Merge pull request #1 from pydata/master

Merge changes since fork

Author: phausamann

.gitattributes

@@ -1,2 +1,3 @@
 # reduce the number of merge conflicts
 doc/whats-new.rst merge=union
+xarray/_version.py export-subst

.github/CONTRIBUTING.md

@@ -1,5 +1,8 @@
 #### Code Sample, a copy-pastable example if possible
 
+A "Minimal, Complete and Verifiable Example" will make it much easier for maintainers to help you:
+http://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports
+
 ```python
 # Your code here
 

.github/ISSUE_TEMPLATE.md

@@ -1,4 +1,3 @@
  - [ ] Closes #xxxx (remove if there is no corresponding issue, which should only be the case for minor changes)
  - [ ] Tests added (for all bug fixes or enhancements)
- - [ ] Tests passed (for all non-documentation changes)
  - [ ] Fully documented, including `whats-new.rst` for all changes and `api.rst` for new API (remove if this change should not be visible to users, e.g., if it is an internal clean-up, or if this is part of a larger project that will be documented later)

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,6 +1,9 @@
 *.py[cod]
 __pycache__
 
+# example caches from Hypothesis
+.hypothesis/
+
 # temp files from docs build
 doc/auto_gallery
 doc/example.nc
@@ -33,6 +36,11 @@ pip-log.txt
 nosetests.xml
 .cache
 .ropeproject/
+.tags*
+.testmon*
+.tmontmp/
+.pytest_cache
+dask-worker-space/
 
 # asv environments
 .asv
@@ -45,10 +53,11 @@ nosetests.xml
 .project
 .pydevproject
 
-# PyCharm and Vim
+# IDEs
 .idea
 *.swp
 .DS_Store
+.vscode/
 
 # xarray specific
 doc/_build

.gitignore

@@ -0,0 +1,12 @@
+# File : .pep8speaks.yml
+
+scanner:
+    diff_only: True  # If True, errors caused by only the patch are shown
+
+pycodestyle:
+    max-line-length: 79
+    ignore:  # Errors and warnings to ignore
+        - E402,  # module level import not at top of file
+        - E731,  # do not assign a lambda expression, use a def
+        - W503   # line break before binary operator
+        - W504   # line break after binary operator

.pep8speaks.yml

@@ -1,5 +1,5 @@
 # Based on http://conda.pydata.org/docs/travis.html
-language: python
+language: minimal
 sudo: false # use container based build
 notifications:
   email: false
@@ -10,74 +10,48 @@ branches:
 matrix:
   fast_finish: true
   include:
-  - python: 2.7
-    env: CONDA_ENV=py27-min
-  - python: 2.7
-    env: CONDA_ENV=py27-cdat+iris+pynio
-  - python: 3.4
-    env: CONDA_ENV=py34
-  - python: 3.5
-    env: CONDA_ENV=py35
-  - python: 3.6
-    env: CONDA_ENV=py36
-  - python: 3.6
-    env:
+  - env: CONDA_ENV=py27-min
+  - env: CONDA_ENV=py27-cdat+iris+pynio
+  - env: CONDA_ENV=py35
+  - env: CONDA_ENV=py36
+  - env: CONDA_ENV=py37
+  - env:
     - CONDA_ENV=py36
     - EXTRA_FLAGS="--run-flaky --run-network-tests"
-  - python: 3.6
-    env: CONDA_ENV=py36-netcdf4-dev
+  - env: CONDA_ENV=py36-netcdf4-dev
     addons:
       apt_packages:
         - libhdf5-serial-dev
         - netcdf-bin
         - libnetcdf-dev
-  - python: 3.6
-    env: CONDA_ENV=py36-dask-dev
-  - python: 3.6
-    env: CONDA_ENV=py36-pandas-dev
-  - python: 3.6
-    env: CONDA_ENV=py36-bottleneck-dev
-  - python: 3.6
-    env: CONDA_ENV=py36-condaforge-rc
-  - python: 3.6
-    env: CONDA_ENV=py36-pynio-dev
-  - python: 3.6
-    env: CONDA_ENV=py36-rasterio1.0alpha
-  - python: 3.6
-    env: CONDA_ENV=py36-zarr-dev
+  - env: CONDA_ENV=py36-dask-dev
+  - env: CONDA_ENV=py36-pandas-dev
+  - env: CONDA_ENV=py36-bottleneck-dev
+  - env: CONDA_ENV=py36-condaforge-rc
+  - env: CONDA_ENV=py36-pynio-dev
+  - env: CONDA_ENV=py36-rasterio-0.36
+  - env: CONDA_ENV=py36-zarr-dev
+  - env: CONDA_ENV=docs
+  - env: CONDA_ENV=py36-hypothesis
+
   allow_failures:
-  - python: 3.6
-    env:
+  - env:
     - CONDA_ENV=py36
     - EXTRA_FLAGS="--run-flaky --run-network-tests"
-  - python: 3.6
-    env: CONDA_ENV=py36-netcdf4-dev
+  - env: CONDA_ENV=py36-netcdf4-dev
     addons:
       apt_packages:
         - libhdf5-serial-dev
         - netcdf-bin
