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bradyrxbradyrx
authoredOct 2, 2020
Update CI to Github Actions (#471)
* Change from Travis CI to Github Actions * require 90% coverage
·
v2.5.0v2.1.1
1 parent 6625e0a commit 80c17f0

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‎.codecov.yml

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coverage:
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status:
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project:
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default:
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# Require 90% coverage.
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target: 90
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patch: false
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changes: false

‎.coveragerc

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This file was deleted.

‎.github/workflows/climpred_installs.yml

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name: climpred installs
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on: [push]
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jobs:
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install-climpred: # Installs climpred on various OS.
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name: Install climpred, ${{ matrix.os }}
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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os: ["ubuntu-latest", "macos-latest", "windows-latest"]
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steps:
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- uses: actions/checkout@v2
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- name: Setup python
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uses: actions/setup-python@v2
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with:
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python-version: 3.6
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install -e .
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python -c "import climpred"

‎.github/workflows/climpred_testing.yml

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name: climpred testing
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on: [push]
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jobs:
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test: # Runs testing suite on various python versions.
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name: Test climpred, python ${{ matrix.python-version }}
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: [3.6, 3.7, 3.8]
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steps:
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- uses: actions/checkout@v2
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- name: Install Conda environment
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uses: conda-incubator/setup-miniconda@v1
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with:
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auto-update-conda: true
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activate-environment: climpred-minimum-tests
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environment-file: ci/requirements/minimum-tests.yml
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python-version: ${{ matrix.python-version }}
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- name: Conda info
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shell: bash -l {0}
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run: conda info
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- name: Conda list
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shell: bash -l {0}
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run: conda list
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- name: Run tests
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shell: bash -l {0}
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run: |
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conda activate climpred-minimum-tests
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pytest --cov=climpred --cov-report=xml
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- name: Upload coverage to codecov
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uses: codecov/codecov-action@v1
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with:
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file: ./coverage.xml
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fail_ci_if_error: true
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docs_notebooks: # Checks that pre-compiled notebooks in docs still work.
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- name: Install Conda environment
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uses: conda-incubator/setup-miniconda@v1
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with:
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auto-update-conda: true
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activate-environment: climpred-docs-notebooks
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environment-file: ci/requirements/docs_notebooks.yml
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python-version: 3.6
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- name: Conda info
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shell: bash -l {0}
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run: conda info
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- name: Conda list
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shell: bash -l {0}
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run: conda list
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- name: Test notebooks in docs
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shell: bash -l {0}
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run: |
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pushd docs
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nbstripout source/*.ipynb source/examples/decadal/*.ipynb source/examples/subseasonal/*.ipynb
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make html
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popd

‎.github/workflows/lint.yml

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name: Lint
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on: [push]
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jobs:
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lint: # Runs linting package checks for code styling.
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python
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uses: actions/setup-python@v2
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with:
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python-version: 3.6
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- name: Install linting dependencies
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run: |
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python -m pip install --upgrade pip
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pip install flake8 black==19.10b0 isort
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- name: Lint with flake8
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shell: bash -l {0}
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run: |
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flake8 climpred
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- name: Lint with black
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shell: bash -l {0}
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run: |
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black --check climpred
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- name: Lint with isort
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shell: bash -l {0}
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run: |
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isort --check-only climpred

‎.github/workflows/python-package.yml

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‎.travis.yml

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‎CHANGELOG.rst

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``matplotlib`` version. Update ``xskillscore`` requirement to 0.0.18 to
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cooperate with new ``xarray`` version. (:pr:`451`, :pr:`449`)
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`Riley X. Brady`_
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- Switch from Travis CI and Coveralls to Github Actions and CodeCov.
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(:pr:`471`) `Riley X. Brady`_
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‎README.rst

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:target: https://requires.io/github/pangeo-data/climpred/requirements/?branch=master
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:alt: Requirements Status
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.. |codecov| image:: https://coveralls.io/repos/github/pangeo-data/climpred/badge.svg?branch=master
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:target: https://coveralls.io/github/pangeo-data/climpred?branch=master
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.. |codecov| image:: https://codecov.io/gh/pangeo-data/climpred/branch/master/graph/badge.svg?token=e53kXaaOqS
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:target: https://codecov.io/gh/pangeo-data/climpred
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.. |conda| image:: https://img.shields.io/conda/vn/conda-forge/climpred.svg
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:target: https://anaconda.org/conda-forge/climpred
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Documentation is in development and can be found on readthedocs_.
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.. _readthedocs: https://climpred.readthedocs.io/en/latest/
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DELETE THIS

‎ci/requirements/environment-dev-3.6.yml ‎ci/requirements/climpred-dev.yml

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channels:
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- conda-forge
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dependencies:
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- python=3.6
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# Documentation
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- nbsphinx
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- nbstripout

