Merge branch 'main' into cupy

* main: (24 commits) Add `packaging` as dependency use engine flox for ordered groups (#266) Update pyproject.toml: py3.12 Bump numpy to >=1.22 (#278) Cleanups (#276) benchmarks updates (#273) repo-review comments (#270) Significantly faster cohorts detection. (#272) Add engine="numbagg" (#72) Support quantile, median, mode with method="blockwise". (#269) Add multidimensional binning demo (#203) [pre-commit.ci] pre-commit autoupdate (#268) Drop python 3.8, test python 3.11 (#209) tests: move xfail out of functions (#265) Bump actions/checkout from 3 to 4 (#267) 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) ...
xarray-contrib · Nov 3, 2023 · eb81f56 · eb81f56
2 parents 796dcd2 + c15572e
commit eb81f56
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diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
@@ -8,7 +8,7 @@ on:
 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.
+    if: ${{ github.event_name == 'pull_request' || github.event_name == 'workflow_dispatch' }} # Always run.
     name: Linux
     runs-on: ubuntu-20.04
     env:
@@ -17,24 +17,20 @@ jobs:
     steps:
       # We need the full repo to avoid this issue
       # https://github.com/actions/checkout/issues/23
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
       - name: Set up conda environment
-        uses: mamba-org/provision-with-micromamba@v15
+        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 }}"
-
-      # - name: Setup some dependencies
-        # shell: bash -l {0}
-        # run: |
-          # pip install asv
-          # sudo apt-get update -y
+          environment-name: flox-bench
+          create-args: >-
+            python=3.10
+            asv
+            mamba
+          init-shell: bash
+          cache-environment: true
 
       - name: Run benchmarks
         shell: bash -l {0}
@@ -46,14 +42,11 @@ jobs:
           ASV_FACTOR: 1.5
           ASV_SKIP_SLOW: 1
         run: |
-          set -x
+          # 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} \

diff --git a/.github/workflows/ci-additional.yaml b/.github/workflows/ci-additional.yaml
@@ -22,7 +22,7 @@ jobs:
     outputs:
       triggered: ${{ steps.detect-trigger.outputs.trigger-found }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 2
       - uses: xarray-contrib/ci-trigger@v1.2
@@ -41,10 +41,10 @@ jobs:
 
     env:
       CONDA_ENV_FILE: ci/environment.yml
-      PYTHON_VERSION: "3.10"
+      PYTHON_VERSION: "3.11"
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0 # Fetch all history for all branches and tags.
 
@@ -53,14 +53,15 @@ jobs:
           echo "TODAY=$(date  +'%Y-%m-%d')" >> $GITHUB_ENV
 
       - name: Setup micromamba
-        uses: mamba-org/provision-with-micromamba@v15
+        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: |
@@ -71,9 +72,12 @@ jobs:
           conda list
       - name: Run doctests
         run: |
-          python -m pytest --doctest-modules flox --ignore flox/tests --cov=./ --cov-report=xml
+          python -m pytest --doctest-modules \
+          flox/aggregations.py flox/core.py flox/xarray.py \
+          --ignore flox/tests \
+          --cov=./ --cov-report=xml
       - name: Upload code coverage to Codecov
-        uses: codecov/codecov-action@v3.1.3
+        uses: codecov/codecov-action@v3.1.4
         with:
           file: ./coverage.xml
           flags: unittests
@@ -91,25 +95,26 @@ jobs:
         shell: bash -l {0}
     env:
       CONDA_ENV_FILE: ci/environment.yml
-      PYTHON_VERSION: "3.10"
+      PYTHON_VERSION: "3.11"
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         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@v15
+        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: |
           python -m pip install --no-deps -e .
@@ -126,7 +131,7 @@ jobs:
           python -m mypy --install-types --non-interactive --cobertura-xml-report mypy_report
 
       - name: Upload mypy coverage to Codecov
-        uses: codecov/codecov-action@v3.1.3
+        uses: codecov/codecov-action@v3.1.4
         with:
           file: mypy_report/cobertura.xml
           flags: mypy

