Add Github Actions system from climpred and xskillscore (#103)

* Add Github Actions system for CI
* Removes Travis CI
* Switches to CodeCov for coverage testing
* Fixes bug with vectorize=True with new dask/xarray

.codecov.yml

@@ -0,0 +1,8 @@
+coverage:
+  status:
+    project:
+      default:
+        # Require 50% coverage.
+        target: 50
+    patch: false
+    changes: false

.github/workflows/esmtools_installs.yml

@@ -0,0 +1,25 @@
+name: esmtools installs
+
+on: pull_request
+
+jobs:
+  install-esmtools:  # Installs esmtools on various OS.
+    name: Install esmtools, ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: ["ubuntu-latest", "macos-latest", "windows-latest"]
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        ref: ${{github.event.pull_request.head.ref}}
+        repository: ${{github.event.pull_request.head.repo.full_name}}
+    - name: Setup python
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.6
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -e .
+        python -c "import esmtools"

.github/workflows/esmtools_testing.yml

@@ -0,0 +1,44 @@
+name: esmtools testing
+
+on: pull_request
+
+jobs:
+  test:  # Runs testing suite on various python versions.
+    name: Test esmtools, python ${{ matrix.python-version }}
+    runs-on: ubuntu-latest
+    defaults:
+        run:
+          shell: bash -l {0}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [3.6, 3.7, 3.8]
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          ref: ${{github.event.pull_request.head.ref}}
+          repository: ${{github.event.pull_request.head.repo.full_name}}
+      - name: Set up conda
+        uses: conda-incubator/setup-miniconda@v1
+        with:
+          auto-update-conda: true
+          channels: conda-forge
+          mamba-version: '*'
+          activate-environment: esmtools-minimum-tests
+          python-version: ${{ matrix.python-version }}
+      - name: Set up conda environment
+        run: |
+          mamba env update -f ci/requirements/minimum-tests.yml
+      - name: Conda info
+        run: conda info
+      - name: Conda list
+        run: conda list
+      - name: Run tests
+        run: |
+          pytest --cov=esmtools --cov-report=xml --verbose
+      - name: Upload coverage to codecov
+        uses: codecov/codecov-action@v1.0.7
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          file: ./coverage.xml
+          fail_ci_if_error: false

.github/workflows/lint.yml

@@ -0,0 +1,19 @@
+
+name: Lint
+
+on: pull_request
+
+jobs:
+  lint:  # Runs linting package checks for code styling.
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          ref: ${{github.event.pull_request.head.ref}}
+          repository: ${{github.event.pull_request.head.repo.full_name}}
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.6
+      - name: Lint via pre-commit checks
+        uses: pre-commit/action@v2.0.0

.pre-commit-config.yaml

@@ -1,37 +1,28 @@
 repos:
 
   -   repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v2.2.3
+      rev: v3.3.0
       hooks:
       -   id: trailing-whitespace
       -   id: end-of-file-fixer
       -   id: check-docstring-first
       -   id: check-yaml
-      -   id: double-quote-string-fixer
       -   id: no-commit-to-branch
       -   id: debug-statements
       -   id: check-merge-conflict
+      -   id: check-added-large-files
 
-  -   repo: https://github.com/ambv/black
-      rev: 19.10b0
+  -   repo: https://github.com/psf/black
+      rev: stable
       hooks:
       - id: black
-        args: ["--line-length", "88", "--skip-string-normalization"]
 
-  -   repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v2.4.0
+  -   repo: https://gitlab.com/pycqa/flake8
+      rev: 3.8.4
       hooks:
       - id: flake8
-        args: ["--max-line-length=88", "--exclude=__init__.py", "--ignore=W605,W503,F722,C901"]
 
   -   repo: https://github.com/pre-commit/mirrors-isort
-      rev: v4.3.21
+      rev: v5.6.4
       hooks:
       -   id: isort
-          args: ["-w", "88"]
-
-  -   repo: https://github.com/PyCQA/doc8
-      rev: 0.8.1rc2
-      hooks:
-      -   id: doc8
-          args: ["--max-line-length", "100", "--ignore-path", "docs/source/setting-up-data.rst", "--allow-long-titles"]

CHANGELOG.rst

@@ -9,6 +9,14 @@ Bug Fixes
 ---------
 - :py:func:`~esmtools.temporal.to_annual` no longer returns ``0.0`` where the original
   dataset had NaNs. (:issue:`75`) (:pr:`95`) `Riley X. Brady`_.
+- :py:func:`~esmtools.stats.rm_poly` and :py:func:`~esmtools.stats.polyfit` now work
+  with newest ``dask`` and ``xarray`` versions. There was an issue with ``vectorize=True``
+  breaking ``xarray.apply_ufunc`` with a single time series. (:pr:`103`) `Riley X. Brady`_.
+
+Internals
+---------
+- We now use Github Actions to do Continuous Integration instead of Travis, similar to
+  ``climpred`` and ``xskillscore`` (:pr:`103`) `Riley X. Brady`_.
 
