Merge branch 'grassia2geo-dist' of https://github.com/ColtAllen/pymc-extras into grassia2geo-dist

Author: ColtAllen

.gitattributes

@@ -17,7 +17,7 @@ jobs:
           fetch-depth: 0
       - uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11"
       - name: Build the sdist and the wheel
         run: |
           pip install build

.github/workflows/pypi.yml

@@ -10,18 +10,29 @@ on:
       - "tests/**"
       - "setup.py"
       - "pyproject.toml"
-      - "buildosx"
       - "conda-envs/**"
       - "codecov.yml"
 
+# Cancels all previous workflow runs for pull requests that have not completed.
+concurrency:
+  # The concurrency group contains the workflow name and the branch name for pull requests
+  # or the commit hash for any other events.
+  group: ${{ github.workflow }}-${{ github.event_name == 'pull_request' && github.head_ref || github.sha }}
+  cancel-in-progress: true
+
 jobs:
   ubuntu:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: ["3.10"]
+        python-version: ["3.11"]
         test-subset:
-          - tests
+          - tests/model
+          - tests/statespace/core/test_statespace.py
+          - tests/statespace/filters/test_kalman_filter.py
+          - tests/statespace --ignore tests/statespace/core/test_statespace.py --ignore tests/statespace/filters/test_kalman_filter.py
+          - tests/distributions
+          - tests --ignore tests/model --ignore tests/statespace --ignore tests/distributions
       fail-fast: false
     runs-on: ${{ matrix.os }}
     env:
@@ -32,7 +43,7 @@ jobs:
         shell: bash -leo pipefail {0}
     steps:
       - uses: actions/checkout@v4
-      - uses: mamba-org/setup-micromamba@v1
+      - uses: mamba-org/setup-micromamba@v2
         with:
           environment-file: conda-envs/environment-test.yml
           create-args: >-
@@ -42,11 +53,12 @@ jobs:
           cache-environment: true
       - name: Install pymc-extras
         run: |
-          pip install -e .
+          pip install -e ".[dev]"
           python --version
+          pip check
       - name: Run tests
         run: |
-          python -m pytest -vv --cov=pymc_extras --cov-append --cov-report=xml --cov-report term --durations=50 $TEST_SUBSET
+          python -m pytest --color=yes -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:
@@ -59,7 +71,12 @@ jobs:
         os: [windows-latest]
         python-version: ["3.12"]
         test-subset:
-          - tests
+          - tests/model
+          - tests/statespace/core/test_statespace.py
+          - tests/statespace/filters/test_kalman_filter.py
+          - tests/statespace --ignore tests/statespace/core/test_statespace.py --ignore tests/statespace/filters/test_kalman_filter.py
+          - tests/distributions
+          - tests --ignore tests/model --ignore tests/statespace --ignore tests/distributions
       fail-fast: false
     runs-on: ${{ matrix.os }}
     env:
@@ -70,27 +87,36 @@ jobs:
         shell: cmd /C call {0}
     steps:
       - uses: actions/checkout@v4
-      - uses: mamba-org/setup-micromamba@v1
+      - uses: mamba-org/setup-micromamba@v2
         with:
-          environment-file: conda-envs/windows-environment-test.yml
-          micromamba-version: "1.5.10-0"  # Until https://github.com/mamba-org/mamba/issues/3467 is not fixed
+          environment-file: conda-envs/environment-test.yml
+          micromamba-version: "latest"
           create-args: >-
             python=${{matrix.python-version}}
           environment-name: pymc-extras-test
           init-shell: cmd.exe
           cache-environment: true
       - name: Install pymc-extras
         run: |
-          pip install -e .
+          pip install -e ".[dev]"
           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_extras --cov-append --cov-report=xml --cov-report term --durations=50 %TEST_SUBSET%
+          python -m pytest --color=yes -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:
           env_vars: TEST_SUBSET
           name: ${{ matrix.os }}
           fail_ci_if_error: false
+
+  all_tests:
+    if: ${{ always() }}
+    runs-on: ubuntu-latest
+    needs: [ ubuntu, windows ]
+    steps:
+      - name: Check all tests pass
+        if: ${{ needs.ubuntu.result != 'success' || needs.windows.result != 'success' }}
+        run: exit 1

.github/workflows/test.yml

@@ -11,6 +11,7 @@ tmtags
 tags
 .DS_Store
 .cache
+_version.py
 # IntelliJ IDE
 .idea
 *.iml

.gitignore

@@ -8,7 +8,7 @@ tasks:
       conda env update -f conda-envs/environment-test.yml -p env
       conda activate /workspace/pymc-extras/env
       pip install -r requirements-dev.txt
-      pip install -e .
+      pip install -e ."[dev]"
     command: |
       conda init bash && echo "conda activate /workspace/pymc-extras/env" >> ~/.bashrc && source ~/.bashrc
 

.gitpod.yml

@@ -26,5 +26,4 @@ repos:
   rev: 0.4.1
   hooks:
     - id: no-print-statements
-      exclude: _version.py
       files: ^pymc_extras/