         - libnetcdf-dev
-  - python: 3.6
-    env: CONDA_ENV=py36-dask-dev
-  - python: 3.6
-    env: CONDA_ENV=py36-pandas-dev
-  - python: 3.6
-    env: CONDA_ENV=py36-bottleneck-dev
-  - python: 3.6
-    env: CONDA_ENV=py36-condaforge-rc
-  - python: 3.6
-    env: CONDA_ENV=py36-pynio-dev
-  - python: 3.6
-    env: CONDA_ENV=py36-rasterio1.0alpha
-  - python: 3.6
-    env: CONDA_ENV=py36-zarr-dev
+  - env: CONDA_ENV=py36-pandas-dev
+  - env: CONDA_ENV=py36-bottleneck-dev
+  - env: CONDA_ENV=py36-condaforge-rc
+  - env: CONDA_ENV=py36-pynio-dev
+  - env: CONDA_ENV=py36-zarr-dev
 
 before_install:
-  - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
-      wget http://repo.continuum.io/miniconda/Miniconda-3.16.0-Linux-x86_64.sh -O miniconda.sh;
-    else
-      wget http://repo.continuum.io/miniconda/Miniconda3-3.16.0-Linux-x86_64.sh -O miniconda.sh;
-    fi
+  - wget http://repo.continuum.io/miniconda/Miniconda3-3.16.0-Linux-x86_64.sh -O miniconda.sh;
   - bash miniconda.sh -b -p $HOME/miniconda
   - export PATH="$HOME/miniconda/bin:$PATH"
   - hash -r
@@ -86,16 +60,28 @@ before_install:
   - conda info -a
 
 install:
-  - conda env create --file ci/requirements-$CONDA_ENV.yml
+  - if [[ "$CONDA_ENV" == "docs" ]]; then
+      conda env create -n test_env --file doc/environment.yml;
+    else
+      conda env create -n test_env --file ci/requirements-$CONDA_ENV.yml;
+    fi
   - source activate test_env
   - conda list
-  - python setup.py install
+  - pip install --no-deps -e .
   - python xarray/util/print_versions.py
 
 script:
-  - flake8 -j auto xarray
+  - which python
+  - python --version
   - python -OO -c "import xarray"
-  - py.test xarray --cov=xarray --cov-config ci/.coveragerc --cov-report term-missing --verbose $EXTRA_FLAGS
+  - if [[ "$CONDA_ENV" == "docs" ]]; then
+      conda install -c conda-forge sphinx sphinx_rtd_theme sphinx-gallery numpydoc;
+      sphinx-build -n -j auto -b html -d _build/doctrees doc _build/html;
+    elif [[ "$CONDA_ENV" == "py36-hypothesis" ]]; then
+      pytest properties ;
+    else
+      py.test xarray --cov=xarray --cov-config ci/.coveragerc --cov-report term-missing --verbose $EXTRA_FLAGS;
+    fi
 
 after_success:
   - coveralls

.travis.yml

@@ -7,21 +7,21 @@ Time required: about an hour.
  2. Look over whats-new.rst and the docs. Make sure "What's New" is complete
     (check the date!) and add a brief summary note describing the release at the
     top.
- 3. Update the version in setup.py and switch to `ISRELEASED = True`.
- 4. If you have any doubts, run the full test suite one final time!
+ 3. If you have any doubts, run the full test suite one final time!
       py.test
- 5. On the master branch, commit the release in git:
+ 4. On the master branch, commit the release in git:
       git commit -a -m 'Release v0.X.Y'
- 6. Tag the release:
+ 5. Tag the release:
       git tag -a v0.X.Y -m 'v0.X.Y'
- 7. Build source and binary wheels for pypi:
+ 6. 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 register and upload the release on pypi. Be careful, you can't
+ 7. 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.
- 9. Push your changes to master:
+ 8. Push your changes to master:
       git push upstream master
       git push upstream --tags
  9. Update the stable branch (used by ReadTheDocs) and switch back to master:
@@ -32,25 +32,18 @@ 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.
-10. Revert ISRELEASED in setup.py back to False. Don't change the version
-    number: in normal development, we keep the version number in setup.py as the
-    last released version.
-11. Add a section for the next release (v.X.(Y+1)) to doc/whats-new.rst.
-12. Commit your changes and push to master again:
+10. Add a section for the next release (v.X.(Y+1)) to doc/whats-new.rst.
+11. Commit your changes and push to master again:
       git commit -a -m 'Revert to dev version'
       git push upstream master
     You're done pushing to master!
-13. Issue the release on GitHub. Click on "Draft a new release" at
