ZnTrack v0.8 (#812)

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* fix hardcoded

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* add `outs_path_no_cache`

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* fix

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* small cleanup

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* basic deps testing

* first draft for loading Nodes

* lazy loading start

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* test state

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* add `state.get_stage()` and `stage.get_stage_lock()`

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* add `ZnTrackOptionEnum`

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* make it a DVCPlugin (part 1)

* small code cleanup

* move `save` to `plugins`

* move `save` functions to `plugins`

* add ABC for plugins

* use sentinel objects

* handle and test loading a node

* test node `repr`

* ruff

* mock `dataclass_transform` in older Python versions

* enable more tests

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* test groups

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* use `typing_extensions`

* cleanup, using nested functions

* test metrics

* ruff

* support plugins via environmental variable

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* add aim plugin

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* remove aim - issue in CI

* add log messages

* save name and module

* bugfix, test combinedconnections

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* bugfix

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* fix convert tests

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* add `ZNTRACK_UNIQUE_OUTPUT_TYPE` info

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* bugfix: rename

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* add `AIMPlugin.finalize()`

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* test outs and use `znjson`, fix aim test

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* set run experiment

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* fix logging metrics

* log run name and run id

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* update mlflow plugin

* first draft of plotting

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* strangest of issues

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* fix `run_cache` commit

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* test and raise errors for extend plots

* prepare for colab

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* fix `with project.group` (#816)

* fix groups

* ruff

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* V08m example1 (#818)

* add project.repro

* make node subclasses kw only

* fix test using positionsl args

* adapt examples from main integration tests

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* fix issue with group nwd (#819)

* fix files test

* fix group nwd

* it does not have to be pretty - it has to work

* add `config.NWD_PATH`

* fix `_extract_group_from_nwd`

* Cli test (#820)

* add project.repro

* make node subclasses kw only

* fix test using positionsl args

* adapt examples from main integration tests

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* activate test

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* Specify the outputs for each Node (#824)

* improve `node_to_output_paths`

* tests for all types of dependencies

* carry over remaining tests from main (#821)

* carry over remaining tests from main

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* fixed test_node_node_getitem (#823)

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* activate actual test

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* xfail mark

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* improve mlflow / aim experience (#826)

* improve mlflow / aim experience

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* bugfix `stage.name` attribute error

* test `NodeWithProperty` and nodes without outputs

* bugfix and better error messages

* use DVCFileSystem only if required and fix extend issue (#829)

* use DVCFileSystem only if required and fix extend issue

* fix tests?

* fix filesystem check test

* use cls default values where possible

* run_count fix (tests needed)

* support plot kwargs for `zntrack.plots` (#828)

* support nodes outside the graph context (#825)

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* fixed test_node_node_getitem (#823)

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* xfail mark

* mark all pending implementation tests

* add files test for nodes outside the graph

* add some TODOs

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* add comment to describe feature on the main

* support `dataclass` for `zntrack.deps`

* update tests

* fix previous tests

* address comments

* update tests / fix iterables

* fix part

* do not use `part_x` key in params but rely on order

* add docs

* more docs

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* merge `zntrack.apply` features from main (#831)

* merge `zntrack.apply` features from main

* files tests for apply

* remove invalid `name` key

* remove `name` to fix tests

* fix dataclass module changing in `deps` (#833)

* add `zntrack.json` path as parameter to `dvc.yaml`

* write to params instead using zntrack.json

* address comments

* fix DVC plotting (#834)

* fix DVC plotting

* fix missing `y` default and update file tests

* fix legacy tests (#835)

* restrict and test init

* remove tests for removed features (node outside graph)

* fix another test

* fix unsupported deps types (needs tests)

* test generic deps types

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* fix more tests

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* fix some more tests

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* MLFlow and AIM support via plugins (#827)

* support for tags

* cache plugins (#830)

* bugfix and better error messages

* use DVCFileSystem only if required and fix extend issue (#829)

* use DVCFileSystem only if required and fix extend issue

* fix tests?

* fix filesystem check test

* use cls default values where possible

* run_count fix (tests needed)

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* rename to `get_plugins_from_env`

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* don't use `repr` (this should not cause issues)

* fix load env vars and move improve mlflow finalize part

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* post commit

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* update lock

* try with options

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* mlflow testing

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* test / fix extend_plots with mlflow

* add todos for testing

* another TODO

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* more mlflow testing

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* set pre-release version

* Pass `node.name` to another node in graph (#832)

* Pass `node.name` to another node in graph

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* add skipped tests (#836)

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* rename file to fix pytest collection

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* add mlflow description

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* add `zntrack mlflow-sync`

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* fix multiple plots

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* more remote tests

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* do not run python 3.13 tests yet

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.github/workflows/test.yaml

@@ -24,6 +24,29 @@ jobs:
         os:
           - ubuntu-latest
 
+    services:
+      # Label used to access the service container
+      mlflow:
+        # Docker Hub image
+        image: pythonf/mlflow:v2.16.0
+        options: >-
+          --health-cmd="curl --fail http://localhost:5000/health || exit 1"
+          --health-interval=10s
+          --health-timeout=5s
+          --health-retries=5
+        ports:
+          - 5000:5000
+      aim:
+        # Docker Hub image
+        image: pythonf/aim:v3.24.0
+        options: >-
+          --health-cmd="curl --fail http://localhost:43800/status || exit 1"
+          --health-interval=10s
+          --health-timeout=5s
+          --health-retries=5
+        ports:
+          - 43800:43800
+
     steps:
       - uses: actions/checkout@v2
       - name: Set up Python ${{ matrix.python-version }}
@@ -37,6 +60,7 @@ jobs:
           virtualenvs-in-project: true
       - name: Install package
         run: |
+          poetry run pip install aim
           poetry install --no-interaction
       - name: Setup git user
         run: |
@@ -60,51 +84,51 @@ jobs:
           flags: fulltest
           verbose: true
 
