@ -83,9 +77,7 @@ def test_save_method_not_found(engine_suds, mock_auth, mock_suds_service, mocker
 
 
 def test_delete(engine_suds, mock_auth, mock_suds_service, mocker):
-    mocker.patch.object(
-        engine_suds, "_get_suds_service", return_value=mock_suds_service
-    )
+    mocker.patch.object(engine_suds, "_get_suds_service", return_value=mock_suds_service)
     mock_convert = mocker.patch.object(engine_suds, "_convert_results")
 
     engine_suds.delete("sample", 123, mock_auth)
@@ -96,9 +88,7 @@ def test_delete(engine_suds, mock_auth, mock_suds_service, mocker):
 
 
 def test_delete_empty_list(engine_suds, mock_auth, mock_suds_service, mocker):
-    mocker.patch.object(
-        engine_suds, "_get_suds_service", return_value=mock_suds_service
-    )
+    mocker.patch.object(engine_suds, "_get_suds_service", return_value=mock_suds_service)
 
     result = engine_suds.delete("sample", [], mock_auth)
 
@@ -109,16 +99,12 @@ def test_delete_empty_list(engine_suds, mock_auth, mock_suds_service, mocker):
 
 
 def test_get_suds_service(engine_suds, mock_client, mocker):
-    mock_client_init = mocker.patch(
-        "bfabric.engine.engine_suds.Client", return_value=mock_client
-    )
+    mock_client_init = mocker.patch("bfabric.engine.engine_suds.Client", return_value=mock_client)
 
     service = engine_suds._get_suds_service("sample")
 
     assert service == mock_client.service
-    mock_client_init.assert_called_once_with(
-        "http://example.com/api/sample?wsdl", cache=None
-    )
+    mock_client_init.assert_called_once_with("http://example.com/api/sample?wsdl", cache=None)
 
     # Test caching
     service2 = engine_suds._get_suds_service("sample")
diff --git a/tests/bfabric/engine/test_engine_zeep.py b/tests/bfabric/engine/test_engine_zeep.py
index 72def595..956d7d85 100644
--- a/tests/bfabric/engine/test_engine_zeep.py
+++ b/tests/bfabric/engine/test_engine_zeep.py
@@ -77,9 +77,7 @@ def test_save(engine_zeep, mock_auth, mock_zeep_client, mocker):
 
 def test_save_method_not_found(engine_zeep, mock_auth, mock_zeep_client, mocker):
     mocker.patch.object(engine_zeep, "_get_client", return_value=mock_zeep_client)
-    mock_zeep_client.service.save.side_effect = AttributeError(
-        "Service has no operation 'save'"
-    )
+    mock_zeep_client.service.save.side_effect = AttributeError("Service has no operation 'save'")
 
     with pytest.raises(
         BfabricRequestError,
@@ -111,9 +109,7 @@ def test_delete_empty_list(engine_zeep, mock_auth, mock_zeep_client, mocker):
 
 
 def test_get_client(engine_zeep, mocker):
-    mock_zeep_client = mocker.patch(
-        "zeep.Client", return_value=MagicMock(spec=zeep.Client)
-    )
+    mock_zeep_client = mocker.patch("zeep.Client", return_value=MagicMock(spec=zeep.Client))
 
     client = engine_zeep._get_client("sample")
 
@@ -186,9 +182,7 @@ def test_zeep_query_append_skipped():
     result_no_overwrite = _zeep_query_append_skipped(query_with_existing, skipped_keys)
     assert result_no_overwrite == query_with_existing
 
-    result_overwrite = _zeep_query_append_skipped(
-        query_with_existing, skipped_keys, overwrite=True
-    )
+    result_overwrite = _zeep_query_append_skipped(query_with_existing, skipped_keys, overwrite=True)
     assert result_overwrite == {"key1": zeep.xsd.SkipValue, "key2": zeep.xsd.SkipValue}
 
 
diff --git a/tests/bfabric/entities/core/test_entity.py b/tests/bfabric/entities/core/test_entity.py
index 5ac43236..7ed028fc 100644
--- a/tests/bfabric/entities/core/test_entity.py
+++ b/tests/bfabric/entities/core/test_entity.py
@@ -83,9 +83,7 @@ def test_find_by_when_found(mocker, mock_client) -> None:
     assert len(entities) == 1
     assert isinstance(entities[1], Entity)
     assert entities[1].data_dict == {"id": 1, "name": "Test Entity"}
-    mock_client.read.assert_called_once_with(
-        "test_endpoint", obj={"id": 1}, max_results=100
-    )
+    mock_client.read.assert_called_once_with("test_endpoint", obj={"id": 1}, max_results=100)
 
 
 def test_find_by_when_not_found(mocker, mock_client) -> None:
@@ -93,9 +91,7 @@ def test_find_by_when_not_found(mocker, mock_client) -> None:
     mocker.patch.object(Entity, "ENDPOINT", new="test_endpoint")
     entities = Entity.find_by({"id": 1}, mock_client)
     assert len(entities) == 0
-    mock_client.read.assert_called_once_with(
-        "test_endpoint", obj={"id": 1}, max_results=100
-    )
+    mock_client.read.assert_called_once_with("test_endpoint", obj={"id": 1}, max_results=100)
 
 
 def test_get_item(mock_entity) -> None:
diff --git a/tests/bfabric/entities/core/test_has_many.py b/tests/bfabric/entities/core/test_has_many.py
index 52815bac..77cbe1fe 100644
--- a/tests/bfabric/entities/core/test_has_many.py
+++ b/tests/bfabric/entities/core/test_has_many.py
@@ -44,9 +44,7 @@ def test_has_many_init():
 
 
 def test_has_many_get(mock_client):
-    mock_obj = MockEntity(
-        data_dict={"test_field": [{"id": 1}, {"id": 2}]}, client=mock_client
-    )
+    mock_obj = MockEntity(data_dict={"test_field": [{"id": 1}, {"id": 2}]}, client=mock_client)
     has_many = HasMany("MockEntity", bfabric_field="test_field")
 
     result = has_many.__get__(mock_obj)
@@ -74,9 +72,7 @@ def test_has_many_get_invalid_config():
     has_many = HasMany("MockEntity")
     mock_obj = MockEntity()
 