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -25,30 +25,31 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest", "windows-latest"]
-        python-version: ["3.8", "3.10"]
+        python-version: ["3.9", "3.11"]
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0 # Fetch all history for all branches and tags.
       - name: Set environment variables
         run: |
           echo "PYTHON_VERSION=${{ matrix.python-version }}" >> $GITHUB_ENV
       - name: Set up conda environment
-        uses: mamba-org/provision-with-micromamba@v15
+        uses: mamba-org/setup-micromamba@v1
         with:
           environment-file: ci/environment.yml
           environment-name: flox-tests
-          cache-env: true
-          extra-specs: |
-            python="${{ matrix.python-version }}"
+          init-shell: bash
+          cache-environment: true
+          create-args: |
+            python=${{ matrix.python-version }}
       - name: Install flox
         run: |
           python -m pip install --no-deps -e .
       - name: Run Tests
         run: |
           pytest -n auto --cov=./ --cov-report=xml
       - name: Upload code coverage to Codecov
-        uses: codecov/codecov-action@v3.1.3
+        uses: codecov/codecov-action@v3.1.4
         with:
           file: ./coverage.xml
           flags: unittests
@@ -58,40 +59,41 @@ jobs:
 
   optional-deps:
     name: ${{ matrix.env }}
-    runs-on: ${{ matrix.os }}
+    runs-on: "ubuntu-latest"
     defaults:
       run:
         shell: bash -l {0}
     strategy:
       fail-fast: false
       matrix:
-        os: ["ubuntu-latest"]
-        env:
-          [
-            "no-xarray",
-            "no-dask",
-            "minimal-requirements",
-          ]
+        python-version: ["3.11"]
+        env: ["no-xarray", "no-dask"]
+        include:
+          - env: "no-numba"
+            python-version: "3.12"
+          - env: "minimal-requirements"
+            python-version: "3.9"
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0 # Fetch all history for all branches and tags.
       - name: Set up conda environment
-        uses: mamba-org/provision-with-micromamba@v15
+        uses: mamba-org/setup-micromamba@v1
         with:
           environment-file: ci/${{ matrix.env }}.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 --cov=./ --cov-report=xml
       - name: Upload code coverage to Codecov
-        uses: codecov/codecov-action@v3.1.3
+        uses: codecov/codecov-action@v3.1.4
         with:
           file: ./coverage.xml
           flags: unittests
@@ -106,18 +108,19 @@ jobs:
       run:
         shell: bash -l {0}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
-          repository: 'pydata/xarray'
+          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@v15
+        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/pypi.yaml b/.github/workflows/pypi.yaml
@@ -8,11 +8,11 @@ jobs:
   deploy:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: '3.x'
+          python-version: "3.x"
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip

diff --git a/.github/workflows/testpypi-release.yaml b/.github/workflows/testpypi-release.yaml
@@ -17,14 +17,14 @@ jobs:
     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
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
       - uses: actions/setup-python@v4
         name: Install Python
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - name: Install dependencies
         run: |
@@ -65,7 +65,7 @@ jobs:
       - uses: actions/setup-python@v4
         name: Install Python
         with:
-          python-version: "3.10"
+          python-version: "3.11"
       - uses: actions/download-artifact@v3
         with:
           name: releases

diff --git a/.github/workflows/upstream-dev-ci.yaml b/.github/workflows/upstream-dev-ci.yaml
@@ -19,28 +19,30 @@ 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' }}
+    if: ${{ (contains(github.event.pull_request.labels.*.name, 'test-upstream') && github.event_name == 'pull_request') || github.event_name == 'workflow_dispatch' }}
     defaults:
       run:
         shell: bash -l {0}
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10"]
+        python-version: ["3.11"]
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0 # Fetch all history for all branches and tags.
       - name: Set environment variables
         run: |
           echo "PYTHON_VERSION=${{ matrix.python-version }}" >> $GITHUB_ENV
       - name: Set up conda environment
-        uses: mamba-org/provision-with-micromamba@v15
+        uses: mamba-org/setup-micromamba@v1
         with:
           environment-file: ci/upstream-dev-env.yml
           environment-name: flox-tests
-          extra-specs: |
-            python="${{ matrix.python-version }}"
+          init-shell: bash
+          cache-environment: true
+          create-args: >-
+            python=${{ matrix.python-version }}
             pytest-reportlog
       - name: Install flox
         run: |

diff --git a/.gitignore b/.gitignore
@@ -1,6 +1,8 @@
+asv_bench/pkgs/
 docs/source/generated/
 html/
 .asv/
+asv_bench/pkgs/
 
 # Byte-compiled / optimized / DLL files
 __pycache__/