Merge branch 'main' into pathfinder_w_pytensor_symbolic

Author: aphc14

.gitattributes

@@ -1 +1 @@
-pymc_experimental/_version.py export-subst
+pymc_extras/_version.py export-subst

.github/workflows/pre-commit.yml

@@ -28,18 +28,18 @@ jobs:
             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
+            venv-sdist/bin/python -m pip install ../dist/pymc_extras*.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__)"
+            venv-sdist/bin/python -c "import pymc_extras 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
+              venv-bdist/bin/python -m pip install ../dist/pymc_extras*.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__)"
+              venv-bdist/bin/python -c "import pymc_extras 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:
@@ -50,13 +50,16 @@ jobs:
     name: upload release to PyPI
     needs: [build]
     runs-on: ubuntu-latest
-    if: github.event_name == 'release' && github.event.action == 'published'
+    if: github.repository_owner == 'pymc-devs' && github.event_name == 'release' && github.event.action == 'published'
+    # Use the `release` GitHub environment to protect the Trusted Publishing (OIDC)
+    # workflow by requiring signoff from a maintainer.
+    environment: release
+    permissions:
+      # write id-token is necessary for trusted publishing (OIDC)
+      id-token: write
     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/pypi.yml

@@ -6,7 +6,7 @@ on:
     branches: [main]
     paths:
       - ".github/workflows/*"
-      - "pymc_experimental/**"
+      - "pymc_extras/**"
       - "tests/**"
       - "setup.py"
       - "pyproject.toml"
@@ -37,16 +37,16 @@ jobs:
           environment-file: conda-envs/environment-test.yml
           create-args: >-
             python=${{matrix.python-version}}
-          environment-name: pymc-experimental-test
+          environment-name: pymc-extras-test
           init-shell: bash
           cache-environment: true
-      - name: Install pymc-experimental
+      - name: Install pymc-extras
         run: |
           pip install -e .
           python --version
       - name: Run tests
         run: |
-          python -m pytest -vv --cov=pymc_experimental --cov-append --cov-report=xml --cov-report term --durations=50 $TEST_SUBSET
+          python -m pytest -vv --cov=pymc_extras --cov-append --cov-report=xml --cov-report term --durations=50 $TEST_SUBSET
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v2
         with:
@@ -76,18 +76,18 @@ jobs:
           micromamba-version: "1.5.10-0"  # Until https://github.com/mamba-org/mamba/issues/3467 is not fixed
           create-args: >-
             python=${{matrix.python-version}}
-          environment-name: pymc-experimental-test
+          environment-name: pymc-extras-test
           init-shell: cmd.exe
           cache-environment: true
-      - name: Install pymc-experimental
+      - name: Install pymc-extras
         run: |
           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: >-
-          python -m pytest -vv --cov=pymc_experimental --cov-append --cov-report=xml --cov-report term --durations=50 %TEST_SUBSET%
+          python -m pytest -vv --cov=pymc_extras --cov-append --cov-report=xml --cov-report term --durations=50 %TEST_SUBSET%
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v2
         with:

.github/workflows/test.yml

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

.gitpod.yml

@@ -27,4 +27,4 @@ repos:
   hooks:
     - id: no-print-statements
       exclude: _version.py
-      files: ^pymc_experimental/
+      files: ^pymc_extras/

.pre-commit-config.yaml

@@ -1,3 +1,3 @@
 # Contributing guide
 
-Page in construction, for now go to https://github.com/pymc-devs/pymc-experimental#questions.
+Page in construction, for now go to https://github.com/pymc-devs/pymc-extras#questions.