-    with pytest.raises(
-        ValueError, match="Exactly one of bfabric_field and ids_property must be set"
-    ):
+    with pytest.raises(ValueError, match="Exactly one of bfabric_field and ids_property must be set"):
         has_many.__get__(mock_obj)
 
 
@@ -109,9 +105,7 @@ def test_has_many_proxy_polars(mocker: MockerFixture, mock_client, mock_proxy):
     result = mock_proxy.polars
 
     assert isinstance(result, DataFrame)
-    DataFrame.__init__.assert_called_once_with(
-        [x.data_dict for x in mock_entities.values()]
-    )
+    DataFrame.__init__.assert_called_once_with([x.data_dict for x in mock_entities.values()])
 
 
 def test_has_many_proxy_getitem(mocker: MockerFixture, mock_client, mock_proxy):
diff --git a/tests/bfabric/entities/core/test_has_one.py b/tests/bfabric/entities/core/test_has_one.py
index c6b3da0b..aa212c8f 100644
--- a/tests/bfabric/entities/core/test_has_one.py
+++ b/tests/bfabric/entities/core/test_has_one.py
@@ -37,9 +37,7 @@ def test_init():
 def test_get_when_cache_not_exists(mocker, mock_client):
     mock_obj = MockEntity(data_dict={"test_field": {"id": 1}}, client=mock_client)
     has_one = HasOne("MockEntity", bfabric_field="test_field")
-    mock_load_entity = mocker.patch.object(
-        HasOne, "_load_entity", return_value="mock_entity"
-    )
+    mock_load_entity = mocker.patch.object(HasOne, "_load_entity", return_value="mock_entity")
     result = has_one.__get__(mock_obj)
     assert result == "mock_entity"
     mock_load_entity.assert_called_once_with(obj=mock_obj)
@@ -49,9 +47,7 @@ def test_get_when_cache_exists(mocker, mock_client):
     mock_obj = MockEntity(data_dict={"test_field": {"id": 1}}, client=mock_client)
     has_one = HasOne("MockEntity", bfabric_field="test_field")
     mock_obj._HasOne__test_field_cache = "mock_entity"
-    mock_load_entity = mocker.patch.object(
-        HasOne, "_load_entity", return_value="mock_entity"
-    )
+    mock_load_entity = mocker.patch.object(HasOne, "_load_entity", return_value="mock_entity")
     result = has_one.__get__(mock_obj)
     assert result == "mock_entity"
     mock_load_entity.assert_not_called()
diff --git a/tests/bfabric/entities/test_dataset.py b/tests/bfabric/entities/test_dataset.py
index f88a3fa5..19a6059f 100644
--- a/tests/bfabric/entities/test_dataset.py
+++ b/tests/bfabric/entities/test_dataset.py
@@ -71,17 +71,11 @@ def test_write_csv(mocker: MockFixture, mock_dataset: Dataset) -> None:
 
 
 def test_repr(mock_empty_dataset: Dataset) -> None:
-    assert (
-        repr(mock_empty_dataset)
-        == "Dataset({'id': 1234, 'attribute': [], 'item': []}, client=None)"
-    )
+    assert repr(mock_empty_dataset) == "Dataset({'id': 1234, 'attribute': [], 'item': []}, client=None)"
 
 
 def test_str(mock_empty_dataset: Dataset) -> None:
-    assert (
-        str(mock_empty_dataset)
-        == "Dataset({'id': 1234, 'attribute': [], 'item': []}, client=None)"
-    )
+    assert str(mock_empty_dataset) == "Dataset({'id': 1234, 'attribute': [], 'item': []}, client=None)"
 
 
 if __name__ == "__main__":
diff --git a/tests/bfabric/entities/test_workunit.py b/tests/bfabric/entities/test_workunit.py
index dfa9046c..c0f82f26 100644
--- a/tests/bfabric/entities/test_workunit.py
+++ b/tests/bfabric/entities/test_workunit.py
@@ -101,13 +101,8 @@ def test_store_output_folder(mocker, mock_workunit) -> None:
         "name": "my app",
     }.__getitem__
     mocker.patch.object(mock_workunit, "application", mock_application)
-    mocker.patch.object(
-        Workunit, "container", mocker.PropertyMock(return_value=mocker.MagicMock(id=12))
-    )
-    assert (
-        Path("xyz12/bfabric/tech/my_app/2024/2024-01/2024-01-02/workunit_30000")
-        == mock_workunit.store_output_folder
-    )
+    mocker.patch.object(Workunit, "container", mocker.PropertyMock(return_value=mocker.MagicMock(id=12)))
+    assert Path("xyz12/bfabric/tech/my_app/2024/2024-01/2024-01-02/workunit_30000") == mock_workunit.store_output_folder
 
 
 def test_repr() -> None:
diff --git a/tests/bfabric/results/test_result_container.py b/tests/bfabric/results/test_result_container.py
index d115265b..6c24aa1e 100644
--- a/tests/bfabric/results/test_result_container.py
+++ b/tests/bfabric/results/test_result_container.py
@@ -10,9 +10,7 @@ class BfabricTestResultContainer(unittest.TestCase):
     def setUp(self):
         self.res1 = ResultContainer([1, 2, 3], total_pages_api=1)
         self.res2 = ResultContainer([4, 5], total_pages_api=1)
-        self.res_with_empty = ResultContainer(
-            [{"a": None, "b": 1, "c": []}, {"a": 2, "b": 3, "c": None}]
-        )
+        self.res_with_empty = ResultContainer([{"a": None, "b": 1, "c": []}, {"a": 2, "b": 3, "c": None}])
 
     def test_str(self):
         self.assertEqual("[1, 2, 3]", str(self.res1))
@@ -56,9 +54,7 @@ def test_assert_success_when_error(self):
         self.res1.errors.append("MockedError")
         with self.assertRaises(RuntimeError) as error:
             self.res1.assert_success()
-        self.assertEqual(
-            "('Query was not successful', ['MockedError'])", str(error.exception)
-        )
+        self.assertEqual("('Query was not successful', ['MockedError'])", str(error.exception))
 
