Merge remote-tracking branch 'upstream/master' into fix/4107

* upstream/master: (46 commits)
  pin netCDF4=1.5.3 in min-all-deps (pydata#4982)
  fix matplotlib errors for single level discrete colormaps (pydata#4256)
  Adapt exception handling in CFTimeIndex.__sub__ and __rsub__ (pydata#5006)
  Update options.py (pydata#5000)
  Adjust tests to use updated pandas syntax for offsets (pydata#4537)
  add a combine_attrs parameter to Dataset.merge (pydata#4895)
  Support for dask.graph_manipulation (pydata#4965)
  raise on passing axis to Dataset.reduce methods (pydata#4940)
  Whatsnew for 0.17.1 (pydata#4963)
  Refinements to how-to-release (pydata#4964)
  DOC: add example for reindex (pydata#4956)
  DOC: rm np import (pydata#4949)
  Add 0.17.0 release notes (pydata#4953)
  document update as inplace (pydata#4932)
  bump the dependencies (pydata#4942)
  Upstream CI: limit runtime (pydata#4946)
  typing for numpy 1.20 (pydata#4878)
  Use definition of DTypeLike from Numpy if found (pydata#4941)
  autoupdate mypy (pydata#4943)
  Add DataArrayCoarsen.reduce and DatasetCoarsen.reduce methods (pydata#4939)
  ...

Author: dcherian

.git_archival.txt

@@ -0,0 +1 @@
+ref-names: $Format:%D$

.gitattributes

@@ -1,2 +1,4 @@
 # reduce the number of merge conflicts
 doc/whats-new.rst merge=union
+# allow installing from git archives
+.git_archival.txt  export-subst

.github/actions/detect-ci-trigger/action.yaml

@@ -19,7 +19,7 @@ jobs:
       - uses: actions/checkout@v2
         with:
           fetch-depth: 2
-      - uses: ./.github/actions/detect-ci-trigger
+      - uses: xarray-contrib/ci-trigger@v1
         id: detect-trigger
         with:
           keyword: "[skip-ci]"
@@ -157,6 +157,50 @@ jobs:
         run: |
           python -m pytest --doctest-modules xarray --ignore xarray/tests
 
+  typing:
+    name: Type checking (mypy)
+    runs-on: "ubuntu-latest"
+    needs: detect-ci-trigger
+    if: needs.detect-ci-trigger.outputs.triggered == 'false'
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+      - name: Cancel previous runs
+        uses: styfle/[email protected]
+        with:
+          access_token: ${{ github.token }}
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0 # Fetch all history for all branches and tags.
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          channels: conda-forge
+          channel-priority: strict
+          mamba-version: "*"
+          activate-environment: xarray-tests
+          auto-update-conda: false
+          python-version: "3.8"
+
+      - name: Install conda dependencies
+        run: |
+          mamba env update -f ci/requirements/environment.yml
+      - name: Install mypy
+        run: |
+          mamba install --file ci/requirements/mypy_only
+      - 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: Run mypy
+        run: |
+          python -m mypy xarray
+
   min-version-policy:
     name: Minimum Version Policy
     runs-on: "ubuntu-latest"
@@ -184,6 +228,6 @@ jobs:
 
       - name: minimum versions policy
         run: |
-          mamba install -y pyyaml conda
+          mamba install -y pyyaml conda python-dateutil
           python ci/min_deps_check.py ci/requirements/py37-bare-minimum.yml
           python ci/min_deps_check.py ci/requirements/py37-min-all-deps.yml

.github/actions/detect-ci-trigger/script.sh

@@ -0,0 +1,44 @@
+name: "pre-commit autoupdate CI"
+
+on:
+  schedule:
+    - cron: "0 0 * * 0"  # every Sunday at 00:00 UTC
+  workflow_dispatch:
+
+
+jobs:
+  autoupdate:
+    name: 'pre-commit autoupdate'
+    runs-on: ubuntu-latest
+    if: github.repository == 'pydata/xarray'
+    steps:
+      - name: checkout
+        uses: actions/checkout@v2
+      - name: Cache pip and pre-commit
+        uses: actions/cache@v2
+        with:
+          path: |
+            ~/.cache/pre-commit
+            ~/.cache/pip
+          key: ${{ runner.os }}-pre-commit-autoupdate
+      - name: setup python
+        uses: actions/setup-python@v2
+      - name: upgrade pip
+        run: python -m pip install --upgrade pip
+      - name: install dependencies
+        run: python -m pip install --upgrade pre-commit pyyaml packaging
+      - name: version info
+        run: python -m pip list
+      - name: autoupdate
+        uses: technote-space/create-pr-action@837dbe469b39f08d416889369a52e2a993625c84
+        with:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          EXECUTE_COMMANDS: |
+            python -m pre_commit autoupdate
+            python .github/workflows/sync_linter_versions.py .pre-commit-config.yaml ci/requirements/mypy_only
+          COMMIT_MESSAGE: 'pre-commit: autoupdate hook versions'
+          COMMIT_NAME: 'github-actions[bot]'
+          COMMIT_EMAIL: 'github-actions[bot]@users.noreply.github.com'
+          PR_TITLE: 'pre-commit: autoupdate hook versions'
+          PR_BRANCH_PREFIX: 'pre-commit/'
+          PR_BRANCH_NAME: 'autoupdate-${PR_ID}'

