Merge remote-tracking branch 'upstream/main' into sparse-unstack

* upstream/main: (39 commits)
  Fixed a mispelling of dimension in dataarray documentation for from_dict (pydata#6020)
  [pre-commit.ci] pre-commit autoupdate (pydata#6014)
  [pre-commit.ci] pre-commit autoupdate (pydata#5990)
  Use set_options for asv bottleneck tests (pydata#5986)
  Fix module name retrieval in `backend.plugins.remove_duplicates()`, plugin tests (pydata#5959)
  Check for py version instead of try/except when importing entry_points (pydata#5988)
  Add "see also" in to_dataframe docs (pydata#5978)
  Alternate method using inline css to hide regular html output in an untrusted notebook (pydata#5880)
  Fix mypy issue with entry_points (pydata#5979)
  Remove pre-commit auto update (pydata#5958)
  Do not change coordinate inplace when throwing error (pydata#5957)
  Create CITATION.cff (pydata#5956)
  Add groupby & resample benchmarks (pydata#5922)
  Fix plot.line crash for data of shape (1, N) in _title_for_slice on format_item (pydata#5948)
  Disable unit test comments (pydata#5946)
  Publish test results from workflow_run only (pydata#5947)
  Generator for groupby reductions (pydata#5871)
  whats-new dev
  whats-new for 0.20.1 (pydata#5943)
  Docs: fix URL for PTSA (pydata#5935)
  ...

.github/workflows/ci.yaml

@@ -108,19 +108,12 @@ jobs:
           name: codecov-umbrella
           fail_ci_if_error: false
 
-  publish-test-results:
-    needs: test
+  event_file:
+    name: "Event File"
     runs-on: ubuntu-latest
-    # the build-and-test job might be skipped, we don't need to run this job then
-    if: success() || failure()
-
     steps:
-      - name: Download Artifacts
-        uses: actions/download-artifact@v2
-        with:
-          path: test-results
-
-      - name: Publish Unit Test Results
-        uses: EnricoMi/publish-unit-test-result-action@v1
+      - name: Upload
+        uses: actions/upload-artifact@v2
         with:
-          files: test-results/**/*.xml
+          name: Event File
+          path: ${{ github.event_path }}

.github/workflows/publish-test-results.yaml

@@ -1,4 +1,4 @@
-# Copied from https://github.com/EnricoMi/publish-unit-test-result-action/blob/v1.18/README.md#support-fork-repositories-and-dependabot-branches
+# Copied from https://github.com/EnricoMi/publish-unit-test-result-action/blob/v1.23/README.md#support-fork-repositories-and-dependabot-branches
 
 name: Publish test results
 
@@ -12,11 +12,7 @@ jobs:
   publish-test-results:
     name: Publish test results
     runs-on: ubuntu-latest
-    if: >
-      github.event.workflow_run.conclusion != 'skipped' && (
-        github.event.sender.login == 'dependabot[bot]' ||
-        github.event.workflow_run.head_repository.full_name != github.repository
-      )
+    if: github.event.workflow_run.conclusion != 'skipped'
 
     steps:
       - name: Download and extract artifacts
@@ -26,13 +22,10 @@ jobs:
           mkdir artifacts && cd artifacts
 
           artifacts_url=${{ github.event.workflow_run.artifacts_url }}
-          artifacts=$(gh api $artifacts_url -q '.artifacts[] | {name: .name, url: .archive_download_url}')
 
-          IFS=$'\n'
-          for artifact in $artifacts
+          gh api "$artifacts_url" -q '.artifacts[] | [.name, .archive_download_url] | @tsv' | while read artifact
           do
-            name=$(jq -r .name <<<$artifact)
-            url=$(jq -r .url <<<$artifact)
+            IFS=$'\t' read name url <<< "$artifact"
             gh api $url > "$name.zip"
             unzip -d "$name" "$name.zip"
           done
@@ -41,4 +34,7 @@ jobs:
         uses: EnricoMi/publish-unit-test-result-action@v1
         with:
           commit: ${{ github.event.workflow_run.head_sha }}
+          event_file: artifacts/Event File/event.json
+          event_name: ${{ github.event.workflow_run.event }}
           files: "artifacts/**/*.xml"
+          comment_mode: off

.github/workflows/upstream-dev-ci.yaml

@@ -122,7 +122,7 @@ jobs:
           shopt -s globstar
           python .github/workflows/parse_logs.py logs/**/*-log
       - name: Report failures
-        uses: actions/github-script@v4.1
+        uses: actions/github-script@v5
         with:
           github-token: ${{ secrets.GITHUB_TOKEN }}
           script: |
@@ -158,15 +158,15 @@ jobs:
             // If no issue is open, create a new issue,
             // else update the body of the existing issue.
             if (result.repository.issues.edges.length === 0) {
-                github.issues.create({
+                github.rest.issues.create({
                     owner: variables.owner,
                     repo: variables.name,
                     body: issue_body,
                     title: title,
                     labels: [variables.label]
                 })
             } else {
-                github.issues.update({
+                github.rest.issues.update({
                     owner: variables.owner,
                     repo: variables.name,
                     issue_number: result.repository.issues.edges[0].node.number,

