Fix JAX warnings in tests

.gitattributes

@@ -0,0 +1 @@
+pymc_experimental/_version.py export-subst

.github/release.yml

@@ -0,0 +1,24 @@
+# This file contains configuration for the automatic generation of release notes in GitHub.
+# It's not perfect, but it makes it a little less laborious to write informative release notes.
+# Also see https://docs.github.com/en/repositories/releasing-projects-on-github/automatically-generated-release-notes
+changelog:
+  exclude:
+    labels:
+      - no releasenotes
+  categories:
+    - title: Major Changes 🛠
+      labels:
+        - major
+    - title: New Features 🎉
+      labels:
+        - enhancements
+        - feature request
+    - title: Bugfixes 🪲
+      labels:
+        - bug
+    - title: Documentation 📖
+      labels:
+        - docs
+    - title: Maintenance 🔧
+      labels:
+        - "*"

.github/workflows/pypi.yml

@@ -0,0 +1,87 @@
+name: PyPI
+on:
+  pull_request:
+    branches: [main]
+  push:
+    branches: [main]
+  release:
+    types: [published]
+
+jobs:
+  build:
+    name: build source distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+      - name: Build the sdist and the wheel
+        run: |
+          pip install build
+          python3 -m build
+      - name: Check the sdist installs and imports
+        run: |
+            mkdir -p test-sdist
+            cd test-sdist
+            python -m venv venv-sdist
+            venv-sdist/bin/python -m pip install numpy
+            venv-sdist/bin/python -m pip install ../dist/pymc-experimental*.tar.gz
+            echo "Checking import and version number (on release)"
+            venv-sdist/bin/python -c "import pymc_experimental as pmx; assert pmx.__version__ == '${{ github.ref_name }}'[1:] if '${{ github.ref_type }}' == 'tag' else True; print(pmx.__version__)"
+            cd ..
+      - name: Check the bdist installs and imports
+        run: |
+              mkdir -p test-bdist
+              cd test-bdist
+              python -m venv venv-bdist
+              venv-bdist/bin/python -m pip install ../dist/pymc_experimental*.whl
+              echo "Checking import and version number (on release)"
+              venv-bdist/bin/python -c "import pymc_experimental as pmx; assert pmx.__version__ == '${{ github.ref_name }}'[1:] if '${{ github.ref_type }}' == 'tag' else pmx.__version__; print(pmx.__version__)"
+              cd ..
+      - uses: actions/upload-artifact@v3
+        with:
+          name: artifact
+          path: dist/*
+  test:
+    name: upload to test PyPI
+    needs: [build]
+    runs-on: ubuntu-latest
+    if: github.event_name == 'release' && github.event.action == 'published'
+    steps:
+      - uses: actions/download-artifact@v3
+        with:
+          name: artifact
+          path: dist
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          skip_existing: true
+          user: __token__
+          password: ${{ secrets.TEST_PYPI_API_TOKEN }}
+          repository_url: https://test.pypi.org/legacy/
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+      - name: Test pip install from test.pypi
+        run: |
+          python -m venv venv-test-pypi
+          venv-test-pypi/bin/python -m pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple pymc-experimental
+          echo "Checking import and version number"
+          venv-test-pypi/bin/python -c "import pymc_experimental; assert pymc_experimental.__version__ == '${{ github.ref_name }}'[1:]"
+
+  publish:
+    name: upload release to PyPI
+    needs: [build, test]
+    runs-on: ubuntu-latest
+    if: github.event_name == 'release' && github.event.action == 'published'
+    steps:
+      - uses: actions/download-artifact@v3
+        with:
+          name: artifact
+          path: dist
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/test.yml

