Merge zarr-developers/master into jakirkham/ensure_text_use_bytes

.github/PULL_REQUEST_TEMPLATE.md

@@ -3,7 +3,6 @@
 TODO:
 * [ ] Unit tests and/or doctests in docstrings
 * [ ] ``tox -e py38`` passes locally
-* [ ] ``tox -e py27`` 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/workflows/ci-osx.yaml

@@ -0,0 +1,33 @@
+name: OSX CI
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: macos-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.5", "3.6", "3.7", "3.8"]
+
+    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 setuptools wheel pytest
+          python -m pip install -v -e .
+
+      - name: List installed packages
+        run: python -m pip list
+
+      - name: Run tests
+        run: pytest -v --pyargs numcodecs

.github/workflows/wheel.yaml

@@ -0,0 +1,101 @@
+name: Wheels
+
+on: [push, pull_request]
+
+jobs:
+  build_wheels:
+    name: Build wheel on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-18.04, windows-latest, macos-latest]
+    env:
+      CIBW_TEST_COMMAND: pytest --pyargs numcodecs
+      CIBW_TEST_REQUIRES: pytest
+      CIBW_SKIP: "*27* pp*"
+      CIBW_ENVIRONMENT: "DISABLE_NUMCODECS_AVX2=1"
+      CIBW_ENVIRONMENT_MACOS: "MACOSX_DEPLOYMENT_TARGET=10.9 DISABLE_NUMCODECS_AVX2=1"
+
+    steps:
+      - uses: actions/checkout@v1
+        with:
+          submodules: true
+
+      - uses: actions/setup-python@v1
+        name: Install Python
+        with:
+          python-version: '3.7'
+
+      - name: Install cibuildwheel
+        run: |
+          python -m pip install cibuildwheel==1.3.0
+
+      - name: Build wheel
+        run: |
+          python -m cibuildwheel --output-dir wheelhouse
+      - uses: actions/upload-artifact@v1
+        with:
+          name: wheels
+          path: ./wheelhouse
+
+  build_sdist:
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v1
+        with:
+          submodules: true
+
+      - uses: actions/setup-python@v2
+        name: Install Python
+        with:
+          python-version: '3.7'
+
+      - name: Build sdist
+        run: python setup.py sdist
+
+      - name: test install
+        run: pip install dist/numcodecs*.tar.gz
+
+      - uses: actions/upload-artifact@v2
+        with:
+          path: dist/*.tar.gz
+
+  test_dist_pypi:
+    needs: [build_wheels, build_sdist]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/download-artifact@v1
+        with:
+          name: artifact
+          path: dist
+      - uses: actions/download-artifact@v1
+        with:
+          name: wheels
+          path: dist
+
+      - name: test
+        run: |
+          ls
+          ls dist
+
+  upload_pypi:
+    needs: [build_wheels, build_sdist]
+    runs-on: ubuntu-latest
+    if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v')
+    steps:
+      - uses: actions/download-artifact@v1
+        with:
+          name: artifact
+          path: dist
+      - uses: actions/download-artifact@v1
+        with:
+          name: wheels
+          path: dist
+
+      - uses: pypa/gh-action-pypi-publish@master
+        with:
+          user: __token__
+          password: ${{ secrets.pypi_password }}
+          # To test: repository_url: https://test.pypi.org/legacy/

.travis.yml

@@ -12,9 +12,6 @@ addons:
 
 matrix:
   include:
-    - os: linux
-      language: python
-      python: 2.7
     - os: linux
       language: python
       python: 3.5
@@ -30,17 +27,14 @@ matrix:
       python: 3.8
       dist: xenial
       sudo: true
-    - os: osx
-      language: generic
 
 install:
   - pip install -U tox-travis coveralls pip setuptools wheel pytest
   - pip install -v -e .
 
 script:
-  - if [ "$TRAVIS_OS_NAME" = "linux" ]; then tox; fi
-  - if [ "$TRAVIS_OS_NAME" = "osx" ]; then pytest -v --pyargs numcodecs; fi
+  - tox
 
 after_success:
-  - if [ "$TRAVIS_OS_NAME" = "linux" ]; then coveralls --service=travis-pro; fi
+  - coveralls --service=travis-pro
 

appveyor.yml

@@ -12,10 +12,6 @@ environment:
 
   matrix:
 
-    - PYTHON: "C:\\Python27-x64"
-      PYTHON_VERSION: "2.7"
-      DISTUTILS_USE_SDK: "1"
-
     - PYTHON: "C:\\Python35-x64"
       PYTHON_VERSION: "3.5"
 

docs/blosc.rst

@@ -13,6 +13,7 @@ Blosc
     .. automethod:: decode
     .. automethod:: get_config
     .. automethod:: from_config
+    .. automethod:: decode_partial
 
