Merge pull request #136 from fgcz/main

bfabricPy 1.13.19

.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'

.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

.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()

.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

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

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:

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

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

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")

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,
         )
 

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)]

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)