Merge pull request #68 from pymc-devs/main

Sync Fork from Upstream Repo

Author: sthagen

.github/ISSUE_TEMPLATE.md renamed to .github/ISSUE_TEMPLATE/bug_report.md

@@ -1,4 +1,8 @@
-If you have questions about a specific use case, or you are not sure whether this is a bug or not, please post it to our discourse channel: https://discourse.pymc.io
+---
+name: 'Bug Report'
+about: Inform about bugs in the PyMC3 library
+
+---
 
 ## Description of your problem
 
@@ -8,10 +12,15 @@ If you have questions about a specific use case, or you are not sure whether thi
 ```
 
 **Please provide the full traceback.**
+
+<details><summary>Complete error traceback</summary>
+
 ```python
-[The error output here]
+[The complete error output here]
 ```
 
+</details>
+
 **Please provide any additional information below.**
 
 

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,8 @@
+blank_issues_enabled: false
+contact_links:
+  - name: PyMC Discourse
+    url: https://discourse.pymc.io/
+    about: Ask usage questions about PyMC3
+  - name: Example notebook error report
+    url: https://github.com/pymc-devs/pymc-examples/issues
+    about: Please report errors or desired extensions to the tutorials and examples here.

.github/workflows/pytest.yml

@@ -5,40 +5,37 @@ on:
   push:
     branches: [main]
 
+
+# Tests are split into multiple jobs to accelerate the CI.
+# Different jobs should be organized to take approximately the same
+# time to complete (and not be prohibitely slow).
+# Because GitHub Actions don't support YAML anchors, we have to place the
+# splitting of testfiles into groups in the strategy/matrix/test-subset
+# and can't re-use the groups across jobs.
+# A pre-commit hook (scripts/check_all_tests_are_covered.py)
+# enforces that test run just once per OS / floatX setting.
+
 jobs:
-  pytest:
+  ubuntu:
     strategy:
       matrix:
         os: [ubuntu-18.04]
         floatx: [float32, float64]
         test-subset:
-        # Tests are split into multiple jobs to accelerate the CI.
-        # The first job (starting in the next block) shouldn't run any tests, but
-        # just ignores tests because that don't work at all, or run in other jobs.'
-        # Any test that was not ignored runs in the first job.
-        # A pre-commit hook (scripts/check_all_tests_are_covered.py) enforces that
-        # test run just once.
-
-        # Because YAML doesn't allow comments in the blocks below, here they are..
-        # 1st block: These tests are temporarily disabled, because they are _very_ broken
-        # 2nd block: The JAX tests run through their own workflow: jaxtests.yml
-        # 3nd & 4rd: These tests are covered by other matrix jobs
-        # 5th block: These tests PASS without a single XFAIL
-        # 6th block: These have some XFAILs
+        # How this works:
+        # 1st block: Only passes --ignore parameters to pytest.
+        # → pytest will run all test_*.py files that are NOT ignored.
+        #
+        # Subsequent blocks: Only pass paths to test files.
+        # → pytest will run only these files
           - |
             --ignore=pymc3/tests/test_distributions_timeseries.py
-            --ignore=pymc3/tests/test_missing.py
             --ignore=pymc3/tests/test_mixture.py
             --ignore=pymc3/tests/test_model_graph.py
             --ignore=pymc3/tests/test_modelcontext.py
             --ignore=pymc3/tests/test_parallel_sampling.py
             --ignore=pymc3/tests/test_profile.py
-            --ignore=pymc3/tests/test_random.py
-            --ignore=pymc3/tests/test_shared.py
-            --ignore=pymc3/tests/test_smc.py
-            --ignore=pymc3/tests/test_starting.py
             --ignore=pymc3/tests/test_step.py
-            --ignore=pymc3/tests/test_tracetab.py
             --ignore=pymc3/tests/test_tuning.py
             --ignore=pymc3/tests/test_types.py
             --ignore=pymc3/tests/test_variational_inference.py
@@ -47,7 +44,6 @@ jobs:
             --ignore=pymc3/tests/test_minibatches.py
             --ignore=pymc3/tests/test_pickling.py
             --ignore=pymc3/tests/test_plots.py
-            --ignore=pymc3/tests/test_special_functions.py
             --ignore=pymc3/tests/test_updates.py
             --ignore=pymc3/tests/test_examples.py
             --ignore=pymc3/tests/test_gp.py
@@ -67,7 +63,6 @@ jobs:
             pymc3/tests/test_minibatches.py
             pymc3/tests/test_pickling.py
             pymc3/tests/test_plots.py
-            pymc3/tests/test_special_functions.py
             pymc3/tests/test_updates.py
 
           - |
@@ -136,3 +131,71 @@ jobs:
           env_vars: OS,PYTHON
           name: codecov-umbrella
           fail_ci_if_error: false
+  windows:
+    strategy:
+      matrix:
+        os: [windows-latest]
+        floatx: [float32, float64]
+        test-subset:
+          - |
+            pymc3/tests/test_distributions_random.py
+          - |
+            pymc3/tests/test_sampling.py