CONTRIBUTING.md

@@ -1,4 +1,5 @@
 include requirements*.txt
 include *.md *.rst
 include LICENSE
-include pymc_experimental/version.txt
+include README.md
+include pymc_extras/version.txt

MANIFEST.in

@@ -1,57 +1,56 @@
-# Welcome to `pymc-experimental`
-<a href="https://gitpod.io/#https://github.com/pymc-devs/pymc-experimental">
+# Welcome to `pymc-extras`
+<a href="https://gitpod.io/#https://github.com/pymc-devs/pymc-extras">
   <img
     src="https://img.shields.io/badge/Contribute%20with-Gitpod-908a85?logo=gitpod"
     alt="Contribute with Gitpod"
   />
 </a>
 <img
-  src="https://codecov.io/gh/pymc-devs/pymc-experimental/branch/main/graph/badge.svg"
+  src="https://codecov.io/gh/pymc-devs/pymc-extras/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.
-To reduce the burden on the main `pymc` repository, this `pymc-experimental` repository can become the aggregator and testing ground for new additions to PyMC.
-This may include unusual probability distributions, advanced model fitting algorithms, innovative yet not fully tested methods or any code that may be inappropriate to include in the `pymc` repository, but may want to be made available to users.
+To reduce the burden on the main `pymc` repository, this `pymc-extras` repository can become the aggregator and testing ground for new additions to PyMC.
+This may include unusual probability distributions, advanced model fitting algorithms, innovative yet not fully tested methods, or niche functionality that might not fit in the main PyMC repository, but still may be of interest to users.
 
-The `pymc-experimental` repository can be understood as the first step in the PyMC development pipeline, where all novel code is introduced until it is obvious that it belongs in the main repository.
+The `pymc-extras` repository can be understood as the first step in the PyMC development pipeline, where all novel code is introduced until it is obvious that it belongs in the main repository.
 We hope that this organization improves the stability and streamlines the testing overhead of the `pymc` repository, while allowing users and developers to test and evaluate cutting-edge methods and not yet fully mature features.
 
-`pymc-experimental` would be designed to mirror the namespaces in `pymc` to make usage and migration as easy as possible.
+`pymc-extras` would be designed to mirror the namespaces in `pymc` to make usage and migration as easy as possible.
 For example, a `ParabolicFractal` distribution could be used analogously to those in `pymc`:
 
 ```python
 import pymc as pm
-import pymc_experimental as pmx
+import pymc_extras as pmx
 
 with pm.Model():
+  alpha = pmx.ParabolicFractal('alpha', b=1, c=1)
 
-    alpha = pmx.ParabolicFractal('alpha', b=1, c=1)
-
-    ...
+  ...
 
 ```
 
 ## Questions
 
-### What belongs in `pymc-experimental`?
+### What belongs in `pymc-extras`?
 
 - newly-implemented statistical methods, for example step methods or model construction helpers
 - distributions that are tricky to sample from or test
 - infrequently-used fitting methods or distributions
 - any code that requires additional optimization before it can be used in practice
 
 
-### What does not belong in `pymc-experimental`?
+### What does not belong in `pymc-extras`?
 - Case studies
 - Implementations that cannot be applied generically, for example because they are tied to variables from a toy example
 
 
 ### Should there be more than one add-on repository?
 
 Since there is a lot of code that we may not want in the main repository, does it make sense to have more than one additional repository?
-For example, `pymc-experimental` may just include methods that are not fully developed, tested and trusted, while code that is known to work well and has adequate test coverage, but is still too specialized to become part of `pymc` could reside in a `pymc-extras` (or similar) repository.
+For example, `pymc-extras` may just include methods that are not fully developed, tested and trusted, while code that is known to work well and has adequate test coverage, but is still too specialized to become part of `pymc` could reside in a `pymc-extras` (or similar) repository.
 
 
 ### Unanswered questions & ToDos

README.md

@@ -1,16 +1,16 @@
-name: pymc-experimental-test
+name: pymc-extras-test
 channels:
 - conda-forge
-- defaults
+- nodefaults
 dependencies:
-- pip
+- pymc>=5.19.1
 - pytest-cov>=2.5
 - pytest>=3.0
 - dask
 - xhistogram
 - statsmodels
+- pip
 - pip:
-  - pymc>=5.17.0  # CI was failing to resolve
   - blackjax
   - scikit-learn
   - better_optimize>=0.0.10