Design Doc: Migrate numcodecs build system from setuptools/setup.py to meson-python

Status: Proposal Date: 2026-03-17 Author: Max (with Claude)

Motivation

numcodecs currently uses a hybrid build system: pyproject.toml declares the setuptools backend, but a 386-line setup.py contains all the C/Cython extension logic. This is problematic because:

setup.py is effectively deprecated. PEP 517/518 moved the ecosystem toward declarative builds. setup.py is imperative, opaque to tooling, and executed during metadata extraction.
distutils imports are fragile. setup.py imports from distutils (removed from stdlib in Python 3.12). This only works because setuptools vendors a copy, which may be dropped in a future major release.
CPU feature detection is incorrect for cross-compilation. py-cpuinfo runs at build time on the build machine, not the target machine. This means cibuildwheel arm64 builds on x86_64 hosts detect x86_64 features. The current workaround is environment variables (DISABLE_NUMCODECS_AVX2, DISABLE_NUMCODECS_SSE2).
System library linking is unsupported. PR #569 has been open since 2023, attempting to add pkg-config-based system library support. The approach adds complexity to an already complex setup.py.
The scientific Python ecosystem has standardized on meson-python. numpy, scipy, scikit-learn, scikit-image, and matplotlib have all migrated. Meson natively handles every concern currently implemented manually in setup.py.

Proposal

Replace setup.py + setuptools with meson.build + meson-python as the build backend. Remove py-cpuinfo as a build dependency. Use meson's native compiler introspection for CPU feature detection and dependency() for optional system library linking.

Current Architecture

Build dependencies

[build-system]
requires = ["setuptools>=77", "setuptools-scm[toml]>=6.2", "Cython", "py-cpuinfo", "numpy>2"]
build-backend = "setuptools.build_meta"

Extension modules (8 total)

Extension	Cython source	C library deps	Assembly	Notes
`blosc`	`blosc.pyx`	c-blosc + vendored lz4, zlib, zstd	zstd `amd64.S` / `aarch64.S`	Most complex; SSE2/AVX2 conditional
`zstd`	`zstd.pyx`	vendored zstd (from c-blosc)	zstd `amd64.S` / `aarch64.S`	Shares zstd sources with blosc
`lz4`	`lz4.pyx`	vendored lz4 (from c-blosc)	None
`vlen`	`vlen.pyx`	None	None	Needs numpy include dirs
`fletcher32`	`fletcher32.pyx`	None	None
`jenkins`	`jenkins.pyx`	None	None	Has `CYTHON_TRACE=1` (likely accidental)
`compat_ext`	`compat_ext.pyx`	None	None
`_shuffle`	`_shuffle.pyx`	None	None

Shared Cython declarations

compat_ext.pxd — PyBytes_RESIZE, ensure_continguous_memoryview (used by blosc, zstd, lz4, vlen)
_utils.pxd — store_le32, load_le32 (used by lz4, fletcher32, vlen)

Vendored C sources (c-blosc git submodule)

c-blosc/
├── blosc/              # Core blosc library (28 files, incl. SIMD shuffle variants)
└── internal-complibs/
    ├── lz4-1.10.0/     # 4 files
    ├── zlib-1.3.1/     # ~58 files
    └── zstd-1.5.6/     # ~90 files across common/, compress/, decompress/, dictBuilder/

Conditional compilation logic in setup.py

CPU detection: py-cpuinfo reads /proc/cpuinfo or equivalent → sets have_sse2, have_avx2
Environment overrides: DISABLE_NUMCODECS_SSE2, DISABLE_NUMCODECS_AVX2, DISABLE_NUMCODECS_CEXT
SIMD sources: SSE2/AVX2 shuffle/bitshuffle .c files included conditionally
SIMD defines: -DSHUFFLE_SSE2_ENABLED, -DSHUFFLE_AVX2_ENABLED, __SSE2__, __AVX2__
Assembly: .S files pre-compiled to .o, passed as extra_objects
Platform flags: -stdlib=libc++ (macOS), -pthread (POSIX), -Wno-implicit-function-declaration (cibuildwheel macOS)