     def test_extend_when_same_lengths(self):
         res1 = ResultContainer([{"a": 1}, {"a": 2}], total_pages_api=5)
@@ -79,31 +75,23 @@ def test_extend_when_different_lengths(self):
         self.assertEqual(203, len(res3))
         self.assertEqual(list(range(200, 400)) + [1, 2, 3], res3.results)
         self.assertEqual(2, res3.total_pages_api)
-        self.assertIn(
-            "Results observed with different total pages counts: 2 != 1", str(error)
-        )
+        self.assertIn("Results observed with different total pages counts: 2 != 1", str(error))
 
     def test_to_list_dict_when_not_drop_empty(self):
         expected = [{"a": None, "b": 1, "c": []}, {"a": 2, "b": 3, "c": None}]
         with self.subTest(case="default"):
             self.assertListEqual(expected, self.res_with_empty.to_list_dict())
         with self.subTest(case="explicit"):
-            self.assertListEqual(
-                expected, self.res_with_empty.to_list_dict(drop_empty=False)
-            )
+            self.assertListEqual(expected, self.res_with_empty.to_list_dict(drop_empty=False))
 
     def test_to_list_dict_when_drop_empty(self):
         expected = [{"b": 1}, {"a": 2, "b": 3}]
-        self.assertListEqual(
-            expected, self.res_with_empty.to_list_dict(drop_empty=True)
-        )
+        self.assertListEqual(expected, self.res_with_empty.to_list_dict(drop_empty=True))
 
     def test_to_polars(self):
         res = ResultContainer([{"a": 1, "b": 2}, {"a": 3, "b": 4}])
         df = res.to_polars()
-        polars.testing.assert_frame_equal(
-            polars.DataFrame({"a": [1, 3], "b": [2, 4]}), df
-        )
+        polars.testing.assert_frame_equal(polars.DataFrame({"a": [1, 3], "b": [2, 4]}), df)
 
 
 if __name__ == "__main__":
diff --git a/tests/bfabric/test_bfabric.py b/tests/bfabric/test_bfabric.py
index 2c29ed4a..1c375930 100644
--- a/tests/bfabric/test_bfabric.py
+++ b/tests/bfabric/test_bfabric.py
@@ -55,9 +55,7 @@ def test_from_config_when_explicit_auth(mocker):
     assert isinstance(client, Bfabric)
     assert client.config == mock_config
     assert client.auth == mock_auth
-    mock_get_system_auth.assert_called_once_with(
-        config_env="TestingEnv", config_path=None
-    )
+    mock_get_system_auth.assert_called_once_with(config_env="TestingEnv", config_path=None)
 
 
 def test_from_config_when_none_auth(mocker):
@@ -74,9 +72,7 @@ def test_from_config_when_none_auth(mocker):
     assert client.config == mock_config
     with pytest.raises(ValueError, match="Authentication not available"):
         _ = client.auth
-    mock_get_system_auth.assert_called_once_with(
-        config_env="TestingEnv", config_path=None
-    )
+    mock_get_system_auth.assert_called_once_with(config_env="TestingEnv", config_path=None)
 
 
 def test_from_config_when_engine_suds(mocker):
@@ -130,9 +126,7 @@ def test_auth_when_missing(bfabric_instance):
 
 def test_auth_when_provided(mock_config, mock_engine):
     mock_auth = MagicMock(name="mock_auth")
-    bfabric_instance = Bfabric(
-        config=mock_config, auth=mock_auth, engine=BfabricAPIEngineType.SUDS
-    )
+    bfabric_instance = Bfabric(config=mock_config, auth=mock_auth, engine=BfabricAPIEngineType.SUDS)
     assert bfabric_instance.auth == mock_auth
 
 
@@ -164,9 +158,7 @@ def test_read_when_no_pages_available_and_check(bfabric_instance, mocker):
     bfabric_instance._auth = mock_auth
 
     mock_engine = mocker.patch.object(bfabric_instance, "_engine")
-    mock_result = MagicMock(
-        name="mock_result", total_pages_api=0, assert_success=MagicMock()
-    )
+    mock_result = MagicMock(name="mock_result", total_pages_api=0, assert_success=MagicMock())
     mock_engine.read.return_value = mock_result
 
     result = bfabric_instance.read(endpoint="mock_endpoint", obj="mock_obj")
@@ -187,9 +179,7 @@ def test_read_when_pages_available_and_check(bfabric_instance, mocker):
     mock_auth = MagicMock(name="mock_auth")
     bfabric_instance._auth = mock_auth
 
-    mock_compute_requested_pages = mocker.patch(
-        "bfabric.bfabric.compute_requested_pages"
-    )
+    mock_compute_requested_pages = mocker.patch("bfabric.bfabric.compute_requested_pages")
     mock_engine = mocker.patch.object(bfabric_instance, "_engine")
 
     mock_page_results = [
@@ -205,9 +195,7 @@ def test_read_when_pages_available_and_check(bfabric_instance, mocker):
     mock_page_results[1].__getitem__.side_effect = lambda i: [6, 7, 8, 9, 10][i]
     mock_page_results[2].__getitem__.side_effect = lambda i: [11, 12, 13, 14, 15][i]
 
-    mock_engine.read.side_effect = lambda **kwargs: mock_page_results[
-        kwargs["page"] - 1
-    ]
+    mock_engine.read.side_effect = lambda **kwargs: mock_page_results[kwargs["page"] - 1]
     mock_compute_requested_pages.return_value = ([1, 2], 4)
 
     result = bfabric_instance.read(endpoint="mock_endpoint", obj="mock_obj")
@@ -301,9 +289,7 @@ def test_delete_when_auth_and_check_false(bfabric_instance, mocker):
 
     assert result == mock_engine.delete.return_value
     method_assert_success.assert_not_called()
-    mock_engine.delete.assert_called_once_with(
-        endpoint="test_endpoint", id=10, auth=mock_auth
-    )
+    mock_engine.delete.assert_called_once_with(endpoint="test_endpoint", id=10, auth=mock_auth)
 
 
 def test_delete_when_auth_and_check_true(bfabric_instance, mocker):
@@ -318,9 +304,7 @@ def test_delete_when_auth_and_check_true(bfabric_instance, mocker):
 
     assert result == mock_engine.delete.return_value
     method_assert_success.assert_called_once()
-    mock_engine.delete.assert_called_once_with(
-        endpoint="test_endpoint", id=10, auth=mock_auth
-    )
+    mock_engine.delete.assert_called_once_with(endpoint="test_endpoint", id=10, auth=mock_auth)
 
 
 def test_exists_when_true(bfabric_instance, mocker):
@@ -363,9 +347,7 @@ def test_exists_when_false(bfabric_instance, mocker):
     mock_read = mocker.patch.object(Bfabric, "read")
     mock_read.return_value.__len__.return_value = 0
 
