File numcodecs-pr569-systemlibs.patch of Package python-numcodecs

Overview Repositories Revisions Requests Users Attributes Meta

File numcodecs-pr569-systemlibs.patch of Package python-numcodecs

From c724de7fa120b5196dad6bf07e729f3399f9d902 Mon Sep 17 00:00:00 2001
From: gorloffslava <gorloff.slava@gmail.com>
Date: Mon, 29 Jul 2024 21:14:14 +0500
Subject: [PATCH 1/3] + Added NUMCODECS_USE_SYSTEM_LIBS capability to build
 numcodecs against system libraries

---
 pyproject.toml |   1 +
 setup.py       | 156 +++++++++++++++++++++++++++++++++++++++++++++++--
 2 files changed, 151 insertions(+), 6 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index af8f040a..910ca0d0 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -5,6 +5,7 @@ requires = [
     "Cython",
     "py-cpuinfo",
     "numpy",
+    "pkgconfig"
 ]
 build-backend = "setuptools.build_meta"
 
diff --git a/setup.py b/setup.py
index e594a203..7e7bf409 100644
--- a/setup.py
+++ b/setup.py
@@ -8,6 +8,7 @@
 from setuptools.errors import CCompilerError, ExecError, PlatformError
 from distutils import ccompiler
 from distutils.command.clean import clean
+import pkgconfig
 
 # determine CPU support for SSE2 and AVX2
 cpu_info = cpuinfo.get_cpu_info()
@@ -16,6 +17,7 @@
 have_avx2 = 'avx2' in flags
 disable_sse2 = 'DISABLE_NUMCODECS_SSE2' in os.environ
 disable_avx2 = 'DISABLE_NUMCODECS_AVX2' in os.environ
+use_system_libraries = 'NUMCODECS_USE_SYSTEM_LIBS' in os.environ
 
 # setup common compile arguments
 have_cflags = 'CFLAGS' in os.environ
@@ -48,8 +50,8 @@ def error(*msg):
     print('[numcodecs]', *msg, **kwargs)
 
 
-def blosc_extension():
-    info('setting up Blosc extension')
+def _blosc_extension_with_vendored_libs():
+    info('setting up Blosc extension from vendored sources')
 
     extra_compile_args = base_compile_args.copy()
     define_macros = []
@@ -124,8 +126,73 @@ def blosc_extension():
     return extensions
 
 
-def zstd_extension():
-    info('setting up Zstandard extension')
+def _blosc_extension_with_system_libs():
+    info('setting up Blosc extension with system libraries')
+
+    extra_compile_args = base_compile_args.copy()
+
+    blosc_package_configuration = pkgconfig.parse("blosc")
+
+    define_macros = blosc_package_configuration["define_macros"]
+    include_dirs = blosc_package_configuration["include_dirs"]
+    libraries = blosc_package_configuration["libraries"]
+    library_dirs = blosc_package_configuration["library_dirs"]
+
+    # remove minizip because Python.h 3.8 tries to include crypt.h
+    include_dirs = [d for d in include_dirs if 'minizip' not in d]
+    define_macros += [
+        ('HAVE_LZ4', 1),
+        # ('HAVE_SNAPPY', 1),
+        ('HAVE_ZLIB', 1),
+        ('HAVE_ZSTD', 1),
+    ]
+    # define_macros += [('CYTHON_TRACE', '1')]
+
+    # SSE2
+    if have_sse2 and not disable_sse2:
+        info('compiling Blosc extension with SSE2 support')
+        extra_compile_args.append('-DSHUFFLE_SSE2_ENABLED')
+        if os.name == 'nt':
+            define_macros += [('__SSE2__', 1)]
+    else:
+        info('compiling Blosc extension without SSE2 support')
+
+    # AVX2
+    if have_avx2 and not disable_avx2:
+        info('compiling Blosc extension with AVX2 support')
+        extra_compile_args.append('-DSHUFFLE_AVX2_ENABLED')
+        if os.name == 'nt':
+            define_macros += [('__AVX2__', 1)]
+    else:
+        info('compiling Blosc extension without AVX2 support')
+
+    sources = ['numcodecs/blosc.pyx']
+
+    # define extension module
+    extensions = [
+        Extension(
+            'numcodecs.blosc',
+            sources=sources,
+            include_dirs=include_dirs,
+            define_macros=define_macros,
+            extra_compile_args=extra_compile_args,
+            libraries=libraries,
+            library_dirs=library_dirs,
+        ),
+    ]
+
+    return extensions
+
+
+def blosc_extension():
+    if use_system_libraries:
+        return _blosc_extension_with_system_libs()
+    else:
+        return _blosc_extension_with_vendored_libs()
+
+
+def _zstd_extension_with_vendored_sources():
+    info('setting up Zstandard extension from vendored sources')
 
     zstd_sources = []
     extra_compile_args = base_compile_args.copy()
@@ -166,8 +233,46 @@ def zstd_extension():
     return extensions
 
