Merge branch 'main' of https://github.com/pandas-dev/pandas into pdep11

Author: rhshadrach

.circleci/config.yml

@@ -6,7 +6,7 @@ jobs:
       image: ubuntu-2004:2022.04.1
     resource_class: arm.large
     environment:
-      ENV_FILE: ci/deps/circle-38-arm64.yaml
+      ENV_FILE: ci/deps/circle-39-arm64.yaml
       PYTEST_WORKERS: auto
       PATTERN: "not single_cpu and not slow and not network and not clipboard and not arm_slow and not db"
       PYTEST_TARGET: "pandas"
@@ -92,4 +92,4 @@ workflows:
               only: /^v.*/
           matrix:
             parameters:
-              cibw-build: ["cp38-manylinux_aarch64", "cp39-manylinux_aarch64", "cp310-manylinux_aarch64", "cp311-manylinux_aarch64"]
+              cibw-build: ["cp39-manylinux_aarch64", "cp310-manylinux_aarch64", "cp311-manylinux_aarch64"]

.circleci/setup_env.sh

@@ -54,10 +54,7 @@ if pip list | grep -q ^pandas; then
     pip uninstall -y pandas || true
 fi
 
-echo "Build extensions"
-python setup.py build_ext -q -j4
-
 echo "Install pandas"
-python -m pip install --no-build-isolation --no-use-pep517 -e .
+python -m pip install --no-build-isolation -ve .
 
 echo "done"

.github/actions/build_pandas/action.yml

@@ -1,5 +1,9 @@
 name: Build pandas
 description: Rebuilds the C extensions and installs pandas
+inputs:
+  editable:
+    description: Whether to build pandas in editable mode (default true)
+    default: true
 runs:
   using: composite
   steps:
@@ -12,9 +16,9 @@ runs:
 
     - name: Build Pandas
       run: |
-        python setup.py build_ext -j $N_JOBS
-        python -m pip install -e . --no-build-isolation --no-use-pep517 --no-index
+        if [[ ${{ inputs.editable }} == "true" ]]; then
+          pip install -e . --no-build-isolation -v
+        else
+          pip install . --no-build-isolation -v
+        fi
       shell: bash -el {0}
-      env:
-        # https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners#supported-runners-and-hardware-resources
-        N_JOBS: ${{ runner.os == 'macOS' && 3 || 2 }}

.github/actions/run-tests/action.yml

@@ -7,7 +7,7 @@ runs:
       shell: bash -el {0}
 
     - name: Publish test results
-      uses: actions/upload-artifact@v2
+      uses: actions/upload-artifact@v3
       with:
         name: Test results
         path: test-data.xml
@@ -19,7 +19,7 @@ runs:
       if: failure()
 
     - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v2
+      uses: codecov/codecov-action@v3
       with:
         flags: unittests
         name: codecov-pandas

.github/actions/setup-conda/action.yml

@@ -13,7 +13,7 @@ runs:
   using: composite
   steps:
     - name: Install ${{ inputs.environment-file }}
-      uses: mamba-org/provision-with-micromamba@v12
+      uses: mamba-org/provision-with-micromamba@v15
       with:
         environment-file: ${{ inputs.environment-file }}
         environment-name: ${{ inputs.environment-name }}

.github/workflows/32-bit-linux.yml

@@ -63,8 +63,24 @@ jobs:
     - name: Build Pandas
       id: build
       uses: ./.github/actions/build_pandas
+      with:
+        editable: false
 
     # The following checks are independent of each other and should still be run if one fails
+
+    # TODO: The doctests have to be run first right now, since the Cython doctests only work
+    # with pandas installed in non-editable mode
+    # This can be removed once pytest-cython doesn't require C extensions to be installed inplace
+    - name: Run doctests
+      run: cd ci && ./code_checks.sh doctests
+      if: ${{ steps.build.outcome == 'success' && always() }}
+
+    - name: Install pandas in editable mode
+      id: build-editable
+      uses: ./.github/actions/build_pandas
+      with:
+        editable: true
+
     - name: Check for no warnings when building single-page docs
       run: ci/code_checks.sh single-docs
       if: ${{ steps.build.outcome == 'success' && always() }}
@@ -73,10 +89,6 @@ jobs:
       run: ci/code_checks.sh code
       if: ${{ steps.build.outcome == 'success' && always() }}
 
-    - name: Run doctests
-      run: ci/code_checks.sh doctests
-      if: ${{ steps.build.outcome == 'success' && always() }}
-
     - name: Run docstring validation
       run: ci/code_checks.sh docstrings
       if: ${{ steps.build.outcome == 'success' && always() }}
@@ -179,7 +191,7 @@ jobs:
         id: setup_python
         uses: actions/setup-python@v4
         with:
-          python-version: '3.8'
+          python-version: '3.10'
           cache: 'pip'
           cache-dependency-path: 'requirements-dev.txt'
 

.github/workflows/code-checks.yml

@@ -18,6 +18,7 @@ jobs:
       actions: read
       contents: read
       security-events: write
+    if: github.repository_owner == 'pandas-dev'
 
     strategy:
       fail-fast: false

.github/workflows/codeql.yml

@@ -14,6 +14,10 @@ on:
 permissions:
   contents: read
 
+defaults:
+  run:
+    shell: bash -el {0}
+
 jobs:
   pip:
     if: ${{ github.event.label.name == 'Build' || contains(github.event.pull_request.labels.*.name, 'Build') || github.event_name == 'push'}}
@@ -38,15 +42,42 @@ jobs:
         id: setup_python
         uses: actions/setup-python@v4
         with:
-          python-version: '3.8'
-
-      - name: Install required dependencies
-        run: |
-          python -m pip install --upgrade pip setuptools wheel python-dateutil pytz numpy cython
-          python -m pip install versioneer[toml]
-        shell: bash -el {0}
+          python-version: '3.10'
 
       - name: Pip install with extra
         run: |
-          python -m pip install -e .[${{ matrix.extra }}] --no-build-isolation
+          python -m pip install .[${{ matrix.extra }}] -v
         shell: bash -el {0}
+  conda_forge_recipe:
+    if: ${{ github.event.label.name == 'Build' || contains(github.event.pull_request.labels.*.name, 'Build') || github.event_name == 'push'}}
+    runs-on: ubuntu-22.04
+    strategy:
+      matrix:
+        python-version: ['3.9', '3.10', '3.11']
+      fail-fast: false
+    name: Test Conda Forge Recipe - Python ${{ matrix.python-version }}
+    concurrency:
+      # https://github.community/t/concurrecy-not-work-for-push/183068/7
+      group: ${{ github.event_name == 'push' && github.run_number || github.ref }}-conda-forge-recipe-${{ matrix.python-version }}
+      cancel-in-progress: true
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: mamba-org/provision-with-micromamba@v15
+        with:
+          environment-file: false
+          environment-name: recipe-test
+          extra-specs: |
+            python=${{ matrix.python-version }}
+            boa
+            conda-verify
+          channels: conda-forge
+          cache-downloads: true
+          cache-env: true
+
+      - name: Build conda package
+        run: conda mambabuild ci --no-anaconda-upload --verify --strict-verify --output --output-folder .