+            pymc3/tests/test_shared.py
+          - |
+            pymc3/tests/test_gp.py
+            pymc3/tests/test_ode.py
+          - |
+            pymc3/tests/test_model.py
+            pymc3/tests/test_model_func.py
+            pymc3/tests/test_modelcontext.py
+            pymc3/tests/test_pickling.py
+
+      fail-fast: false
+    runs-on: ${{ matrix.os }}
+    env:
+      TEST_SUBSET: ${{ matrix.test-subset }}
+      AESARA_FLAGS: floatX=${{ matrix.floatx }},gcc__cxxflags='-march=core2'
+    defaults:
+      run:
+        shell: cmd
+    steps:
+      - uses: actions/checkout@v2
+      - name: Cache conda
+        uses: actions/cache@v1
+        env:
+          # Increase this value to reset cache if conda-envs/environment-dev-py38.yml has not changed
+          CACHE_NUMBER: 0
+        with:
+          path: ~/conda_pkgs_dir
+          key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
+            hashFiles('conda-envs/windows-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
+          channel-priority: strict
+          environment-file: conda-envs/windows-environment-dev-py38.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-py38
+          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 pymc3-dev-py38 &&
+          python -m pytest -vv --cov=pymc3 --cov-report=xml --cov-report term --durations=50 %TEST_SUBSET%

.github/workflows/windows.yml

@@ -1,7 +1,7 @@
 exclude: ^(docs/logos|pymc3/tests/data)/
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v3.4.0
+  rev: v4.0.1
   hooks:
     -   id: check-merge-conflict
     -   id: check-toml
@@ -14,28 +14,29 @@ repos:
         exclude: ^requirements-dev\.txt$
     -   id: trailing-whitespace
 - repo: https://github.com/PyCQA/isort
-  rev: 5.8.0
+  rev: 5.9.0
   hooks:
     - id: isort
       name: isort
 - repo: https://github.com/asottile/pyupgrade
-  rev: v2.11.0
+  rev: v2.19.4
   hooks:
     - id: pyupgrade
       args: [--py37-plus]
 - repo: https://github.com/psf/black
-  rev: 20.8b1
+  rev: 21.6b0
   hooks:
     - id: black
 - repo: https://github.com/PyCQA/pylint
-  rev: pylint-2.7.4
+  rev: v2.8.3
   hooks:
     - id: pylint
       args: [--rcfile=.pylintrc]
       files: ^pymc3/
 - repo: local
   hooks:
     - id: check-no-tests-are-ignored
+      additional_dependencies: [pandas,pyyaml]
       entry: python scripts/check_all_tests_are_covered.py
       files: ^\.github/workflows/pytest\.yml$
       language: python

.pre-commit-config.yaml

@@ -7,7 +7,8 @@
 - The GLM submodule has been removed, please use [Bambi](https://bambinos.github.io/bambi/) instead.
 - The `Distribution` keyword argument `testval` has been deprecated in favor of `initval`.
 - `pm.sample` now returns results as `InferenceData` instead of `MultiTrace` by default (see [#4744](https://github.com/pymc-devs/pymc3/pull/4744)).
-- ...
+- `pm.sample_prior_predictive` no longer returns transformed variable values by default. Pass them by name in `var_names` if you want to obtain these draws (see [4769](https://github.com/pymc-devs/pymc3/pull/4769)).
+...
 
 ### New Features
 - The `CAR` distribution has been added to allow for use of conditional autoregressions which often are used in spatial and network models.

RELEASE-NOTES.md

@@ -3,21 +3,29 @@ channels:
 - conda-forge
 - defaults
 dependencies:
+- aesara>=2.0.9
+- arviz>=0.11.2
+- cachetools>=4.2.1
+- dill
+- fastprogress>=0.2.0
 - h5py>=2.7
 - ipython>=7.16
 - libblas=*=*mkl
 - mkl-service
-- nbsphinx>=0.4
+- myst-nb
 - numpy=1.15
 - numpydoc>=0.9
 - pandas=0.24
 - pre-commit>=2.8.0
+- pydata-sphinx-theme
 - pytest-cov>=2.5
 - pytest>=3.0
 - python-graphviz
 - python=3.7
 - recommonmark>=0.4
-- scipy=1.2
+- scipy>1.4.1
 - sphinx-autobuild>=0.7
+- sphinx-panels
 - sphinx>=1.5
+- typing-extensions
 - watermark

conda-envs/environment-dev-py37.yml

@@ -3,18 +3,30 @@ channels:
 - conda-forge
 - defaults
 dependencies:
+- aesara>=2.0.9
+- arviz>=0.11.2
+- cachetools>=4.2.1
+- dill
+- fastprogress>=0.2.0
 - h5py>=2.7
 - ipython>=7.16
 - libblas=*=*mkl
 - mkl-service
+- myst-nb
 - nbsphinx>=0.4
+- numpy>=1.15.0
 - numpydoc>=0.9
+- pandas
 - pre-commit>=2.8.0
+- pydata-sphinx-theme
 - pytest-cov>=2.5
 - pytest>=3.0
 - python-graphviz
 - python=3.8
 - recommonmark>=0.4
+- scipy>1.4.1
 - sphinx-autobuild>=0.7
+- sphinx-panels
 - sphinx>=1.5
+- typing-extensions>=3.7.4
 - watermark

conda-envs/environment-dev-py38.yml

@@ -3,18 +3,30 @@ channels:
 - conda-forge
 - defaults
 dependencies:
+- aesara>=2.0.9
+- arviz>=0.11.2
+- cachetools>=4.2.1
+- dill
+- fastprogress>=0.2.0
 - h5py>=2.7
 - ipython>=7.16
 - libblas=*=*mkl
 - mkl-service
+- myst-nb
 - nbsphinx>=0.4
+- numpy>=1.15.0
 - numpydoc>=0.9
+- pandas>=0.24.0
 - pre-commit>=2.8.0
+- pydata-sphinx-theme
 - pytest-cov>=2.5
 - pytest>=3.0
 - python-graphviz
 - python=3.9
 - recommonmark>=0.4
+- scipy>1.4.1
 - sphinx-autobuild>=0.7
+- sphinx-panels
 - sphinx>=1.5
+- typing-extensions>=3.7.4
 - watermark