‎ci/requirements/docs_notebooks.yml

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name: climpred-docs-notebooks
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channels:
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- conda-forge
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dependencies:
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- xesmf
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- esmpy
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- bottleneck
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- cartopy>=0.18.0
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- esmtools>=1.1.3
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- importlib_metadata
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- jupyterlab
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- matplotlib
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- nbsphinx
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- nbstripout
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- nc-time-axis
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- netcdf4
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- numpy
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- pandas
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- pygments==2.6.1
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- sphinx
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- sphinxcontrib-napoleon
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- sphinx_rtd_theme
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- toolz
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- tqdm
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- xarray>=0.16.1
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- pip
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- pip:
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# Install latest version of climpred.
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- -e ../..

‎ci/requirements/minimum-tests.yml

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name: climpred-minimum-tests
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channels:
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- conda-forge
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- defaults
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dependencies:
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- xesmf
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- esmpy
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- dask
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- netcdf4
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- ipython
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- nc-time-axis
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- coveralls
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- pytest
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- pytest-cov
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- pip
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- pip:
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- pytest-lazy-fixture
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- -e ../..

‎ci/run-linter.sh

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echo "Code Styling with (black, flake8, isort)"
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source activate climpred-dev
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echo "[flake8]"
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flake8 climpred --exclude=__init__.py
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‎climpred/comparisons.py

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"""
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Compare ensemble mean forecast to single member verification.
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If the initialized dataset is concatinated in a way that the first member
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is taken from the control simulation, this compares the member mean of all
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is taken from the control simulation, this compares the member mean of all
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other member forecasts to the control simulation.
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Args:

‎climpred/tests/test_perfectModelEnsemble_class.py

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pm = pm.add_control(PM_ds_control_1d)
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assert "does not match" in str(excinfo.value)
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def test_HindcastEnsemble_as_PerfectModelEnsemble(hindcast_recon_1d_mm):
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"""Test that initialized dataset for HindcastEnsemble can also be used for
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PerfectModelEnsemble."""
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.isnull()
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.any()
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)
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# try PerfectModelEnsemble predictability
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init = hindcast.get_initialized()
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print(init.lead)
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.isnull()
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.any()
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# generate_uninitialized
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pm = pm.generate_uninitialized()
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assert (
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pm.bootstrap(iterations=2, metric="acc", comparison="m2e", dim=["member", "init"])
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def test_verify_no_need_for_control(PM_da_initialized_1d, PM_da_control_1d):
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"""Tests that no error is thrown when no control present
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when calling verify(reference=['uninitialized'])."""

‎climpred/tests/test_versioning.py

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import pytest
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from climpred.versioning.print_versions import main, show_versions
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from climpred.versioning.print_versions import show_versions
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@pytest.mark.parametrize("as_json", [True, False])
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def test_show_versions(as_json):
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show_versions(as_json=as_json)
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def test_main():
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main()

‎climpred/versioning/print_versions.py

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("setuptools", lambda mod: mod.__version__),
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("pip", lambda mod: mod.__version__),
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("conda", lambda mod: mod.__version__),
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("pytest", lambda mod: mod.__version__),
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# Misc.
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("IPython", lambda mod: mod.__version__),
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("sphinx", lambda mod: mod.__version__),

‎docs/source/contributing.rst

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.. code:: bash
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$ conda env update -f ci/requirements/environment-dev-3.6.yml
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$ conda env update -f ci/requirements/climpred-dev.yml
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$ cd docs
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#. Install dependencies into a new conda environment::
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$ conda env update -f ci/requirements/environment-dev-3.6.yml
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$ conda env update -f ci/requirements/climpred-dev.yml
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$ conda activate climpred-dev
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#. Make an editable install of climpred by running::

‎docs/source/index.rst

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:target: https://requires.io/github/pangeo-data/climpred/requirements/?branch=master
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:alt: Requirements Status
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.. |codecov| image:: https://coveralls.io/repos/github/pangeo-data/climpred/badge.svg?branch=master
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:target: https://coveralls.io/github/pangeo-data/climpred?branch=master
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.. |codecov| image:: https://codecov.io/gh/pangeo-data/climpred/branch/master/graph/badge.svg?token=e53kXaaOqS
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:target: https://codecov.io/gh/pangeo-data/climpred
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.. |conda| image:: https://img.shields.io/conda/vn/conda-forge/climpred.svg
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:target: https://anaconda.org/conda-forge/climpred

‎requirements.txt

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cftime>=1.1.2
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eofs
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esmtools>=1.1.3
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ipython
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matplotlib
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numpy
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pandas
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scipy
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toolz
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tqdm
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xarray>=0.16.1
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xrft==0.2.0

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