Merge branch 'main' into allow-dtype

* main: Update ci-additional.yaml (#167) Refactor before redoing cohorts (#164) Fix mypy errors in core.py (#150) Add link to numpy_groupies (#160) Bump codecov/codecov-action from 3.1.0 to 3.1.1 (#159) Use math.prod instead of np.prod (#157) Remove None output from _get_expected_groups (#152) Fix mypy errors in xarray.py, xrutils.py, cache.py (#144) Raise error if multiple by's are used with Ellipsis (#149) pre-commit autoupdate (#148) Add mypy ignores (#146) Get pre commit bot to update (#145) Remove duplicate examples headers (#147) Add ci additional (#143) Bump mamba-org/provision-with-micromamba from 12 to 13 (#141) Add ASV benchmark CI workflow (#139) Fix func count for dtype O with numpy and numba (#138)
xarray-contrib · Oct 9, 2022 · 08dff04 · 08dff04
2 parents a32a40c + a1fb701
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diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
@@ -0,0 +1,78 @@
+name: Benchmark
+
+on:
+  pull_request:
+    types: [opened, reopened, synchronize, labeled]
+  workflow_dispatch:
+
+jobs:
+  benchmark:
+    # if: ${{ contains( github.event.pull_request.labels.*.name, 'run-benchmark') && github.event_name == 'pull_request' || github.event_name == 'workflow_dispatch' }}  # Run if the PR has been labelled correctly.
+    if: ${{ github.event_name == 'pull_request' || github.event_name == 'workflow_dispatch' }}  # Always run.
+    name: Linux
+    runs-on: ubuntu-20.04
+    env:
+      ASV_DIR: "./asv_bench"
+
+    steps:
+      # We need the full repo to avoid this issue
+      # https://github.com/actions/checkout/issues/23
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Set up conda environment
+        uses: mamba-org/provision-with-micromamba@v13
+        with:
+          environment-file: ci/environment.yml
+          environment-name: flox-tests
+          cache-env: true
+          # extra-specs: |
+          #   python="${{ matrix.python-version }}"
+
+      # - name: Setup some dependencies
+        # shell: bash -l {0}
+        # run: |
+          # pip install asv
+          # sudo apt-get update -y
+
+      - 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:  ${{ github.event.pull_request.base.sha }} (${{ github.event.pull_request.base.label }})"
+          echo "Contender: ${GITHUB_SHA} (${{ github.event.pull_request.head.label }})"
+          # 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 ${{ github.event.pull_request.base.sha }} ${GITHUB_SHA} \
+              | sed "/Traceback \|failed$\|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/ci-additional.yaml b/.github/workflows/ci-additional.yaml
@@ -0,0 +1,118 @@
+name: CI Additional
+on:
+  push:
+    branches:
+      - "main"
+  pull_request:
+    branches:
+      - "*"
+  workflow_dispatch: # allows you to trigger manually
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  detect-ci-trigger:
+    name: detect ci trigger
+    runs-on: ubuntu-latest
+    if: |
+      github.repository == 'xarray-contrib/flox'
+      && (github.event_name == 'push' || github.event_name == 'pull_request')
+    outputs:
+      triggered: ${{ steps.detect-trigger.outputs.trigger-found }}
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 2
+      - uses: xarray-contrib/ci-trigger@v1.1
+        id: detect-trigger
+        with:
+          keyword: "[skip-ci]"
+
+  doctest:
+    name: Doctests
+    runs-on: "ubuntu-latest"
+    needs: detect-ci-trigger
+    if: needs.detect-ci-trigger.outputs.triggered == 'false'
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    env:
+      CONDA_ENV_FILE: ci/environment.yml
+      PYTHON_VERSION: "3.10"
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0 # Fetch all history for all branches and tags.
+
+      - name: set environment variables
+        run: |
+          echo "TODAY=$(date  +'%Y-%m-%d')" >> $GITHUB_ENV
+
+      - name: Setup micromamba
+        uses: mamba-org/provision-with-micromamba@34071ca7df4983ccd272ed0d3625818b27b70dcc
+        with:
+          environment-file: ${{env.CONDA_ENV_FILE}}
+          environment-name: flox-tests
+          extra-specs: |
+            python=${{env.PYTHON_VERSION}}
+          cache-env: true
+          cache-env-key: "${{runner.os}}-${{runner.arch}}-py${{env.PYTHON_VERSION}}-${{env.TODAY}}-${{hashFiles(env.CONDA_ENV_FILE)}}"
+
+      - name: Install flox
+        run: |
+          python -m pip install --no-deps -e .
+      - name: Version info
+        run: |
+          conda info -a
+          conda list
+      - name: Run doctests
+        run: |
+          python -m pytest --doctest-modules flox --ignore flox/tests
+
+  mypy:
+    name: Mypy
+    runs-on: "ubuntu-latest"
+    needs: detect-ci-trigger
+    if: needs.detect-ci-trigger.outputs.triggered == 'false'
+    defaults:
+      run:
+        shell: bash -l {0}
+    env:
+      CONDA_ENV_FILE: ci/environment.yml
+      PYTHON_VERSION: "3.10"
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0 # Fetch all history for all branches and tags.
+
+      - name: set environment variables
+        run: |
+          echo "TODAY=$(date +'%Y-%m-%d')" >> $GITHUB_ENV
+      - name: Setup micromamba
+        uses: mamba-org/provision-with-micromamba@34071ca7df4983ccd272ed0d3625818b27b70dcc
+        with:
+          environment-file: ${{env.CONDA_ENV_FILE}}
+          environment-name: xarray-tests
+          extra-specs: |
+            python=${{env.PYTHON_VERSION}}
+          cache-env: true
+          cache-env-key: "${{runner.os}}-${{runner.arch}}-py${{env.PYTHON_VERSION}}-${{env.TODAY}}-${{hashFiles(env.CONDA_ENV_FILE)}}"
+      - name: Install xarray
+        run: |
+          python -m pip install --no-deps -e .
+      - name: Version info
+        run: |
+          conda info -a
+          conda list
+      - name: Install mypy
+        run: |
+          python -m pip install mypy
+
+      - name: Run mypy
+        run: |
+          python -m mypy --install-types --non-interactive
diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -34,7 +34,7 @@ jobs:
         run: |
           echo "PYTHON_VERSION=${{ matrix.python-version }}" >> $GITHUB_ENV
       - name: Set up conda environment
-        uses: mamba-org/provision-with-micromamba@v12
+        uses: mamba-org/provision-with-micromamba@v13
         with:
           environment-file: ci/environment.yml
           environment-name: flox-tests
@@ -49,7 +49,7 @@ jobs:
         run: |
           pytest -n auto --cov=./ --cov-report=xml
       - name: Upload code coverage to Codecov
-        uses: codecov/codecov-action@v3.1.0
+        uses: codecov/codecov-action@v3.1.1
         with:
           file: ./coverage.xml
           flags: unittests
@@ -78,7 +78,7 @@ jobs:
         with:
           fetch-depth: 0 # Fetch all history for all branches and tags.
       - name: Set up conda environment
-        uses: mamba-org/provision-with-micromamba@v12
+        uses: mamba-org/provision-with-micromamba@v13
         with:
           environment-file: ci/${{ matrix.env }}.yml
           environment-name: flox-tests
@@ -101,7 +101,7 @@ jobs:
     steps:
       - uses: actions/checkout@v3
       - name: Set up conda environment
-        uses: mamba-org/provision-with-micromamba@v12
+        uses: mamba-org/provision-with-micromamba@v13
         with:
           environment-file: ci/upstream-dev-env.yml
           environment-name: flox-tests
@@ -123,7 +123,7 @@ 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@v12
+        uses: mamba-org/provision-with-micromamba@v13
         with:
           environment-file: ci/requirements/environment.yml
           environment-name: xarray-tests

