Multi-tile-output

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.2.1
+current_version = 0.2.2
 commit = True
 tag = True
 

.gitattributes

@@ -0,0 +1 @@
+xmitgcm/_version.py export-subst

.github/workflows/ci.yaml

@@ -0,0 +1,98 @@
+# This uses actios:
+#  checkout: https://github.com/actions/checkout
+#  cache: https://github.com/actions/cache
+#  codecov-action: https://github.com/codecov/codecov-action
+
+name: CI
+on:
+  push:
+    branches:
+      - "*"
+  pull_request:
+    branches:
+      - "*"
+        # Nothing scheduled, just PRs and pushes
+        #  schedule:
+        #    - cron: "0 0 * * *" # Daily at midnight
+
+jobs:
+  build:
+    name: Build (${{ matrix.python-version }} | ${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-latest"]
+        python-version: ["3.7", "3.8", "3.9"]
+    steps:
+      - uses: actions/checkout@v2
+      - name: Cache conda
+        uses: actions/cache@v2
+        env:
+          # Increase this value to reset cache if ci/environment.yml has not changed
+          CACHE_NUMBER: 0
+        with:
+          path: ~/conda_pkgs_dir
+          key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('ci/environment.yml') }}
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: test_env # Defined in ci/environment*.yml
+          auto-update-conda: false
+          python-version: ${{ matrix.python-version }}
+          environment-file: ci/environment-py${{ matrix.python-version }}.yml
+          use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
+      - name: Set up conda environment
+        shell: bash -l {0}
+        run: |
+          python -m pip install -e .
+          conda list
+      - name: Run Tests
+        shell: bash -l {0}
+        run: |
+          py.test --cov=./ --cov-report=xml
+      - name: Upload code coverage to Codecov
+        uses: codecov/codecov-action@v1
+        with:
+          file: ./coverage.xml
+          flags: unittests
+          env_vars: OS,PYTHON
+          name: codecov-umbrella
+          fail_ci_if_error: false
+
+  xarray-master:
+    name: Build xarray-master
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: Cache conda
+      uses: actions/cache@v2
+      env:
+        # Increase this value to reset cache if ci/environment-upstream-dev.yml has not changed
+        CACHE_NUMBER: 0
+      with:
+        path: ~/conda_pkgs_dir
+        key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('ci/environment-upstream-dev.yml') }}
+    - uses: conda-incubator/setup-miniconda@v2
+      with:
+        activate-environment: test_env # Defined in ci/environment-*.yml
+        auto-update-conda: false
+        python-version: 3.7
+        environment-file: ci/environment-py37-xarraymaster.yml
+        use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
+    - name: Set up conda environment
+      shell: bash -l {0}
+      run: |
+        python -m pip install -e .
+        conda list
+    - name: Run Tests
+      shell: bash -l {0}
+      run: |
+        py.test --cov=./ --cov-report=xml
+    - name: Upload code coverage to Codecov
+      uses: codecov/codecov-action@v1
+      with:
+        file: ./coverage.xml
+        flags: unittests
+        env_vars: OS,PYTHON
+        name: codecov-umbrella
+        fail_ci_if_error: false

.github/workflows/pythonpublish.yaml

@@ -0,0 +1,26 @@
+name: Upload Python Package
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v1
+      - name: Set up Python
+        uses: actions/setup-python@v1
+        with:
+          python-version: '3.x'
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install setuptools setuptools-scm wheel twine
+      - name: Build and publish
+        env:
+          TWINE_USERNAME: "__token__"
+          TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
+        run: |
+          python setup.py sdist bdist_wheel
+          twine upload dist/*

.stickler.yml

@@ -0,0 +1,5 @@
+linters:
+  flake8:
+    fixer: true
+fixers:
+  enable: true

MANIFEST.in

@@ -0,0 +1,3 @@
+include LICENSE
+include versioneer.py
+include xmitgcm/_version.py

README.rst

@@ -10,20 +10,20 @@ parallel, out-of-core_ analysis of MITgcm output data.
 Links
 -----
 
--  HTML documentation: http://xmitgcm.readthedocs.org
--  Issue tracker: http://github.com/xgcm/xmitgcm/issues
--  Source code: http://github.com/xgcm/xmitgcm
+-  HTML documentation: https://xmitgcm.readthedocs.org
+-  Issue tracker: https://github.com/MITgcm/xmitgcm/issues
+-  Source code: https://github.com/MITgcm/xmitgcm
 
 Installation
 ------------
 
 Requirements
 ^^^^^^^^^^^^
 
-xmitgcm is compatible with python 3 and python 2.7. It requires xarray_
-(>= version 0.8.2) and dask_ (>= version 0.11.2).
+xmitgcm is compatible with python >=3.7. It requires xarray_
+(>= version 0.11.0) and dask_ (>= version 1.0).
 These packages are most reliably installed via the
-`conda <http://conda.pydata.org/docs/>`_ environment management
+`conda <https://conda.pydata.org/docs/>`_ environment management
 system, which is part of the Anaconda_ python distribution. Assuming you have
 conda available on your system, the dependencies can be installed with the
 command::
@@ -47,10 +47,10 @@ Installation from github
 ^^^^^^^^^^^^^^^^^^^^^^^^
 
 xmitgcm is under active development. To obtain the latest development version,
-you may clone the `source repository <https://github.com/xgcm/xmitgcm>`_
+you may clone the `source repository <https://github.com/MITgcm/xmitgcm>`_
 and install it::
 