Proposed Architecture

Build dependencies

[build-system]
requires = ["meson-python>=0.17", "meson>=1.6.0", "Cython>=3.0", "numpy>=2"]
build-backend = "mesonpy"

Removed: setuptools, setuptools-scm, py-cpuinfo

File structure

numcodecs/
├── meson.build                    # Root: project(), subdir()
├── meson.options                  # Build options (system libs, SIMD toggles)
├── numcodecs/
│   └── meson.build                # Extension modules
├── c-blosc/                       # Unchanged submodule
├── pyproject.toml                 # Updated build-backend
└── setup.py                       # DELETED

Root meson.build

project(
  'numcodecs',
  'c', 'cython',
  version: run_command('python', '-m', 'setuptools_scm', '--version', check: true).stdout().strip(),
  default_options: [
    'c_std=c11',
    'warning_level=1',
  ],
  meson_version: '>=1.6.0',
)

py = import('python').find_installation(pure: false)
cy = meson.get_compiler('cython')
cc = meson.get_compiler('c')

# NumPy include directory (needed for vlen extension)
numpy_dep = dependency('numpy')

subdir('numcodecs')

Note on versioning: meson-python has native setuptools-scm integration — see meson-python docs on dynamic versioning. The version field can use run_command to call setuptools-scm, or we can switch to meson-python's built-in VCS versioning. This will need to replace the current write_to = "numcodecs/version.py" approach — meson-python generates version metadata at build time via importlib.metadata instead of writing a file.

meson.options

option('system_blosc', type: 'feature', value: 'auto',
       description: 'Use system-installed Blosc library')
option('system_zstd', type: 'feature', value: 'auto',
       description: 'Use system-installed Zstandard library')
option('system_lz4', type: 'feature', value: 'auto',
       description: 'Use system-installed LZ4 library')

With value: 'disabled', meson always uses the vendored sources by default, matching the old setup.py behavior. Users who want to link against system libraries opt in with -Dsystem_blosc=enabled etc. This replaces the NUMCODECS_USE_SYSTEM_LIBS env var from PR #569 with a standard meson idiom.

numcodecs/meson.build (core of the migration)

This is the most complex file. The design below is broken into sections.

Compiler flags

# Platform-specific flags
c_args = []
link_args = []

if host_machine.system() == 'darwin'
  c_args += ['-stdlib=libc++']
endif

if host_machine.system() != 'windows'
  c_args += ['-pthread']
  link_args += ['-pthread']
endif

SIMD detection (replaces py-cpuinfo)

# SIMD support — detected via compiler capability, NOT runtime CPU flags.
# This is correct for cross-compilation: we check what the *target* supports.
have_sse2 = false
have_avx2 = false

if host_machine.cpu_family() == 'x86_64'
  have_sse2 = cc.has_argument('-msse2')
  have_avx2 = cc.has_argument('-mavx2')
endif

# Allow disabling via meson configure (replaces DISABLE_NUMCODECS_* env vars)
# cibuildwheel can pass -Dsse2=disabled instead of DISABLE_NUMCODECS_SSE2=1

This fixes the cross-compilation bug: host_machine.cpu_family() reflects the target architecture (from a meson cross file or native detection), not the build machine.

Vendored libraries as static dependencies

# --- Vendored zstd ---
zstd_dep = dependency('libzstd', required: get_option('system_zstd'))

if not zstd_dep.found()
  zstd_sources = files(
    # common/
    'c-blosc/internal-complibs/zstd-1.5.6/common/entropy_common.c',
    'c-blosc/internal-complibs/zstd-1.5.6/common/error_private.c',
    # ... (enumerate all .c files)
  )