-    assert not bfabric_instance.exists(
-        endpoint="test_endpoint", key="key", value="value"
-    )
+    assert not bfabric_instance.exists(endpoint="test_endpoint", key="key", value="value")
 
     mock_read.assert_called_once_with(
         endpoint="test_endpoint",
@@ -401,18 +383,14 @@ def test_upload_resource(bfabric_instance, mocker):
 def test_get_version_message(mock_config, bfabric_instance):
     mock_config.base_url = "dummy_url"
     line1, line2 = bfabric_instance._get_version_message()
-    pattern = (
-        r"bfabricPy v\d+\.\d+\.\d+ \(EngineSUDS, dummy_url, U=None, PY=\d\.\d+\.\d+\)"
-    )
+    pattern = r"bfabricPy v\d+\.\d+\.\d+ \(EngineSUDS, dummy_url, U=None, PY=\d\.\d+\.\d+\)"
     assert re.match(pattern, line1)
     year = datetime.datetime.now().year
     assert line2 == f"Copyright (C) 2014-{year} Functional Genomics Center Zurich"
 
 
 def test_log_version_message(mocker, bfabric_instance):
-    mocker.patch.object(
-        Bfabric, "_get_version_message", return_value=("line1", "line2")
-    )
+    mocker.patch.object(Bfabric, "_get_version_message", return_value=("line1", "line2"))
     mock_logger = mocker.patch("bfabric.bfabric.logger")
     bfabric_instance._log_version_message()
     assert mock_logger.info.mock_calls == [call("line1"), call("line2")]
diff --git a/tests/bfabric/test_bfabric_config.py b/tests/bfabric/test_bfabric_config.py
index ec1dfa55..bb1ddd70 100644
--- a/tests/bfabric/test_bfabric_config.py
+++ b/tests/bfabric/test_bfabric_config.py
@@ -19,9 +19,7 @@ def test_read_yml_bypath_all_fields(example_config_path: Path) -> None:
         "Proteomics/DUCK_666": 12,
     }
 
-    job_notification_emails_ground_truth = (
-        "john.snow@fgcz.uzh.ch billy.the.kid@fgcz.ethz.ch"
-    )
+    job_notification_emails_ground_truth = "john.snow@fgcz.uzh.ch billy.the.kid@fgcz.ethz.ch"
 
     assert auth.login == "my_epic_test_login"
     assert auth.password == "012345678901234567890123456789ff"
@@ -36,11 +34,7 @@ def test_read_yml_when_empty_optional(example_config_path: Path, logot: Logot) -
     assert config.base_url == "https://standby-server.uzh.ch/mystandby"
     assert config.application_ids == {}
     assert config.job_notification_emails == ""
-    logot.assert_logged(
-        logged.debug(
-            f"Reading configuration from: {str(example_config_path.absolute())}"
-        )
-    )
+    logot.assert_logged(logged.debug(f"Reading configuration from: {str(example_config_path.absolute())}"))
 
 
 if __name__ == "__main__":
diff --git a/tests/bfabric/wrapper_creator/test_slurm.py b/tests/bfabric/wrapper_creator/test_slurm.py
index cddbfefb..38f793f5 100644
--- a/tests/bfabric/wrapper_creator/test_slurm.py
+++ b/tests/bfabric/wrapper_creator/test_slurm.py
@@ -15,9 +15,7 @@ def mock_slurm() -> SLURM:
 
 
 @pytest.mark.parametrize("path", ["/tmp/hello/world.txt", Path("/tmp/hello/world.txt")])
-def test_sbatch_when_success(
-    mocker: MockerFixture, mock_slurm: SLURM, path: Path | str
-) -> None:
+def test_sbatch_when_success(mocker: MockerFixture, mock_slurm: SLURM, path: Path | str) -> None:
     mock_is_file = mocker.patch.object(Path, "is_file", return_value=True)
     mocker.patch("os.environ", new={"x": "y"})
     mock_run = mocker.patch(
@@ -38,9 +36,7 @@ def test_sbatch_when_success(
     assert mock_is_file.call_count == 2
 
 
-def test_sbatch_when_script_not_exists(
-    mocker: MockerFixture, mock_slurm: SLURM, logot: Logot
-) -> None:
+def test_sbatch_when_script_not_exists(mocker: MockerFixture, mock_slurm: SLURM, logot: Logot) -> None:
     mocker.patch("bfabric.wrapper_creator.slurm.Path", side_effect=lambda x: x)
     mock_script = mocker.MagicMock(name="script", is_file=lambda: False)
     result = mock_slurm.sbatch(script=mock_script)
@@ -48,14 +44,10 @@ def test_sbatch_when_script_not_exists(
     logot.assert_logged(logged.error(f"Script not found: {mock_script}"))
 
