Merge remote-tracking branch 'upstream/master' into fix-contourf-set_…

…under * upstream/master: (71 commits) Optimize isel for lazy array equality checking (pydata#3588) pin msgpack (pydata#3793) concat now handles non-dim coordinates only present in one dataset (pydata#3769) Add new h5netcdf backend phony_dims kwarg (pydata#3753) always use dask_array_type for isinstance calls (pydata#3787) allow formatting the diff of ndarray attributes (pydata#3728) Pint support for variables (pydata#3706) Format issue template comment as md comment (pydata#3790) Avoid running test_open_mfdataset_list_attr without dask (pydata#3780) remove seaborn.apionly compatibility (pydata#3749) 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) ...
johnomotani · Feb 24, 2020 · 103657d · 103657d
2 parents 061ddf2 + f468a06
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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/.coveragerc b/.coveragerc
@@ -5,4 +5,3 @@ omit =
     xarray/core/npcompat.py
     xarray/core/pdcompat.py
     xarray/core/pycompat.py
-    xarray/_version.py
diff --git a/.gitattributes b/.gitattributes
@@ -1,3 +1,2 @@
 # reduce the number of merge conflicts
 doc/whats-new.rst merge=union
-xarray/_version.py export-subst
diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -24,6 +24,6 @@ assignees: ''
 
 #### Output of ``xr.show_versions()``
 <details>
-# Paste the output here xr.show_versions() here
+<!-- Paste the output here xr.show_versions() here -->
 
 </details>
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/.gitignore b/.gitignore
@@ -15,6 +15,7 @@ doc/savefig
 # Packages
 *.egg
 *.egg-info
+.eggs
 dist
 build
 eggs
@@ -65,7 +66,6 @@ dask-worker-space/
 # xarray specific
 doc/_build
 doc/generated
-xarray/version.py
 xarray/tests/data/*.grib.*.idx
 
 # Sync tools

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,20 +1,24 @@
 # 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:
       - id: flake8
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.730  # Must match ci/requirements/*.yml
+    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/MANIFEST.in b/MANIFEST.in
@@ -4,6 +4,4 @@ recursive-include doc *
 prune doc/_build
 prune doc/generated
 global-exclude .DS_Store
-include versioneer.py
-include xarray/_version.py
 recursive-include xarray/static *
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'
@@ -110,5 +122,5 @@ jobs:
   - bash: |
       source activate xarray-tests
       cd doc
-      sphinx-build -n -j auto -b html -d _build/doctrees . _build/html
+      sphinx-build -W --keep-going -j auto -b html -d _build/doctrees . _build/html
     displayName: Build HTML docs
diff --git a/ci/azure/install.yml b/ci/azure/install.yml
@@ -6,34 +6,37 @@ 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 \
         git+https://github.com/dask/distributed \
         git+https://github.com/zarr-developers/zarr \
         git+https://github.com/Unidata/cftime \
         git+https://github.com/mapbox/rasterio \
+        git+https://github.com/hgrecco/pint \
         git+https://github.com/pydata/bottleneck
   condition: eq(variables['UPSTREAM_DEV'], 'true')
   displayName: Install upstream dev dependencies
 
 - 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
@@ -14,11 +14,13 @@ dependencies:
   - jupyter_client
   - nbsphinx
   - netcdf4
+  - numba
   - numpy
   - numpydoc
-  - pandas<0.25  # Hack around https://github.com/pydata/xarray/issues/3369
+  - 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=1.14
-  - pandas=0.24
+  - 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
@@ -15,22 +15,24 @@ dependencies:
   - cfgrib=0.9
   - cftime=1.0
   - coveralls
-  - dask=1.2
-  - distributed=1.27
+  - dask=2.2
+  - distributed=2.2
   - flake8
   - h5netcdf=0.7
   - h5py=2.9  # Policy allows for 2.10, but it's a conflict-fest
   - hdf5=1.10
   - hypothesis
   - iris=2.2
+  - isort
   - lxml=4.4  # Optional dep of pydap
   - matplotlib=3.1
-  - mypy=0.730  # Must match .pre-commit-config.yaml
+  - msgpack-python=0.6  # remove once distributed is bumped. distributed GH3491
+  - mypy=0.761  # Must match .pre-commit-config.yaml
   - nc-time-axis=1.2
   - netcdf4=1.4
   - numba=0.44
-  - numpy=1.14
-  - pandas=0.24
+  - numpy=1.15
+  - pandas=0.25
   # - pint  # See py36-min-nep18.yml
   - pip
   - pseudonetcdf=3.0
@@ -40,8 +42,9 @@ dependencies:
   - pytest-cov
   - pytest-env
   - rasterio=1.0
-  - scipy=1.0  # Policy allows for 1.2, but scipy>=1.1 breaks numpy=1.14
+  - 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
@@ -8,11 +8,14 @@ dependencies:
   - coveralls
   - dask=2.4
   - distributed=2.4
+  - msgpack-python=0.6  # remove once distributed is bumped. distributed GH3491
   - numpy=1.17
-  - pandas=0.24
+  - 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
@@ -19,9 +19,10 @@ dependencies:
   - hdf5
   - hypothesis
   - iris
-  - lxml    # optional dep of pydap
+  - isort
+  - lxml    # Optional dep of pydap
   - matplotlib
-  - mypy=0.730  # Must match .pre-commit-config.yaml
+  - mypy=0.761  # Must match .pre-commit-config.yaml
   - nc-time-axis
   - netcdf4
   - numba
@@ -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=0.730  # Must match .pre-commit-config.yaml
+  - 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
@@ -19,9 +19,10 @@ dependencies:
   - hdf5
   - hypothesis
   - iris
+  - isort
   - lxml    # Optional dep of pydap
   - matplotlib
-  - mypy=0.730  # Must match .pre-commit-config.yaml
+  - mypy=0.761  # Must match .pre-commit-config.yaml
   - nc-time-axis
   - netcdf4
   - numba
@@ -38,6 +39,7 @@ dependencies:
   - rasterio
   - scipy
   - seaborn
+  - setuptools
   - sparse
   - toolz
   - zarr