Merge branch 'master' of github.com:pydata/xarray into remove-old-aut…

…o-combine

* 'master' of github.com:pydata/xarray: (81 commits)
  use builtin python types instead of the numpy alias (pydata#4170)
  Revise pull request template (pydata#4039)
  pint support for Dataset (pydata#3975)
  drop eccodes in docs (pydata#4162)
  Update issue templates inspired/based on dask (pydata#4154)
  Fix failing upstream-dev build & remove docs build (pydata#4160)
  Improve typehints of xr.Dataset.__getitem__ (pydata#4144)
  provide a error summary for assert_allclose (pydata#3847)
  built-in accessor documentation (pydata#3988)
  Recommend installing cftime when time decoding fails. (pydata#4134)
  parameter documentation for DataArray.sel (pydata#4150)
  speed up map_blocks (pydata#4149)
  Remove outdated note from datetime accessor docstring (pydata#4148)
  Fix the upstream-dev pandas build failure (pydata#4138)
  map_blocks: Allow passing dask-backed objects in args (pydata#3818)
  keep attrs in reset_index (pydata#4103)
  Fix open_rasterio() for WarpedVRT with specified src_crs (pydata#4104)
  Allow non-unique and non-monotonic coordinates in get_clean_interp_index and polyfit (pydata#4099)
  update numpy's intersphinx url (pydata#4117)
  xr.infer_freq (pydata#4033)
  ...

.deepsource.toml

@@ -0,0 +1,18 @@
+version = 1
+
+test_patterns = [
+    "*/tests/**",
+    "*/test_*.py"
+]
+
+exclude_patterns = [
+    "doc/**",
+    "ci/**"
+]
+
+[[analyzers]]
+name = "python"
+enabled = true
+
+  [analyzers.meta]
+  runtime_version = "3.x.x"

.github/ISSUE_TEMPLATE/bug-report.md

@@ -0,0 +1,39 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+<!-- Please include a self-contained copy-pastable example that generates the issue if possible.
+
+Please be concise with code posted. See guidelines below on how to provide a good bug report:
+
+- Craft Minimal Bug Reports: http://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports
+- Minimal Complete Verifiable Examples: https://stackoverflow.com/help/mcve
+
+Bug reports that follow these guidelines are easier to diagnose, and so are often handled much more quickly.
+-->
+
+**What happened**:
+
+**What you expected to happen**:
+
+**Minimal Complete Verifiable Example**:
+
+```python
+# Put your MCVE code here
+```
+
+**Anything else we need to know?**:
+
+**Environment**:
+
+<details><summary>Output of <tt>xr.show_versions()</tt></summary>
+
+<!-- Paste the output here xr.show_versions() here -->
+
+
+</details>

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,5 @@
+blank_issues_enabled: true
+contact_links:
+  - name: General Question
+    url: https://stackoverflow.com/questions/tagged/python-xarray
+    about: "If you have a question like *How do I append to an xarray.Dataset?* then please ask on Stack Overflow using the #python-xarray tag."

.github/ISSUE_TEMPLATE/feature-request.md

@@ -0,0 +1,22 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+<!-- Please do a quick search of existing issues to make sure that this has not been asked before. -->
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context about the feature request here.

.github/PULL_REQUEST_TEMPLATE.md

@@ -3,4 +3,5 @@
  - [ ] Closes #xxxx
  - [ ] Tests added
  - [ ] Passes `isort -rc . && black . && mypy . && flake8`
- - [ ] Fully documented, including `whats-new.rst` for all changes and `api.rst` for new API
+ - [ ] User visible changes (including notable bug fixes) are documented in `whats-new.rst`
+ - [ ] New functions/methods are listed in `api.rst`

.pre-commit-config.yaml

@@ -16,7 +16,7 @@ repos:
     hooks:
       - id: flake8
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.761  # Must match ci/requirements/*.yml
+    rev: v0.780  # Must match ci/requirements/*.yml
     hooks:
       - id: mypy
   # run this occasionally, ref discussion https://github.com/pydata/xarray/pull/3194

HOW_TO_RELEASE.md

@@ -1,12 +1,21 @@
-How to issue an xarray release in 16 easy steps
+# How to issue an xarray release in 17 easy steps
 
 Time required: about an hour.
 