 
-def test_sbatch_when_sbatch_not_exists(
-    mocker: MockerFixture, mock_slurm: SLURM, logot: Logot
-) -> None:
+def test_sbatch_when_sbatch_not_exists(mocker: MockerFixture, mock_slurm: SLURM, logot: Logot) -> None:
     mocker.patch("bfabric.wrapper_creator.slurm.Path", side_effect=lambda x: x)
     mock_script = mocker.MagicMock(name="script", is_file=lambda: True)
-    mock_sbatch = mocker.patch.object(
-        mock_slurm, "_sbatch_bin", mocker.MagicMock(is_file=lambda: False)
-    )
+    mock_sbatch = mocker.patch.object(mock_slurm, "_sbatch_bin", mocker.MagicMock(is_file=lambda: False))
     result = mock_slurm.sbatch(script=mock_script)
     assert result is None
     logot.assert_logged(logged.error(f"sbatch binary not found: {mock_sbatch}"))
diff --git a/tests/app_runner/__init__.py b/tests/bfabric_app_runner/__init__.py
similarity index 100%
rename from tests/app_runner/__init__.py
rename to tests/bfabric_app_runner/__init__.py
diff --git a/tests/app_runner/app_runner/__init__.py b/tests/bfabric_app_runner/app_runner/__init__.py
similarity index 100%
rename from tests/app_runner/app_runner/__init__.py
rename to tests/bfabric_app_runner/app_runner/__init__.py
diff --git a/tests/bfabric_app_runner/app_runner/test_prepare_file_spec.py b/tests/bfabric_app_runner/app_runner/test_prepare_file_spec.py
new file mode 100644
index 00000000..55495175
--- /dev/null
+++ b/tests/bfabric_app_runner/app_runner/test_prepare_file_spec.py
@@ -0,0 +1,190 @@
+from pathlib import Path
+from shutil import SameFileError
+from subprocess import CalledProcessError
+
+import pytest
+from logot import Logot, logged
+
+from bfabric_app_runner.input_preparation.prepare_file_spec import (
+    prepare_file_spec,
+    _operation_copy_rsync,
+    _operation_copy_cp,
+    _operation_link_symbolic,
+    _operation_copy_scp,
+)
+from bfabric_app_runner.specs.inputs.file_copy_spec import FileSpec
+from bfabric import Bfabric
+
+
+@pytest.fixture
+def mock_subprocess(mocker):
+    return mocker.patch("subprocess.run")
+
+
+@pytest.fixture
+def mock_shutil_copyfile(mocker):
+    return mocker.patch("shutil.copyfile")
+
+
+@pytest.fixture
+def mock_client(mocker):
+    return mocker.MagicMock(spec=Bfabric)
+
+
+@pytest.fixture
+def operation_copy_rsync(mocker):
+    return mocker.patch(
+        "bfabric_app_runner.input_preparation.prepare_file_spec._operation_copy_rsync", return_value=False
+    )
+
+
+@pytest.fixture
+def operation_copy_scp(mocker):
+    return mocker.patch(
+        "bfabric_app_runner.input_preparation.prepare_file_spec._operation_copy_scp", return_value=False
+    )
+
+
+@pytest.fixture
+def operation_copy_cp(mocker):
+    return mocker.patch("bfabric_app_runner.input_preparation.prepare_file_spec._operation_copy_cp", return_value=False)
+
+
+@pytest.fixture
+def operation_link_symbolic(mocker):
+    return mocker.patch(
+        "bfabric_app_runner.input_preparation.prepare_file_spec._operation_link_symbolic", return_value=False
+    )
+
+
+# TODO should absolute path  for filename be mandatory in the future? -> this could also have unwanted side effects
+
+
+def test_prepare_local_copy_when_rsync_success(mock_client, operation_copy_rsync) -> None:
+    spec = FileSpec.model_validate({"source": {"local": "/source.txt"}, "filename": "destination.txt"})
+    operation_copy_rsync.return_value = True
+    prepare_file_spec(spec=spec, client=mock_client, working_dir=Path("../integration/working_dir"), ssh_user=None)
+    operation_copy_rsync.assert_called_once_with(spec, Path("../integration/working_dir") / "destination.txt", None)
+
+
+def test_prepare_local_copy_when_fallback_success(mock_client, operation_copy_rsync, operation_copy_cp) -> None:
+    spec = FileSpec.model_validate({"source": {"local": "/source.txt"}, "filename": "destination.txt"})
+    operation_copy_rsync.return_value = False
+    operation_copy_cp.return_value = True
+    prepare_file_spec(spec=spec, client=mock_client, working_dir=Path("../integration/working_dir"), ssh_user=None)
+    operation_copy_rsync.assert_called_once_with(spec, Path("../integration/working_dir") / "destination.txt", None)
+    operation_copy_cp.assert_called_once_with(spec, Path("../integration/working_dir") / "destination.txt")
+
+
+def test_prepare_local_link_when_success(mock_client, operation_link_symbolic):
+    spec = FileSpec.model_validate({"source": {"local": "/source.txt"}, "filename": "destination.txt", "link": True})
+    operation_link_symbolic.return_value = True
+    prepare_file_spec(spec=spec, client=mock_client, working_dir=Path("../integration/working_dir"), ssh_user=None)
+    operation_link_symbolic.assert_called_once_with(spec, Path("../integration/working_dir") / "destination.txt")
+
+
+def test_prepare_remote_copy_when_rsync_success(mock_client, operation_copy_rsync):
+    spec = FileSpec.model_validate(
+        {"source": {"ssh": {"host": "host", "path": "/source.txt"}}, "filename": "destination.txt"}
+    )
+    operation_copy_rsync.return_value = True
+    prepare_file_spec(spec=spec, client=mock_client, working_dir=Path("../integration/working_dir"), ssh_user="user")
+    operation_copy_rsync.assert_called_once_with(spec, Path("../integration/working_dir") / "destination.txt", "user")
+
+
+def test_prepare_remote_copy_when_fallback_success(mock_client, operation_copy_rsync, operation_copy_scp):
+    spec = FileSpec.model_validate(
+        {"source": {"ssh": {"host": "host", "path": "/source.txt"}}, "filename": "destination.txt"}
+    )
+    operation_copy_rsync.return_value = False
+    operation_copy_scp.return_value = True
+    prepare_file_spec(spec=spec, client=mock_client, working_dir=Path("../integration/working_dir"), ssh_user="user")
+    operation_copy_rsync.assert_called_once_with(spec, Path("../integration/working_dir") / "destination.txt", "user")
+    operation_copy_scp.assert_called_once_with(spec, Path("../integration/working_dir") / "destination.txt", "user")
+
+
+def test_operation_copy_rsync_local(mock_subprocess, logot: Logot):
+    spec = FileSpec.model_validate({"source": {"local": "/source.txt"}, "filename": "destination.txt"})
+    mock_subprocess.return_value.returncode = 0
+    result = _operation_copy_rsync(spec=spec, output_path=Path("mock_output.txt"), ssh_user=None)
+    mock_subprocess.assert_called_once_with(["rsync", "-Pav", "/source.txt", "mock_output.txt"], check=False)
+    logot.assert_logged(logged.info("rsync -Pav /source.txt mock_output.txt"))
+    assert result
+
+
+def test_operation_copy_rsync_ssh_default(mock_subprocess, logot: Logot):
+    spec = FileSpec.model_validate(
+        {"source": {"ssh": {"host": "host", "path": "/source.txt"}}, "filename": "destination.txt"}
+    )
+    mock_subprocess.return_value.returncode = 0
+    result = _operation_copy_rsync(spec=spec, output_path=Path("mock_output.txt"), ssh_user=None)
+    mock_subprocess.assert_called_once_with(["rsync", "-Pav", "host:/source.txt", "mock_output.txt"], check=False)
+    logot.assert_logged(logged.info("rsync -Pav host:/source.txt mock_output.txt"))
+    assert result
+
+
+def test_operation_copy_rsync_ssh_custom_user(mock_subprocess, logot: Logot):
+    spec = FileSpec.model_validate(
+        {"source": {"ssh": {"host": "host", "path": "/source.txt"}}, "filename": "destination.txt"}
+    )
+    mock_subprocess.return_value.returncode = 0
+    result = _operation_copy_rsync(spec=spec, output_path=Path("mock_output.txt"), ssh_user="user")
+    mock_subprocess.assert_called_once_with(["rsync", "-Pav", "user@host:/source.txt", "mock_output.txt"], check=False)
+    logot.assert_logged(logged.info("rsync -Pav user@host:/source.txt mock_output.txt"))
+    assert result
+
+
+def test_operation_copy_scp(mocker):
+    mock_scp = mocker.patch("bfabric_app_runner.input_preparation.prepare_file_spec.scp")
+    spec = FileSpec.model_validate(
+        {"source": {"ssh": {"host": "host", "path": "/source.txt"}}, "filename": "destination.txt"}
+    )
+    result = _operation_copy_scp(spec=spec, output_path=Path("mock_output.txt"), ssh_user="user")
+    mock_scp.assert_called_once_with(source="host:/source.txt", target=Path("mock_output.txt"), user="user")
+    assert result
+
+
+def test_operation_copy_scp_when_error(mocker):
+    mock_scp = mocker.patch(
+        "bfabric_app_runner.input_preparation.prepare_file_spec.scp", side_effect=CalledProcessError(1, "scp")
+    )
+    spec = FileSpec.model_validate(
+        {"source": {"ssh": {"host": "host", "path": "/source.txt"}}, "filename": "destination.txt"}
+    )
+    result = _operation_copy_scp(spec=spec, output_path=Path("mock_output.txt"), ssh_user="user")
+    mock_scp.assert_called_once_with(source="host:/source.txt", target=Path("mock_output.txt"), user="user")
+    assert not result
+
+
+def test_operation_copy_cp(mock_shutil_copyfile, logot: Logot):
+    spec = FileSpec.model_validate({"source": {"local": "/source.txt"}, "filename": "destination.txt"})
+    result = _operation_copy_cp(spec=spec, output_path=Path("mock_output.txt"))
+    mock_shutil_copyfile.assert_called_once_with("/source.txt", "mock_output.txt")
+    logot.assert_logged(logged.info("cp /source.txt mock_output.txt"))
+    assert result
+
+
+def test_operation_copy_cp_when_error(mock_shutil_copyfile, logot: Logot):
+    mock_shutil_copyfile.side_effect = SameFileError
+    spec = FileSpec.model_validate({"source": {"local": "/source.txt"}, "filename": "destination.txt"})
+    result = _operation_copy_cp(spec=spec, output_path=Path("mock_output.txt"))
+    mock_shutil_copyfile.assert_called_once_with("/source.txt", "mock_output.txt")
+    logot.assert_logged(logged.info("cp /source.txt mock_output.txt"))
+    assert not result
+
+
+@pytest.mark.parametrize(
+    "source,dest,expected_target",
+    [
+        ("/E/source.txt", "/E/dir/destination.txt", "../source.txt"),
+        ("/X/source.txt", "/E/dir/destination.txt", "../../X/source.txt"),
+        ("/work/source.txt", "/work/destination.txt", "source.txt"),
+    ],
+)
+def test_operation_link_symbolic(mock_subprocess, logot: Logot, source, dest, expected_target):
+    spec = FileSpec.model_validate({"source": {"local": source}, "filename": "IGNORED", "link": True})
+    mock_subprocess.return_value.returncode = 0
+    result = _operation_link_symbolic(spec=spec, output_path=Path(dest))
+    mock_subprocess.assert_called_once_with(["ln", "-s", expected_target, str(dest)], check=False)
+    logot.assert_logged(logged.info(f"ln -s {expected_target} {dest}"))
+    assert result
diff --git a/tests/app_runner/app_runner/test_runner.py b/tests/bfabric_app_runner/app_runner/test_runner.py
similarity index 86%
rename from tests/app_runner/app_runner/test_runner.py
rename to tests/bfabric_app_runner/app_runner/test_runner.py
index 92ebbe07..d91e73a6 100644
--- a/tests/app_runner/app_runner/test_runner.py
+++ b/tests/bfabric_app_runner/app_runner/test_runner.py
@@ -4,7 +4,7 @@
 import yaml
 from pydantic import BaseModel
 