  # Assembly files — meson handles .S natively
  if host_machine.cpu_family() == 'x86_64'
    zstd_sources += files('c-blosc/internal-complibs/zstd-1.5.6/decompress/huf_decompress_amd64.S')
  elif host_machine.cpu_family() == 'aarch64'
    zstd_sources += files('c-blosc/internal-complibs/zstd-1.5.6/decompress/huf_decompress_aarch64.S')
  endif

  zstd_inc = include_directories(
    'c-blosc/internal-complibs/zstd-1.5.6',
    'c-blosc/internal-complibs/zstd-1.5.6/common',
    'c-blosc/internal-complibs/zstd-1.5.6/compress',
    'c-blosc/internal-complibs/zstd-1.5.6/decompress',
    'c-blosc/internal-complibs/zstd-1.5.6/dictBuilder',
  )

  zstd_lib = static_library('zstd_vendored', zstd_sources,
    include_directories: zstd_inc,
    c_args: c_args,
  )
  zstd_dep = declare_dependency(
    link_with: zstd_lib,
    include_directories: zstd_inc,
  )
endif

# --- Vendored lz4 ---
lz4_dep = dependency('liblz4', required: get_option('system_lz4'))

if not lz4_dep.found()
  lz4_sources = files(
    'c-blosc/internal-complibs/lz4-1.10.0/lz4.c',
    'c-blosc/internal-complibs/lz4-1.10.0/lz4hc.c',
  )
  lz4_inc = include_directories('c-blosc/internal-complibs/lz4-1.10.0')

  lz4_lib = static_library('lz4_vendored', lz4_sources,
    include_directories: lz4_inc,
    c_args: c_args,
  )
  lz4_dep = declare_dependency(
    link_with: lz4_lib,
    include_directories: lz4_inc,
  )
endif

# --- Vendored zlib ---
zlib_sources = files(
  'c-blosc/internal-complibs/zlib-1.3.1/adler32.c',
  'c-blosc/internal-complibs/zlib-1.3.1/crc32.c',
  'c-blosc/internal-complibs/zlib-1.3.1/deflate.c',
  'c-blosc/internal-complibs/zlib-1.3.1/inflate.c',
  'c-blosc/internal-complibs/zlib-1.3.1/inffast.c',
  'c-blosc/internal-complibs/zlib-1.3.1/inftrees.c',
  'c-blosc/internal-complibs/zlib-1.3.1/trees.c',
  'c-blosc/internal-complibs/zlib-1.3.1/uncompr.c',
  'c-blosc/internal-complibs/zlib-1.3.1/zutil.c',
)
zlib_inc = include_directories('c-blosc/internal-complibs/zlib-1.3.1')

zlib_lib = static_library('zlib_vendored', zlib_sources,
  include_directories: zlib_inc,
  c_args: c_args,
)
zlib_dep = declare_dependency(
  link_with: zlib_lib,
  include_directories: zlib_inc,
)

Blosc extension (most complex)

# --- Vendored blosc ---
blosc_dep = dependency('blosc', required: get_option('system_blosc'))

if not blosc_dep.found()
  blosc_sources = files(
    'c-blosc/blosc/blosc.c',
    'c-blosc/blosc/blosclz.c',
    'c-blosc/blosc/fastcopy.c',
    'c-blosc/blosc/shuffle.c',
    'c-blosc/blosc/shuffle-generic.c',
    'c-blosc/blosc/bitshuffle-generic.c',
  )

  blosc_c_args = c_args
  blosc_c_args += ['-DHAVE_LZ4', '-DHAVE_ZLIB', '-DHAVE_ZSTD']

  if have_sse2
    blosc_sources += files(
      'c-blosc/blosc/shuffle-sse2.c',
      'c-blosc/blosc/bitshuffle-sse2.c',
    )
    blosc_c_args += ['-DSHUFFLE_SSE2_ENABLED', '-msse2']
    if host_machine.system() == 'windows'
      blosc_c_args += ['-D__SSE2__']
    endif
  endif

  if have_avx2
    blosc_sources += files(
      'c-blosc/blosc/shuffle-avx2.c',
      'c-blosc/blosc/bitshuffle-avx2.c',
    )
    blosc_c_args += ['-DSHUFFLE_AVX2_ENABLED', '-mavx2']
    if host_machine.system() == 'windows'
      blosc_c_args += ['-D__AVX2__']
    endif
  endif

  blosc_inc = include_directories('c-blosc/blosc')

  blosc_lib = static_library('blosc_vendored', blosc_sources,
    include_directories: blosc_inc,
    dependencies: [lz4_dep, zlib_dep, zstd_dep],
    c_args: blosc_c_args,
  )
  blosc_dep = declare_dependency(
    link_with: blosc_lib,
    include_directories: blosc_inc,
  )
endif

