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Jackson Maxfield Brownjakirkham
Jackson Maxfield Brown
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jakirkham
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Build + Support Py39 and Various CI Updates (#270)
* Support Py39 in tests * Remove old CI configs * Add or upgrade CI for GH-Actions * Update doc references to py39 * Remove references to py35 * Fix build docs check on linux ci * Test new README badge targets * Point badges at zarr-developers org * Update GitHub PR Template * More specificity in ci linux on os versions * Upgrade wheel CI to use py39 * Upgrade tox docs test to use py39 * Update cibuildwheel to support py39 * Add back pypi package classifiers * Swap wheel builds for ubuntu 18 + 20 for latest * Linux CI install deps instead of dev deps * Rename OSX steps + change env setup * Add Windows CI * Add newline character to ci-linux * Mark pickle backwards compat xfail on windows * Add link to GH Issue for windows xfail test Co-authored-by: jakirkham <[email protected]> Co-authored-by: jakirkham <[email protected]>
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‎.github/PULL_REQUEST_TEMPLATE.md‎

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[Description of PR]
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TODO:
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* [ ] Unit tests and/or doctests in docstrings
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* [ ] ``tox -e py38`` passes locally
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* [ ] Docstrings and API docs for any new/modified user-facing classes and functions
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* [ ] Changes documented in docs/release.rst
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* [ ] ``tox -e docs`` passes locally
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* [ ] AppVeyor and Travis CI passes
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* [ ] Test coverage to 100% (Coveralls passes)
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- [ ] Unit tests and/or doctests in docstrings
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- [ ] `tox -e py39` passes locally
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- [ ] Docstrings and API docs for any new/modified user-facing classes and functions
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- [ ] Changes documented in docs/release.rst
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- [ ] `tox -e docs` passes locally
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- [ ] GitHub Actions CI passes
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- [ ] Test coverage to 100% (Coveralls passes)

‎.github/workflows/ci-linux.yaml‎

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name: Linux CI
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on: [push, pull_request]
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jobs:
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build:
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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python-version: ["3.6", "3.7", "3.8", "3.9"]
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os: [ubuntu-18.04, ubuntu-20.04]
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steps:
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- name: Checkout source
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uses: actions/checkout@v2
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with:
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submodules: recursive
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- name: Set up Python
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uses: actions/setup-python@v1
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install numcodecs
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run: |
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python -m pip install -U pip -r requirements_test.txt -r requirements.txt
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python -m pip install -v -e .
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- name: List installed packages
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run: python -m pip list
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- name: Run tests
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run: pytest -v --cov=numcodecs --doctest-modules --doctest-glob=*.pyx numcodecs
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- name: Flake8
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run: flake8 numcodecs
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- name: Build Docs
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run: |
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pip install -r requirements_rtfd.txt
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cd docs
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sphinx-build -W -b html -d {envtmpdir}/doctrees . {envtmpdir}/html

‎.github/workflows/ci-osx.yaml‎

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strategy:
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fail-fast: false
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matrix:
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python-version: ["3.6", "3.7", "3.8"]
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python-version: ["3.6", "3.7", "3.8", "3.9"]
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steps:
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- name: Checkout source
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python-version: ${{ matrix.python-version }}
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env:
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ACTIONS_ALLOW_UNSECURE_COMMANDS: true
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- name: Install numcodecs
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- name: Set up env
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shell: "bash -l {0}"
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run: |
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conda create -n env python==${{matrix.python-version}} wheel cython numpy msgpack-python pytest wheel pip compilers
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conda create -n env python==${{matrix.python-version}} wheel pip compilers
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conda activate env
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which pip
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pip install -r requirements_test.txt -r requirements.txt
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conda env export
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- name: Install numcodecs
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shell: "bash -l {0}"
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run: |

‎.github/workflows/ci-windows.yaml‎

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name: Windows CI
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on: [push, pull_request]
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jobs:
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build:
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runs-on: windows-latest
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strategy:
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fail-fast: false
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matrix:
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python-version: ["3.6", "3.7", "3.8", "3.9"]
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steps:
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- name: Checkout source
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uses: actions/checkout@v2
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with:
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submodules: recursive
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- name: Set up Python
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uses: conda-incubator/setup-miniconda@master
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with:
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channels: conda-forge
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python-version: ${{ matrix.python-version }}
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env:
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ACTIONS_ALLOW_UNSECURE_COMMANDS: true
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- name: Set up env
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shell: "bash -l {0}"
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run: |
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conda create -n env python==${{matrix.python-version}} wheel pip compilers
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conda activate env
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which pip
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pip install -r requirements_test.txt -r requirements.txt
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conda env export
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- name: Install numcodecs
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shell: "bash -l {0}"
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run: |
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conda activate env
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export CC=clang
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python setup.py build
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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 env
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pytest -v --pyargs numcodecs

