numcodecs 0.13.0__tar.gz → 0.14.0__tar.gz

numcodecs-0.14.0/.github/workflows/ci.yaml

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+name: Tests
+
+on: [push, pull_request]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build:
+    runs-on: ${{ matrix.platform }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.11", "3.12", "3.13"]
+        # macos-13 is an intel runner, macos-14 is a arm64 runner
+        platform: [ubuntu-latest, windows-latest, macos-13, macos-14]
+
+    steps:
+      - name: Checkout source
+        uses: actions/checkout@v4
+        with:
+          submodules: recursive
+
+      - name: Set up Conda
+        uses: conda-incubator/setup-miniconda@v3.1.0
+        with:
+            channels: conda-forge
+            miniforge-version: latest
+            python-version: ${{ matrix.python-version }}
+
+      - name: Show info about `base` environment
+        shell: "bash -l {0}"
+        run: |
+          conda info
+          conda config --show-sources
+          conda list --show-channel-urls
+
+      - name: Set up `env`
+        shell: "bash -l {0}"
+        run: >
+          conda create -n env
+          c-compiler cxx-compiler
+          python=${{matrix.python-version}} wheel pip
+
+      - name: Install clang
+        shell: "bash -l {0}"
+        if: matrix.platform == 'macos-13'
+        run: |
+          conda activate env
+          conda install -y 'clang>=12.0.1,<17'
+
+      - name: Show info about `env` environment
+        shell: "bash -l {0}"
+        run: |
+          conda list --show-channel-urls -n env
+
+      - name: Install numcodecs
+        shell: "bash -l {0}"
+        run: |
+          conda activate env
+          export DISABLE_NUMCODECS_AVX2=""
+          # TODO: put back zfpy import when it supports numpy 2.0
+          python -m pip install -v -e .[test,test_extras,msgpack,crc32c]
+
+      - name: Install pcodec
+        if: matrix.python-version != '3.13'
+        shell: "bash -l {0}"
+        run: |
+            conda activate env
+            python -m pip install -v ".[pcodec]"
+
+      - name: Install zarr-python
+        shell: "bash -l {0}"
+        # Since zarr v3 requires numpy >= 1.25, on Python 3.11 leave it out
+        # so we can have some tests of our minimum version of numpy (1.24)
+        if: matrix.python-version != '3.11'
+        run: |
+          conda activate env
+          # TODO: remove --pre option when zarr v3 is out
+          python -m pip install --pre zarr
+
+      # This is used to test with zfpy, which does not yet support numpy 2.0
+      - name: Install older numpy and zfpy
+        if: matrix.python-version == '3.11'
+        shell: "bash -l {0}"
+        run: |
+          conda activate env
+          python -m pip install -v ".[zfpy]"
+
+      - name: List installed packages
+        shell: "bash -l {0}"
+        run: |
+          conda activate env
+          python -m pip list
+
+      - name: Run tests
+        shell: "bash -l {0}"
+        run: |
+          conda activate env
+          pytest -v
+
+      - uses: codecov/codecov-action@v4
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          verbose: true

numcodecs-0.14.0/.github/workflows/wheel.yaml

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+name: Wheels
+
+on: [push, pull_request]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build_wheels:
+    name: Build wheel on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        # macos-13 is an intel runner, macos-14 is a arm64 runner
+        os: [ubuntu-latest, windows-latest, macos-13, macos-14]
+    env:
+      CIBW_TEST_COMMAND: python -c "import numcodecs"
+      CIBW_BUILD: "cp311-* cp312-* cp313-*"
+      CIBW_SKIP: "pp* *-musllinux_* *win32 *_i686 *_s390x"
+      # note: CIBW_ENVIRONMENT is now set in pyproject.toml
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: true
+
+      - uses: pypa/cibuildwheel@v2.21.3
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: wheels-${{ matrix.os }}
+          path: ./wheelhouse
+
+  build_sdist:
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: true
+
+      - uses: actions/setup-python@v5
+        name: Install Python
+        with:
+          python-version: "3.11"
+
+      - name: Build sdist
+        run: pipx run build --sdist
+
+      - name: test install
+        run: pip install dist/numcodecs*.tar.gz
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: sdist
+          path: dist/*.tar.gz
+
+  test_dist_pypi:
+    needs: [build_wheels, build_sdist]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: sdist
+          path: dist
+      - uses: actions/download-artifact@v4
+        with:
+          pattern: wheels-*
+          path: dist
+          merge-multiple: true
+
+      - 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@v4
+        with:
+          name: sdist
+          path: dist
+      - uses: actions/download-artifact@v4
+        with:
+          pattern: wheels-*
+          path: dist
+          merge-multiple: true
+
+      - uses: pypa/gh-action-pypi-publish@master
+        with:
+          user: __token__
+          password: ${{ secrets.pypi_password }}
+          # To test: repository_url: https://test.pypi.org/legacy/