@@ -17,13 +17,15 @@ jobs:
   ubuntu:
     strategy:
       matrix:
-        os: [ubuntu-18.04]
-        floatx: [float32, float64]
+        os: [ubuntu-latest]
+        python-version: ["3.9"]
+        test-subset:
+          - pymc_experimental/tests
       fail-fast: false
     runs-on: ${{ matrix.os }}
     env:
       TEST_SUBSET: ${{ matrix.test-subset }}
-      AESARA_FLAGS: floatX=${{ matrix.floatx }},gcc__cxxflags='-march=native'
+      PYTENSOR_FLAGS: gcc__cxxflags='-march=native'
     defaults:
       run:
         shell: bash -l {0}
@@ -32,12 +34,12 @@ jobs:
       - name: Cache conda
         uses: actions/cache@v1
         env:
-          # Increase this value to reset cache if environment-test-py38.yml has not changed
+          # Increase this value to reset cache if environment-test.yml has not changed
           CACHE_NUMBER: 0
         with:
           path: ~/conda_pkgs_dir
-          key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
-            hashFiles('conda-envs/environment-test-py38.yml') }}
+          key: ${{ runner.os }}-py${{matrix.python-version}}-conda-${{ env.CACHE_NUMBER }}-${{
+            hashFiles('conda-envs/environment-test.yml') }}
       - name: Cache multiple paths
         uses: actions/cache@v2
         env:
@@ -55,36 +57,39 @@ jobs:
           miniforge-variant: Mambaforge
           miniforge-version: latest
           mamba-version: "*"
-          activate-environment: pymc-test-py38
+          activate-environment: pymc-experimental-test
           channel-priority: strict
-          environment-file: conda-envs/environment-test-py38.yml
+          environment-file: conda-envs/environment-test.yml
+          python-version: ${{matrix.python-version}}
           use-mamba: true
           use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
-      - name: Install-pymc
+      - name: Install pymc-experimental
         run: |
-          conda activate pymc-test-py38
+          conda activate pymc-experimental-test
           pip install -e .
           python --version
       - name: Run tests
         run: |
-          conda activate pymc-test-py38
+          conda activate pymc-experimental-test
           python -m pytest -vv --cov=pymc_experimental --cov-append --cov-report=xml --cov-report term --durations=50 $TEST_SUBSET
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v2
         with:
           env_vars: TEST_SUBSET
-          name: ${{ matrix.os }} ${{ matrix.floatx }}
+          name: ${{ matrix.os }}
           fail_ci_if_error: false
   windows:
     strategy:
       matrix:
         os: [windows-latest]
-        floatx: [float32, float64]
+        python-version: ["3.11"]
+        test-subset:
+          - pymc_experimental/tests
       fail-fast: false
     runs-on: ${{ matrix.os }}
     env:
       TEST_SUBSET: ${{ matrix.test-subset }}
-      AESARA_FLAGS: floatX=${{ matrix.floatx }},gcc__cxxflags='-march=core2'
+      PYTENSOR_FLAGS: gcc__cxxflags='-march=core2'
     defaults:
       run:
         shell: cmd
@@ -93,12 +98,12 @@ jobs:
       - name: Cache conda
         uses: actions/cache@v1
         env:
-          # Increase this value to reset cache if conda-envs/environment-test-py37.yml has not changed
+          # Increase this value to reset cache if conda-envs/windows-environment-test.yml has not changed
           CACHE_NUMBER: 0
         with:
           path: ~/conda_pkgs_dir
-          key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
-            hashFiles('conda-envs/windows-environment-test-py37.yml') }}
+          key: ${{ runner.os }}-py${{matrix.python-version}}-conda-${{ env.CACHE_NUMBER }}-${{
+            hashFiles('conda-envs/windows-environment-test.yml') }}
       - name: Cache multiple paths
         uses: actions/cache@v2
         env:
@@ -116,25 +121,26 @@ jobs:
           miniforge-variant: Mambaforge
           miniforge-version: latest
           mamba-version: "*"
-          activate-environment: pymc-test-py37
+          activate-environment: pymc-experimental-test
           channel-priority: strict
-          environment-file: conda-envs/windows-environment-test-py37.yml
+          environment-file: conda-envs/windows-environment-test.yml
+          python-version: ${{matrix.python-version}}
           use-mamba: true
           use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
-      - name: Install-pymc
+      - name: Install pymc-experimental
         run: |
-          conda activate pymc-test-py37
+          conda activate pymc-experimental-test
           pip install -e .
           python --version
       - name: Run tests
         # This job uses a cmd shell, therefore the environment variable syntax is different!
         # The ">-" in the next line replaces newlines with spaces (see https://stackoverflow.com/a/66809682).
         run: >-
-          conda activate pymc-test-py37 &&
-          python -m pytest -vv --cov=pymc_experimental --doctest-modules pymc_experimental --cov-append --cov-report=xml --cov-report term --durations=50 %TEST_SUBSET%
+          conda activate pymc-experimental-test &&
+          python -m pytest -vv --cov=pymc_experimental --cov-append --cov-report=xml --cov-report term --durations=50 %TEST_SUBSET%
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v2
         with:
           env_vars: TEST_SUBSET
-          name: ${{ matrix.os }} ${{ matrix.floatx }}
+          name: ${{ matrix.os }}
           fail_ci_if_error: false