 
-def lz4_extension():
-    info('setting up LZ4 extension')
+def _zstd_extension_with_system_libs():
+    info('setting up Zstandard extension with system libraries')
+
+    extra_compile_args = base_compile_args.copy()
+
+    zstd_package_configuration = pkgconfig.parse("libzstd")
+    include_dirs = zstd_package_configuration["include_dirs"]
+    define_macros = zstd_package_configuration["define_macros"]
+    libraries = zstd_package_configuration["libraries"]
+    library_dirs = zstd_package_configuration["library_dirs"]
+
+    # define_macros += [('CYTHON_TRACE', '1')]
+
+    sources = ['numcodecs/zstd.pyx']
+
+    # define extension module
+    extensions = [
+        Extension(
+            'numcodecs.zstd',
+            sources=sources,
+            include_dirs=include_dirs,
+            define_macros=define_macros,
+            extra_compile_args=extra_compile_args,
+            libraries=libraries,
+            library_dirs=library_dirs,
+        ),
+    ]
+
+    return extensions
+
+
+def zstd_extension():
+    if use_system_libraries:
+        return _zstd_extension_with_system_libs()
+    else:
+        return _zstd_extension_with_vendored_sources()
+
+
+def _lz4_extension_with_vendored_sources():
+    info('setting up LZ4 extension from vendored sources')
 
     extra_compile_args = base_compile_args.copy()
     define_macros = []
@@ -194,6 +299,45 @@ def lz4_extension():
     return extensions
 
 
+def _lz4_extension_with_system_libs():
+    info('setting up LZ4 extension with system libraries')
+
+    extra_compile_args = base_compile_args.copy()
+
+    lz4_package_configuration = pkgconfig.parse("liblz4")
+    include_dirs = lz4_package_configuration["include_dirs"]
+    define_macros = lz4_package_configuration["define_macros"]
+    libraries = lz4_package_configuration["libraries"]
+    library_dirs = lz4_package_configuration["library_dirs"]
+
+    include_dirs += ['numcodecs']
+    # define_macros += [('CYTHON_TRACE', '1')]
+
+    sources = ['numcodecs/lz4.pyx']
+
+    # define extension module
+    extensions = [
+        Extension(
+            'numcodecs.lz4',
+            sources=sources,
+            include_dirs=include_dirs,
+            define_macros=define_macros,
+            extra_compile_args=extra_compile_args,
+            libraries=libraries,
+            library_dirs=library_dirs,
+        ),
+    ]
+
+    return extensions
+
+
+def lz4_extension():
+    if use_system_libraries:
+        return _lz4_extension_with_system_libs()
+    else:
+        return _lz4_extension_with_vendored_sources()
+
+
 def vlen_extension():
     info('setting up vlen extension')
     import numpy

From f925fdb3b79faa9bf0e9ca087b84785ef6568aa4 Mon Sep 17 00:00:00 2001
From: Benjamin Leff <benjamin.w.leff@gmail.com>
Date: Tue, 6 Aug 2024 12:53:48 -0400
Subject: [PATCH 2/3] docs(deps): added readme system libs instructions

---
 README.rst | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/README.rst b/README.rst
index c9e58f52..89244ad1 100644
--- a/README.rst
+++ b/README.rst
@@ -18,3 +18,12 @@ codecs for use in data storage and communication applications.
 
 .. image:: https://codecov.io/gh/zarr-developers/numcodecs/branch/main/graph/badge.svg
     :target: https://codecov.io/gh/zarr-developers/numcodecs
+
+---
+If you already have native Blosc, Zstd, and LZ4 installed on your system and want to use these system libraries instead of the vendored sources, you
+should set the `NUMCODECS_USE_SYSTEM_LIBS=1` environment variable when building the wheel, like this:
+
+    $ NUMCODECS_USE_SYSTEM_LIBS=1 pip install numcodecs --no-binary numcodecs
+
+Blosc, Zstd, and LZ4 are found via the `pkg-config` utility. Moreover, you must build all 3 `blosc`, `libzstd`, and `liblz4`
+components. C-Blosc comes with full sources for LZ4, LZ4HC, Snappy, Zlib and Zstd and in general, you should not worry about not having (or CMake not finding) the libraries in your system because by default the included sources will be automatically compiled and included in the C-Blosc library. This effectively means that you can be confident in having a complete support for all the codecs in all the Blosc deployments (unless you are explicitly excluding support for some of them). To compile blosc, see these [instructions](https://github.com/Blosc/c-blosc?tab=readme-ov-file#compiling-the-blosc-library).
\ No newline at end of file

From 45fdddb1b818a4e796b4e83bafc8e2d92f54360b Mon Sep 17 00:00:00 2001
From: Benjamin Leff <benjamin.w.leff@gmail.com>
Date: Fri, 23 Aug 2024 13:05:49 -0400
Subject: [PATCH 3/3] Cleaned define_macros from blosc system

---
 setup.py | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/setup.py b/setup.py
index 7e7bf409..e5a0b985 100644
--- a/setup.py
+++ b/setup.py
@@ -140,12 +140,7 @@ def _blosc_extension_with_system_libs():
 
     # remove minizip because Python.h 3.8 tries to include crypt.h
     include_dirs = [d for d in include_dirs if 'minizip' not in d]
-    define_macros += [
-        ('HAVE_LZ4', 1),
-        # ('HAVE_SNAPPY', 1),
-        ('HAVE_ZLIB', 1),
-        ('HAVE_ZSTD', 1),
-    ]
+
     # define_macros += [('CYTHON_TRACE', '1')]
 
     # SSE2

Places

File numcodecs-pr569-systemlibs.patch of Package python-numcodecs

Places