Merge remote-tracking branch 'upstream/master' into groupby-plot

* upstream/master: Python 3.8 CI (pydata#3727) PKG: Explicitly add setuptools dependency (pydata#3628) update whats-new Typo in Universal Functions section (pydata#3663) Release v0.15.0 fix setup.cfg Documentation fixes (pydata#3732) Remove extra && in PR template (pydata#3730) Remove garbage text inserted in DASK_LICENSE (pydata#3729) Avoid unsafe use of pip (pydata#3726) remove PR pre-black instructions (pydata#3707) Fix whats-new for 0.15 (pydata#3723) Add isort to CI (pydata#3721) setuptools-scm (3) (pydata#3724) Fix Sphinx links on contributing doc page (pydata#3710)
dcherian · Jan 31, 2020 · c83c617 · c83c617
2 parents e694a50 + 4c96d53
commit c83c617
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diff --git a/.binder/environment.yml b/.binder/environment.yml
@@ -2,7 +2,7 @@ name: xarray-examples
 channels:
   - conda-forge
 dependencies:
-  - python=3.7
+  - python=3.8
   - boto3
   - bottleneck
   - cartopy
@@ -31,6 +31,7 @@ dependencies:
   - rasterio
   - scipy
   - seaborn
+  - setuptools
   - sparse
   - toolz
   - xarray

diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -2,5 +2,5 @@
 
  - [ ] Closes #xxxx
  - [ ] Tests added
- - [ ] Passes `black . && mypy . && flake8`
+ - [ ] Passes `isort -rc . && black . && mypy . && flake8`
  - [ ] Fully documented, including `whats-new.rst` for all changes and `api.rst` for new API
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,11 +1,15 @@
 # https://pre-commit.com/
-# https://github.com/python/black#version-control-integration
 repos:
+  # isort should run before black as black sometimes tweaks the isort output
+  - repo: https://github.com/timothycrosley/isort
+    rev: 4.3.21-2
+    hooks:
+      - id: isort
+  # https://github.com/python/black#version-control-integration
   - repo: https://github.com/python/black
     rev: stable
     hooks:
       - id: black
-        language_version: python3.7
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v2.2.3
     hooks:
@@ -14,7 +18,7 @@ repos:
     rev: v0.761  # Must match ci/requirements/*.yml
     hooks:
       - id: mypy
-  # run these occasionally, ref discussion https://github.com/pydata/xarray/pull/3194
+  # run this occasionally, ref discussion https://github.com/pydata/xarray/pull/3194
   # - repo: https://github.com/asottile/pyupgrade
   #   rev: v1.22.1
   #   hooks:
@@ -23,7 +27,3 @@ repos:
   #         - "--py3-only"
   #         # remove on f-strings in Py3.7
   #         - "--keep-percent-format"
-  # - repo: https://github.com/timothycrosley/isort
-  #   rev: 4.3.21-2
-  #   hooks:
-  #     - id: isort
diff --git a/asv_bench/asv.conf.json b/asv_bench/asv.conf.json
@@ -40,7 +40,7 @@
 
     // The Pythons you'd like to test against.  If not provided, defaults
     // to the current version of Python used to run `asv`.
-    "pythons": ["3.6"],
+    "pythons": ["3.8"],
 
     // The matrix of dependencies to test.  Each key is the name of a
     // package (in PyPI) and the values are version numbers.  An empty

diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -20,11 +20,11 @@ jobs:
         conda_env: py37
       py38:
         conda_env: py38
-      py37-upstream-dev:
-        conda_env: py37
+      py38-upstream-dev:
+        conda_env: py38
         upstream_dev: true
-      py36-flaky:
-        conda_env: py36
+      py38-flaky:
+        conda_env: py38
         pytest_extra_flags: --run-flaky --run-network-tests
         allow_failure: true
   pool:
@@ -35,8 +35,8 @@ jobs:
 - job: MacOSX
   strategy:
     matrix:
-      py36:
-        conda_env: py36
+      py38:
+        conda_env: py38
   pool:
     vmImage: 'macOS-10.13'
   steps:
@@ -74,7 +74,7 @@ jobs:
 
 - job: TypeChecking
   variables:
-    conda_env: py37
+    conda_env: py38
   pool:
     vmImage: 'ubuntu-16.04'
   steps:
@@ -84,6 +84,18 @@ jobs:
       mypy .
     displayName: mypy type checks
 
