Merge branch 'main' into numbagg

* main: (68 commits) convert datetime: micro-optimizations (#261) compatibility with `numpy>=2.0` (#257) replace the deprecated `provision-with-micromamba` with `setup-micromamba` (#258) Fix some typing errors in asv_bench and tests (#253) [pre-commit.ci] pre-commit autoupdate (#250) typing fixes (#235) Fix test failure on i386 (#248) Delete resample_reduce (#246) Bump codecov/codecov-action from 3.1.3 to 3.1.4 (#243) Enable nanargmax, nanargmin (#171) Support nanfirst, nanlast with simple combine algo (#240) Check method only for dask reductions. (#241) Optimize broadcasting (#230) Handle min_count=0 (#238) Try and fix dtypes on 3.8,3.10 windows Preserve input dtypes now that pandas can do it. Add pytest-pretty to envs factorize early as much as possible Bump codecov/codecov-action from 3.1.1 to 3.1.3 (#239) [pre-commit.ci] pre-commit autoupdate (#229) ...
xarray-contrib · Sep 28, 2023 · 4c78f8e · 4c78f8e
2 parents fea47a5 + 5ea713e
commit 4c78f8e
Show file tree

Hide file tree

Showing 60 changed files with 22,487 additions and 2,356 deletions.
diff --git a/.git_archival.txt b/.git_archival.txt
@@ -0,0 +1,4 @@
+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true)$
+ref-names: $Format:%D$
diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
@@ -22,12 +22,13 @@ jobs:
           fetch-depth: 0
 
       - name: Set up conda environment
-        uses: mamba-org/provision-with-micromamba@v13
+        uses: mamba-org/setup-micromamba@v1
         with:
           environment-file: ci/environment.yml
           environment-name: flox-tests
-          cache-env: true
-          # extra-specs: |
+          init-shell: bash
+          cache-environment: true
+          # create-args: |
           #   python="${{ matrix.python-version }}"
 
       # - name: Setup some dependencies

diff --git a/.github/workflows/ci-additional.yaml b/.github/workflows/ci-additional.yaml
@@ -25,7 +25,7 @@ jobs:
       - uses: actions/checkout@v3
         with:
           fetch-depth: 2
-      - uses: xarray-contrib/ci-trigger@v1.1
+      - uses: xarray-contrib/ci-trigger@v1.2
         id: detect-trigger
         with:
           keyword: "[skip-ci]"
@@ -53,14 +53,15 @@ jobs:
           echo "TODAY=$(date  +'%Y-%m-%d')" >> $GITHUB_ENV
 
       - name: Setup micromamba
-        uses: mamba-org/provision-with-micromamba@34071ca7df4983ccd272ed0d3625818b27b70dcc
+        uses: mamba-org/setup-micromamba@v1
         with:
           environment-file: ${{env.CONDA_ENV_FILE}}
           environment-name: flox-tests
-          extra-specs: |
-            python=${{env.PYTHON_VERSION}}
-          cache-env: true
+          init-shell: bash
+          cache-environment: true
           cache-env-key: "${{runner.os}}-${{runner.arch}}-py${{env.PYTHON_VERSION}}-${{env.TODAY}}-${{hashFiles(env.CONDA_ENV_FILE)}}"
+          create-args: |
+            python=${{ env.PYTHON_VERSION }}
 
       - name: Install flox
         run: |
@@ -71,7 +72,15 @@ jobs:
           conda list
       - name: Run doctests
         run: |
-          python -m pytest --doctest-modules flox --ignore flox/tests
+          python -m pytest --doctest-modules flox --ignore flox/tests --cov=./ --cov-report=xml
+      - name: Upload code coverage to Codecov
+        uses: codecov/[email protected]
+        with:
+          file: ./coverage.xml
+          flags: unittests
+          env_vars: RUNNER_OS
+          name: codecov-umbrella
+          fail_ci_if_error: false
 
   mypy:
     name: Mypy
@@ -94,15 +103,16 @@ jobs:
         run: |
           echo "TODAY=$(date +'%Y-%m-%d')" >> $GITHUB_ENV
       - name: Setup micromamba
-        uses: mamba-org/provision-with-micromamba@34071ca7df4983ccd272ed0d3625818b27b70dcc
+        uses: mamba-org/setup-micromamba@v1
         with:
           environment-file: ${{env.CONDA_ENV_FILE}}
-          environment-name: xarray-tests
-          extra-specs: |
-            python=${{env.PYTHON_VERSION}}
-          cache-env: true
+          environment-name: flox-tests
+          init-shell: bash
+          cache-environment: true
           cache-env-key: "${{runner.os}}-${{runner.arch}}-py${{env.PYTHON_VERSION}}-${{env.TODAY}}-${{hashFiles(env.CONDA_ENV_FILE)}}"
-      - name: Install xarray
+          create-args: |
+            python=${{ env.PYTHON_VERSION }}
+      - name: Install flox
         run: |
           python -m pip install --no-deps -e .
       - name: Version info
@@ -115,4 +125,13 @@ jobs:
 