-from app_runner.app_runner.runner import Runner, run_app
+from bfabric_app_runner.app_runner.runner import Runner, run_app
 
 
 # Mock classes to represent dependencies
@@ -87,14 +87,12 @@ def test_runner_run_dispatch(mocker, mock_app_version, mock_bfabric, tmp_path):
 
     runner.run_dispatch(workunit_ref, work_dir)
 
-    mock_run.assert_called_once_with(
-        ["mock-command", str(workunit_ref), str(work_dir)], check=True
-    )
+    mock_run.assert_called_once_with(["mock-command", str(workunit_ref), str(work_dir)], check=True)
 
 
 def test_runner_run_prepare_input(mocker, mock_app_version, mock_bfabric, tmp_path):
     """Test Runner.run_prepare_input method"""
-    mock_prepare = mocker.patch("app_runner.app_runner.runner.prepare_folder")
+    mock_prepare = mocker.patch("bfabric_app_runner.app_runner.runner.prepare_folder")
     runner = Runner(spec=mock_app_version, client=mock_bfabric, ssh_user="test_user")
     chunk_dir = tmp_path / "chunk"
     chunk_dir.mkdir()
@@ -122,9 +120,7 @@ def test_runner_run_process(mocker, mock_app_version, mock_bfabric, tmp_path):
     mock_run.assert_called_once_with(["mock-command", str(chunk_dir)], check=True)
 
