Merge branch 'main' into glum-v3

.github/workflows/build_wheels.yml

@@ -16,12 +16,10 @@ jobs:
 
     steps:
       - uses: actions/checkout@v3
-
       - name: Build wheels
         uses: pypa/[email protected]
         env:
           CIBW_ARCHS_MACOS: x86_64 arm64
-
       - uses: actions/upload-artifact@v3
         with:
           path: ./wheelhouse/*.whl
@@ -31,17 +29,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
-
       - uses: actions/setup-python@v4
         name: Install Python
         with:
           python-version: '3.8'
-
       - name: Install build dependencies
         run: python -m pip install setuptools setuptools-scm wheel Cython numpy scikit-learn
       - name: Build sdist
         run: python setup.py sdist
-
       - uses: actions/upload-artifact@v3
         with:
           path: dist/*.tar.gz
@@ -55,12 +50,11 @@ jobs:
         with:
           name: artifact
           path: dist
-
-      - uses: pypa/[email protected]
+      - uses: pypa/[email protected]
         with:
           user: __token__
           password: ${{ secrets.GH_TESTPYPI_UPLOAD }}
-          repository_url: https://test.pypi.org/legacy/
+          repository-url: https://test.pypi.org/legacy/
 
   upload_pypi:
     needs: [build_wheels, build_sdist, upload_testpypi]
@@ -71,8 +65,7 @@ jobs:
         with:
           name: artifact
           path: dist
-
-      - uses: pypa/[email protected]
+      - uses: pypa/[email protected]
         with:
           user: __token__
           password: ${{ secrets.GH_PYPI_UPLOAD }}

.github/workflows/ci.yml

@@ -2,62 +2,76 @@ name: CI
 on: [push]
 
 jobs:
-  linter:
-    name: "Linter (pre-commit)"
+  pre-commit-checks:
+    name: Linux - pre-commit checks - Python 3.10
+    timeout-minutes: 30
     runs-on: ubuntu-latest
     env:
-      CI: True
-    strategy:
-      fail-fast: true
+      PRE_COMMIT_USE_MICROMAMBA: 1
     steps:
-     - name: Pull image
-       run: docker pull condaforge/mambaforge:latest
-     - name: Checkout branch
-       uses: actions/checkout@v3
-       with:
-         ref: ${{ github.head_ref }}
-     - name: Run linter inside of container
-       uses: ./.github/actions/linter
-  linux:
-    name: "Linux - tests - Py${{ matrix.PYTHON_VERSION }}"
-    runs-on: ubuntu-latest
-    env:
-      CI: True
-    strategy:
-      fail-fast: true
-      matrix:
-        PYTHON_VERSION: ['3.8', '3.9', '3.10']
-    steps:
-     - name: Pull image
-       run: docker pull condaforge/mambaforge:latest
-     - name: Checkout branch
-       uses: actions/checkout@v3
-       with:
-         ref: ${{ github.head_ref }}
-     - name: Run CI inside of container
-       uses: ./.github/actions/unittests
-       with:
-         python_version: ${{ matrix.PYTHON_VERSION }}
-  linux-conda-build:
-    name: "Linux - conda-build - Python ${{ matrix.CONDA_BUILD_YML }}"
-    runs-on: ubuntu-latest
+      - name: Checkout branch
+        uses: actions/[email protected]
+      - name: Set up micromamba
+        uses: mamba-org/setup-micromamba@d05808540d968a55ca33c798e0661fb98f533c73
+      - name: Add micromamba to GITHUB_PATH
+        run: echo "${HOME}/micromamba-bin" >> "$GITHUB_PATH"
+      - name: Install Python 3.10
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+      - name: Run pre-commit checks
+        uses: pre-commit/[email protected]
+
+  unit-tests:
+    name: Tests - ${{ matrix.os }} - Py${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
     env:
       CI: True
     strategy:
       fail-fast: true
       matrix:
-        CONDA_BUILD_YML:
-          - linux_64_numpy1.20python3.8.____cpython
+        include:
+          - { os: ubuntu-latest, python-version: '3.8' }
+          - { os: ubuntu-latest, python-version: '3.9' }
+          - { os: ubuntu-latest, python-version: '3.10' }
+          - { os: ubuntu-latest, python-version: '3.11' }
+          - { os: macos-latest, python-version: '3.10' }
+          - { os: windows-latest, python-version: '3.10' }
     steps:
-      - name: Pull image
-        run: docker pull condaforge/mambaforge:latest
       - name: Checkout branch
         uses: actions/checkout@v3
+      - name: Set up conda env
+        uses: mamba-org/setup-micromamba@875557da4ee020f18df03b8910a42203fbf02da1
         with:
-          ref: ${{ github.head_ref }}
-      - name: Fetch full git history
-        run: git fetch --prune --unshallow
-      - name: Run CI inside of container
-        uses: ./.github/actions/conda-build
-        with:
-          conda_build_yml: ${{ matrix.CONDA_BUILD_YML }}
+          environment-file: environment.yml
+          init-shell: ${{ matrix.os == 'windows-latest' && 'powershell' || 'bash' }}
+          cache-environment: true
+          create-args: >-
+            python=${{ matrix.python-version }}
+      - name: Install repository (unix)
+        if: matrix.os != 'windows-latest'
+        shell: bash -el {0}
+        run: pip install --no-use-pep517 --no-deps --disable-pip-version-check -e .
+      - name: Install repository (windows)
+        if: matrix.os == 'windows-latest'
+        shell: powershell
+        run: pip install --no-use-pep517 --no-deps --disable-pip-version-check -e .
+      - name: Run pytest (unix)
+        if: matrix.os != 'windows-latest'
+        shell: bash -el {0}
+        run: pytest -nauto tests/glm --doctest-modules src/glum
+      - name: Run pytest (windows)
+        if: matrix.os == 'windows-latest'
+        shell: powershell
+        run: pytest -nauto .\tests\glm --doctest-modules .\src\glum
+      - name: Run doctest
+        if: matrix.os != 'windows-latest'
+        shell: bash -el {0}
+        # Check that the readme example will work by running via doctest.
+        # We run outside the repo to make the test a bit more similar to
+        # a user running after installing with conda.
+        run: |
+          mkdir ../temp
+          cp README.md ../temp
+          cd ../temp
+          python -m doctest -v README.md