numcodecs-0.14.0/.pre-commit-config.yaml

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+exclude: ^fixture/  # files with trailing whitespaces on purpose
+ci:
+  autoupdate_commit_msg: "chore: update pre-commit hooks"
+  autofix_commit_msg: "style: pre-commit fixes"
+  autofix_prs: false
+default_stages: [pre-commit, pre-push]
+default_language_version:
+  python: python3
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+    - id: trailing-whitespace
+    - id: check-yaml
+    - id: debug-statements
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.7.3
+    hooks:
+    - id: ruff
+      args: ["--fix", "--show-fixes"]
+    - id: ruff-format
+
+  - repo: https://github.com/scientific-python/cookie
+    rev: 2024.08.19
+    hooks:
+    - id: sp-repo-review
+
+  -   repo: https://github.com/pre-commit/mirrors-mypy
+      rev: 'v1.4.0'
+      hooks:
+      -   id: mypy
+          args: [--config-file, pyproject.toml]
+          additional_dependencies: [numpy, pytest, zfpy, 'zarr==3.0.0b1']

numcodecs-0.14.0/.pyup.yml

@@ -0,0 +1,4 @@
+# autogenerated pyup.io config file
+# see https://pyup.io/docs/configuration/ for all available options
+
+schedule: every month

numcodecs-0.14.0/.readthedocs.yaml

@@ -0,0 +1,25 @@
+version: 2
+
+submodules:
+  include: all
+
+build:
+  os: ubuntu-20.04
+  tools:
+    python: "3.12"
+  jobs:
+    post_install:
+      - python -m pip install --pre 'zarr'
+
+sphinx:
+  configuration: docs/conf.py
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs
+        - msgpack
+        - zfpy
+        - crc32c

numcodecs-0.14.0/PKG-INFO

@@ -0,0 +1,66 @@
+Metadata-Version: 2.1
+Name: numcodecs
+Version: 0.14.0
+Summary: A Python package providing buffer compression and transformation codecs for use in data storage and communication applications.
+Maintainer-email: Alistair Miles <alimanfoo@googlemail.com>
+License: MIT
+Project-URL: Bug Tracker, https://github.com/zarr-developers/numcodecs/issues
+Project-URL: Changelog, https://numcodecs.readthedocs.io/en/stable/release.html
+Project-URL: Documentation, https://numcodecs.readthedocs.io/
+Project-URL: Homepage, https://github.com/zarr-developers/numcodecs
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Information Technology
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Classifier: Operating System :: Unix
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Requires-Python: >=3.11
+Description-Content-Type: text/x-rst
+License-File: LICENSE.txt
+Requires-Dist: numpy>=1.24
+Provides-Extra: docs
+Requires-Dist: sphinx; extra == "docs"
+Requires-Dist: sphinx-issues; extra == "docs"
+Requires-Dist: pydata-sphinx-theme; extra == "docs"
+Requires-Dist: numpydoc; extra == "docs"
+Requires-Dist: mock; extra == "docs"
+Provides-Extra: test
+Requires-Dist: coverage; extra == "test"
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"
+Provides-Extra: test-extras
+Requires-Dist: importlib_metadata; extra == "test-extras"
+Provides-Extra: msgpack
+Requires-Dist: msgpack; extra == "msgpack"
+Provides-Extra: zfpy
+Requires-Dist: zfpy>=1.0.0; extra == "zfpy"
+Requires-Dist: numpy<2.0.0; extra == "zfpy"
+Provides-Extra: pcodec
+Requires-Dist: pcodec<0.3,>=0.2; extra == "pcodec"
+Provides-Extra: crc32c
+Requires-Dist: crc32c>=2.7; extra == "crc32c"
+
+Numcodecs
+=========
+
+Numcodecs is a Python package providing buffer compression and transformation
+codecs for use in data storage and communication applications.
+
+.. image:: https://readthedocs.org/projects/numcodecs/badge/?version=latest
+    :target: https://numcodecs.readthedocs.io/en/latest/?badge=latest
+
+.. image:: https://github.com/zarr-developers/numcodecs/workflows/Linux%20CI/badge.svg?branch=main
+    :target: https://github.com/zarr-developers/numcodecs/actions?query=workflow%3A%22Linux+CI%22
+
+.. image:: https://github.com/zarr-developers/numcodecs/workflows/OSX%20CI/badge.svg?branch=main
+    :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=main
+    :target: https://github.com/zarr-developers/numcodecs/actions?query=workflow%3AWheels
+
+.. image:: https://codecov.io/gh/zarr-developers/numcodecs/branch/main/graph/badge.svg
+    :target: https://codecov.io/gh/zarr-developers/numcodecs

