Build + Support Py39 and Various CI Updates

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,10 +1,11 @@
 [Description of PR]
 
 TODO:
-* [ ] Unit tests and/or doctests in docstrings
-* [ ] ``tox -e py38`` passes locally
-* [ ] Docstrings and API docs for any new/modified user-facing classes and functions
-* [ ] Changes documented in docs/release.rst
-* [ ] ``tox -e docs`` passes locally
-* [ ] AppVeyor and Travis CI passes
-* [ ] Test coverage to 100% (Coveralls passes)
+
+- [ ] Unit tests and/or doctests in docstrings
+- [ ] `tox -e py39` passes locally
+- [ ] Docstrings and API docs for any new/modified user-facing classes and functions
+- [ ] Changes documented in docs/release.rst
+- [ ] `tox -e docs` passes locally
+- [ ] GitHub Actions CI passes
+- [ ] Test coverage to 100% (Coveralls passes)

.github/workflows/ci-linux.yaml

@@ -0,0 +1,43 @@
+name: Linux CI
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.6", "3.7", "3.8", "3.9"]
+        os: [ubuntu-18.04, ubuntu-20.04]
+
+    steps:
+      - name: Checkout source
+        uses: actions/checkout@v2
+        with:
+          submodules: recursive
+
+      - name: Set up Python
+        uses: actions/setup-python@v1
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install numcodecs
+        run: |
+          python -m pip install -U pip -r requirements_test.txt -r requirements.txt
+          python -m pip install -v -e .
+
+      - name: List installed packages
+        run: python -m pip list
+
+      - name: Run tests
+        run: pytest -v --cov=numcodecs --doctest-modules --doctest-glob=*.pyx numcodecs
+
+      - name: Flake8
+        run: flake8 numcodecs
+
+      - name: Build Docs
+        run: |
+          pip install -r requirements_rtfd.txt
+          cd docs
+          sphinx-build -W -b html -d {envtmpdir}/doctrees . {envtmpdir}/html

.github/workflows/ci-osx.yaml

@@ -8,7 +8,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.6", "3.7", "3.8"]
+        python-version: ["3.6", "3.7", "3.8", "3.9"]
 
     steps:
       - name: Checkout source
@@ -23,13 +23,16 @@ jobs:
             python-version: ${{ matrix.python-version }}
         env:
             ACTIONS_ALLOW_UNSECURE_COMMANDS: true
-      - name: Install numcodecs
+
+      - name: Set up env
         shell: "bash -l {0}"
         run: |
-          conda create -n env python==${{matrix.python-version}} wheel cython numpy msgpack-python pytest wheel pip compilers
+          conda create -n env python==${{matrix.python-version}} wheel pip compilers
           conda activate env
           which pip
+          pip install -r requirements_test.txt -r requirements.txt
           conda env export
+
       - name: Install numcodecs
         shell: "bash -l {0}"
         run: |

.github/workflows/ci-windows.yaml

@@ -0,0 +1,47 @@
+name: Windows CI
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: windows-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.6", "3.7", "3.8", "3.9"]
+
+    steps:
+      - name: Checkout source
+        uses: actions/checkout@v2
+        with:
+          submodules: recursive
+
+      - name: Set up Python
+        uses: conda-incubator/setup-miniconda@master
+        with:
+            channels: conda-forge
+            python-version: ${{ matrix.python-version }}
+        env:
+            ACTIONS_ALLOW_UNSECURE_COMMANDS: true
+
+      - name: Set up env
+        shell: "bash -l {0}"
+        run: |
+          conda create -n env python==${{matrix.python-version}} wheel pip compilers
+          conda activate env
+          which pip
+          pip install -r requirements_test.txt -r requirements.txt
+          conda env export
+
+      - name: Install numcodecs
+        shell: "bash -l {0}"
+        run: |
+          conda activate env
+          export CC=clang
+          python setup.py build
+
+      - name: Run tests
+        shell: "bash -l {0}"
+        run: |
+          conda activate env
+          pytest -v --pyargs numcodecs

