Merge branch 'main' into numbagg

* main: (44 commits) Rename repo to xarray-contrib/flox (#125) Propagate attrs better (#124) Update README.md (#123) Update README.md micromamba in CI (#122) Many optimizations (#120) Add xarray groupby test (#121) Update README.md Update README.md Add NASA Xarray grant [pre-commit.ci] pre-commit autoupdate (#118) Allow custom numpy aggregations for "blockwise" (#117) Don't execute hourly climatology notebook (#98) Bump actions/setup-python from 3 to 4 (#116) Fix factorizing some more. (#115) Correctly factorize values outside bin edges Better error message Avoid a copy. Fix bug where we had extra groups in expected_groups. (#112) Fix binning by nD variable ...
xarray-contrib · Jul 13, 2022 · e4ca066 · e4ca066
2 parents acfd0ec + bed52b1
commit e4ca066
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diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -0,0 +1,6 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "monthly"
diff --git a/.github/workflows/cancel-duplicate-runs.yaml b/.github/workflows/cancel-duplicate-runs.yaml
diff --git a/.github/workflows/ci-additional.yaml b/.github/workflows/ci-additional.yaml
diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -10,6 +10,10 @@ on:
     - cron: "0 0 * * *" # Daily “At 00:00”
   workflow_dispatch: # allows you to trigger manually
 
+concurrency:
+  group: ${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   build:
     name: Build (${{ matrix.python-version }}, ${{ matrix.os }})
@@ -21,77 +25,132 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest"]
-        python-version: ["3.7", "3.8", "3.9"]
+        python-version: ["3.8", "3.10"]
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           fetch-depth: 0 # Fetch all history for all branches and tags.
       - name: Set environment variables
         run: |
-          echo "CONDA_ENV_FILE=ci/environment.yml" >> $GITHUB_ENV
           echo "PYTHON_VERSION=${{ matrix.python-version }}" >> $GITHUB_ENV
-      - name: Cache conda
-        uses: actions/cache@v2
-        with:
-          path: ~/conda_pkgs_dir
-          key:
-            ${{ runner.os }}-conda-py${{ matrix.python-version }}-${{
-            hashFiles('ci/**.yml') }}
-      - uses: conda-incubator/setup-miniconda@v2
-        with:
-          channels: conda-forge
-          channel-priority: strict
-          mamba-version: "*"
-          activate-environment: flox-tests
-          auto-update-conda: false
-          python-version: ${{ matrix.python-version }}
-          use-only-tar-bz2: true
-
-      - name: Install conda dependencies
-        run: |
-          mamba env update -f $CONDA_ENV_FILE
-
       - name: Set up conda environment
-        shell: bash -l {0}
+        uses: mamba-org/provision-with-micromamba@v12
+        with:
+          environment-file: ci/environment.yml
+          environment-name: flox-tests
+          cache-env: true
+          extra-specs: |
+            python="${{ matrix.python-version }}"
+      - name: Install flox
         run: |
           python -m pip install -e .
           conda list
-
       - name: Run Tests
-        shell: bash -l {0}
         run: |
           pytest -n auto --cov=./ --cov-report=xml
-
       - name: Upload code coverage to Codecov
-        uses: codecov/codecov-action@v1
+        uses: codecov/codecov-action@v3.1.0
         with:
           file: ./coverage.xml
           flags: unittests
           env_vars: RUNNER_OS,PYTHON_VERSION
           name: codecov-umbrella
           fail_ci_if_error: false
 
-  # docs-build:
-  #   name: Documentation build
-  #   runs-on: ubuntu-latest
-  #   steps:
-  #     - name: Checkout
-  #       uses: actions/checkout@v2
-  #     - name: set up Python 3.8
-  #       uses: actions/setup-python@v2
-  #       with:
-  #           python-version: 3.8
-
-  #     - name: Install package
-  #       run: |
-  #         python -m pip install --upgrade pip
-  #         python -m pip install -e .
+  optional-deps:
+    name: ${{ matrix.env }}
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -l {0}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-latest"]
+        env:
+          [
+            "no-xarray",
+            "no-dask",
+            "minimal-requirements",
+          ]
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0 # Fetch all history for all branches and tags.
+      - name: Set up conda environment
+        uses: mamba-org/provision-with-micromamba@v12
+        with:
+          environment-file: ci/${{ matrix.env }}.yml
+          environment-name: flox-tests
+          cache-env: true
+          extra-specs: |
+            python="${{ matrix.python-version }}"
+      - name: Install flox
+        run: |
+          python -m pip install --no-deps -e .
+      - name: Run tests
+        run: |
+          python -m pytest -n auto
 
-  #     - name: Install documentation dependencies
-  #       run: |
-  #         python -m pip install -r docs/requirements-docs.txt
+  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@v12
+        with:
+          environment-file: ci/upstream-dev-env.yml
+          environment-name: flox-tests
+          extra-specs: |
+            python="3.10"
+      - name: Run Tests
+        run: |
+          pytest -n 2
 