  1. Ensure your master branch is synced to upstream:
       ```
       git pull upstream master
       ```
- 2. Look over whats-new.rst and the docs. Make sure "What's New" is complete
+ 2. Get a list of contributors with:
+    ```
+    git log "$(git tag --sort="v:refname" | sed -n 'x;$p').." --format=%aN | sort -u | perl -pe 's/\n/$1, /'
+    ```
+    or by substituting the _previous_ release in:
+    ```
+    git log v0.X.Y-1.. --format=%aN | sort -u | perl -pe 's/\n/$1, /'
+    ```
+    Add these into `whats-new.rst` somewhere :)
+ 3. Look over whats-new.rst and the docs. Make sure "What's New" is complete
     (check the date!) and consider adding a brief summary note describing the
     release at the top.
     Things to watch out for:
@@ -16,41 +25,41 @@ Time required: about an hour.
       due to a bad merge. Check for these before a release by using git diff,
       e.g., `git diff v0.X.Y whats-new.rst` where 0.X.Y is the previous
       release.
- 3. If you have any doubts, run the full test suite one final time!
+ 4. If you have any doubts, run the full test suite one final time!
       ```
       pytest
       ```
- 4. Check that the ReadTheDocs build is passing.
- 5. On the master branch, commit the release in git:
+ 5. Check that the ReadTheDocs build is passing.
+ 6. On the master branch, commit the release in git:
       ```
       git commit -am 'Release v0.X.Y'
       ```
- 6. Tag the release:
+ 7. Tag the release:
       ```
       git tag -a v0.X.Y -m 'v0.X.Y'
       ```
- 7. Build source and binary wheels for pypi:
+ 8. Build source and binary wheels for pypi:
       ```
       git clean -xdf  # this deletes all uncommited changes!
       python setup.py bdist_wheel sdist
       ```
- 8. Use twine to check the package build:
+ 9. Use twine to check the package build:
       ```
       twine check dist/xarray-0.X.Y*
       ```
- 9. Use twine to register and upload the release on pypi. Be careful, you can't
+10. Use twine to register and upload the release on pypi. Be careful, you can't
     take this back!
       ```
       twine upload dist/xarray-0.X.Y*
       ```
     You will need to be listed as a package owner at
     https://pypi.python.org/pypi/xarray for this to work.
-10. Push your changes to master:
+11. Push your changes to master:
       ```
       git push upstream master
       git push upstream --tags
       ```
-11. Update the stable branch (used by ReadTheDocs) and switch back to master:
+12. Update the stable branch (used by ReadTheDocs) and switch back to master:
      ```
       git checkout stable
       git rebase master
@@ -60,7 +69,7 @@ Time required: about an hour.
     It's OK to force push to 'stable' if necessary. (We also update the stable 
     branch with `git cherrypick` for documentation only fixes that apply the 
     current released version.)
-12. Add a section for the next release (v.X.Y+1) to doc/whats-new.rst:
+13. Add a section for the next release (v.X.Y+1) to doc/whats-new.rst:
      ```
      .. _whats-new.0.X.Y+1:
 
@@ -86,19 +95,19 @@ Time required: about an hour.
      Internal Changes
      ~~~~~~~~~~~~~~~~
      ```
-13. Commit your changes and push to master again:
+14. Commit your changes and push to master again:
       ```
       git commit -am 'New whatsnew section'
       git push upstream master
       ```
     You're done pushing to master!
-14. Issue the release on GitHub. Click on "Draft a new release" at
+15. Issue the release on GitHub. Click on "Draft a new release" at
     https://github.com/pydata/xarray/releases. Type in the version number, but
     don't bother to describe it -- we maintain that on the docs instead.
-15. Update the docs. Login to https://readthedocs.org/projects/xray/versions/
+16. Update the docs. Login to https://readthedocs.org/projects/xray/versions/
     and switch your new release tag (at the bottom) from "Inactive" to "Active".
     It should now build automatically.
-16. Issue the release announcement! For bug fix releases, I usually only email
+17. Issue the release announcement! For bug fix releases, I usually only email
     xarray@googlegroups.com. For major/feature releases, I will email a broader
     list (no more than once every 3-6 months):
       - pydata@googlegroups.com
@@ -109,18 +118,8 @@ Time required: about an hour.
 
