Merge branch 'main' into hypothesis-strategies

TomNicholas · Jul 20, 2023 · 4dcbc60 · 4dcbc60
2 parents 9777c2a + 2bf15f8
commit 4dcbc60
Show file tree

Hide file tree

Showing 219 changed files with 27,196 additions and 10,452 deletions.
diff --git a/.coveragerc b/.coveragerc
diff --git a/.git_archival.txt b/.git_archival.txt
@@ -1 +1,4 @@
+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$
 ref-names: $Format:%D$
diff --git a/.github/config.yml b/.github/config.yml
@@ -0,0 +1,23 @@
+# Comment to be posted to on first time issues
+newIssueWelcomeComment: >
+  Thanks for opening your first issue here at xarray! Be sure to follow the issue template!
+
+  If you have an idea for a solution, we would really welcome a Pull Request with proposed changes.
+
+  See the [Contributing Guide](https://docs.xarray.dev/en/latest/contributing.html) for more.
+
+  It may take us a while to respond here, but we really value your contribution. Contributors like you help make xarray better.
+
+  Thank you!
+
+# Comment to be posted to on PRs from first time contributors in your repository
+newPRWelcomeComment: >
+  Thank you for opening this pull request! It may take us a few days to respond here, so thank you for being patient.
+
+  If you have questions, some answers may be found in our [contributing guidelines](http://docs.xarray.dev/en/stable/contributing.html).
+
+# Comment to be posted to on pull requests merged by a first time user
+firstPRMergeComment: >
+  Congratulations on completing your first pull request! Welcome to Xarray!
+  We are proud of you, and hope to see you again!
+  ![celebration gif](https://media.giphy.com/media/umYMU8G2ixG5mJBDo5/giphy.gif)
diff --git a/.github/labeler.yml b/.github/labeler.yml
@@ -54,10 +54,6 @@ topic-indexing:
   - xarray/core/indexes.py
   - xarray/core/indexing.py
 
-run-benchmark:
-  - asv_bench/benchmarks/*
-  - asv_bench/benchmarks/**/*
-
 topic-performance:
   - asv_bench/benchmarks/*
   - asv_bench/benchmarks/**/*

diff --git a/.github/workflows/benchmarks-last-release.yml b/.github/workflows/benchmarks-last-release.yml
@@ -0,0 +1,79 @@
+name: Benchmark compare last release
+
+on:
+  push:
+    branches:
+      - main
+  workflow_dispatch:
+
+jobs:
+  benchmark:
+    name: Linux
+    runs-on: ubuntu-20.04
+    env:
+      ASV_DIR: "./asv_bench"
+      CONDA_ENV_FILE: ci/requirements/environment.yml
+
+    steps:
+      # We need the full repo to avoid this issue
+      # https://github.com/actions/checkout/issues/23
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Set up conda environment
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: ${{env.CONDA_ENV_FILE}}
+          environment-name: xarray-tests
+          cache-environment: true
+          cache-environment-key: "${{runner.os}}-${{runner.arch}}-py${{env.PYTHON_VERSION}}-${{env.TODAY}}-${{hashFiles(env.CONDA_ENV_FILE)}}-benchmark"
+          create-args: >-
+            asv
+
+      - name: 'Get Previous tag'
+        id: previoustag
+        uses: "WyriHaximus/github-action-get-previous-tag@v1"
+        # with:
+        #   fallback: 1.0.0 # Optional fallback tag to use when no tag can be found
+
+      - name: Run benchmarks
+        shell: bash -l {0}
+        id: benchmark
+        env:
+          OPENBLAS_NUM_THREADS: 1
+          MKL_NUM_THREADS: 1
+          OMP_NUM_THREADS: 1
+          ASV_FACTOR: 1.5
+          ASV_SKIP_SLOW: 1
+        run: |
+          set -x
+          # ID this runner
+          asv machine --yes
+          echo "Baseline: ${{ steps.previoustag.outputs.tag }} "
+          echo "Contender: ${{ github.sha }}"
+          # Use mamba for env creation
+          # export CONDA_EXE=$(which mamba)
+          export CONDA_EXE=$(which conda)
+          # Run benchmarks for current commit against base
+          ASV_OPTIONS="--split --show-stderr --factor $ASV_FACTOR"
+          asv continuous $ASV_OPTIONS ${{ steps.previoustag.outputs.tag }}  ${{ github.sha }} \
+              | sed "/Traceback \|failed$\|PERFORMANCE DECREASED/ s/^/::error::/" \
+              | tee benchmarks.log
+          # Report and export results for subsequent steps
+          if grep "Traceback \|failed\|PERFORMANCE DECREASED" benchmarks.log > /dev/null ; then
+              exit 1
+          fi
+        working-directory: ${{ env.ASV_DIR }}
+
+      - name: Add instructions to artifact
+        if: always()
+        run: |
+          cp benchmarks/README_CI.md benchmarks.log .asv/results/
+        working-directory: ${{ env.ASV_DIR }}
+
+      - uses: actions/upload-artifact@v3
+        if: always()
+        with:
+          name: asv-benchmark-results-${{ runner.os }}
+          path: ${{ env.ASV_DIR }}/.asv/results
diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
@@ -7,11 +7,12 @@ on:
 
 jobs:
   benchmark:
-    if: ${{ contains( github.event.pull_request.labels.*.name, 'run-benchmark') && github.event_name == 'pull_request' || github.event_name == 'workflow_dispatch' }}
+    if: ${{ contains( github.event.pull_request.labels.*.name, 'run-benchmark') && github.event_name == 'pull_request' || contains( github.event.pull_request.labels.*.name, 'topic-performance') && github.event_name == 'pull_request' || github.event_name == 'workflow_dispatch' }}
     name: Linux
     runs-on: ubuntu-20.04
     env:
       ASV_DIR: "./asv_bench"
+      CONDA_ENV_FILE: ci/requirements/environment.yml
 
     steps:
       # We need the full repo to avoid this issue
@@ -20,17 +21,16 @@ jobs:
         with:
           fetch-depth: 0
 
