numcodecs 0.12.1__tar.gz → 0.13.1__tar.gz

numcodecs-0.13.1/.github/workflows/ci.yaml

@@ -0,0 +1,97 @@
+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: ["3.10", "3.11", "3.12", "3.13.0"]
+        # macos-12 is an intel runner, macos-14 is a arm64 runner
+        platform: [ubuntu-latest, windows-latest, macos-12, macos-14]
+
+    steps:
+      - name: Checkout source
+        uses: actions/checkout@v4
+        with:
+          submodules: recursive
+
+      - name: Set up Conda
+        uses: conda-incubator/setup-miniconda@v3.0.4
+        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-12'
+        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]
+
+      - name: Install pcodec
+        if: matrix.python-version != '3.13.0'
+        shell: "bash -l {0}"
+        run: |
+            conda activate env
+            python -m pip install -v pcodec
+
+
+      # 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 == '3.10'
+        shell: "bash -l {0}"
+        run: |
+          conda activate env
+          python -m pip install "zfpy>=1" "numpy<2"
+
+      - 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-0.13.1/.github/workflows/codeql-analysis.yml

@@ -0,0 +1,62 @@
+name: "Code Scanning - Action"
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+  schedule:
+    #        ┌───────────── minute (0 - 59)
+    #        │  ┌───────────── hour (0 - 23)
+    #        │  │ ┌───────────── day of the month (1 - 31)
+    #        │  │ │ ┌───────────── month (1 - 12 or JAN-DEC)
+    #        │  │ │ │ ┌───────────── day of the week (0 - 6 or SUN-SAT)
+    #        │  │ │ │ │
+    #        │  │ │ │ │
+    #        │  │ │ │ │
+    #        *  * * * *
+    - cron: '22 2 * * 5'
+
+jobs:
+  CodeQL-Build:
+    # CodeQL runs on ubuntu-latest, windows-latest, and macos-latest
+    runs-on: ubuntu-latest
+
+    permissions:
+      # required for all workflows
+      security-events: write
+
+      # only required for workflows in private repositories
+      actions: read
+      contents: read
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      # Initializes the CodeQL tools for scanning.
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@v3
+        with:
+          languages: python
+          # languages: python, cpp
+          # queries: +security-extended
+
+      # Autobuild attempts to build any compiled languages (C/C++, C#, or Java).
+      # If this step fails, then you should remove it and run the build manually (see below).
+      - name: Autobuild
+        uses: github/codeql-action/autobuild@v3
+
+      # ℹ️ Command-line programs to run using the OS shell.
+      # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
+
+      # ✏️ If the Autobuild fails above, remove it and uncomment the following
+      #    three lines and modify them (or add more) to build your code if your
+      #    project uses a compiled language
+
+      #- run: |
+      #     make bootstrap
+      #     make release
+
+      - name: Perform CodeQL Analysis
+        uses: github/codeql-action/analyze@v3

numcodecs-0.13.1/.github/workflows/wheel.yaml

@@ -0,0 +1,98 @@
+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: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        # macos-12 is an intel runner, macos-14 is a arm64 runner
+        os: [ubuntu-latest, windows-latest, macos-12, macos-14]
+    env:
+      CIBW_TEST_COMMAND: python -c "import numcodecs"
+      CIBW_BUILD: "cp310-* cp311-* cp312-* cp313-*"
+      CIBW_SKIP: "pp* *-musllinux_* *win32 *_i686 *_s390x"
+      # note: CIBW_ENVIRONMENT is now set in pyproject.toml
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: true
+
+      - uses: pypa/cibuildwheel@v2.21.2
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: wheels-${{ 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: "3.10"
+
+      - 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-0.13.1/.gitignore

@@ -0,0 +1,106 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+numcodecs/**/*.c
+numcodecs/**/*.h
+*.so
+
+# editor
+*~
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+.hypothesis/
+cover/
+
+# Cython annotation files
+numcodecs/*.html
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# IPython Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# dotenv
+.env
+
+# virtualenv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+
+# Rope project settings
+.ropeproject
+
+# PyCharm
+.idea
+
+# setuptools-scm
+numcodecs/version.py
+
+# Cython generated
+numcodecs/*.c

numcodecs-0.13.1/.pre-commit-config.yaml

@@ -0,0 +1,27 @@
+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: [commit, push]
+default_language_version:
+  python: python3
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+    - id: trailing-whitespace
+    - id: check-yaml
+    - id: debug-statements
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.6.9
+    hooks:
+    - id: ruff
+      args: ["--fix", "--show-fixes"]
+    - id: ruff-format
+
+  - repo: https://github.com/scientific-python/cookie
+    rev: 2024.04.23
+    hooks:
+    - id: sp-repo-review

numcodecs-0.13.1/.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-0.13.1/.readthedocs.yaml

@@ -0,0 +1,21 @@
+version: 2
+
+submodules:
+  include: all
+
+build:
+  os: ubuntu-20.04
+  tools:
+    python: "3.12"
+
+sphinx:
+  configuration: docs/conf.py
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs
+        - msgpack
+        - zfpy

numcodecs-0.13.1/PKG-INFO

@@ -0,0 +1,64 @@
+Metadata-Version: 2.1
+Name: numcodecs
+Version: 0.13.1
+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: >=3.10
+Description-Content-Type: text/x-rst
+License-File: LICENSE.txt
+Requires-Dist: numpy>=1.7
+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>=0.2.0; extra == "pcodec"
+
+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-0.13.1/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-0.13.1/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-0.13.1/c-blosc/.github/dependabot.yml