 esmtools v1.1.3 (2020-07-17)
 ============================

README.rst

@@ -2,27 +2,60 @@
 
 a toolbox for Earth System Model analysis
 
-.. image:: https://travis-ci.org/bradyrx/esmtools.svg?branch=master
-    :target: https://travis-ci.org/bradyrx/esmtools
+..
+    Table version of badges inspired by pySTEPS.
+
+.. list-table::
+    :stub-columns: 1
+    :widths: 10 90
+
+    * - docs
+      - |docs|
+    * - tests
+      - |requires| |codecov|
+    * - package
+      - |conda| |pypi|
+    * - license
+      - |license|
+    * - community
+      - |contributors| |downloads|
+    * - tutorials
+      - |gallery|
+
+.. |docs| image:: https://img.shields.io/readthedocs/esmtools/stable.svg?style=flat
+    :target: https://esmtools.readthedocs.io/en/stable/?badge=stable
+    :alt: Documentation Status
+
+.. |requires| image:: https://requires.io/github/bradyrx/esmtools/requirements.svg?branch=master
+     :target: https://requires.io/github/bradyrx/esmtools/requirements/?branch=master
+     :alt: Requirements Status
 
-.. image:: https://img.shields.io/pypi/v/esmtools.svg
-    :target: https://pypi.python.org/pypi/esmtools/
+.. |codecov| image:: https://codecov.io/gh/bradyrx/esmtools/branch/master/graph/badge.svg
+      :target: https://codecov.io/gh/bradyrx/esmtools
 
-.. image:: https://img.shields.io/conda/vn/conda-forge/esmtools.svg
+.. |conda| image:: https://img.shields.io/conda/vn/conda-forge/esmtools.svg
     :target: https://anaconda.org/conda-forge/esmtools
     :alt: Conda Version
 
-.. image:: https://coveralls.io/repos/github/bradyrx/esmtools/badge.svg?branch=master
-    :target: https://coveralls.io/github/bradyrx/esmtools?branch=master
-
-.. image:: https://img.shields.io/readthedocs/esmtools/stable.svg?style=flat
-    :target: https://esmtools.readthedocs.io/en/stable/?badge=stable
-    :alt: Documentation Status
+.. |pypi| image:: https://img.shields.io/pypi/v/esmtools.svg
+   :target: https://pypi.python.org/pypi/esmtools/
 
-.. image:: https://img.shields.io/github/license/bradyrx/esmtools.svg
+.. |license| image:: https://img.shields.io/github/license/bradyrx/esmtools.svg
     :alt: license
     :target: LICENSE.txt
 
+.. |contributors| image:: https://img.shields.io/github/contributors/bradyrx/esmtools
+    :alt: GitHub contributors
+    :target: https://github.com/bradyrx/esmtools/graphs/contributors
+
+.. |downloads| image:: https://img.shields.io/conda/dn/conda-forge/esmtools
+    :alt: Conda downloads
+    :target: https://anaconda.org/conda-forge/esmtools
+
+.. |gallery| image:: https://img.shields.io/badge/esmtools-example_gallery-ed7b0e.svg
+    :alt: climpred gallery
+    :target: https://esmtools.readthedocs.io/en/stable/examples.html
+
 Installation
 ============
 

ci/requirements/docs.yml

@@ -0,0 +1,26 @@
+name: esmtools-docs
+channels:
+  - conda-forge
+dependencies:
+  - python=3.6
+  - bottleneck
+  - cartopy>=0.18.0
+  - importlib_metadata
+  - jupyterlab
+  - matplotlib
+  - nbsphinx
+  - nc-time-axis
+  - netcdf4
+  - numpy
+  - pandas
+  - pygments==2.6.1
+  - sphinx
+  - sphinxcontrib-napoleon
+  - sphinx_rtd_theme
+  - toolz
+  - tqdm
+  - xarray>=0.16.1
+  - pip
+  - pip:
+    # Install latest version of climpred.
+    - -e ../..

ci/environment-dev-3.6.yml → ci/requirements/esmtools-dev.yml

@@ -2,7 +2,6 @@ name: esmtools-dev
 channels:
   - conda-forge
 dependencies:
-  - python=3.6
   # Documentation
   - nbsphinx
   - nbstripout

ci/requirements/minimum-tests.yml

@@ -0,0 +1,19 @@
+name: esmtools-minimum-tests
+channels:
+  - conda-forge
+dependencies:
+  - cftime
+  - coveralls
+  - dask
+  - ipython
+  - nc-time-axis
+  - netcdf4
+  - pip
+  - pytest
+  - pytest-cov
+  - scipy
+  - xarray
+  - xskillscore
+  - pip:
+    - pytest-lazy-fixture
+    - -e ../..