-  nbtest:
-    runs-on: ubuntu-latest
-    needs: [ pytest ]
-    steps:
-      - uses: actions/checkout@v2
-      - name: Set up Python 3.11
-        uses: actions/setup-python@v4
-        with:
-          python-version: "3.11"
-      - name: Install Poetry
-        uses: snok/install-poetry@v1
-        with:
-          virtualenvs-create: true
-          virtualenvs-in-project: true
-      - name: Install package
-        run: |
-          poetry install
-      - name: Setup git user
-        run: |
-          git config --global user.name "John Doe"
-          git config --global user.email johndoe@example.com
-          git config --global init.defaultBranch "main"
-      - name: Pytest
-        run: |
-          poetry run pytest --nbmake ./examples
+  # nbtest:
+  #   runs-on: ubuntu-latest
+  #   needs: [ pytest ]
+  #   steps:
+  #     - uses: actions/checkout@v2
+  #     - name: Set up Python 3.11
+  #       uses: actions/setup-python@v4
+  #       with:
+  #         python-version: "3.11"
+  #     - name: Install Poetry
+  #       uses: snok/install-poetry@v1
+  #       with:
+  #         virtualenvs-create: true
+  #         virtualenvs-in-project: true
+  #     - name: Install package
+  #       run: |
+  #         poetry install
+  #     - name: Setup git user
+  #       run: |
+  #         git config --global user.name "John Doe"
+  #         git config --global user.email johndoe@example.com
+  #         git config --global init.defaultBranch "main"
+  #     - name: Pytest
+  #       run: |
+  #         poetry run pytest --nbmake ./examples
 
-  doctest:
-    runs-on: ubuntu-latest
-    needs: [ pytest, nbtest ]
-    steps:
-      - uses: actions/checkout@v2
-      - name: Set up Python 3.11
-        uses: actions/setup-python@v4
-        with:
-          python-version: "3.11"
-      - name: Install Poetry
-        uses: snok/install-poetry@v1
-        with:
-          virtualenvs-create: true
-          virtualenvs-in-project: true
-      - name: Install package
-        run: |
-          sudo apt install pandoc
-          poetry install --with=docs
-      - name: Build documentation
-        run: |
-          cd ./docs
-          poetry run make html
+  # doctest:
+  #   runs-on: ubuntu-latest
+  #   needs: [ pytest, nbtest ]
+  #   steps:
+  #     - uses: actions/checkout@v2
+  #     - name: Set up Python 3.11
+  #       uses: actions/setup-python@v4
+  #       with:
+  #         python-version: "3.11"
+  #     - name: Install Poetry
+  #       uses: snok/install-poetry@v1
+  #       with:
+  #         virtualenvs-create: true
+  #         virtualenvs-in-project: true
+  #     - name: Install package
+  #       run: |
+  #         sudo apt install pandoc
+  #         poetry install --with=docs
+  #     - name: Build documentation
+  #       run: |
+  #         cd ./docs
+  #         poetry run make html

.gitignore

@@ -1,17 +1,170 @@
-.vscode/
-tmp/
-/tests/basic/.git
-/docs/build
-.idea
-PyTrack.egg-info
-htmlcov
-.coverage
-venv
-/build/
-/dist/
-/py_track.egg-info/
+# Byte-compiled / optimized / DLL files
 __pycache__/
-.pymon
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
 .ipynb_checkpoints
-_examples/
-prof/
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+tmp/
+params.yaml
+zntrack.json
+dvc.yaml
+.dvc
+nodes/
+.vscode/

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "zntrack-examples"]
+	path = zntrack-examples
+	url = https://github.com/PythonFZ/zntrack-examples.git

README.md

@@ -78,20 +78,20 @@ print(hello_world.random_number)
 
 > ## Tip
 >
-> You can easily load this Node directly from a repository.
+> You can easily load a Node directly from a repository.
 >
 > ```python
 > import zntrack
 >
 > node = zntrack.from_rev(
->     "HelloWorld",
->     remote="https://github.com/PythonFZ/ZnTrackExamples.git",
->     rev="890c714",
+>     "ParamsToMetrics",
+>     remote="https://github.com/PythonFZ/zntrack-examples",
+>     rev="8d0c992"
 > )
 > ```
 >
-> Try accessing the `max_number` parameter and `random_number` output. All Nodes
-> from this and many other repositories can be loaded like this.
+> Try accessing the `params` parameter and `metrics` output. All Nodes from this
+> and many other repositories can be loaded like this.
 
 An overview of all the ZnTrack features as well as more detailed examples can be
 found in the [ZnTrack Documentation](https://zntrack.readthedocs.io/en/latest/).

docs/source/index.rst

@@ -21,6 +21,11 @@ Welcome to ZnTrack, the first developer package from zincware <https://github.co
 We're excited to have you on board!
 ZnTrack is designed to simplify code sharing and reproducibility.
 
+.. note::
+
+   This documentation has not been updated to the newest version of ZnTrack.
+   Features and changes in :code:`v0.8.0` and newer are not included in this documentation.
+
 - :ref:`userdoc-get-started`
 - :ref:`userdoc-examples`
 - :ref:`userdoc-theory`