       - name: Run mypy
         run: |
-          python -m mypy --install-types --non-interactive
+          python -m mypy --install-types --non-interactive --cobertura-xml-report mypy_report
+
+      - name: Upload mypy coverage to Codecov
+        uses: codecov/[email protected]
+        with:
+          file: mypy_report/cobertura.xml
+          flags: mypy
+          env_vars: PYTHON_VERSION
+          name: codecov-umbrella
+          fail_ci_if_error: false
diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -24,7 +24,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: ["ubuntu-latest"]
+        os: ["ubuntu-latest", "windows-latest"]
         python-version: ["3.8", "3.10"]
     steps:
       - uses: actions/checkout@v3
@@ -34,22 +34,22 @@ jobs:
         run: |
           echo "PYTHON_VERSION=${{ matrix.python-version }}" >> $GITHUB_ENV
       - name: Set up conda environment
-        uses: mamba-org/provision-with-micromamba@v13
+        uses: mamba-org/setup-micromamba@v1
         with:
           environment-file: ci/environment.yml
           environment-name: flox-tests
-          cache-env: true
-          extra-specs: |
-            python="${{ matrix.python-version }}"
+          init-shell: bash
+          cache-environment: true
+          create-args: |
+            python=${{ matrix.python-version }}
       - name: Install flox
         run: |
-          python -m pip install -e .
-          conda list
+          python -m pip install --no-deps -e .
       - name: Run Tests
         run: |
           pytest -n auto --cov=./ --cov-report=xml
       - name: Upload code coverage to Codecov
-        uses: codecov/[email protected].1
+        uses: codecov/[email protected].4
         with:
           file: ./coverage.xml
           flags: unittests
@@ -78,38 +78,28 @@ jobs:
         with:
           fetch-depth: 0 # Fetch all history for all branches and tags.
       - name: Set up conda environment
-        uses: mamba-org/provision-with-micromamba@v13
+        uses: mamba-org/setup-micromamba@v1
         with:
-          environment-file: ci/${{ matrix.env }}.yml
+          environment-file: ci/environment.yml
           environment-name: flox-tests
-          cache-env: true
-          extra-specs: |
-            python="${{ matrix.python-version }}"
+          init-shell: bash
+          cache-environment: true
+          create-args: |
+            python=${{ matrix.python-version }}
       - name: Install flox
         run: |
           python -m pip install --no-deps -e .
       - name: Run tests
         run: |
-          python -m pytest -n auto
-
-  upstream-dev:
-    name: upstream-dev
-    runs-on: ubuntu-latest
-    defaults:
-      run:
-        shell: bash -l {0}
-    steps:
-      - uses: actions/checkout@v3
-      - name: Set up conda environment
-        uses: mamba-org/provision-with-micromamba@v13
+          python -m pytest -n auto --cov=./ --cov-report=xml
+      - name: Upload code coverage to Codecov
+        uses: codecov/[email protected]
         with:
-          environment-file: ci/upstream-dev-env.yml
-          environment-name: flox-tests
-          extra-specs: |
-            python="3.10"
-      - name: Run Tests
-        run: |
-          pytest -n 2
+          file: ./coverage.xml
+          flags: unittests
+          env_vars: RUNNER_OS
+          name: codecov-umbrella
+          fail_ci_if_error: false
 
   xarray-groupby:
     name: xarray-groupby
@@ -123,13 +113,14 @@ jobs:
           repository: 'pydata/xarray'
           fetch-depth: 0 # Fetch all history for all branches and tags.
       - name: Set up conda environment
-        uses: mamba-org/provision-with-micromamba@v13
+        uses: mamba-org/setup-micromamba@v1
         with:
           environment-file: ci/requirements/environment.yml
           environment-name: xarray-tests
-          cache-env: true
-          extra-specs: |
-            python="3.10"
+          init-shell: bash
+          cache-environment: true
+          create-args: |
+            python=3.10
       - name: Install xarray
         run: |
           python -m pip install --no-deps .