Extension module declarations

# --- Cython extension modules ---

# Extensions with C library dependencies
py.extension_module('blosc',
  'blosc.pyx',
  dependencies: [blosc_dep, lz4_dep, zlib_dep, zstd_dep],
  link_args: link_args,
  install: true,
  subdir: 'numcodecs',
)

py.extension_module('zstd',
  'zstd.pyx',
  dependencies: [zstd_dep],
  link_args: link_args,
  install: true,
  subdir: 'numcodecs',
)

py.extension_module('lz4',
  'lz4.pyx',
  dependencies: [lz4_dep],
  include_directories: include_directories('.'),
  link_args: link_args,
  install: true,
  subdir: 'numcodecs',
)

py.extension_module('vlen',
  'vlen.pyx',
  dependencies: [numpy_dep],
  include_directories: include_directories('.'),
  install: true,
  subdir: 'numcodecs',
)

# Pure-Cython extensions (no C library deps)
foreach ext : ['fletcher32', 'jenkins', 'compat_ext', '_shuffle']
  py.extension_module(ext,
    ext + '.pyx',
    include_directories: include_directories('.'),
    install: true,
    subdir: 'numcodecs',
  )
endforeach

# --- Pure Python sources ---
py.install_sources(
  '__init__.py',
  'abc.py',
  'compat.py',
  'registry.py',
  # ... all .py files
  subdir: 'numcodecs',
)

Version management

Option A: meson-python + setuptools-scm (minimal change)

Keep setuptools-scm as a build dependency and use run_command() in meson.build:

project('numcodecs', 'c', 'cython',
  version: run_command(
    py, ['-m', 'setuptools_scm', '--version'], check: true
  ).stdout().strip(),
)

At runtime, version is read via importlib.metadata.version('numcodecs') instead of a generated version.py. Update __init__.py:

from importlib.metadata import version
__version__ = version("numcodecs")

Option B: meson's built-in VCS tagging

Use vcs_tag() to generate a version file from git tags, removing the setuptools-scm dependency entirely. This is what numpy does.

Recommendation: Option A — keep setuptools-scm for now, swap to vcs_tag() later if desired.

pyproject.toml changes

[build-system]
requires = ["meson-python>=0.17", "meson>=1.6.0", "Cython>=3.0", "numpy>=2"]
build-backend = "mesonpy"

[project]
# ... unchanged ...

[tool.meson-python.args]
# Pass default meson options
setup = ['--default-library=static']

# Replace setuptools-scm config
[tool.setuptools_scm]  # REMOVE this section

# Replace setuptools config
[tool.setuptools]      # REMOVE this section

cibuildwheel changes

The DISABLE_NUMCODECS_* environment variables are replaced by meson configure options:

[tool.cibuildwheel]
# Meson cross-compilation handles SIMD correctly — no env vars needed
# AVX2 still disabled for portable wheels (not all x86_64 CPUs have it)
config-settings = "setup-args=-Davx2=disabled"

[tool.cibuildwheel.macos]
# No need for MACOSX_DEPLOYMENT_TARGET — meson-python handles this
# No need for -Wno-implicit-function-declaration — meson compiles correctly

[[tool.cibuildwheel.overrides]]
select = "*-macosx_arm64"
config-settings = "setup-args=-Davx2=disabled -Dsse2=disabled"

Files deleted

setup.py (386 lines)
MANIFEST.in (meson-python builds sdists from version control, like setuptools-scm)
numcodecs/version.py (replaced by importlib.metadata)

Files added

meson.build (root, ~20 lines)
meson.options (~15 lines)
numcodecs/meson.build (~180 lines)

Files updated

docs/contributing.rst (rewritten — see Contributing Guide Updates below)

Migration Plan

numcodecs has limited maintenance bandwidth. A phased migration (the numpy/scipy approach of running two build systems in parallel for multiple releases) would double the maintenance surface during the transition. Instead, this should be a single PR that swaps everything at once.