     Google search will turn up examples of prior release announcements (look for
     "ANN xarray").
-    You can get a list of contributors with:
-    ```
-    git log "$(git tag --sort="v:refname" | sed -n 'x;$p').." --format="%aN" | sort -u
-    ```
-    or by substituting the _previous_ release in:
-    ```
-    git log v0.X.Y-1.. --format="%aN" | sort -u
-    ```
-    NB: copying this output into a Google Groups form can cause 
-    [issues](https://groups.google.com/forum/#!topic/xarray/hK158wAviPs) with line breaks, so take care
 
-Note on version numbering:
+## Note on version numbering
 
 We follow a rough approximation of semantic version. Only major releases (0.X.0)
 should include breaking changes. Minor releases (0.X.Y) are for bug fixes and

azure-pipelines.yml

@@ -20,6 +20,8 @@ jobs:
         conda_env: py37
       py38:
         conda_env: py38
+      py38-all-but-dask:
+        conda_env: py38-all-but-dask
       py38-upstream-dev:
         conda_env: py38
         upstream_dev: true
@@ -106,21 +108,3 @@ jobs:
       python ci/min_deps_check.py ci/requirements/py36-bare-minimum.yml
       python ci/min_deps_check.py ci/requirements/py36-min-all-deps.yml
     displayName: minimum versions policy
-
-- job: Docs
-  pool:
-    vmImage: 'ubuntu-16.04'
-  steps:
-  - template: ci/azure/install.yml
-    parameters:
-      env_file: ci/requirements/doc.yml
-  - bash: |
-      source activate xarray-tests
-      # Replicate the exact environment created by the readthedocs CI
-      conda install --yes --quiet -c pkgs/main mock pillow sphinx sphinx_rtd_theme
-    displayName: Replicate readthedocs CI environment
-  - bash: |
-      source activate xarray-tests
-      cd doc
-      sphinx-build -W --keep-going -j auto -b html -d _build/doctrees . _build/html
-    displayName: Build HTML docs

ci/azure/install.yml

@@ -10,16 +10,37 @@ steps:
     conda env create -n xarray-tests --file ${{ parameters.env_file }}
   displayName: Install conda dependencies
 
+# TODO: add sparse back in, once Numba works with the development version of
+# NumPy again: https://github.com/pydata/xarray/issues/4146 
 - bash: |
     source activate xarray-tests
+    conda uninstall -y --force \
+        numpy \
+        scipy \
+        pandas \
+        matplotlib \
+        dask \
+        distributed \
+        zarr \
+        cftime \
+        rasterio \
+        pint \
+        bottleneck \
+        sparse
     python -m pip install \
-        -f https://7933911d6844c6c53a7d-47bd50c35cd79bd838daf386af554a83.ssl.cf2.rackcdn.com \
+        -i https://pypi.anaconda.org/scipy-wheels-nightly/simple \
         --no-deps \
         --pre \
         --upgrade \
-        matplotlib \
         numpy \
-        scipy
+        scipy \
+        pandas
+    python -m pip install \
+        -f https://7933911d6844c6c53a7d-47bd50c35cd79bd838daf386af554a83.ssl.cf2.rackcdn.com \
+        --no-deps \
+        --pre \
+        --upgrade \
+        matplotlib
     python -m pip install \
         --no-deps \
         --upgrade \
@@ -29,8 +50,7 @@ steps:
         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/pandas-dev/pandas
+        git+https://github.com/pydata/bottleneck
   condition: eq(variables['UPSTREAM_DEV'], 'true')
   displayName: Install upstream dev dependencies
 

ci/requirements/doc.yml

@@ -17,11 +17,10 @@ dependencies:
   - netcdf4>=1.5
   - numba
   - numpy>=1.17
-  - numpydoc
   - pandas>=1.0
   - rasterio>=1.1
   - seaborn
   - setuptools
   - sphinx>=2.3
   - sphinx_rtd_theme>=0.4
-  - zarr>=2.4
+  - zarr>=2.4

ci/requirements/py36-min-all-deps.yml

@@ -15,8 +15,8 @@ dependencies:
   - cfgrib=0.9
   - cftime=1.0
   - coveralls
-  - dask=2.2
-  - distributed=2.2
+  - dask=2.5
+  - distributed=2.5
   - flake8
   - h5netcdf=0.7
   - h5py=2.9  # Policy allows for 2.10, but it's a conflict-fest

ci/requirements/py36-min-nep18.yml

@@ -6,12 +6,12 @@ dependencies:
   # require drastically newer packages than everything else
   - python=3.6
   - coveralls
-  - dask=2.4
-  - distributed=2.4
+  - dask=2.5
+  - distributed=2.5
   - msgpack-python=0.6  # remove once distributed is bumped. distributed GH3491
   - numpy=1.17
   - pandas=0.25
-  - pint=0.11
+  - pint
   - pip
   - pytest
   - pytest-cov