Only pin theano-pymc in requirements.txt (#4322)

* 🔨 add scripts to check theano-pymc pins, to generate requirements-dev from conda, to sort conda deps * 🔧 update conda envs and requirements-dev.txt * 📝 fix typo * 📝 add docstrings * 📝 update pip-to-conda docstring * noop * 🔥 remove pin theano checks, just use requirements.txt * local install in arviz compat * 📝 switch -> checkout, note beginner friendly label * 📝 link to beginner friendly issues * run generate pip deps from conda on all conda env files * 🔧 make sure all conda-envs files generate requirements-dev * 🔀 reorder some tests * 🎨 remove trailing comma * Update scripts/generate_pip_deps_from_conda.py Co-authored-by: Thomas Wiecki <thomas.wiecki@gmail.com>
pymc-devs · Dec 11, 2020 · eb4be99 · eb4be99
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diff --git a/.github/workflows/arviz_compat.yml b/.github/workflows/arviz_compat.yml
@@ -33,6 +33,18 @@ jobs:
           path: ~/conda_pkgs_dir
           key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
             hashFiles('conda-envs/environment-dev-py38.yml') }}
+      - name: Cache multiple paths
+        uses: actions/cache@v2
+        env:
+          # Increase this value to reset cache if requirements.txt has not changed
+          CACHE_NUMBER: 0
+        with:
+          path: |
+            ~/.cache/pip
+            $RUNNER_TOOL_CACHE/Python/*
+            ~\AppData\Local\pip\Cache
+          key: ${{ runner.os }}-build-${{ matrix.python-version }}-${{
+            hashFiles('requirements.txt') }}
       - uses: conda-incubator/setup-miniconda@v2
         with:
           activate-environment: pymc3-dev-py38
@@ -47,7 +59,7 @@ jobs:
       - name: Install latest arviz
         run: |
           conda activate pymc3-dev-py38
-          conda remove arviz -y
+          pip uninstall arviz -y
           pip install git+git://github.com/arviz-devs/arviz.git
       - name: Run tests
         run: |

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
@@ -21,6 +21,7 @@ jobs:
             --ignore=pymc3/tests/test_examples.py
             --ignore=pymc3/tests/test_gp.py
             --ignore=pymc3/tests/test_mixture.py
+            --ignore=pymc3/tests/test_ode.py
             --ignore=pymc3/tests/test_parallel_sampling.py
             --ignore=pymc3/tests/test_posteriors.py
             --ignore=pymc3/tests/test_quadpotential.py
@@ -43,6 +44,7 @@ jobs:
           - |
             pymc3/tests/test_examples.py
             pymc3/tests/test_mixture.py
+            pymc3/tests/test_ode.py
             pymc3/tests/test_posteriors.py
             pymc3/tests/test_quadpotential.py
           - |
@@ -74,6 +76,18 @@ jobs:
           path: ~/conda_pkgs_dir
           key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
             hashFiles('conda-envs/environment-dev-py36.yml') }}
+      - name: Cache multiple paths
+        uses: actions/cache@v2
+        env:
+          # Increase this value to reset cache if requirements.txt has not changed
+          CACHE_NUMBER: 0
+        with:
+          path: |
+            ~/.cache/pip
+            $RUNNER_TOOL_CACHE/Python/*
+            ~\AppData\Local\pip\Cache
+          key: ${{ runner.os }}-build-${{ matrix.python-version }}-${{
+            hashFiles('requirements.txt') }}
       - uses: conda-incubator/setup-miniconda@v2
         with:
           activate-environment: pymc3-dev-py36