-    https://github.com/pydata/xarray/releases and paste in the latest from
-    whats-new.rst.
-14. Update the docs. Login to https://readthedocs.org/projects/xray/versions/
+12. 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.
+13. 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.
-15. Update conda-forge. Clone https://github.com/conda-forge/xarray-feedstock
-    and update the version number and sha256 in meta.yaml. (On OS X, you can
-    calculate sha256 with `shasum -a 256 xarray-0.X.Y.tar.gz`). Submit a pull
-    request (and merge it, once CI passes).
-16. Issue the release announcement! For bug fix releases, I usually only email
+14. Issue the release announcement! For bug fix releases, I usually only email
     [email protected]. For major/feature releases, I will email a broader
     list (no more than once every 3-6 months):
       [email protected], [email protected],

HOW_TO_RELEASE

@@ -4,3 +4,5 @@ recursive-include doc *
 prune doc/_build
 prune doc/generated
 global-exclude .DS_Store
+include versioneer.py
+include xarray/_version.py

MANIFEST.in

@@ -7,12 +7,16 @@ xarray: N-D labeled arrays and datasets
    :target: https://ci.appveyor.com/project/shoyer/xray
 .. image:: https://coveralls.io/repos/pydata/xarray/badge.svg
    :target: https://coveralls.io/r/pydata/xarray
+.. image:: https://readthedocs.org/projects/xray/badge/?version=latest
+   :target: http://xarray.pydata.org/
 .. image:: https://img.shields.io/pypi/v/xarray.svg
    :target: https://pypi.python.org/pypi/xarray/
 .. image:: https://zenodo.org/badge/13221727.svg
   :target: https://zenodo.org/badge/latestdoi/13221727
 .. image:: http://img.shields.io/badge/benchmarked%20by-asv-green.svg?style=flat
-  :target: https://tomaugspurger.github.io/asv-collection/xarray/
+  :target: http://pandas.pydata.org/speed/xarray/
+.. image:: https://img.shields.io/badge/powered%20by-NumFOCUS-orange.svg?style=flat&colorA=E1523D&colorB=007D8A
+  :target: http://numfocus.org
 
 **xarray** (formerly **xray**) is an open source project and Python package that aims to bring the
 labeled data power of pandas_ to the physical sciences, by providing
@@ -84,6 +88,11 @@ Documentation
 
 The official documentation is hosted on ReadTheDocs at http://xarray.pydata.org/
 
+Contributing
+------------
+
+You can find information about contributing to xarray at our `Contributing page <http://xarray.pydata.org/en/latest/contributing.html#>`_.
+
 Get in touch
 ------------
 
@@ -96,20 +105,36 @@ Get in touch
 .. _mailing list: https://groups.google.com/forum/#!forum/xarray
 .. _on GitHub: http://github.com/pydata/xarray
 
+NumFOCUS
+--------
+
+.. image:: https://numfocus.org/wp-content/uploads/2017/07/NumFocus_LRG.png
+   :scale: 25 %
+   :target: https://numfocus.org/
+
+Xarray is a fiscally sponsored project of NumFOCUS_, a nonprofit dedicated
+to supporting the open source scientific computing community. If you like
+Xarray and want to support our mission, please consider making a donation_
+to support our efforts.
+
+.. _donation: https://www.flipcause.com/secure/cause_pdetails/NDE2NTU=
+
 History
 -------
 
 xarray is an evolution of an internal tool developed at `The Climate
 Corporation`__. It was originally written by Climate Corp researchers Stephan
 Hoyer, Alex Kleeman and Eugene Brevdo and was released as open source in
-May 2014. The project was renamed from "xray" in January 2016.
+May 2014. The project was renamed from "xray" in January 2016. Xarray became a
+fiscally sponsored project of NumFOCUS_ in August 2018.
 
 __ http://climate.com/
+.. _NumFOCUS: https://numfocus.org
 
 License
 -------
 
-Copyright 2014-2017, xarray Developers
+Copyright 2014-2018, xarray Developers
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.

README.rst

@@ -63,7 +63,8 @@
         "netcdf4": [""],
         "scipy": [""],
         "bottleneck": ["", null],
-        "dask": ["", null],
+        "dask": [""],
+        "distributed": [""],
     },