.github/workflows/ci-additional.yaml

@@ -19,7 +19,7 @@ jobs:
       - uses: actions/checkout@v2
         with:
           fetch-depth: 2
-      - uses: ./.github/actions/detect-ci-trigger
+      - uses: xarray-contrib/ci-trigger@v1
         id: detect-trigger
         with:
           keyword: "[skip-ci]"

.github/workflows/ci-pre-commit-autoupdate.yaml

@@ -18,7 +18,7 @@ def extract_short_test_summary_info(lines):
     )
     up_to_section_content = itertools.islice(up_to_start_of_section, 1, None)
     section_content = itertools.takewhile(
-        lambda l: l.startswith("FAILED"), up_to_section_content
+        lambda l: l.startswith("FAILED") or l.startswith("ERROR"), up_to_section_content
     )
     content = "\n".join(section_content)
 

.github/workflows/ci.yaml

@@ -0,0 +1,76 @@
+#!/usr/bin/env python
+import argparse
+import itertools
+import pathlib
+import re
+
+import yaml
+from packaging import version
+from packaging.requirements import Requirement
+
+operator_re = re.compile("=+")
+
+
+def extract_versions(config):
+    repos = config.get("repos")
+    if repos is None:
+        raise ValueError("invalid pre-commit configuration")
+
+    extracted_versions = (
+        ((hook["id"], version.parse(repo["rev"])) for hook in repo["hooks"])
+        for repo in repos
+    )
+    return dict(itertools.chain.from_iterable(extracted_versions))
+
+
+def update_requirement(line, new_versions):
+    # convert to pep-508 compatible
+    preprocessed = operator_re.sub("==", line)
+    requirement = Requirement(preprocessed)
+
+    specifier, *_ = requirement.specifier
+    old_version = specifier.version
+    new_version = new_versions.get(requirement.name, old_version)
+
+    new_line = f"{requirement.name}={new_version}"
+
+    return new_line
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--dry", action="store_true")
+    parser.add_argument(
+        metavar="pre-commit-config", dest="pre_commit_config", type=pathlib.Path
+    )
+    parser.add_argument("requirements", type=pathlib.Path)
+    args = parser.parse_args()
+
+    with args.pre_commit_config.open() as f:
+        config = yaml.safe_load(f)
+
+    versions = extract_versions(config)
+    mypy_version = versions["mypy"]
+
+    requirements_text = args.requirements.read_text()
+    requirements = requirements_text.split("\n")
+    new_requirements = [
+        update_requirement(line, versions)
+        if line and not line.startswith("# ")
+        else line
+        for line in requirements
+    ]
+    new_requirements_text = "\n".join(new_requirements)
+
+    if args.dry:
+        separator = "\n" + "—" * 80 + "\n"
+        print(
+            "contents of the old requirements file:",
+            requirements_text,
+            "contents of the new requirements file:",
+            new_requirements_text,
+            sep=separator,
+            end=separator,
+        )
+    else:
+        args.requirements.write_text(new_requirements_text)

.github/workflows/parse_logs.py

@@ -21,7 +21,7 @@ jobs:
       - uses: actions/checkout@v2
         with:
           fetch-depth: 2
-      - uses: ./.github/actions/detect-ci-trigger
+      - uses: xarray-contrib/ci-trigger@v1
         id: detect-trigger
         with:
           keyword: "[test-upstream]"
@@ -77,7 +77,7 @@ jobs:
         id: status
         run: |
           set -euo pipefail
-          python -m pytest -rf | tee output-${{ matrix.python-version }}-log || (
+          python -m pytest --timeout=60 -rf | tee output-${{ matrix.python-version }}-log || (
               echo '::set-output name=ARTIFACTS_AVAILABLE::true' && false
           )
       - name: Upload artifacts

.github/workflows/sync_linter_versions.py

@@ -30,7 +30,8 @@ repos:
   #     - id: velin
   #       args: ["--write", "--compact"]
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.800
+    # version must correspond to the one in .github/workflows/ci-additional.yaml
+    rev: v0.812
     hooks:
       - id: mypy
         exclude: "properties|asv_bench"