diff --git a/.github/workflows/windows.yml b/.github/workflows/windows.yml
@@ -32,12 +32,29 @@ jobs:
           path: ~/conda_pkgs_dir
           key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
             hashFiles('conda-envs/environment-dev-py37.yml') }}
+      - name: Cache multiple paths
+        uses: actions/cache@v2
+        env:
+          # Increase this value to reset cache if requirements.txt has not changed
+          CACHE_NUMBER: 0
+        with:
+          path: |
+            ~/.cache/pip
+            $RUNNER_TOOL_CACHE/Python/*
+            ~\AppData\Local\pip\Cache
+          key: ${{ runner.os }}-build-${{ matrix.python-version }}-${{
+            hashFiles('requirements.txt') }}
       - uses: conda-incubator/setup-miniconda@v2
         with:
           activate-environment: pymc3-dev-py37
           channel-priority: strict
           environment-file: conda-envs/environment-dev-py37.yml
           use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
+      - name: Install-pymc3
+        run: |
+          conda activate pymc3-dev-py37
+          pip install -e .
+          python --version
       - run: |
           conda activate pymc3-dev-py37
           python -m pytest -vv --cov=pymc3 --cov-report=xml --cov-report term --durations=50 $TEST_SUBSET
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -11,6 +11,7 @@ repos:
     -   id: no-commit-to-branch
         args: [--branch, master]
     -   id: requirements-txt-fixer
+        exclude: ^requirements-dev\.txt$
     -   id: trailing-whitespace
 - repo: https://github.com/nbQA-dev/nbQA
   rev: 0.5.4
@@ -61,6 +62,19 @@ repos:
       language: python
       name: Check no tests are ignored
       pass_filenames: false
+    - id: conda-env-sort
+      additional_dependencies: [pyyaml]
+      entry: python scripts/sort_conda_envs.py
+      files: ^conda-envs/
+      language: python
+      name: Sort dependencies in conda envs
+      types: [yaml]
+    - id: pip-from-conda
+      additional_dependencies: [pyyaml]
+      entry: python scripts/generate_pip_deps_from_conda.py
+      files: ^conda-envs/
+      language: python
+      name: Generate pip dependency from conda
     - id: no-relative-imports
       name: No relative imports
       entry: from \.[\.\w]* import

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -15,6 +15,8 @@ We appreciate being notified of problems with the existing PyMC code. We prefer
 
 Please verify that your issue is not being currently addressed by other issues or pull requests by using the GitHub search tool to look for key words in the project issue tracker.
 
+Filter on the ["beginner friendly"](https://github.com/pymc-devs/pymc3/issues?q=is%3Aopen+is%3Aissue+label%3A%22beginner+friendly%22) label for issues which are good for new contributors.
+
 # Contributing code via pull requests
 
 While issue reporting is valuable, we strongly encourage users who are inclined to do so to submit patches for new or existing issues via pull requests. This is particularly the case for simple fixes, such as typos or tweaks to documentation, which do not require a heavy investment of time and attention.
@@ -38,7 +40,7 @@ The preferred workflow for contributing to PyMC3 is to fork the [GitHub reposito
 3. Create a ``feature`` branch to hold your development changes:
 
    ```bash
-   $ git switch -c my-feature
+   $ git checkout -b my-feature
    ```
 
    Always use a ``feature`` branch. It's good practice to never routinely work on the ``master`` branch of any repository.
@@ -147,4 +149,6 @@ Follow [TensorFlow's style guide](https://www.tensorflow.org/community/contribut
 
 For documentation strings, we *prefer* [numpy style](https://numpydoc.readthedocs.io/en/latest/format.html) to comply with the style that predominates in our upstream dependencies.
 