.github/workflows/wheel.yaml

@@ -9,7 +9,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-18.04, windows-latest, macos-latest]
+        os: [ubuntu-latest, windows-latest, macos-latest]
     env:
       CIBW_TEST_COMMAND: pytest --pyargs numcodecs
       CIBW_TEST_REQUIRES: pytest
@@ -25,11 +25,11 @@ jobs:
       - uses: actions/setup-python@v1
         name: Install Python
         with:
-          python-version: '3.7'
+          python-version: '3.9'
 
       - name: Install cibuildwheel
         run: |
-          python -m pip install cibuildwheel==1.3.0 wheel
+          python -m pip install cibuildwheel==1.8.0 wheel
 
       - name: Build wheel
         run: |
@@ -50,7 +50,7 @@ jobs:
       - uses: actions/setup-python@v2
         name: Install Python
         with:
-          python-version: '3.7'
+          python-version: '3.9'
 
       - name: Build sdist
         run: python setup.py sdist

README.rst

@@ -7,11 +7,14 @@ codecs for use in data storage and communication applications.
 .. image:: https://readthedocs.org/projects/numcodecs/badge/?version=latest
     :target: http://numcodecs.readthedocs.io/en/latest/?badge=latest
 
-.. image:: https://travis-ci.org/zarr-developers/numcodecs.svg?branch=master
-    :target: https://travis-ci.org/zarr-developers/numcodecs
+.. image:: https://github.com/zarr-developers/numcodecs/workflows/Linux%20CI/badge.svg?branch=master
+    :target: https://github.com/zarr-developers/numcodecs/actions?query=workflow%3A%22Linux+CI%22
 
-.. image:: https://ci.appveyor.com/api/projects/status/jhaaaxotvel24n9g?svg=true
-    :target: https://ci.appveyor.com/project/zarr-developers/numcodecs
+.. image:: https://github.com/zarr-developers/numcodecs/workflows/OSX%20CI/badge.svg?branch=master
+    :target: https://github.com/zarr-developers/numcodecs/actions?query=workflow%3A%22OSX+CI%22
+
+.. image:: https://github.com/zarr-developers/numcodecs/workflows/Wheels/badge.svg?branch=master
+    :target: https://github.com/zarr-developers/numcodecs/actions?query=workflow%3AWheels
 
 .. image:: https://coveralls.io/repos/github/zarr-developers/numcodecs/badge.svg?branch=master
     :target: https://coveralls.io/github/zarr-developers/numcodecs?branch=master

docs/contributing.rst

@@ -90,7 +90,7 @@ you have cloned the NumCodecs source code and your current working directory is
 the repository, you can do something like the following::
 
     $ mkdir -p ~/pyenv/numcodecs-dev
-    $ virtualenv --no-site-packages --python=/usr/bin/python3.8 ~/pyenv/numcodecs-dev
+    $ virtualenv --no-site-packages --python=/usr/bin/python3.9 ~/pyenv/numcodecs-dev
     $ source ~/pyenv/numcodecs-dev/bin/activate
     $ pip install -r requirements_dev.txt
     $ python setup.py build_ext --inplace
@@ -145,11 +145,11 @@ To also run the doctests within docstrings, run::
 Tests can be run under different Python versions using tox. E.g. (assuming you have the
 corresponding Python interpreters installed on your system)::
 
-    $ tox -e py35,py36,py37,py38
+    $ tox -e py36,py37,py38,py39
 
-NumCodecs currently supports Python 3.5-3.8, so the above command must
-succeed before code can be accepted into the main code base. Note that only the py38
-tox environment runs the doctests, i.e., doctests only need to succeed under Python 3.8.
+NumCodecs currently supports Python 6-3.9, so the above command must
+succeed before code can be accepted into the main code base. Note that only the py39
+tox environment runs the doctests, i.e., doctests only need to succeed under Python 3.9.
 
