Merge branch 'main' into groupby-aggs-using-numpy-groupies

* main: (68 commits) Bump actions/setup-python from 2 to 3 (pydata#6338) Bump actions/checkout from 2 to 3 (pydata#6337) In documentation on adding a new backend, add missing import and tweak headings (pydata#6330) Lengthen underline, correct spelling, and reword (pydata#6326) quantile: use skipna=None (pydata#6303) New whatsnew section v2022.03.0 release notes (pydata#6319) fix typos (using codespell) (pydata#6316) Add General issue template (pydata#6314) Disable CI runs on forks (pydata#6315) Enable running sphinx-build on Windows (pydata#6237) Fix class attributes versus init parameters (pydata#6312) On Windows, enable successful test of opening a dataset containing a cftime index (pydata#6305) from_dict: doctest (pydata#6302) Drop duplicates over multiple dims, and add Dataset.drop_duplicates (pydata#6307) Amended docs on how to add a new backend (pydata#6292) Adding the new wrapper gsw-xarray (pydata#6294) Amended docstring to reflect the actual behaviour of Dataset.map (pydata#6232) Align language def in bugreport.yml with schema (pydata#6290) Move Zarr up in io.rst (pydata#6289) ...
andersy005 · Mar 9, 2022 · e348c76 · e348c76
2 parents 3f3a197 + d293f50
commit e348c76
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diff --git a/.binder/environment.yml b/.binder/environment.yml
@@ -23,6 +23,7 @@ dependencies:
   - netcdf4
   - numba
   - numpy
+  - packaging
   - pandas
   - pint
   - pip

diff --git a/.github/ISSUE_TEMPLATE/bugreport.yml b/.github/ISSUE_TEMPLATE/bugreport.yml
@@ -1,8 +1,6 @@
 name: Bug Report
 description: File a bug report to help us improve
-title: '[Bug]: '
-labels: [bug, 'needs triage']
-assignees: []
+labels: [bug, "needs triage"]
 body:
   - type: textarea
     id: what-happened
@@ -35,14 +33,14 @@ body:
 
         Bug reports that follow these guidelines are easier to diagnose, and so are often handled much more quickly.
         This will be automatically formatted into code, so no need for markdown backticks.
-      render: python
+      render: Python
 
   - type: textarea
     id: log-output
     attributes:
       label: Relevant log output
       description: Please copy and paste any relevant output. This will be automatically formatted into code, so no need for markdown backticks.
-      render: python
+      render: Python
 
   - type: textarea
     id: extra
@@ -54,8 +52,8 @@ body:
   - type: textarea
     id: show-versions
     attributes:
-     label: Environment
-     description: |
-       Paste the output of `xr.show_versions()` here
+      label: Environment
+      description: |
+        Paste the output of `xr.show_versions()` here
     validations:
       required: true
diff --git a/.github/ISSUE_TEMPLATE/misc.yml b/.github/ISSUE_TEMPLATE/misc.yml
@@ -0,0 +1,17 @@
+name: Issue
+description: General Issue or discussion topic. For usage questions, please follow the "Usage question" link
+labels: ["needs triage"]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Please describe your issue here.
+  - type: textarea
+    id: issue-description
+    attributes:
+      label: What is your issue?
+      description: |
+        Thank you for filing an issue! Please give us further information on how we can help you.
+      placeholder: Please describe your issue.
+    validations:
+      required: true
diff --git a/.github/ISSUE_TEMPLATE/newfeature.yml b/.github/ISSUE_TEMPLATE/newfeature.yml
@@ -1,8 +1,6 @@
 name: Feature Request
 description: Suggest an idea for xarray
-title: '[FEATURE]: '
 labels: [enhancement]
-assignees: []
 body:
   - type: textarea
     id: description

diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
@@ -16,7 +16,7 @@ jobs:
     steps:
       # We need the full repo to avoid this issue
       # https://github.com/actions/checkout/issues/23
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           fetch-depth: 0
 

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
@@ -8,6 +8,10 @@ on:
       - "*"
   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
@@ -18,7 +22,7 @@ jobs:
     outputs:
       triggered: ${{ steps.detect-trigger.outputs.trigger-found }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           fetch-depth: 2
       - uses: xarray-contrib/ci-trigger@v1.1
@@ -49,7 +53,7 @@ jobs:
             "py39-flaky",
           ]
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           fetch-depth: 0 # Fetch all history for all branches and tags.
 