+- job: isort
+  variables:
+    conda_env: py38
+  pool:
+    vmImage: 'ubuntu-16.04'
+  steps:
+  - template: ci/azure/install.yml
+  - bash: |
+      source activate xarray-tests
+      isort -rc --check .
+    displayName: isort formatting checks
+
 - job: MinimumVersionsPolicy
   pool:
     vmImage: 'ubuntu-16.04'

diff --git a/ci/azure/install.yml b/ci/azure/install.yml
@@ -6,20 +6,22 @@ steps:
 - template: add-conda-to-path.yml
 
 - bash: |
+    conda update -y conda
     conda env create -n xarray-tests --file ${{ parameters.env_file }}
   displayName: Install conda dependencies
 
 - bash: |
     source activate xarray-tests
-    pip install -f https://7933911d6844c6c53a7d-47bd50c35cd79bd838daf386af554a83.ssl.cf2.rackcdn.com \
+    python -m pip install \
+        -f https://7933911d6844c6c53a7d-47bd50c35cd79bd838daf386af554a83.ssl.cf2.rackcdn.com \
         --no-deps \
         --pre \
         --upgrade \
         matplotlib \
         numpy \
         pandas \
         scipy
-    pip install \
+    python -m pip install \
         --no-deps \
         --upgrade \
         git+https://github.com/dask/dask \
@@ -33,7 +35,7 @@ steps:
 
 - bash: |
     source activate xarray-tests
-    pip install --no-deps -e .
+    python -m pip install --no-deps -e .
   displayName: Install xarray
 
 - bash: |

diff --git a/ci/min_deps_check.py b/ci/min_deps_check.py
@@ -15,6 +15,7 @@
     "coveralls",
     "flake8",
     "hypothesis",
+    "isort",
     "mypy",
     "pip",
     "pytest",

diff --git a/ci/requirements/doc.yml b/ci/requirements/doc.yml
@@ -3,7 +3,7 @@ channels:
   # Don't change to pkgs/main, as it causes random timeouts in readthedocs
   - conda-forge
 dependencies:
-  - python=3.7
+  - python=3.8
   - bottleneck
   - cartopy
   - cfgrib
@@ -20,6 +20,7 @@ dependencies:
   - pandas
   - rasterio
   - seaborn
+  - setuptools
   - sphinx
   - sphinx_rtd_theme
   - zarr
diff --git a/ci/requirements/py36-bare-minimum.yml b/ci/requirements/py36-bare-minimum.yml
@@ -4,8 +4,10 @@ channels:
 dependencies:
   - python=3.6
   - coveralls
+  - pip
   - pytest
   - pytest-cov
   - pytest-env
   - numpy=1.15
   - pandas=0.25
+  - setuptools=41.2
diff --git a/ci/requirements/py36-min-all-deps.yml b/ci/requirements/py36-min-all-deps.yml
@@ -23,6 +23,7 @@ dependencies:
   - hdf5=1.10
   - hypothesis
   - iris=2.2
+  - isort
   - lxml=4.4  # Optional dep of pydap
   - matplotlib=3.1
   - mypy=0.761  # Must match .pre-commit-config.yaml
@@ -42,6 +43,7 @@ dependencies:
   - rasterio=1.0
   - scipy=1.3
   - seaborn=0.9
+  - setuptools=41.2
   # - sparse  # See py36-min-nep18.yml
   - toolz=0.10
   - zarr=2.3

diff --git a/ci/requirements/py36-min-nep18.yml b/ci/requirements/py36-min-nep18.yml
@@ -11,8 +11,10 @@ dependencies:
   - numpy=1.17
   - pandas=0.25
   - pint=0.9  # Actually not enough as it doesn't implement __array_function__yet!
+  - pip
   - pytest
   - pytest-cov
   - pytest-env
   - scipy=1.2
+  - setuptools=41.2
   - sparse=0.8
diff --git a/ci/requirements/py36.yml b/ci/requirements/py36.yml
@@ -19,7 +19,8 @@ dependencies:
   - hdf5
   - hypothesis
   - iris
-  - lxml    # optional dep of pydap
+  - isort
+  - lxml    # Optional dep of pydap
   - matplotlib
   - mypy=0.761  # Must match .pre-commit-config.yaml
   - nc-time-axis
@@ -38,6 +39,7 @@ dependencies:
   - rasterio
   - scipy
   - seaborn
+  - setuptools
   - sparse
   - toolz
   - zarr

diff --git a/ci/requirements/py37-windows.yml b/ci/requirements/py37-windows.yml
@@ -19,13 +19,14 @@ dependencies:
   - hdf5
   - hypothesis
   - iris
+  - isort
   - lxml    # Optional dep of pydap
   - matplotlib
   - mypy=0.761  # Must match .pre-commit-config.yaml
   - nc-time-axis
   - netcdf4
   - numba
-  - numpy<1.18  # FIXME https://github.com/pydata/xarray/issues/3409
+  - numpy
   - pandas
   - pint
   - pip
@@ -38,6 +39,7 @@ dependencies:
   - rasterio
   - scipy
   - seaborn
+  - setuptools
   - sparse
   - toolz
   - zarr