.pre-commit-config.yaml

@@ -8,21 +8,22 @@ repos:
       - id: check-yaml
   # isort should run before black as black sometimes tweaks the isort output
   - repo: https://github.com/PyCQA/isort
-    rev: 5.9.3
+    rev: 5.10.1
     hooks:
       - id: isort
   # https://github.com/python/black#version-control-integration
   - repo: https://github.com/psf/black
-    rev: 21.9b0
+    rev: 21.11b1
     hooks:
       - id: black
       - id: black-jupyter
   - repo: https://github.com/keewis/blackdoc
     rev: v0.3.4
     hooks:
       - id: blackdoc
-  - repo: https://gitlab.com/pycqa/flake8
-    rev: 3.9.2
+        exclude: "generate_reductions.py"
+  - repo: https://github.com/PyCQA/flake8
+    rev: 4.0.1
     hooks:
       - id: flake8
   # - repo: https://github.com/Carreau/velin

CITATION.cff

@@ -0,0 +1,96 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+- family-names: "Hoyer"
+  given-names: "Stephan"
+  orcid: "https://orcid.org/0000-0002-5207-0380"
+- family-names: "Roos"
+  given-names: "Maximilian"
+- family-names: "Joseph"
+  given-names: "Hamman"
+  orcid: "https://orcid.org/0000-0001-7479-8439"
+- family-names: "Magin"
+  given-names: "Justus"
+- family-names: "Cherian"
+  given-names: "Deepak"
+  orcid: "https://orcid.org/0000-0002-6861-8734"
+- family-names: "Fitzgerald"
+  given-names: "Clark"
+  orcid: "https://orcid.org/0000-0003-3446-6389"
+- family-names: "Hauser"
+  given-names: "Mathias"
+  orcid: "https://orcid.org/0000-0002-0057-4878"
+- family-names: "Fujii"
+  given-names: "Keisuke"
+  orcid: "https://orcid.org/0000-0003-0390-9984"
+- family-names: "Maussion"
+  given-names: "Fabien"
+  orcid: "https://orcid.org/0000-0002-3211-506X"
+- family-names: "Imperiale"
+  given-names: "Guido"
+- family-names: "Clark"
+  given-names: "Spencer"
+  orcid: "https://orcid.org/0000-0001-5595-7895"
+- family-names: "Kleeman"
+  given-names: "Alex"
+- family-names: "Nicholas"
+  given-names: "Thomas"
+  orcid: "https://orcid.org/0000-0002-2176-0530"
+- family-names: "Kluyver"
+  given-names: "Thomas"
+  orcid: "https://orcid.org/0000-0003-4020-6364"
+- family-names: "Westling"
+  given-names: "Jimmy"
+- family-names: "Munroe"
+  given-names: "James"
+  orcid: "https://orcid.org/0000-0001-9098-6309"
+- family-names: "Amici"
+  given-names: "Alessandro"
+  orcid: "https://orcid.org/0000-0002-1778-4505"
+- family-names: "Barghini"
+  given-names: "Aureliana"
+- family-names: "Banihirwe"
+  given-names: "Anderson"
+  orcid: "https://orcid.org/0000-0001-6583-571X"
+- family-names: "Bell"
+  given-names: "Ray"
+  orcid: "https://orcid.org/0000-0003-2623-0587"
+- family-names: "Hatfield-Dodds"
+  given-names: "Zac"
+  orcid: "https://orcid.org/0000-0002-8646-8362"
+- family-names: "Abernathey"
+  given-names: "Ryan"
+  orcid: "https://orcid.org/0000-0001-5999-4917"
+- family-names: "Bovy"
+  given-names: "Benoît"
+- family-names: "Omotani"
+  given-names: "John"
+  orcid: "https://orcid.org/0000-0002-3156-8227"
+- family-names: "Mühlbauer"
+  given-names: "Kai"
+  orcid: "https://orcid.org/0000-0001-6599-1034"
+- family-names: "Roszko"
+  given-names: "Maximilian K."
+  orcid: "https://orcid.org/0000-0001-9424-2526"
+- family-names: "Wolfram"
+  given-names: "Phillip J."
+  orcid: "https://orcid.org/0000-0001-5971-4241"
+title: "xarray"
+doi: 10.5281/zenodo.598201
+url: "https://github.com/pydata/xarray"
+preferred-citation:
+  type: article
+  authors:
+  - family-names: "Hoyer"
+    given-names: "Stephan"
+    orcid: "https://orcid.org/0000-0002-5207-0380"
+  - family-names: "Joseph"
+    given-names: "Hamman"
+    orcid: "https://orcid.org/0000-0001-7479-8439"
+  doi: "10.5334/jors.148"
+  journal: "Journal of Open Research Software"
+  month: 4
+  title: "xarray: N-D labeled Arrays and Datasets in Python"
+  volume: 5
+  issue: 1
+  year: 2017

asv_bench/asv.conf.json

@@ -62,7 +62,7 @@
         "pandas": [""],
         "netcdf4": [""],
         "scipy": [""],
-        "bottleneck": ["", null],
+        "bottleneck": [""],
         "dask": [""],
         "distributed": [""],
         "sparse": [""]

asv_bench/benchmarks/dataarray_missing.py

@@ -16,13 +16,6 @@ def make_bench_data(shape, frac_nan, chunks):
     return da
 
 
-def requires_bottleneck():
-    try:
-        import bottleneck  # noqa: F401
-    except ImportError:
-        raise NotImplementedError()
-
-
 class DataArrayMissingInterpolateNA:
     def setup(self, shape, chunks, limit):
         if chunks is not None:
@@ -46,7 +39,6 @@ def time_interpolate_na(self, shape, chunks, limit):
 
 class DataArrayMissingBottleneck:
     def setup(self, shape, chunks, limit):
-        requires_bottleneck()
         if chunks is not None:
             requires_dask()
         self.da = make_bench_data(shape, 0.1, chunks)