-  #     - name: Build docs
-  #       run: |
-  #         cd docs
-  #         make html
+  xarray-groupby:
+    name: xarray-groupby
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          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
+        with:
+          environment-file: ci/requirements/environment.yml
+          environment-name: xarray-tests
+          cache-env: true
+          extra-specs: |
+            python="3.10"
+      - name: Install xarray
+        run: |
+          python -m pip install --no-deps .
+      - name: Install upstream flox
+        run: |
+          python -m pip install --no-deps \
+            git+https://github.com/dcherian/flox.git@${{ github.ref }}
+      - name: Version info
+        run: |
+          conda info -a
+          conda list
+          python xarray/util/print_versions.py
+      - name: import xarray
+        run: |
+          python -c 'import xarray'
+      - name: import flox
+        run: |
+          python -c 'import flox'
+      - name: Run Tests
+        if: success()
+        id: status
+        run: |
+          set -euo pipefail
+          python -m pytest -n auto xarray/tests/test_groupby.py
diff --git a/.github/workflows/pypi.yaml b/.github/workflows/pypi.yaml
@@ -8,9 +8,9 @@ jobs:
   deploy:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: '3.x'
       - name: Install dependencies

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -3,14 +3,14 @@ ci:
 
 repos:
     - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.1.0
+      rev: v4.3.0
       hooks:
         - id: trailing-whitespace
         - id: end-of-file-fixer
         - id: check-docstring-first
 
     - repo: https://github.com/psf/black
-      rev: 22.3.0
+      rev: 22.6.0
       hooks:
         - id: black
 

diff --git a/README.md b/README.md
@@ -1,4 +1,13 @@
-[![GitHub Workflow CI Status](https://img.shields.io/github/workflow/status/dcherian/flox/CI?logo=github&style=flat)](https://github.com/dcherian/flox/actions)[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/dcherian/flox/main.svg)](https://results.pre-commit.ci/latest/github/dcherian/flox/main)[![image](https://img.shields.io/codecov/c/github/dcherian/flox.svg?style=flat)](https://codecov.io/gh/dcherian/flox)[![PyPI](https://img.shields.io/pypi/v/flox.svg?style=flat)](https://pypi.org/project/flox/)[![Conda-forge](https://img.shields.io/conda/vn/conda-forge/flox.svg?style=flat)](https://anaconda.org/conda-forge/flox)[![Documentation Status](https://readthedocs.org/projects/flox/badge/?version=latest)](https://flox.readthedocs.io/en/latest/?badge=latest)[![NASA-80NSSC18M0156](https://img.shields.io/badge/NASA-80NSSC18M0156-blue)](https://earthdata.nasa.gov/esds/competitive-programs/access/pangeo-ml)
+[![GitHub Workflow CI Status](https://img.shields.io/github/workflow/status/xarray-contrib/flox/CI?logo=github&style=flat)](https://github.com/xarray-contrib/flox/actions)
+[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/xarray-contrib/flox/main.svg)](https://results.pre-commit.ci/latest/github/xarray-contrib/flox/main)
+[![image](https://img.shields.io/codecov/c/github/xarray-contrib/flox.svg?style=flat)](https://codecov.io/gh/xarray-contrib/flox)
+[![Documentation Status](https://readthedocs.org/projects/flox/badge/?version=latest)](https://flox.readthedocs.io/en/latest/?badge=latest)
+
+[![PyPI](https://img.shields.io/pypi/v/flox.svg?style=flat)](https://pypi.org/project/flox/)
+[![Conda-forge](https://img.shields.io/conda/vn/conda-forge/flox.svg?style=flat)](https://anaconda.org/conda-forge/flox)
+
+[![NASA-80NSSC18M0156](https://img.shields.io/badge/NASA-80NSSC18M0156-blue)](https://earthdata.nasa.gov/esds/competitive-programs/access/pangeo-ml)
+[![NASA-80NSSC22K0345](https://img.shields.io/badge/NASA-80NSSC22K0345-blue)](https://science.nasa.gov/open-science-overview)
 
 # flox
 
@@ -16,8 +25,12 @@ about this package, from the Pangeo Showcase).
 
 ## Acknowledgements
 
-This work was funded in part by NASA-ACCESS 80NSSC18M0156 "Community tools for analysis of NASA Earth Observing System
-Data in the Cloud" (PI J. Hamman), and [NCAR's Earth System Data Science Initiative](https://ncar.github.io/esds/).
+This work was funded in part by
+1. NASA-ACCESS 80NSSC18M0156 "Community tools for analysis of NASA Earth Observing System
+Data in the Cloud" (PI J. Hamman, NCAR),
+2. NASA-OSTFL 80NSSC22K0345 "Enhancing analysis of NASA data with the open-source Python Xarray Library" (PIs Scott Henderson, University of Washington; Deepak Cherian, NCAR; Jessica Scheick, University of New Hampshire), and
+3. [NCAR's Earth System Data Science Initiative](https://ncar.github.io/esds/).
+
 It was motivated by [very](https://github.com/pangeo-data/pangeo/issues/266) [very](https://github.com/pangeo-data/pangeo/issues/271) [many](https://github.com/dask/distributed/issues/2602) [discussions](https://github.com/pydata/xarray/issues/2237) in the [Pangeo](https://pangeo.io) community.
 
 ## API

diff --git a/ci/docs.yml b/ci/docs.yml
@@ -16,4 +16,4 @@ dependencies:
   - ipykernel
   - jupyter
   - pip:
-    - git+https://github.com/dcherian/flox
+    - git+https://github.com/xarray-contrib/flox
diff --git a/ci/environment.yml b/ci/environment.yml
@@ -13,7 +13,7 @@ dependencies:
   - pytest-xdist
   - xarray
   - pre-commit
-  - numpy_groupies
+  - numpy_groupies>=0.9.15
   - pooch
   - toolz
   - numba