 
-def test_run_app_full_workflow(
-    mocker, mock_app_version, mock_bfabric, mock_workunit_definition, setup_work_dir
-):
+def test_run_app_full_workflow(mocker, mock_app_version, mock_bfabric, mock_workunit_definition, setup_work_dir):
     """Test complete run_app workflow"""
     # Setup mocks
     mocker.patch(
@@ -132,8 +128,8 @@ def test_run_app_full_workflow(
         return_value=mock_workunit_definition,
     )
     mock_run = mocker.patch("subprocess.run")
-    mock_prepare = mocker.patch("app_runner.app_runner.runner.prepare_folder")
-    mock_register = mocker.patch("app_runner.app_runner.runner.register_outputs")
+    mock_prepare = mocker.patch("bfabric_app_runner.app_runner.runner.prepare_folder")
+    mock_register = mocker.patch("bfabric_app_runner.app_runner.runner.register_outputs")
 
     # Run the app
     run_app(
@@ -166,8 +162,8 @@ def test_run_app_read_only_mode(
         return_value=mock_workunit_definition,
     )
     mocker.patch("subprocess.run")
-    mocker.patch("app_runner.app_runner.runner.prepare_folder")
-    mocker.patch("app_runner.app_runner.runner.register_outputs")
+    mocker.patch("bfabric_app_runner.app_runner.runner.prepare_folder")
+    mocker.patch("bfabric_app_runner.app_runner.runner.register_outputs")
 
     run_app(
         app_spec=mock_app_version,
@@ -194,8 +190,8 @@ def test_run_app_with_path_workunit_ref(
         return_value=mock_workunit_definition,
     )
     mocker.patch("subprocess.run")
-    mocker.patch("app_runner.app_runner.runner.prepare_folder")
-    mocker.patch("app_runner.app_runner.runner.register_outputs")
+    mocker.patch("bfabric_app_runner.app_runner.runner.prepare_folder")
+    mocker.patch("bfabric_app_runner.app_runner.runner.register_outputs")
 
     run_app(
         app_spec=mock_app_version,
diff --git a/tests/app_runner/integration/__init__.py b/tests/bfabric_app_runner/integration/__init__.py
similarity index 100%
rename from tests/app_runner/integration/__init__.py
rename to tests/bfabric_app_runner/integration/__init__.py
diff --git a/tests/app_runner/integration/test_cli_commands.py b/tests/bfabric_app_runner/integration/test_cli_commands.py
similarity index 100%
rename from tests/app_runner/integration/test_cli_commands.py
rename to tests/bfabric_app_runner/integration/test_cli_commands.py
diff --git a/tests/app_runner/specs/__init__.py b/tests/bfabric_app_runner/specs/__init__.py
similarity index 100%
rename from tests/app_runner/specs/__init__.py
rename to tests/bfabric_app_runner/specs/__init__.py
diff --git a/tests/app_runner/specs/app/__init__.py b/tests/bfabric_app_runner/specs/app/__init__.py
similarity index 100%
rename from tests/app_runner/specs/app/__init__.py
rename to tests/bfabric_app_runner/specs/app/__init__.py
diff --git a/tests/app_runner/specs/app/test_commands_spec.py b/tests/bfabric_app_runner/specs/app/test_commands_spec.py
similarity index 94%
rename from tests/app_runner/specs/app/test_commands_spec.py
rename to tests/bfabric_app_runner/specs/app/test_commands_spec.py
index e0eec37c..00bd556b 100644
--- a/tests/app_runner/specs/app/test_commands_spec.py
+++ b/tests/bfabric_app_runner/specs/app/test_commands_spec.py
@@ -1,7 +1,7 @@
 import os
 from pathlib import Path
 
-from app_runner.specs.app.commands_spec import MountOptions, CommandDocker, CommandShell
+from bfabric_app_runner.specs.app.commands_spec import MountOptions, CommandDocker, CommandShell
 
 
 def test_mount_options_default_behavior(tmp_path):
@@ -81,9 +81,7 @@ def test_command_shell_with_quotes():
 
 def test_command_shell_complex_command():
     """Test complex shell command with multiple arguments and quotes"""
-    cmd = CommandShell(
-        command="python3 -c \"import sys; print('Hello from Python')\" --verbose"
-    )
+    cmd = CommandShell(command="python3 -c \"import sys; print('Hello from Python')\" --verbose")
     result = cmd.to_shell()
     assert result == [
         "python3",
@@ -129,9 +127,7 @@ def test_command_docker_with_options(tmp_path):
         mac_address="00:00:00:00:00:00",
         custom_args=["--network=host"],
         hostname="myhost",
-        mounts=MountOptions(
-            share_bfabric_config=False
-        ),  # Disable bfabric mount for simpler testing
+        mounts=MountOptions(share_bfabric_config=False),  # Disable bfabric mount for simpler testing
     )
 
     work_dir = tmp_path / "work"
diff --git a/tests/app_runner/specs/app/test_versions.py b/tests/bfabric_app_runner/specs/app/test_versions.py
similarity index 93%
rename from tests/app_runner/specs/app/test_versions.py
rename to tests/bfabric_app_runner/specs/app/test_versions.py
index d31b580a..b6ed01d9 100644
--- a/tests/app_runner/specs/app/test_versions.py
+++ b/tests/bfabric_app_runner/specs/app/test_versions.py
@@ -2,7 +2,7 @@
 
 import pytest
 
-from app_runner.specs.app.app_spec import AppSpec
+from bfabric_app_runner.specs.app.app_spec import AppSpec
 
 
 @pytest.fixture()
diff --git a/tests/app_runner/specs/app/test_versions.yml b/tests/bfabric_app_runner/specs/app/test_versions.yml
similarity index 100%
rename from tests/app_runner/specs/app/test_versions.yml
rename to tests/bfabric_app_runner/specs/app/test_versions.yml
diff --git a/tests/app_runner/specs/test_app_spec.py b/tests/bfabric_app_runner/specs/test_app_spec.py
similarity index 88%
rename from tests/app_runner/specs/test_app_spec.py
rename to tests/bfabric_app_runner/specs/test_app_spec.py
index 198dda7d..5c6c5c42 100644
--- a/tests/app_runner/specs/test_app_spec.py
+++ b/tests/bfabric_app_runner/specs/test_app_spec.py
@@ -1,14 +1,14 @@
 import pytest
 import yaml
 