Single-PR migration

One PR, one release. The PR:

Adds meson.build, meson.options, numcodecs/meson.build
Deletes setup.py, MANIFEST.in
Updates pyproject.toml: new [build-system], removes [tool.setuptools], [tool.setuptools_scm], [tool.setuptools.package-data]
Updates numcodecs/__init__.py: version from importlib.metadata
Updates cibuildwheel config in pyproject.toml
Updates CI workflows (pixi tasks, wheel building)
Updates .gitignore (remove numcodecs/version.py)
Updates docs/contributing.rst: new dev setup instructions for pixi and uv, removes outdated references
Closes PR #569 (system library support is native via -Dsystem_blosc=enabled)

Validation checklist

Before merging, verify:

Risk of a clean break

The main risk is that a broken build blocks the next release. This is mitigated by:

The test matrix is comprehensive. CI already tests 5 OS/arch combos x 4 Python versions. If the meson build passes CI, it works.
meson-python is battle-tested. numpy, scipy, scikit-learn all use it for projects with far more complex C/Cython builds than numcodecs.
Rollback is trivial. If something goes wrong post-release, revert the PR and cut a patch release. The old setup.py is in git history.

Contributing Guide Updates

The current docs/contributing.rst is significantly outdated (references Python 3.8/3.9, Travis CI, AppVeyor, bare pip install -e . without a venv manager). The meson migration is a natural point to rewrite the development setup section.

Current problems with the contributing guide

Recommends manual python3 -m venv + pip install -e . — works but requires the user to have a C compiler, Cython, and numpy already available, with no guidance on obtaining them
No mention of pixi or uv, which are already configured in the project
References Python 3.8, 3.9, Travis CI, and AppVeyor (all outdated)
No mention of meson or how to pass build options
No guidance on building against system libraries

Proposed "Creating a development environment" section

The guide should present two supported paths (pixi and uv) and explicitly discourage developing without an isolated environment. The following replaces the "Creating a development environment" and "Running the test suite" sections.

Creating a development environment
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

NumCodecs contains C and Cython extensions, so you need a C compiler and
build tooling in addition to Python. We support two development workflows:
**pixi** (recommended) and **uv**. Both manage isolated environments and
are tested in CI. **Do not** install numcodecs into your system Python or a
manually-managed virtualenv — the C compilation dependencies are
difficult to get right by hand.

Whichever tool you use, first clone the repository with its submodules::

    $ git clone --recursive git@github.com:your-user-name/numcodecs.git
    $ cd numcodecs
    $ git remote add upstream https://github.com/zarr-developers/numcodecs.git

Using pixi (recommended)
"""""""""""""""""""""""""

`pixi <https://pixi.sh>`_ manages Python, the C compiler toolchain, and all
dependencies via conda-forge. This is the easiest way to get started,
especially on macOS or if you don't have a system C compiler.

Install pixi, then::

    $ pixi run -e test-py313 run-tests     # build + test in one step

This will create an isolated environment with Python 3.13, install the C
toolchain from conda-forge, build the Cython extensions, and run the test
suite. Available test environments::

    test-py311, test-py312, test-py313, test-py314

To get a shell inside a pixi environment for interactive development::

    $ pixi shell -e test-py313

Using uv
""""""""

`uv <https://docs.astral.sh/uv/>`_ is a fast Python package manager. It
manages virtualenvs and dependencies but does **not** provide a C compiler —
you must have ``cc`` / ``gcc`` / ``clang`` available on your ``PATH``.

On Debian/Ubuntu::

    $ sudo apt install build-essential

On macOS (Xcode command line tools)::

    $ xcode-select --install

Then::

    $ uv sync --extra test --extra msgpack
    $ uv run pytest -v

uv will create a ``.venv``, build the extensions, and install numcodecs in
editable mode.

Passing build options
"""""""""""""""""""""

NumCodecs uses `meson <https://mesonbuild.com>`_ as its build system. You can
pass meson options via pip's ``--config-settings`` or via environment variables
when building.