 Helper functions
 ----------------
@@ -28,3 +29,4 @@ Helper functions
 .. autofunction:: cbuffer_metainfo
 .. autofunction:: compress
 .. autofunction:: decompress
+.. autofunction:: decompress_partial

docs/conf.py

@@ -16,16 +16,7 @@
 
 import sys
 import os
-
-
-PY2 = sys.version_info[0] == 2
-
-
-if PY2:  # pragma: py3 no cover
-    from mock import Mock as MagicMock
-else:    # pragma: py2 no cover
-    from unittest.mock import Mock as MagicMock
-
+from unittest.mock import Mock as MagicMock
 
 class Mock(MagicMock):
     @classmethod
@@ -34,10 +25,6 @@ def __getattr__(cls, name):
 
 
 MOCK_MODULES = ['msgpack']
-if PY2:
-    MOCK_MODULES.append('lzma')
-
-
 sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES)
 
 

docs/contributing.rst

@@ -145,9 +145,9 @@ 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 py27,py35,py36,py37,py38
+    $ tox -e py35,py36,py37,py38
 
-NumCodecs currently supports Python 2.7 and Python 3.5-3.8, so the above command must
+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.
 
@@ -305,10 +305,8 @@ Tag the version (where "X.X.X" stands for the version number, e.g., "2.2.0")::
     $ git tag -a v$version -m v$version
     $ git push --tags
 
-Release source code to PyPI::
-
-    $ python setup.py register sdist
-    $ twine upload dist/numcodecs-${version}.tar.gz
+This will trigger a GitHub Action which will build the source
+distribution as well as wheels for all major platforms.
 
 Obtain checksum for release to conda-forge::
 

docs/index.rst

@@ -24,7 +24,9 @@ Alternatively, install via conda::
     $ conda install -c conda-forge numcodecs
 
 Numcodecs includes a C extension providing integration with the Blosc_
-library. Installing via conda will install a pre-compiled binary distribution.
+library. Wheels are available for most platforms.
+
+Installing a wheel or via conda will install a pre-compiled binary distribution.
 However, if you have a newer CPU that supports the AVX2 instruction set (e.g.,
 Intel Haswell, Broadwell or Skylake) then installing via pip is preferable,
 because this will compile the Blosc library from source with optimisations
@@ -36,7 +38,7 @@ To disable compilation with AVX2 support regardless of the machine
 architecture::
 
     $ export DISABLE_NUMCODECS_AVX2=
-    $ pip install -v --no-cache-dir numcodecs
+    $ pip install -v --no-cache-dir --no-binary numcodecs numcodecs
 
 To work with Numcodecs source code in development, install from GitHub::
 
@@ -91,6 +93,9 @@ documentation, code reviews, comments and/or ideas:
 * :user:`John Kirkham <jakirkham>`
 * :user:`Alistair Miles <alimanfoo>`
 * :user:`Jeff Reback <jreback>`
+* :user:`Trevor Manz <manzt>`
+* :user:`Grzegorz Bokota <Czaki>`
+* :user:`Josh Moore <joshmoore>`
 
 Numcodecs bundles the `c-blosc <https://github.com/Blosc/c-blosc>`_ library.
 

docs/release.rst

@@ -1,6 +1,54 @@
 Release notes
 =============
 
+.. _release_0.7.2:
+
+0.7.2
+-----
+
+* Disable avx2 for wheel.
+  By :user:`Grzegorz Bokota <Czaki>`, :issue:`253`.
+
+* Add Base64 fixtures.
+  By :user:`John Kirkham <jakirkham>`, :issue:`251`.
+
+* Update docs regarding wheels.
+  By :user:`Josh Moore <joshmoore>`, :issue:`250`.
+
+.. _release_0.7.1:
+
+0.7.1
+-----
+
+* Fix build of wheels.
+  By :user:`Grzegorz Bokota <Czaki>`, :issue:`244`.
+
+.. _release_0.7.0:
+
+0.7.0
+-----
+
+* Automatically release to PyPI.
+  By :user:`Josh Moore <joshmoore>`, :issue:`241`.
+
+* Build wheels on github actions.
+  By :user:`Grzegorz Bokota <Czaki>`, :issue:`224`.
+
+* Add Base64 codec.
+  By :user:`Trevor Manz <manzt>`, :issue:`176`.
+
+* Add partial decompression of Blosc compressed arrays.
+  By :user:`Andrew Fulton <andrewfulton9>`, :issue:`235`.
+
+* Remove LegacyJSON codec.
+  By :user:`James Bourbeau  <jrbourbeau>`, :issue:`226`.
+
+* Remove LegacyMsgPack codec.
+  By :user:`James Bourbeau  <jrbourbeau>`, :issue:`218`.
+
+* Drop support for Python 2.
+  By :user:`James Bourbeau <jrbourbeau>`, :issue:`220`.
+
 
 .. _release_0.6.4:
 

fixture/base64/codec.00/config.json

@@ -0,0 +1,3 @@
+{
+    "id": "base64"
+}

fixture/base64/codec.00/encoded.00.dat

@@ -0,0 +1 @@
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