Merge branch 'master' of https://github.com/pydata/xarray into dev

Author: Matthias Göbel

.github/dependabot.yml

@@ -0,0 +1,7 @@
+version: 2
+updates:
+  - package-ecosystem: 'github-actions'
+    directory: '/'
+    schedule:
+      # Check for updates once a week
+      interval: 'weekly'

.github/workflows/cancel-duplicate-runs.yaml

@@ -9,6 +9,6 @@ jobs:
     name: Cancel previous runs
     runs-on: ubuntu-latest
     steps:
-    - uses: styfle/cancel-workflow-action@0.8.0
+    - uses: styfle/cancel-workflow-action@0.9.0
       with:
         workflow_id: ${{ github.event.workflow.id }}

.github/workflows/ci-additional.yaml

@@ -181,7 +181,7 @@ jobs:
           python xarray/util/print_versions.py
       - name: Run mypy
         run: |
-          python -m mypy xarray
+          python -m mypy .
 
   min-version-policy:
     name: Minimum Version Policy

.github/workflows/ci-pre-commit.yml

@@ -13,4 +13,4 @@ jobs:
     steps:
       - uses: actions/checkout@v2
       - uses: actions/setup-python@v2
-      - uses: pre-commit/[email protected].0
+      - uses: pre-commit/[email protected].3

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

@@ -48,6 +48,8 @@ jobs:
       artifacts_availability: ${{ steps.status.outputs.ARTIFACTS_AVAILABLE }}
     steps:
       - 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
@@ -60,6 +62,9 @@ jobs:
         run: |
           mamba env update -f ci/requirements/environment.yml
           bash ci/install-upstream-wheels.sh
+      - name: Install xarray
+        run: |
+          python -m pip install --no-deps -e .
       - name: Version info
         run: |
           conda info -a
@@ -117,7 +122,7 @@ jobs:
           shopt -s globstar
           python .github/workflows/parse_logs.py logs/**/*-log
       - name: Report failures
-        uses: actions/github-script@v3
+        uses: actions/github-script@v4.0.2
         with:
           github-token: ${{ secrets.GITHUB_TOKEN }}
           script: |

.pre-commit-config.yaml

@@ -8,20 +8,20 @@ repos:
       - id: check-yaml
   # isort should run before black as black sometimes tweaks the isort output
   - repo: https://github.com/PyCQA/isort
-    rev: 5.7.0
+    rev: 5.8.0
     hooks:
       - id: isort
   # https://github.com/python/black#version-control-integration
   - repo: https://github.com/psf/black
-    rev: 20.8b1
+    rev: 21.4b2
     hooks:
       - id: black
   - repo: https://github.com/keewis/blackdoc
     rev: v0.3.3
     hooks:
       - id: blackdoc
   - repo: https://gitlab.com/pycqa/flake8
-    rev: 3.8.4
+    rev: 3.9.1
     hooks:
       - id: flake8
   # - repo: https://github.com/Carreau/velin
@@ -34,6 +34,7 @@ repos:
     rev: v0.812
     hooks:
       - id: mypy
+        # Copied from setup.cfg
         exclude: "properties|asv_bench"
   # run this occasionally, ref discussion https://github.com/pydata/xarray/pull/3194
   # - repo: https://github.com/asottile/pyupgrade

ci/install-upstream-wheels.sh

@@ -1,8 +1,5 @@
 #!/usr/bin/env bash
 
-# TODO: add sparse back in, once Numba works with the development version of
-# NumPy again: https://github.com/pydata/xarray/issues/4146
-
 conda uninstall -y --force \
     numpy \
     scipy \
@@ -15,7 +12,8 @@ conda uninstall -y --force \
     rasterio \
     pint \
     bottleneck \
-    sparse
+    sparse \
+    xarray
 # to limit the runtime of Upstream CI
 python -m pip install pytest-timeout
 python -m pip install \
@@ -41,5 +39,5 @@ python -m pip install \
     git+https://github.com/Unidata/cftime \
     git+https://github.com/mapbox/rasterio \
     git+https://github.com/hgrecco/pint \
-    git+https://github.com/pydata/bottleneck # \
-    # git+https://github.com/pydata/sparse
+    git+https://github.com/pydata/bottleneck \
+    git+https://github.com/pydata/sparse

ci/min_deps_check.py

@@ -7,7 +7,7 @@
 from datetime import datetime
 from typing import Dict, Iterator, Optional, Tuple
 
-import conda.api
+import conda.api  # type: ignore[import]
 import yaml
 from dateutil.relativedelta import relativedelta
 
@@ -76,9 +76,9 @@ def parse_requirements(fname) -> Iterator[Tuple[str, int, int, Optional[int]]]:
             raise ValueError("non-numerical version: " + row)
 
         if len(version_tup) == 2:
-            yield (pkg, *version_tup, None)  # type: ignore
+            yield (pkg, *version_tup, None)  # type: ignore[misc]
         elif len(version_tup) == 3:
-            yield (pkg, *version_tup)  # type: ignore
+            yield (pkg, *version_tup)  # type: ignore[misc]
         else:
             raise ValueError("expected major.minor or major.minor.patch: " + row)
 

ci/requirements/doc.yml

@@ -20,6 +20,7 @@ dependencies:
   - numba
   - numpy>=1.17
   - pandas>=1.0
+  - pooch
   - pip
   - pydata-sphinx-theme>=0.4.3
   - rasterio>=1.1
@@ -30,7 +31,7 @@ dependencies:
   - sphinx-book-theme >= 0.0.38
   - sphinx-copybutton
   - sphinx-panels
-  - sphinx>=3.3
+  - sphinx<4
   - zarr>=2.4
   - pip:
       - sphinxext-rediraffe

ci/requirements/environment.yml

@@ -26,7 +26,8 @@ dependencies:
   - numpy
   - pandas
   - pint
-  - pip=20.2
+  - pip
+  - pooch
   - pre-commit
   - pseudonetcdf
   - pydap

ci/requirements/mypy_only

@@ -1,3 +1,4 @@
 # used for the "Type checking (mypy)" CI run
 # version must correspond to the one in .pre-commit-config.yaml
+# See https://github.com/pydata/xarray/issues/4881 for more details.
 mypy=0.812

ci/requirements/py37-min-all-deps.yml

@@ -8,27 +8,27 @@ dependencies:
   # When upgrading python, numpy, or pandas, must also change
   # doc/installing.rst and setup.py.
   - python=3.7
-  - boto3=1.12
+  - boto3=1.13
   - bottleneck=1.3
   - cartopy=0.17
   - cdms2=3.1
   - cfgrib=0.9
-  - cftime=1.0
+  - cftime=1.1
   - coveralls
-  - dask=2.11
-  - distributed=2.11
+  - dask=2.15
+  - distributed=2.15
   - h5netcdf=0.8
   - h5py=2.10
   - hdf5=1.10
   - hypothesis
   - iris=2.4
   - lxml=4.5  # Optional dep of pydap
-  - matplotlib-base=3.1
+  - matplotlib-base=3.2
   - nc-time-axis=1.2
 # netcdf follows a 1.major.minor[.patch] convention (see https://github.com/Unidata/netcdf4-python/issues/1090)
 # bumping the netCDF4 version is currently blocked by #4491
   - netcdf4=1.5.3
-  - numba=0.48
+  - numba=0.49
   - numpy=1.17
   - pandas=1.0
   # - pint  # See py37-min-nep18.yml