-      - name: Setup Miniconda
-        uses: conda-incubator/setup-miniconda@v2
+      - name: Set up conda environment
+        uses: mamba-org/setup-micromamba@v1
         with:
-          # installer-url: https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh
-          installer-url: https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh
+          environment-file: ${{env.CONDA_ENV_FILE}}
+          environment-name: xarray-tests
+          cache-environment: true
+          cache-environment-key: "${{runner.os}}-${{runner.arch}}-py${{env.PYTHON_VERSION}}-${{env.TODAY}}-${{hashFiles(env.CONDA_ENV_FILE)}}-benchmark"
+          create-args: >-
+            asv
 
-      - name: Setup some dependencies
-        shell: bash -l {0}
-        run: |
-          pip install asv
-          sudo apt-get update -y
 
       - name: Run benchmarks
         shell: bash -l {0}

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
         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: ${{env.CONDA_ENV_FILE}}
           environment-name: xarray-tests
-          extra-specs: |
+          create-args: >-
             python=${{env.PYTHON_VERSION}}
-          cache-env: true
-          cache-env-key: "${{runner.os}}-${{runner.arch}}-py${{env.PYTHON_VERSION}}-${{env.TODAY}}-${{hashFiles(env.CONDA_ENV_FILE)}}"
+            conda
+          cache-environment: true
+          cache-environment-key: "${{runner.os}}-${{runner.arch}}-py${{env.PYTHON_VERSION}}-${{env.TODAY}}-${{hashFiles(env.CONDA_ENV_FILE)}}"
 
       - name: Install xarray
         run: |
@@ -72,7 +73,10 @@ jobs:
           python xarray/util/print_versions.py
       - name: Run doctests
         run: |
-          python -m pytest --doctest-modules xarray --ignore xarray/tests
+          # Raise an error if there are warnings in the doctests, with `-Werror`.
+          # This is a trial; if it presents an problem, feel free to remove.
+          # See https://github.com/pydata/xarray/issues/7164 for more info.
+          python -m pytest --doctest-modules xarray --ignore xarray/tests -Werror
 
   mypy:
     name: Mypy
@@ -96,14 +100,15 @@ 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: ${{env.CONDA_ENV_FILE}}
           environment-name: xarray-tests
-          extra-specs: |
+          create-args: >-
             python=${{env.PYTHON_VERSION}}
-          cache-env: true
-          cache-env-key: "${{runner.os}}-${{runner.arch}}-py${{env.PYTHON_VERSION}}-${{env.TODAY}}-${{hashFiles(env.CONDA_ENV_FILE)}}"
+            conda
+          cache-environment: true
+          cache-environment-key: "${{runner.os}}-${{runner.arch}}-py${{env.PYTHON_VERSION}}-${{env.TODAY}}-${{hashFiles(env.CONDA_ENV_FILE)}}"
       - name: Install xarray
         run: |
           python -m pip install --no-deps -e .
@@ -114,11 +119,76 @@ jobs:
           python xarray/util/print_versions.py
       - name: Install mypy
         run: |
-          python -m pip install mypy
+          python -m pip install mypy --force-reinstall
 
       - 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
+
+  mypy39:
+    name: Mypy 3.9
+    runs-on: "ubuntu-latest"
+    needs: detect-ci-trigger
+    defaults:
+      run:
+        shell: bash -l {0}
+    env:
+      CONDA_ENV_FILE: ci/requirements/environment.yml
+      PYTHON_VERSION: "3.9"
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0 # Fetch all history for all branches and tags.
+
+      - name: set environment variables
+        run: |
+          echo "TODAY=$(date +'%Y-%m-%d')" >> $GITHUB_ENV
+      - name: Setup micromamba
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: ${{env.CONDA_ENV_FILE}}
+          environment-name: xarray-tests
+          create-args: >-
+            python=${{env.PYTHON_VERSION}}
+            conda
+          cache-environment: true
+          cache-environment-key: "${{runner.os}}-${{runner.arch}}-py${{env.PYTHON_VERSION}}-${{env.TODAY}}-${{hashFiles(env.CONDA_ENV_FILE)}}"
+      - name: Install xarray
+        run: |
+          python -m pip install --no-deps -e .
+      - name: Version info
+        run: |
+          conda info -a
+          conda list
+          python xarray/util/print_versions.py
+      - name: Install mypy
+        run: |
+          python -m pip install mypy --force-reinstall
+
+      - name: Run mypy
+        run: |
+          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: mypy39
+          env_vars: PYTHON_VERSION
+          name: codecov-umbrella
+          fail_ci_if_error: false
+
+
 
   min-version-policy:
     name: Minimum Version Policy
@@ -140,16 +210,14 @@ jobs:
           fetch-depth: 0 # Fetch all history for all branches and tags.
 
       - name: Setup micromamba
-        uses: mamba-org/provision-with-micromamba@34071ca7df4983ccd272ed0d3625818b27b70dcc
+        uses: mamba-org/setup-micromamba@v1
         with:
           environment-name: xarray-tests
-          environment-file: false
-          extra-specs: |
+          create-args: >-
             python=3.10
             pyyaml
             conda
             python-dateutil
-          channels: conda-forge
 
       - name: minimum versions policy
         run: |