Merge branch 'master' of github.com:pymc-devs/pymc3 into feature-oprobit

Author: tohtsky

.github/workflows/arviz_compat.yml

@@ -18,7 +18,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     env:
       TEST_SUBSET: ${{ matrix.test-subset }}
-      THEANO_FLAGS: floatX=${{ matrix.floatx }},gcc.cxxflags='-march=native'
+      THEANO_FLAGS: floatX=${{ matrix.floatx }},gcc__cxxflags='-march=native'
     defaults:
       run:
         shell: bash -l {0}
@@ -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: |

.github/workflows/dispatched_pre-commit.yml

@@ -0,0 +1,33 @@
+name: run pre-commit
+
+on:
+  repository_dispatch:
+    types: [pre-commit-run-command]
+jobs:
+  runPreCommit:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          repository: ${{github.event.client_payload.pull_request.head.repo.full_name}}
+          ref: ${{github.event.client_payload.pull_request.head.ref}}
+          token: ${{ secrets.ACTION_TRIGGER_TOKEN }}
+      - name: Cache multiple paths
+        uses: actions/cache@v2
+        with:
+          path: |
+            ~/.cache/pre-commit
+            ~/.cache/pip
+          key: pre-commit-dispatched-${{ runner.os }}-build
+      - uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+      - name: install-pre-commit
+        run: python -m pip install --upgrade pre-commit
+      - name: Slash Command Dispatch
+        run: pre-commit run --all-files || (exit 0)
+      - run: |
+          git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com"
+          git config --local user.name "github-actions[bot]"
+          git commit -m "Run pre-commit" -a
+          git push

.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
           - |
@@ -59,7 +61,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     env:
       TEST_SUBSET: ${{ matrix.test-subset }}
-      THEANO_FLAGS: floatX=${{ matrix.floatx }},gcc.cxxflags='-march=native'
+      THEANO_FLAGS: floatX=${{ matrix.floatx }},gcc__cxxflags='-march=native'
     defaults:
       run:
         shell: bash -l {0}
@@ -68,26 +70,38 @@ jobs:
       - name: Cache conda
         uses: actions/cache@v1
         env:
-          # Increase this value to reset cache if environment-dev-py36.yml has not changed
+          # Increase this value to reset cache if environment-dev-py39.yml has not changed
           CACHE_NUMBER: 0
         with:
           path: ~/conda_pkgs_dir
           key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
-            hashFiles('conda-envs/environment-dev-py36.yml') }}
+            hashFiles('conda-envs/environment-dev-py39.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
+          activate-environment: pymc3-dev-py39
           channel-priority: strict
-          environment-file: conda-envs/environment-dev-py36.yml
+          environment-file: conda-envs/environment-dev-py39.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-py36
+          conda activate pymc3-dev-py39
           pip install -e .
           python --version
       - name: Run tests
         run: |
-          conda activate pymc3-dev-py36
+          conda activate pymc3-dev-py39
           python -m pytest -vv --cov=pymc3 --cov-report=xml --cov-report term --durations=50 $TEST_SUBSET
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v1

.github/workflows/slash_dispatch.yml

@@ -0,0 +1,15 @@
+name: Slash Command Dispatch
+on:
+  issue_comment:
+    types: [created]
+jobs:
+  slashCommandDispatch:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Slash Command Dispatch
+        uses: peter-evans/slash-command-dispatch@v2
+        with:
+          token: ${{ secrets.ACTION_TRIGGER_TOKEN }}
+          issue-type: pull-request
+          commands: |
+            pre-commit-run

.github/workflows/windows.yml

@@ -17,7 +17,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     env:
       TEST_SUBSET: ${{ matrix.test-subset }}
-      THEANO_FLAGS: floatX=${{ matrix.floatx }},gcc.cxxflags='-march=core2'
+      THEANO_FLAGS: floatX=${{ matrix.floatx }},gcc__cxxflags='-march=core2'
     defaults:
       run:
         shell: bash -l {0}
@@ -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

.pre-commit-config.yaml

@@ -11,16 +11,18 @@ 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
+  rev: 0.5.5
   hooks:
     - id: nbqa-black
       additional_dependencies: [black==20.8b1]
     - id: nbqa-isort
       additional_dependencies: [isort==5.6.4]
     - id: nbqa-pyupgrade
       additional_dependencies: [pyupgrade==2.7.4]
+      args: [--py37-plus]
 - repo: https://github.com/PyCQA/isort
   rev: 5.6.4
   hooks:
@@ -30,7 +32,7 @@ repos:
   rev: v2.7.4
   hooks:
     - id: pyupgrade
-      args: [--py36-plus]
+      args: [--py37-plus]
 - repo: https://github.com/psf/black
   rev: 20.8b1
   hooks:
@@ -61,6 +63,19 @@ 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

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.
@@ -38,16 +40,16 @@ 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.
 
 4. Project requirements are in ``requirements.txt``, and libraries used for development are in ``requirements-dev.txt``. The easiest (and recommended) way to set up a development environment is via [miniconda](https://docs.conda.io/en/latest/miniconda.html):
 
    ```bash
-   $ conda env create -f conda-envs/environment-dev-py36.yml  # or py37 or py38
-   $ conda activate pymc3-dev-py36
+   $ conda env create -f conda-envs/environment-dev-py37.yml  # or py38 or py39
+   $ conda activate pymc3-dev-py37
    $ pip install -e .
    ```
 
@@ -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)

README.rst

@@ -120,7 +120,7 @@ Dependencies
 ============
 
 PyMC3 is tested on Python 3.6, 3.7, and 3.8 and depends on `Theano-PyMC <https://github.com/pymc-devs/Theano-PyMC>`__,
-NumPy, SciPy, and Pandas
+NumPy, SciPy, and pandas
 (see `requirements.txt <https://github.com/pymc-devs/pymc3/blob/master/requirements.txt>`__ for version
 information).
 

RELEASE-NOTES.md

@@ -1,5 +1,15 @@
 # Release Notes
 
+## PyMC3 4.0.0 (on deck)
+
+This is the first release to support Python3.9 and to drop Python3.6.
+
+### Maintenance
+- Fixed bug whereby partial traces returns after keyboard interrupt during parallel sampling had fewer draws than would've been available [#4318](https://github.com/pymc-devs/pymc3/pull/4318)
+- Make `sample_shape` same across all contexts in `draw_values` (see [#4305](https://github.com/pymc-devs/pymc3/pull/4305)).
+- Removed `theanof.set_theano_config` because it illegally touched Theano's privates (see [#4329](https://github.com/pymc-devs/pymc3/pull/4329)).
+
+
 ## PyMC3 3.10.0 (7 December 2020)
 
 This is a major release with many exciting new features. The biggest change is that we now rely on our own fork of [Theano-PyMC](https://github.com/pymc-devs/Theano-PyMC). This is in line with our [big announcement about our commitment to PyMC3 and Theano](https://pymc-devs.medium.com/the-future-of-pymc3-or-theano-is-dead-long-live-theano-d8005f8a0e9b).

conda-envs/environment-dev-py36.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==1.0.11
-  - 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