Merge pull request #1 from pymc-devs/main

Sync forked repo

Author: ciguaran

.github/workflows/arviz_compat.yml

@@ -65,3 +65,9 @@ jobs:
       - name: Run tests
         run: |
           python -m pytest -vv --cov=pymc --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: ArviZ compat - ${{ matrix.os }} ${{ matrix.floatx }}
+          fail_ci_if_error: false

.github/workflows/jaxtests.yml

@@ -62,3 +62,9 @@ jobs:
       - name: Run tests
         run: |
           python -m pytest -vv --cov=pymc --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: JAX tests - ${{ matrix.os }} ${{ matrix.floatx }}
+          fail_ci_if_error: false

.github/workflows/pytest.yml

@@ -46,7 +46,6 @@ jobs:
             --ignore=pymc/tests/test_dist_math.py
             --ignore=pymc/tests/test_minibatches.py
             --ignore=pymc/tests/test_pickling.py
-            --ignore=pymc/tests/test_plots.py
             --ignore=pymc/tests/test_updates.py
             --ignore=pymc/tests/test_gp.py
             --ignore=pymc/tests/test_model.py
@@ -68,7 +67,6 @@ jobs:
             pymc/tests/test_dist_math.py
             pymc/tests/test_minibatches.py
             pymc/tests/test_pickling.py
-            pymc/tests/test_plots.py
             pymc/tests/test_updates.py
             pymc/tests/test_transforms.py
 
@@ -141,10 +139,10 @@ jobs:
           conda activate pymc-test-py37
           python -m pytest -vv --cov=pymc --cov-append --cov-report=xml --cov-report term --durations=50 $TEST_SUBSET
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v1
+        uses: codecov/codecov-action@v2
         with:
-          env_vars: OS,PYTHON
-          name: codecov-umbrella
+          env_vars: TEST_SUBSET
+          name: ${{ matrix.os }} ${{ matrix.floatx }}
           fail_ci_if_error: false
   windows:
     strategy:
@@ -223,3 +221,9 @@ jobs:
         run: >-
           conda activate pymc-test-py38 &&
           python -m pytest -vv --cov=pymc --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 }}
+          fail_ci_if_error: false

.github/workflows/release.yml

@@ -9,7 +9,7 @@ jobs:
   release-job:
     runs-on: ubuntu-latest
     env:
-      PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }}
+      PYPI_TOKEN: ${{ secrets.PYPI_TOKEN_PYMC }}
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python
@@ -39,7 +39,7 @@ jobs:
     - name: Publish to PyPI
       run: |
         twine check dist/*
-        twine upload --repository pypi --username __token__ --password ${PYPI_TOKEN} dist/*
+        twine upload --repository pypi --username __token__ --password ${PYPI_TOKEN_PYMC} dist/*
   test-install-job:
     needs: release-job
     runs-on: ubuntu-latest

.gitignore

@@ -18,6 +18,7 @@ tags
 # Sphinx
 _build
 docs/jupyter_execute
+docs/**/generated/*
 
 # Merge tool
 *.orig

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 exclude: ^(docs/logos|pymc/tests/data)/
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.0.1
+  rev: v4.1.0
   hooks:
     -   id: check-merge-conflict
     -   id: check-toml
@@ -19,16 +19,16 @@ repos:
     - id: isort
       name: isort
 - repo: https://github.com/asottile/pyupgrade
-  rev: v2.29.1
+  rev: v2.31.0
   hooks:
     - id: pyupgrade
       args: [--py37-plus]
 - repo: https://github.com/psf/black
-  rev: 21.11b1
+  rev: 21.12b0
   hooks:
     - id: black
 - repo: https://github.com/PyCQA/pylint
-  rev: v2.12.1
+  rev: v2.12.2
   hooks:
     - id: pylint
       args: [--rcfile=.pylintrc]

CONTRIBUTING.md

@@ -146,9 +146,9 @@ docker exec -it pymc jupyter notebook list
 ## Style guide
 
 We have configured a pre-commit hook that checks for `black`-compliant code style.
-We encourage you to configure the pre-commit hook as described in the [PyMC Python Code Style Wiki Page](https://github.com/pymc-devs/pymc/wiki/Python-Code-Style), because it will automatically enforce the code style on your commits.
+We encourage you to configure the pre-commit hook as described in the [PyMC Python Code Style Wiki Page](https://docs.pymc.io/en/latest/contributing/python_style.html), because it will automatically enforce the code style on your commits.
 
-Similarly, consult the [PyMC's Jupyter Notebook Style](https://github.com/pymc-devs/pymc/wiki/PyMC-Jupyter-Notebook-Style-Guide) guides for notebooks.
+Similarly, consult the [PyMC's Jupyter Notebook Style](https://docs.pymc.io/en/latest/contributing/jupyter_style.html) guides for notebooks.
 
 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.