To build against system-installed Blosc, Zstd, and LZ4 instead of the
vendored copies::

    $ pip install -e . --no-build-isolation \
        --config-settings=setup-args=-Dsystem_blosc=enabled \
        --config-settings=setup-args=-Dsystem_zstd=enabled \
        --config-settings=setup-args=-Dsystem_lz4=enabled

To disable SIMD optimizations (e.g. for portable debugging)::

    $ pip install -e . --no-build-isolation \
        --config-settings=setup-args=-Davx2=disabled \
        --config-settings=setup-args=-Dsse2=disabled

Running the test suite
~~~~~~~~~~~~~~~~~~~~~~

With pixi::

    $ pixi run -e test-py313 run-tests

With uv::

    $ uv run pytest -v

To run tests for specific Zarr integration versions::

    $ pixi run test-zarr-312
    $ pixi run test-zarr-313
    $ pixi run test-zarr-main

All tests are automatically run via GitHub Actions for every pull request
across Linux (x86_64, aarch64, i386), macOS (x86_64, arm64), and Windows
(x86_64), with Python 3.12 through 3.14.

Other sections to update

The rest of the contributing guide needs lighter touch-ups as part of this PR:

"Code standards" — already correct (references pre-commit run ruff), no change needed
"Test coverage" — update Python version reference from "3.9" to "3.13" (or just say "the latest stable release")
"Documentation" — update Python version reference, otherwise fine
"Bug reports" — update the Python session example from 3.8 to a current version
"Running the test suite" (old) — replace entirely (covered above)
Remove all references to Travis CI and AppVeyor — CI is GitHub Actions only

Risks and Mitigations

Risk: Meson doesn't support a platform/arch that setuptools did

Mitigation: Meson supports all platforms numcodecs targets (Linux x86_64/aarch64/i386, macOS x86_64/arm64, Windows x86_64). The i386 Alpine CI job (ci-i386.yml) needs verification — meson may need a cross file for 32-bit builds inside the Alpine container.

Risk: Cython version incompatibilities

Mitigation: Pin Cython>=3.0 in build-requires. Meson's Cython support requires Cython 3. This drops Cython 0.x support, which is already effectively unsupported.

Risk: sdist contents change

Mitigation: meson-python includes all files tracked by git (plus submodules) in sdists by default, matching setuptools-scm behavior. The MANIFEST.in is not needed. Verify with python -m build --sdist and compare contents.

Risk: Editable installs behave differently

Mitigation: meson-python supports editable installs via pip install -e . --no-build-isolation. The experience differs from setuptools (meson-python uses import hooks rather than .egg-link). The pixi-based dev workflow should still work. Test editable installs explicitly in Phase 1.

Risk: Windows MSVC compatibility

Mitigation: Meson has excellent MSVC support. The SIMD flag logic (-msse2, -mavx2) is GCC/Clang-specific; MSVC equivalents (/arch:SSE2, /arch:AVX2) are needed. Meson's cc.get_id() can branch on compiler. Current setup.py already handles this partially (the __SSE2__/__AVX2__ defines for os.name == 'nt').

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File metadata and controls

Design Doc: Migrate numcodecs build system from setuptools/setup.py to meson-python

Motivation

Proposal

Current Architecture

Build dependencies

Extension modules (8 total)

Shared Cython declarations

Vendored C sources (c-blosc git submodule)

Conditional compilation logic in setup.py

Proposed Architecture

Build dependencies

File structure

Root meson.build

meson.options

numcodecs/meson.build (core of the migration)

Compiler flags

SIMD detection (replaces py-cpuinfo)

Vendored libraries as static dependencies

Blosc extension (most complex)

Extension module declarations

Version management

pyproject.toml changes

cibuildwheel changes

Files deleted

Files added

Files updated

Migration Plan

Single-PR migration

Validation checklist

Risk of a clean break

Contributing Guide Updates

Current problems with the contributing guide

Proposed "Creating a development environment" section

Other sections to update

Risks and Mitigations

Risk: Meson doesn't support a platform/arch that setuptools did

Risk: Cython version incompatibilities

Risk: sdist contents change

Risk: Editable installs behave differently

Risk: Windows MSVC compatibility

References