.gitignore

@@ -44,3 +44,4 @@ pytestdebug.log
 
 # Codespaces
 pythonenv*
+env/

.gitpod.yml

@@ -3,14 +3,14 @@ tasks:
   - name: initialize
     init: |
       mkdir -p .vscode
-      echo '{"python.defaultInterpreterPath": "/home/gitpod/.conda/envs/pymc-test-py39/bin/python"}' > .vscode/settings.json
+      echo '{"python.defaultInterpreterPath": "/workspace/pymc-experimental/env/bin/python"}' > .vscode/settings.json
       conda init bash && source ~/.bashrc
-      conda env update -f conda-envs/environment-test-py39.yml
-      conda activate pymc-test-py39
+      conda env update -f conda-envs/environment-test.yml -p env
+      conda activate /workspace/pymc-experimental/env
       pip install -r requirements-dev.txt
       pip install -e .
     command: |
-      conda init bash && echo "conda activate pymc-test-py39" >> ~/.bashrc && source ~/.bashrc && conda activate pymc-test-py39
+      conda init bash && echo "conda activate /workspace/pymc-experimental/env" >> ~/.bashrc && source ~/.bashrc
 
 vscode:
   extensions:

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.3.0
+  rev: v4.5.0
   hooks:
     -   id: check-merge-conflict
     -   id: check-toml
@@ -11,30 +11,31 @@ repos:
         args: [--branch, main]
     -   id: trailing-whitespace
 - repo: https://github.com/PyCQA/isort
-  rev: 5.10.1
+  rev: 5.13.2
   hooks:
     - id: isort
       name: isort
 - repo: https://github.com/asottile/pyupgrade
-  rev: v2.37.1
+  rev: v3.15.0
   hooks:
     - id: pyupgrade
       args: [--py37-plus]
 - repo: https://github.com/psf/black
-  rev: 22.6.0
+  rev: 24.1.1
   hooks:
     - id: black
     - id: black-jupyter
 - repo: https://github.com/PyCQA/pylint
-  rev: v2.14.5
+  rev: v3.0.3
   hooks:
     - id: pylint
       args: [--rcfile=.pylintrc]
       files: ^pymc_experimental/
 - repo: https://github.com/MarcoGorelli/madforhooks
-  rev: 0.3.0
+  rev: 0.4.1
   hooks:
     - id: no-print-statements
+      exclude: _version.py
       files: ^pymc_experimental/
 - repo: local
   hooks:

.readthedocs.yaml

@@ -13,3 +13,7 @@ python:
    - requirements: requirements.txt
    - method: pip
      path: .
+
+sphinx:
+  fail_on_warning: false
+  configuration: docs/conf.py

MANIFEST.in

@@ -0,0 +1,4 @@
+include requirements*.txt
+include *.md *.rst
+include LICENSE
+include pymc_experimental/version.txt

README.md

@@ -5,6 +5,10 @@
     alt="Contribute with Gitpod"
   />
 </a>
+<img
+  src="https://codecov.io/gh/pymc-devs/pymc-experimental/branch/main/graph/badge.svg"
+  alt="Codecov Badge"
+/>
 
 As PyMC continues to mature and expand its functionality to accommodate more domains of application, we increasingly see cutting-edge methodologies, highly specialized statistical distributions, and complex models appear.
 While this adds to the functionality and relevance of the project, it can also introduce instability and impose a burden on testing and quality control.
@@ -54,7 +58,5 @@ For example, `pymc-experimental` may just include methods that are not fully dev
 This project is still young and many things have not been answered or implemented.
 Please get involved!
 
-* What are guidlines for organizing submodules?
+* What are guidelines for organizing submodules?
   * Proposal: No default imports of WIP/unstable submodules. By importing manually we can avoid breaking the package if a submodule breaks, for example because of an updated dependency.
-* How can we minimize the additional burden of additional project repositories?
-* ToDo: Setting up a basic CI pipeline

conda-envs/environment-test.yml

@@ -0,0 +1,16 @@
+name: pymc-experimental-test
+channels:
+- conda-forge
+- defaults
+dependencies:
+- pip
+
+- pytest-cov>=2.5
+- pytest>=3.0
+- dask
+- xhistogram
+- statsmodels
+- pip:
+  - pymc>=5.10.0  # CI was failing to resolve
+  - blackjax
+  - scikit-learn