-    git clone https://github.com/xgcm/xmitgcm.git
+    git clone https://github.com/MITgcm/xmitgcm.git
     cd xmitgcm
     python setup.py install
 
@@ -73,7 +73,7 @@ This will create a directory called ``global_oce_latlon`` which we will use
 for the rest of these examples. If you have your own data, replace this with
 the path to your mitgcm files.
 
-To opean MITgcm MDS data as an xarray.Dataset, do the following in python::
+To open MITgcm MDS data as an xarray.Dataset, do the following in python::
 
     from xmitgcm import open_mdsdataset
     data_dir = './global_oce_latlon'
@@ -85,29 +85,29 @@ try to determine the file prefixes and iteration numbers to read. In some
 configurations, the ``open_mdsdataset`` function may work without further
 keyword arguments. In most cases, you will have to specify further details.
 
-Consult the `online documentation <http://xmitgcm.readthedocs.org>`_ for
+Consult the `online documentation <https://xmitgcm.readthedocs.org>`_ for
 more details.
 
 .. |DOI| image:: https://zenodo.org/badge/70649781.svg
    :target: https://zenodo.org/badge/latestdoi/70649781
-.. |Build Status| image:: https://travis-ci.org/xgcm/xmitgcm.svg?branch=master
-   :target: https://travis-ci.org/xgcm/xmitgcm
+.. |Build Status| image:: https://travis-ci.org/MITgcm/xmitgcm.svg?branch=master
+   :target: https://travis-ci.org/MITgcm/xmitgcm
    :alt: travis-ci build status
-.. |codecov| image:: https://codecov.io/github/xgcm/xmitgcm/coverage.svg?branch=master
-   :target: https://codecov.io/github/xgcm/xmitgcm?branch=master
+.. |codecov| image:: https://codecov.io/github/MITgcm/xmitgcm/coverage.svg?branch=master
+   :target: https://codecov.io/github/MITgcm/xmitgcm?branch=master
    :alt: code coverage
 .. |pypi| image:: https://badge.fury.io/py/xmitgcm.svg
    :target: https://badge.fury.io/py/xmitgcm
    :alt: pypi package
-.. |docs| image:: http://readthedocs.org/projects/xmitgcm/badge/?version=stable
-   :target: http://xmitgcm.readthedocs.org/en/stable/?badge=stable
+.. |docs| image:: https://readthedocs.org/projects/xmitgcm/badge/?version=stable
+   :target: https://xmitgcm.readthedocs.org/en/stable/?badge=stable
    :alt: documentation status
 
-.. _dask: http://dask.pydata.org
-.. _xarray: http://xarray.pydata.org
-.. _Comodo: http://pycomodo.forge.imag.fr/norm.html
-.. _issues: https://github.com/xgcm/xmitgcm/issues
-.. _`pull requests`: https://github.com/xgcm/xmitgcm/pulls
+.. _dask: https://dask.pydata.org
+.. _xarray: https://xarray.pydata.org
+.. _Comodo: https://pycomodo.forge.imag.fr/norm.html
+.. _issues: https://github.com/MITgcm/xmitgcm/issues
+.. _`pull requests`: https://github.com/MITgcm/xmitgcm/pulls
 .. _MITgcm: http://mitgcm.org/public/r2_manual/latest/online_documents/node277.html
 .. _out-of-core: https://en.wikipedia.org/wiki/Out-of-core_algorithm
 .. _Anaconda: https://www.continuum.io/downloads

ci/environment-py36.yml → ci/environment-py3.7.yml

@@ -1,11 +1,18 @@
 name: test_env
+channels:
+  - conda-forge
 dependencies:
-  - python=3.6
+  - python=3.7
   - xarray
   - dask
   - numpy
   - pytest
   - future
+  - zarr
+  - cftime
+  - aiohttp
   - pip:
+    - cachetools
+    - fsspec
     - codecov
     - pytest-cov

ci/environment-py3.8.yml

@@ -0,0 +1,17 @@
+name: test_env
+channels:
+  - conda-forge
+dependencies:
+  - python=3.8
+  - xarray
+  - dask
+  - numpy
+  - pytest
+  - future
+  - zarr
+  - cftime
+  - aiohttp
+  - pytest-cov
+  - codecov
+  - fsspec
+  - cachetools

ci/environment-py3.9.yml

@@ -0,0 +1,17 @@
+name: test_env
+channels:
+  - conda-forge
+dependencies:
+  - python=3.9
+  - xarray
+  - dask
+  - numpy
+  - pytest
+  - future
+  - zarr
+  - cftime
+  - aiohttp
+  - pytest-cov
+  - codecov
+  - fsspec
+  - cachetools