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -10,12 +10,12 @@ repos:
         - id: check-docstring-first
 
     - repo: https://github.com/psf/black
-      rev: 22.6.0
+      rev: 22.8.0
       hooks:
         - id: black
 
     - repo: https://github.com/PyCQA/flake8
-      rev: 4.0.1
+      rev: 5.0.4
       hooks:
         - id: flake8
 

diff --git a/README.md b/README.md
@@ -16,7 +16,7 @@ It was motivated by
 
 1.  Dask Dataframe GroupBy
     [blogpost](https://blog.dask.org/2019/10/08/df-groupby)
-2.  numpy_groupies in Xarray
+2.  [numpy_groupies](https://github.com/ml31415/numpy-groupies) in Xarray
     [issue](https://github.com/pydata/xarray/issues/4473)
 
 (See a

diff --git a/asv.conf.json → asv_bench/asv.conf.json b/asv.conf.json → asv_bench/asv.conf.json
@@ -11,7 +11,7 @@
 
     // The URL or local path of the source code repository for the
     // project being benchmarked
-    "repo": ".",
+    "repo": "..",
 
     // The Python project's subdirectory in your repo.  If missing or
     // the empty string, the project is assumed to be located at the root
@@ -37,7 +37,7 @@
     // determined from "repo" by looking at the protocol in the URL
     // (if remote), or by looking for special directories, such as
     // ".git" (if local).
-    // "dvcs": "git",
+    "dvcs": "git",
 
     // The tool to use to create environments.  May be "conda",
     // "virtualenv" or other value depending on the plugins in use.
@@ -48,10 +48,10 @@
 
     // timeout in seconds for installing any dependencies in environment
     // defaults to 10 min
-    //"install_timeout": 600,
+    "install_timeout": 600,
 
     // the base URL to show a commit for the project.
-    "show_commit_url": "http://github.com/dcherian/flox/commit/",
+    "show_commit_url": "http://github.com/xarray-contrib/flox/commit/",
 
     // The Pythons you'd like to test against.  If not provided, defaults
     // to the current version of Python used to run `asv`.
@@ -114,7 +114,7 @@
 
     // The directory (relative to the current directory) that benchmarks are
     // stored in.  If not provided, defaults to "benchmarks"
-    // "benchmark_dir": "benchmarks",
+    "benchmark_dir": "benchmarks",
 
     // The directory (relative to the current directory) to cache the Python
     // environments in.  If not provided, defaults to "env"