+Finally, see the [PyMC3 Python Code Style](https://github.com/pymc-devs/pymc3/wiki/PyMC3-Python-Code-Style) and the [PyMC's Jupyter Notebook Style](https://github.com/pymc-devs/pymc3/wiki/PyMC's-Jupyter-Notebook-Style) guides.
+
 #### This guide was derived from the [scikit-learn guide to contributing](https://github.com/scikit-learn/scikit-learn/blob/master/CONTRIBUTING.md)
diff --git a/conda-envs/environment-dev-py36.yml b/conda-envs/environment-dev-py36.yml
@@ -1,31 +1,22 @@
 name: pymc3-dev-py36
 channels:
-  - conda-forge
-  - defaults
+- conda-forge
+- defaults
 dependencies:
-  - python=3.6
-  - arviz>=0.9
-  - theano-pymc==1.0.12
-  - numpy>=1.13
-  - scipy>=0.18
-  - pandas>=0.18
-  - patsy>=0.5
-  - fastprogress>=0.2
-  - h5py>=2.7
-  - typing-extensions>=3.7
-  - python-graphviz
-  - ipython>=7.16
-  - nbsphinx>=0.4
-  - numpydoc>=0.9
-  - pre-commit>=2.8.0
-  - pytest-cov>=2.5
-  - pytest>=3.0
-  - recommonmark>=0.4
-  - sphinx-autobuild>=0.7
-  - sphinx>=1.5
-  - watermark
-  - dataclasses  # python_version < 3.7
-  - contextvars  # python_version < 3.7
-  - mkl-service
-  - dill
-  - libblas=*=*mkl
+- contextvars
+- dataclasses
+- h5py>=2.7
+- ipython>=7.16
+- libblas=*=*mkl
+- mkl-service
+- nbsphinx>=0.4
+- numpydoc>=0.9
+- pre-commit>=2.8.0
+- pytest-cov>=2.5
+- pytest>=3.0
+- python-graphviz
+- python=3.6
+- recommonmark>=0.4
+- sphinx-autobuild>=0.7
+- sphinx>=1.5
+- watermark
diff --git a/conda-envs/environment-dev-py37.yml b/conda-envs/environment-dev-py37.yml
@@ -1,29 +1,20 @@
 name: pymc3-dev-py37
 channels:
-  - conda-forge
-  - defaults
+- conda-forge
+- defaults
 dependencies:
-  - python=3.7
-  - arviz>=0.9
-  - theano-pymc==1.0.12
-  - numpy>=1.13
-  - scipy>=0.18
-  - pandas>=0.18
-  - patsy>=0.5
-  - fastprogress>=0.2
-  - h5py>=2.7
-  - typing-extensions>=3.7
-  - python-graphviz
-  - ipython>=7.16
-  - nbsphinx>=0.4
-  - numpydoc>=0.9
-  - pre-commit>=2.8.0
-  - pytest-cov>=2.5
-  - pytest>=3.0
-  - recommonmark>=0.4
-  - sphinx-autobuild>=0.7
-  - sphinx>=1.5
-  - watermark
-  - mkl-service
-  - dill
-  - libblas=*=*mkl
+- h5py>=2.7
+- ipython>=7.16
+- libblas=*=*mkl
+- mkl-service
+- nbsphinx>=0.4
+- numpydoc>=0.9
+- pre-commit>=2.8.0
+- pytest-cov>=2.5
+- pytest>=3.0
+- python-graphviz
+- python=3.7
+- recommonmark>=0.4
+- sphinx-autobuild>=0.7
+- sphinx>=1.5
+- watermark
diff --git a/conda-envs/environment-dev-py38.yml b/conda-envs/environment-dev-py38.yml
@@ -1,29 +1,20 @@
 name: pymc3-dev-py38
 channels:
-  - conda-forge
-  - defaults
+- conda-forge
+- defaults
 dependencies:
-  - python=3.8
-  - arviz>=0.9
-  - theano-pymc==1.0.12
-  - numpy>=1.13
-  - scipy>=0.18
-  - pandas>=0.18
-  - patsy>=0.5
-  - fastprogress>=0.2
-  - h5py>=2.7
-  - typing-extensions>=3.7
-  - python-graphviz
-  - ipython>=7.16
-  - nbsphinx>=0.4
-  - numpydoc>=0.9
-  - pre-commit>=2.8.0
-  - pytest-cov>=2.5
-  - pytest>=3.0
-  - recommonmark>=0.4
-  - sphinx-autobuild>=0.7
-  - sphinx>=1.5
-  - watermark
-  - mkl-service
-  - dill
-  - libblas=*=*mkl
+- h5py>=2.7
+- ipython>=7.16
+- libblas=*=*mkl
+- mkl-service
+- nbsphinx>=0.4
+- numpydoc>=0.9
+- pre-commit>=2.8.0
+- pytest-cov>=2.5
+- pytest>=3.0
+- python-graphviz
+- python=3.8
+- recommonmark>=0.4
+- sphinx-autobuild>=0.7
+- sphinx>=1.5
+- watermark
diff --git a/requirements-dev.txt b/requirements-dev.txt
@@ -1,22 +1,14 @@
-bokeh>=0.12.13
-coverage>=5.1
-dill
-graphviz>=0.8.3
-ipython
-nbsphinx>=0.4.2
-nose>=1.3.7
-nose-parameterized==0.6.0
-numpydoc>=0.9.1
-parameterized
+# This file is auto-generated from by scripts/generate_pip_deps_from_conda.py, do not modify.
+# See that file for comments about the need/usage of each dependency.
+
+h5py>=2.7
+ipython>=7.16
+nbsphinx>=0.4
+numpydoc>=0.9
 pre-commit>=2.8.0
-pycodestyle>=2.3.1
-pyflakes>=1.5.0
-pylint>=1.7.4
-pytest>=3.0.7
-pytest-cov>=2.5.1
-pytest-xdist
-recommonmark>=0.4.0
-seaborn>=0.8.1
-sphinx>=1.5.5
-sphinx-autobuild==0.7.1
+pytest-cov>=2.5
+pytest>=3.0
+recommonmark>=0.4
+sphinx-autobuild>=0.7
+sphinx>=1.5
 watermark