diff --git a/.github/workflows/testpypi-release.yaml b/.github/workflows/testpypi-release.yaml
@@ -0,0 +1,89 @@
+name: Build and Upload to TestPyPI
+
+on:
+  push:
+    branches:
+      - "main"
+  pull_request:
+    types: [opened, reopened, synchronize, labeled]
+    branches:
+      - "*"
+  workflow_dispatch:
+
+# no need for concurrency limits
+
+jobs:
+  build-artifacts:
+    if: ${{ contains( github.event.pull_request.labels.*.name, 'test-build') && github.event_name == 'pull_request' || github.event_name == 'workflow_dispatch' }}
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - uses: actions/setup-python@v4
+        name: Install Python
+        with:
+          python-version: "3.10"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install build twine
+          python -m pip install tomli tomli_w
+
+      # - name: Disable local versions
+      #   run: |
+      #     python .github/workflows/configure-testpypi-version.py pyproject.toml
+      #     git update-index --assume-unchanged pyproject.toml
+      #     cat pyproject.toml
+
+      - name: Build tarball and wheels
+        run: |
+          git clean -xdf
+          python -m build
+
+      - name: Check built artifacts
+        run: |
+          python -m twine check --strict dist/*
+          if [ -f dist/flox-999.tar.gz ]; then
+            echo "❌ INVALID VERSION NUMBER"
+            exit 1
+          else
+            echo "✅ Looks good"
+          fi
+
+      - uses: actions/upload-artifact@v3
+        with:
+          name: releases
+          path: dist
+
+  test-built-dist:
+    needs: build-artifacts
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/setup-python@v4
+        name: Install Python
+        with:
+          python-version: "3.10"
+      - uses: actions/download-artifact@v3
+        with:
+          name: releases
+          path: dist
+      - name: List contents of built dist
+        run: |
+          ls -ltrh
+          ls -ltrh dist
+
+      - name: Verify the built dist/wheel is valid
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install dist/flox*.whl
+          # python -m cf_xarray.scripts.print_versions
+
+      # - name: Publish package to TestPyPI
+      #   uses: pypa/[email protected]
+      #   with:
+      #     password: ${{ secrets.TESTPYPI_TOKEN }}
+      #     repository_url: https://test.pypi.org/legacy/
+      #     verbose: true
diff --git a/.github/workflows/upstream-dev-ci.yaml b/.github/workflows/upstream-dev-ci.yaml
@@ -0,0 +1,64 @@
+name: CI Upstream
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    types: [opened, reopened, synchronize, labeled]
+    branches:
+      - main
+  schedule:
+    - cron: "0 0 * * *" # Daily “At 00:00” UTC
+  workflow_dispatch: # allows you to trigger the workflow run manually
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  upstream-dev:
+    name: upstream-dev
+    runs-on: ubuntu-latest
+    if: ${{ (contains(github.event.pull_request.labels.*.name, 'test-upstream') && github.event_name == 'pull_request') || github.event_name == 'workflow_dispatch' }}
+    defaults:
+      run:
+        shell: bash -l {0}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10"]
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0 # Fetch all history for all branches and tags.
+      - name: Set environment variables
+        run: |
+          echo "PYTHON_VERSION=${{ matrix.python-version }}" >> $GITHUB_ENV
+      - name: Set up conda environment
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: ci/upstream-dev-env.yml
+          environment-name: flox-tests
+          init-shell: bash
+          cache-environment: true
+          create-args: >-
+            python=${{ matrix.python-version }}
+            pytest-reportlog
+      - name: Install flox
+        run: |
+          python -m pip install --no-deps -e .
+      - name: Run Tests
+        if: success()
+        id: status
+        run: |
+          pytest -rf -n auto --cov=./ --cov-report=xml \
+            --report-log output-${{ matrix.python-version }}-log.jsonl
+      - name: Generate and publish the report
+        if: |
+          failure()
+          && steps.status.outcome == 'failure'
+          && github.event_name == 'schedule'
+          && github.repository_owner == 'xarray-contrib'
+        uses: xarray-contrib/issue-from-pytest-log@v1
+        with:
+          log-path: output-${{ matrix.python-version }}-log.jsonl