@@ -115,13 +119,13 @@ jobs:
   doctest:
     name: Doctests
     runs-on: "ubuntu-latest"
-    if: github.repository == 'pydata/xarray'
+    if: needs.detect-ci-trigger.outputs.triggered == 'false'
     defaults:
       run:
         shell: bash -l {0}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           fetch-depth: 0 # Fetch all history for all branches and tags.
       - uses: conda-incubator/setup-miniconda@v2
@@ -158,7 +162,7 @@ jobs:
         shell: bash -l {0}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           fetch-depth: 0 # Fetch all history for all branches and tags.
       - uses: conda-incubator/setup-miniconda@v2

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -8,6 +8,10 @@ on:
       - "*"
   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
@@ -18,7 +22,7 @@ jobs:
     outputs:
       triggered: ${{ steps.detect-trigger.outputs.trigger-found }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           fetch-depth: 2
       - uses: xarray-contrib/ci-trigger@v1.1
@@ -38,9 +42,9 @@ jobs:
       matrix:
         os: ["ubuntu-latest", "macos-latest", "windows-latest"]
         # Bookend python versions
-        python-version: ["3.8", "3.9"]
+        python-version: ["3.8", "3.9", "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
@@ -111,6 +115,7 @@ jobs:
   event_file:
     name: "Event File"
     runs-on: ubuntu-latest
+    if: github.repository == 'pydata/xarray'
     steps:
       - name: Upload
         uses: actions/upload-artifact@v2

diff --git a/.github/workflows/publish-test-results.yaml b/.github/workflows/publish-test-results.yaml
@@ -8,6 +8,10 @@ on:
     types:
       - completed
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   publish-test-results:
     name: Publish test results

diff --git a/.github/workflows/pypi-release.yaml b/.github/workflows/pypi-release.yaml
@@ -12,10 +12,10 @@ jobs:
     runs-on: ubuntu-latest
     if: github.repository == 'pydata/xarray'
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           fetch-depth: 0
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v3
         name: Install Python
         with:
           python-version: 3.8
@@ -50,7 +50,7 @@ jobs:
     needs: build-artifacts
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v3
         name: Install Python
         with:
           python-version: 3.8
@@ -62,6 +62,14 @@ jobs:
         run: |
           ls -ltrh
           ls -ltrh dist
+
+      - name: Verify the built dist/wheel is valid
+        if: github.event_name == 'push'
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install dist/xarray*.whl
+          python -m xarray.util.print_versions
+
       - name: Publish package to TestPyPI
         if: github.event_name == 'push'
         uses: pypa/gh-action-pypi-publish@v1.5.0
@@ -71,13 +79,6 @@ jobs:
           repository_url: https://test.pypi.org/legacy/
           verbose: true
 
-      - name: Check uploaded package
-        if: github.event_name == 'push'
-        run: |
-          sleep 3
-          python -m pip install --upgrade pip
-          python -m pip install --extra-index-url https://test.pypi.org/simple --upgrade xarray
-          python -m xarray.util.print_versions
 