numcodecs-0.14.0/README.rst

@@ -0,0 +1,20 @@
+Numcodecs
+=========
+
+Numcodecs is a Python package providing buffer compression and transformation
+codecs for use in data storage and communication applications.
+
+.. image:: https://readthedocs.org/projects/numcodecs/badge/?version=latest
+    :target: https://numcodecs.readthedocs.io/en/latest/?badge=latest
+
+.. image:: https://github.com/zarr-developers/numcodecs/workflows/Linux%20CI/badge.svg?branch=main
+    :target: https://github.com/zarr-developers/numcodecs/actions?query=workflow%3A%22Linux+CI%22
+
+.. image:: https://github.com/zarr-developers/numcodecs/workflows/OSX%20CI/badge.svg?branch=main
+    :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=main
+    :target: https://github.com/zarr-developers/numcodecs/actions?query=workflow%3AWheels
+
+.. image:: https://codecov.io/gh/zarr-developers/numcodecs/branch/main/graph/badge.svg
+    :target: https://codecov.io/gh/zarr-developers/numcodecs

numcodecs-0.14.0/adhoc/blosc_memleak_check.py

@@ -0,0 +1,14 @@
+import sys
+
+import numpy as np
+from numpy.testing import assert_array_equal
+
+import numcodecs
+
+codec = numcodecs.Blosc()
+data = np.arange(int(sys.argv[1]))
+for _ in range(int(sys.argv[2])):
+    enc = codec.encode(data)
+    dec = codec.decode(enc)
+    arr = np.frombuffer(dec, dtype=data.dtype)
+    assert_array_equal(data, arr)

numcodecs-0.14.0/c-blosc/.github/workflows/fuzz.yml

@@ -0,0 +1,23 @@
+name: CI Fuzz
+on: [push, pull_request]
+jobs:
+  Fuzzing:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Build Fuzzers
+      uses: google/oss-fuzz/infra/cifuzz/actions/build_fuzzers@master
+      with:
+        oss-fuzz-project-name: 'c-blosc'
+        dry-run: false
+    - name: Run Fuzzers
+      uses: google/oss-fuzz/infra/cifuzz/actions/run_fuzzers@master
+      with:
+        oss-fuzz-project-name: 'c-blosc'
+        fuzz-seconds: 600
+        dry-run: false
+    - name: Upload Crash
+      uses: actions/upload-artifact@v4
+      if: failure()
+      with:
+        name: artifacts
+        path: ./out/artifacts

numcodecs-0.14.0/c-blosc/ANNOUNCE.rst

@@ -0,0 +1,52 @@
+===============================================================
+ Announcing C-Blosc 1.21.6
+ A blocking, shuffling and lossless compression library for C
+===============================================================
+
+What is new?
+============
+
+This is a maintenance release. Here, we are providing new versions of
+internal Zlib and Zstd compressors, which are now 1.3.1 and 1.5.6
+respectively.
+
+For more info, please see the release notes in:
+
+https://github.com/Blosc/c-blosc/blob/main/RELEASE_NOTES.rst
+
+
+What is it?
+===========
+
+Blosc (https://www.blosc.org) is a high performance meta-compressor
+optimized for binary data.  It has been designed to transmit data to
+the processor cache faster than the traditional, non-compressed,
+direct memory fetch approach via a memcpy() OS call.
+
+Blosc has internal support for different compressors like its internal
+BloscLZ, but also LZ4, LZ4HC, Snappy, Zlib and Zstd.  This way these can
+automatically leverage the multithreading and pre-filtering
+(shuffling) capabilities that comes with Blosc.
+
+
+Download sources
+================
+
+The github repository is over here:
+
+https://github.com/Blosc
+
+Blosc is distributed using the BSD license, see LICENSE.txt for
+details.
+
+
+Mailing list
+============
+
+There is an official Blosc mailing list at:
+
+blosc@googlegroups.com
+https://groups.google.com/g/blosc
+
+
+Enjoy Data!