@@ -0,0 +1,7 @@
+# https://docs.github.com/en/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"

numcodecs-0.13.1/c-blosc/.github/workflows/cmake.yml

@@ -0,0 +1,155 @@
+name: CI CMake
+on: [push, pull_request]
+jobs:
+  ci-cmake:
+    name: ${{ matrix.name }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        name: [
+          Ubuntu GCC,
+          Ubuntu GCC OSB,
+          Ubuntu GCC External LZ4,
+          Ubuntu GCC External SNAPPY,
+          Ubuntu GCC External ZLIB,
+          Ubuntu GCC External ZSTD,
+          Ubuntu Clang,
+          Ubuntu Clang No SSE2,
+          Ubuntu Clang No AVX2,
+          Ubuntu Clang No AVX2 No SSE2,
+          Ubuntu Clang No LZ4,
+          Ubuntu Clang No ZLIB,
+          Ubuntu Clang No ZSTD,
+          Windows MSVC Win32,
+          Windows MSVC Win64,
+          macOS Clang,
+          macOS GCC
+        ]
+        include:
+          - name: Ubuntu GCC
+            os: ubuntu-latest
+            compiler: gcc
+
+          # Out of source build
+          - name: Ubuntu GCC OSB
+            os: ubuntu-latest
+            compiler: gcc
+            build-dir: ../build
+            build-src-dir: ../c-blosc
+
+          - name: Ubuntu GCC External LZ4
+            os: ubuntu-latest
+            compiler: gcc
+            packages: liblz4-1 liblz4-dev
+            cmake-args: -DPREFER_EXTERNAL_LZ4=ON
+
+          - name: Ubuntu GCC External SNAPPY
+            os: ubuntu-latest
+            compiler: gcc
+            packages: libsnappy-dev
+            cmake-args: -DDEACTIVATE_SNAPPY=OFF
+
+          - name: Ubuntu GCC External ZLIB
+            os: ubuntu-latest
+            compiler: gcc
+            packages: zlib1g-dev
+            cmake-args: -DPREFER_EXTERNAL_ZLIB=ON
+
+          - name: Ubuntu GCC External ZSTD
+            os: ubuntu-latest
+            compiler: gcc
+            packages: zstd libzstd-dev
+            cmake-args: -DPREFER_EXTERNAL_ZSTD=ON
+
+          - name: Ubuntu Clang
+            os: ubuntu-latest
+            compiler: clang
+
+          - name: Ubuntu Clang No SSE2
+            os: ubuntu-latest
+            compiler: clang
+            cmake-args: -DDEACTIVATE_SSE2=ON
+
+          - name: Ubuntu Clang No AVX2
+            os: ubuntu-latest
+            compiler: clang
+            cmake-args: -DDEACTIVATE_AVX2=ON
+
+          - name: Ubuntu Clang No AVX2 No SSE2
+            os: ubuntu-latest
+            compiler: clang
+            cmake-args: -DDEACTIVATE_AVX2=ON -DDEACTIVATE_SSE2=ON
+
+          - name: Ubuntu Clang No LZ4
+            os: ubuntu-latest
+            compiler: clang
+            cmake-args: -DDEACTIVATE_LZ4=ON
+
+          - name: Ubuntu Clang No ZLIB
+            os: ubuntu-latest
+            compiler: clang
+            cmake-args: -DDEACTIVATE_ZLIB=ON
+
+          - name: Ubuntu Clang No ZSTD
+            os: ubuntu-latest
+            compiler: clang
+            cmake-args: -DDEACTIVATE_ZSTD=ON
+
+          - name: Windows MSVC Win32
+            os: windows-latest
+            compiler: cl
+            cmake-args: -A Win32
+
+          - name: Windows MSVC Win64
+            os: windows-latest
+            compiler: cl
+            cmake-args: -A x64
+
+          - name: macOS Clang
+            os: macOS-latest
+            compiler: clang
+
+          - name: macOS GCC
+            os: macOS-latest
+            compiler: gcc
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Install packages (Ubuntu)
+      if: runner.os == 'Linux' && matrix.packages
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y ${{ matrix.packages }}
+
+    - name: Install packages (Windows)
+      if: runner.os == 'Windows'
+      run: |
+        choco install ninja ${{ matrix.packages }}
+
+    - name: Install packages (macOS)
+      if: runner.os == 'macOS'
+      run: |
+        brew install ninja ${{ matrix.packages }}
+
+    - name: Generate project files
+      run: |
+        mkdir ${{ matrix.build-dir || '.not-used' }}
+        cd ${{ matrix.build-dir || '.' }}
+        cmake ${{ matrix.build-src-dir || '.' }} ${{ matrix.cmake-args }} -DCMAKE_BUILD_TYPE=${{ matrix.build-config || 'Release' }} -DBUILD_SHARED_LIBS=OFF -DBUILD_FUZZERS=ON
+      env:
+        CC: ${{ matrix.compiler }}
+        CFLAGS: ${{ matrix.cflags }}
+        LDFLAGS: ${{ matrix.ldflags }}
+        CI: true
+
+    - name: Compile source code
+      run: |
+        cd ${{ matrix.build-dir || '.' }}
+        cmake --build . --config ${{ matrix.build-config || 'Release' }}
+
+    - name: Run test cases
+      run: |
+        cd ${{ matrix.build-dir || '.' }}
+        ctest -C Release --output-on-failure --max-width 120