diff --git a/ci/requirements/py37.yml b/ci/requirements/py37.yml
@@ -19,6 +19,7 @@ dependencies:
   - hdf5
   - hypothesis
   - iris
+  - isort
   - lxml    # Optional dep of pydap
   - matplotlib
   - mypy=0.761  # Must match .pre-commit-config.yaml
@@ -38,6 +39,7 @@ dependencies:
   - rasterio
   - scipy
   - seaborn
+  - setuptools
   - sparse
   - toolz
   - zarr

diff --git a/ci/requirements/py38.yml b/ci/requirements/py38.yml
@@ -3,13 +3,45 @@ channels:
   - conda-forge
 dependencies:
   - python=3.8
+  - black
+  - boto3
+  - bottleneck
+  - cartopy
+  - cdms2
+  - cfgrib
+  - cftime
+  - coveralls
+  - dask
+  - distributed
+  - flake8
+  - h5netcdf
+  - h5py
+  - hdf5
+  - hypothesis
+  - iris
+  - isort
+  - lxml    # Optional dep of pydap
+  - matplotlib
+  - mypy=0.761  # Must match .pre-commit-config.yaml
+  - nc-time-axis
+  - netcdf4
+  - numba
+  - numpy
+  - pandas
+  - pint
   - pip
+  - pseudonetcdf
+  - pydap
+  - pynio
+  - pytest
+  - pytest-cov
+  - pytest-env
+  - rasterio
+  - scipy
+  - seaborn
+  - setuptools
+  - sparse
+  - toolz
+  - zarr
   - pip:
-      - coveralls
-      - dask
-      - distributed
-      - numpy
-      - pandas
-      - pytest
-      - pytest-cov
-      - pytest-env
+    - numbagg
diff --git a/doc/api-hidden.rst b/doc/api-hidden.rst
@@ -583,15 +583,13 @@
    CFTimeIndex.factorize
    CFTimeIndex.fillna
    CFTimeIndex.format
-   CFTimeIndex.get_duplicates
    CFTimeIndex.get_indexer
    CFTimeIndex.get_indexer_for
    CFTimeIndex.get_indexer_non_unique
    CFTimeIndex.get_level_values
    CFTimeIndex.get_loc
    CFTimeIndex.get_slice_bound
    CFTimeIndex.get_value
-   CFTimeIndex.get_values
    CFTimeIndex.groupby
    CFTimeIndex.holds_integer
    CFTimeIndex.identical
@@ -603,7 +601,6 @@
    CFTimeIndex.is_floating
    CFTimeIndex.is_integer
    CFTimeIndex.is_interval
-   CFTimeIndex.is_lexsorted_for_tuple
    CFTimeIndex.is_mixed
    CFTimeIndex.is_numeric
    CFTimeIndex.is_object
@@ -635,7 +632,6 @@
    CFTimeIndex.sort_values
    CFTimeIndex.sortlevel
    CFTimeIndex.strftime
-   CFTimeIndex.summary
    CFTimeIndex.symmetric_difference
    CFTimeIndex.take
    CFTimeIndex.to_datetimeindex
@@ -656,16 +652,12 @@
    CFTimeIndex.T
    CFTimeIndex.array
    CFTimeIndex.asi8
-   CFTimeIndex.base
-   CFTimeIndex.data
    CFTimeIndex.date_type
    CFTimeIndex.day
    CFTimeIndex.dayofweek
    CFTimeIndex.dayofyear
    CFTimeIndex.dtype
-   CFTimeIndex.dtype_str
    CFTimeIndex.empty
-   CFTimeIndex.flags
    CFTimeIndex.has_duplicates
    CFTimeIndex.hasnans
    CFTimeIndex.hour
@@ -675,7 +667,6 @@
    CFTimeIndex.is_monotonic_increasing
    CFTimeIndex.is_monotonic_decreasing
    CFTimeIndex.is_unique
-   CFTimeIndex.itemsize
    CFTimeIndex.microsecond
    CFTimeIndex.minute
    CFTimeIndex.month
@@ -687,7 +678,6 @@
    CFTimeIndex.second
    CFTimeIndex.shape
    CFTimeIndex.size
-   CFTimeIndex.strides
    CFTimeIndex.values
    CFTimeIndex.year