   upload-to-pypi:
     needs: test-built-dist

diff --git a/.github/workflows/upstream-dev-ci.yaml b/.github/workflows/upstream-dev-ci.yaml
@@ -10,6 +10,10 @@ on:
     - 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:
   detect-ci-trigger:
     name: detect upstream-dev ci trigger
@@ -20,7 +24,7 @@ jobs:
     outputs:
       triggered: ${{ steps.detect-trigger.outputs.trigger-found }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           fetch-depth: 2
       - uses: xarray-contrib/ci-trigger@v1.1
@@ -44,11 +48,11 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9"]
+        python-version: ["3.10"]
     outputs:
       artifacts_availability: ${{ steps.status.outputs.ARTIFACTS_AVAILABLE }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           fetch-depth: 0 # Fetch all history for all branches and tags.
       - uses: conda-incubator/setup-miniconda@v2
@@ -106,8 +110,8 @@ jobs:
       run:
         shell: bash
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v3
         with:
           python-version: "3.x"
       - uses: actions/download-artifact@v2
@@ -122,7 +126,7 @@ jobs:
           shopt -s globstar
           python .github/workflows/parse_logs.py logs/**/*-log
       - name: Report failures
-        uses: actions/github-script@v5
+        uses: actions/github-script@v6
         with:
           github-token: ${{ secrets.GITHUB_TOKEN }}
           script: |

diff --git a/.gitignore b/.gitignore
@@ -5,8 +5,9 @@ __pycache__
 .hypothesis/
 
 # temp files from docs build
+doc/*.nc
 doc/auto_gallery
-doc/example.nc
+doc/rasm.zarr
 doc/savefig
 
 # C extensions
@@ -72,4 +73,3 @@ xarray/tests/data/*.grib.*.idx
 Icon*
 
 .ipynb_checkpoints
-doc/rasm.zarr
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -6,14 +6,27 @@ repos:
       - id: trailing-whitespace
       - id: end-of-file-fixer
       - id: check-yaml
-  # isort should run before black as black sometimes tweaks the isort output
+      - id: debug-statements
+      - id: mixed-line-ending
+    # This wants to go before isort & flake8
+  - repo: https://github.com/myint/autoflake
+    rev: "v1.4"
+    hooks:
+      - id: autoflake # isort should run before black as black sometimes tweaks the isort output
+        args: ["--in-place", "--ignore-init-module-imports"]
   - repo: https://github.com/PyCQA/isort
     rev: 5.10.1
     hooks:
       - id: isort
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v2.31.0
+    hooks:
+      - id: pyupgrade
+        args:
+          - "--py38-plus"
   # https://github.com/python/black#version-control-integration
   - repo: https://github.com/psf/black
-    rev: 21.12b0
+    rev: 22.1.0
     hooks:
       - id: black
       - id: black-jupyter
@@ -35,9 +48,11 @@ repos:
     rev: v0.931
     hooks:
       - id: mypy
-        # `properies` & `asv_bench` are copied from setup.cfg.
-        # `_typed_ops.py` is added since otherwise mypy will complain (but notably only in pre-commit)
-        exclude: "properties|asv_bench|_typed_ops.py"
+        # Copied from setup.cfg
+        exclude: "properties|asv_bench"
+        # This is slow and so we take it out of the fast-path; requires passing
+        # `--hook-stage manual` to pre-commit
+        stages: [manual]
         additional_dependencies: [
             # Type stubs
             types-python-dateutil,
@@ -47,12 +62,3 @@ repos:
             typing-extensions==3.10.0.0,
             numpy,
           ]
-  # run this occasionally, ref discussion https://github.com/pydata/xarray/pull/3194
-  # - repo: https://github.com/asottile/pyupgrade
-  #   rev: v1.22.1
-  #   hooks:
-  #     - id: pyupgrade
-  #       args:
-  #         - "--py3-only"
-  #         # remove on f-strings in Py3.7
-  #         - "--keep-percent-format"
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -1 +1 @@
-Xarray's contributor guidelines [can be found in our online documentation](http://xarray.pydata.org/en/stable/contributing.html)
+Xarray's contributor guidelines [can be found in our online documentation](http://docs.xarray.dev/en/stable/contributing.html)