‎.github/workflows/wheel.yaml‎

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matrix:
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os: [ubuntu-18.04, windows-latest, macos-latest]
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os: [ubuntu-latest, windows-latest, macos-latest]
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env:
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CIBW_TEST_COMMAND: pytest --pyargs numcodecs
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CIBW_TEST_REQUIRES: pytest
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- uses: actions/setup-python@v1
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name: Install Python
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with:
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python-version: '3.7'
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python-version: '3.9'
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- name: Install cibuildwheel
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run: |
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python -m pip install cibuildwheel==1.3.0 wheel
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python -m pip install cibuildwheel==1.8.0 wheel
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- name: Build wheel
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- uses: actions/setup-python@v2
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name: Install Python
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with:
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python-version: '3.7'
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python-version: '3.9'
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- name: Build sdist
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run: python setup.py sdist

‎.travis.yml‎

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‎README.rst‎

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.. image:: https://readthedocs.org/projects/numcodecs/badge/?version=latest
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:target: http://numcodecs.readthedocs.io/en/latest/?badge=latest
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.. image:: https://travis-ci.org/zarr-developers/numcodecs.svg?branch=master
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:target: https://travis-ci.org/zarr-developers/numcodecs
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.. image:: https://github.com/zarr-developers/numcodecs/workflows/Linux%20CI/badge.svg?branch=master
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:target: https://github.com/zarr-developers/numcodecs/actions?query=workflow%3A%22Linux+CI%22
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.. image:: https://ci.appveyor.com/api/projects/status/jhaaaxotvel24n9g?svg=true
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:target: https://ci.appveyor.com/project/zarr-developers/numcodecs
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.. image:: https://github.com/zarr-developers/numcodecs/workflows/OSX%20CI/badge.svg?branch=master
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:target: https://github.com/zarr-developers/numcodecs/actions?query=workflow%3A%22OSX+CI%22
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.. image:: https://github.com/zarr-developers/numcodecs/workflows/Wheels/badge.svg?branch=master
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:target: https://github.com/zarr-developers/numcodecs/actions?query=workflow%3AWheels
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.. image:: https://coveralls.io/repos/github/zarr-developers/numcodecs/badge.svg?branch=master
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:target: https://coveralls.io/github/zarr-developers/numcodecs?branch=master

‎appveyor.yml‎

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‎docs/contributing.rst‎

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the repository, you can do something like the following::
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$ mkdir -p ~/pyenv/numcodecs-dev
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$ virtualenv --no-site-packages --python=/usr/bin/python3.8 ~/pyenv/numcodecs-dev
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$ virtualenv --no-site-packages --python=/usr/bin/python3.9 ~/pyenv/numcodecs-dev
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$ source ~/pyenv/numcodecs-dev/bin/activate
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$ pip install -r requirements_dev.txt
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$ python setup.py build_ext --inplace
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Tests can be run under different Python versions using tox. E.g. (assuming you have the
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$ tox -e py35,py36,py37,py38
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$ tox -e py36,py37,py38,py39
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NumCodecs currently supports Python 3.5-3.8, so the above command must
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succeed before code can be accepted into the main code base. Note that only the py38
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tox environment runs the doctests, i.e., doctests only need to succeed under Python 3.8.
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NumCodecs currently supports Python 6-3.9, so the above command must
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succeed before code can be accepted into the main code base. Note that only the py39
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tox environment runs the doctests, i.e., doctests only need to succeed under Python 3.9.
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All tests are automatically run via Travis (Linux) and AppVeyor (Windows) continuous
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integration services for every pull request. Tests must pass under both services before
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This is automatically run when invoking ``tox -e py38``.
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This is automatically run when invoking ``tox -e py39``.
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Test coverage
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NumCodecs maintains 100% test coverage under the latest Python stable release (currently
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Python 3.8). Both unit tests and docstring doctests are included when computing
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coverage. Running ``tox -e py38`` will automatically run the test suite with coverage
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Python 3.9). Both unit tests and docstring doctests are included when computing
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coverage. Running ``tox -e py39`` will automatically run the test suite with coverage
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and produce a coverage report. This should be 100% before code can be accepted into the
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main code base.
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Docstrings for user-facing classes and functions should follow the `numpydoc
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<https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt>`_ standard,
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including sections for Parameters and Examples. All examples will be run as doctests
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under Python 3.8.
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under Python 3.9.
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NumCodecs uses Sphinx for documentation, hosted on readthedocs.org. Documentation is
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‎numcodecs/tests/test_pickles.py‎

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@pytest.mark.skipif(sys.byteorder != 'little',
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# Details on xfail
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# https://stackoverflow.com/questions/58194852/modulenotfounderror-no-module-named-numpy-core-multiarray-r
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@pytest.mark.skipif(
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sys.byteorder != "little", reason="Pickle does not restore byte orders"
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)
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@pytest.mark.xfail(
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sys.platform == "win32", reason=(
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"Pickle fails to read w/ Windows carriage return "
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"( https://github.com/zarr-developers/numcodecs/issues/271 )"
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)
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)
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def test_backwards_compatibility():
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check_backwards_compatibility(Pickle.codec_id, arrays, codecs)

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