 All tests are automatically run via Travis (Linux) and AppVeyor (Windows) continuous
 integration services for every pull request. Tests must pass under both services before
@@ -164,14 +164,14 @@ Conformance can be checked by running::
 
     $ flake8 --max-line-length=100 numcodecs
 
-This is automatically run when invoking ``tox -e py38``.
+This is automatically run when invoking ``tox -e py39``.
 
 Test coverage
 ~~~~~~~~~~~~~
 
 NumCodecs maintains 100% test coverage under the latest Python stable release (currently
-Python 3.8). Both unit tests and docstring doctests are included when computing
-coverage. Running ``tox -e py38`` will automatically run the test suite with coverage
+Python 3.9). Both unit tests and docstring doctests are included when computing
+coverage. Running ``tox -e py39`` will automatically run the test suite with coverage
 and produce a coverage report. This should be 100% before code can be accepted into the
 main code base.
 
@@ -185,7 +185,7 @@ Documentation
 Docstrings for user-facing classes and functions should follow the `numpydoc
 <https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt>`_ standard,
 including sections for Parameters and Examples. All examples will be run as doctests
-under Python 3.8.
+under Python 3.9.
 
 NumCodecs uses Sphinx for documentation, hosted on readthedocs.org. Documentation is
 written in the RestructuredText markup language (.rst files) in the ``docs`` folder.

numcodecs/tests/test_pickles.py

@@ -43,7 +43,16 @@ def test_repr():
     check_repr("Pickle(protocol=-1)")
 
 
-@pytest.mark.skipif(sys.byteorder != 'little',
-                    reason='Pickle does not restore byte orders')
+# Details on xfail
+# https://stackoverflow.com/questions/58194852/modulenotfounderror-no-module-named-numpy-core-multiarray-r
+@pytest.mark.skipif(
+    sys.byteorder != "little", reason="Pickle does not restore byte orders"
+)
+@pytest.mark.xfail(
+    sys.platform == "win32", reason=(
+        "Pickle fails to read w/ Windows carriage return "
+        "( https://github.com/zarr-developers/numcodecs/issues/271 )"
+    )
+)
 def test_backwards_compatibility():
     check_backwards_compatibility(Pickle.codec_id, arrays, codecs)

requirements_dev.txt

@@ -1,3 +1,3 @@
-Cython==0.29.6
-msgpack==0.6.1
-numpy==1.16.2
+Cython==0.29.21
+msgpack==1.0.2
+numpy==1.19.0

setup.py

@@ -322,18 +322,19 @@ def run_setup(with_extensions):
         python_requires=">=3.6, <4",
         packages=["numcodecs", "numcodecs.tests"],
         classifiers=[
-            'Development Status :: 4 - Beta',
-            'Intended Audience :: Developers',
-            'Intended Audience :: Information Technology',
-            'Intended Audience :: Science/Research',
-            'License :: OSI Approved :: MIT License',
-            'Programming Language :: Python',
-            'Topic :: Software Development :: Libraries :: Python Modules',
-            'Operating System :: Unix',
-            'Programming Language :: Python :: 3',
-            'Programming Language :: Python :: 3.6',
-            'Programming Language :: Python :: 3.7',
-            'Programming Language :: Python :: 3.8',
+            "Development Status :: 4 - Beta",
+            "Intended Audience :: Developers",
+            "Intended Audience :: Information Technology",
+            "Intended Audience :: Science/Research",
+            "License :: OSI Approved :: MIT License",
+            "Programming Language :: Python",
+            "Topic :: Software Development :: Libraries :: Python Modules",
+            "Operating System :: Unix",
+            "Programming Language :: Python :: 3",
+            "Programming Language :: Python :: 3.6",
+            "Programming Language :: Python :: 3.7",
+            "Programming Language :: Python :: 3.8",
+            "Programming Language :: Python :: 3.9",
         ],
         author='Alistair Miles',
         author_email='[email protected]',