-from app_runner.specs.app.app_version import AppVersion
-from app_runner.specs.app.commands_spec import (
+from bfabric_app_runner.specs.app.app_version import AppVersion
+from bfabric_app_runner.specs.app.commands_spec import (
     CommandShell,
     CommandDocker,
     MountOptions,
     CommandsSpec,
 )
-from app_runner.specs.submitter_ref import SubmitterRef
+from bfabric_app_runner.specs.submitter_ref import SubmitterRef
 
 
 @pytest.fixture()
diff --git a/tests/app_runner/specs/test_config_interpolation.py b/tests/bfabric_app_runner/specs/test_config_interpolation.py
similarity index 93%
rename from tests/app_runner/specs/test_config_interpolation.py
rename to tests/bfabric_app_runner/specs/test_config_interpolation.py
index a9665590..f501e5d0 100644
--- a/tests/app_runner/specs/test_config_interpolation.py
+++ b/tests/bfabric_app_runner/specs/test_config_interpolation.py
@@ -2,7 +2,7 @@
 from mako.exceptions import MakoException
 from pydantic import ValidationError
 
-from app_runner.specs.config_interpolation import (
+from bfabric_app_runner.specs.config_interpolation import (
     Variables,
     VariablesApp,
     interpolate_config_strings,
@@ -11,9 +11,7 @@
 
 @pytest.fixture
 def basic_variables():
-    return Variables(
-        app=VariablesApp(id="test-app", name="Test Application", version="1.0.0")
-    )
+    return Variables(app=VariablesApp(id="test-app", name="Test Application", version="1.0.0"))
 
 
 def test_variables_app_model():
@@ -93,9 +91,7 @@ def test_invalid_template_syntax(basic_variables):
 
 def test_missing_variable(basic_variables):
     template = "${app.missing}"
-    with pytest.raises(
-        Exception
-    ):  # Could be more specific depending on Mako's behavior
+    with pytest.raises(Exception):  # Could be more specific depending on Mako's behavior
         interpolate_config_strings(template, basic_variables)
 
 
diff --git a/tests/app_runner/specs/test_inputs_spec.py b/tests/bfabric_app_runner/specs/test_inputs_spec.py
similarity index 79%
rename from tests/app_runner/specs/test_inputs_spec.py
rename to tests/bfabric_app_runner/specs/test_inputs_spec.py
index 6a78d514..9a049224 100644
--- a/tests/app_runner/specs/test_inputs_spec.py
+++ b/tests/bfabric_app_runner/specs/test_inputs_spec.py
@@ -1,9 +1,9 @@
 import pytest
 import yaml
 
-from app_runner.specs.inputs_spec import InputsSpec
-from app_runner.specs.inputs.bfabric_dataset_spec import BfabricDatasetSpec
-from app_runner.specs.inputs.bfabric_resource_spec import BfabricResourceSpec
+from bfabric_app_runner.specs.inputs_spec import InputsSpec
+from bfabric_app_runner.specs.inputs.bfabric_dataset_spec import BfabricDatasetSpec
+from bfabric_app_runner.specs.inputs.bfabric_resource_spec import BfabricResourceSpec
 
 
 @pytest.fixture()
diff --git a/tests/app_runner/specs/test_outputs_spec.py b/tests/bfabric_app_runner/specs/test_outputs_spec.py
similarity index 92%
rename from tests/app_runner/specs/test_outputs_spec.py
rename to tests/bfabric_app_runner/specs/test_outputs_spec.py
index 6846adb4..ade870ea 100644
--- a/tests/app_runner/specs/test_outputs_spec.py
+++ b/tests/bfabric_app_runner/specs/test_outputs_spec.py
@@ -1,7 +1,7 @@
 import pytest
 import yaml
 
-from app_runner.specs.outputs_spec import OutputsSpec, CopyResourceSpec, SaveDatasetSpec
+from bfabric_app_runner.specs.outputs_spec import OutputsSpec, CopyResourceSpec, SaveDatasetSpec
 
 
 @pytest.fixture()
diff --git a/tests/bfabric_scripts/test_bfabric_list_not_existing_storage_directories.py b/tests/bfabric_scripts/test_bfabric_list_not_existing_storage_directories.py
index c32d9d4a..44f2558b 100644
--- a/tests/bfabric_scripts/test_bfabric_list_not_existing_storage_directories.py
+++ b/tests/bfabric_scripts/test_bfabric_list_not_existing_storage_directories.py
@@ -21,9 +21,7 @@ def test_list_not_existing_storage_directories(
 
     # mock a client
     client = mocker.MagicMock()
-    client.read.return_value = ResultContainer(
-        [{"id": 3000}, {"id": 3050}, {"id": 3100}, {"id": 3200}, {"id": 3300}]
-    )
+    client.read.return_value = ResultContainer([{"id": 3000}, {"id": 3050}, {"id": 3100}, {"id": 3200}, {"id": 3300}])
 
     # call the function
     list_not_existing_storage_dirs(client, tmp_path, cache_path=tmp_path / "cache.json")
diff --git a/tests/bfabric_scripts/test_bfabric_save_csv2dataset.py b/tests/bfabric_scripts/test_bfabric_save_csv2dataset.py
index af55cf4d..1198112b 100644
--- a/tests/bfabric_scripts/test_bfabric_save_csv2dataset.py
+++ b/tests/bfabric_scripts/test_bfabric_save_csv2dataset.py
@@ -55,9 +55,7 @@ def test_check_for_invalid_characters_empty_dataframe():
 
 
 def test_check_for_invalid_characters_non_string_columns():
-    data = pl.DataFrame(
-        {"col1": [1, 2, 3], "col2": [4.5, 5.6, 6.7], "col3": ["abc", "def", "ghi"]}
-    )
+    data = pl.DataFrame({"col1": [1, 2, 3], "col2": [4.5, 5.6, 6.7], "col3": ["abc", "def", "ghi"]})
     invalid_characters = "!@#"
 
     # Should not raise an exception