{data}[foss/2022a] PyTables v3.8.0

easybuild/easyconfigs/b/Blosc2/Blosc2-2.6.1-GCCcore-11.3.0.eb

@@ -0,0 +1,31 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Denis Kristak
+# Update: Thomas Hoffmann (EMBL)
+easyblock = 'CMakeMake'
+
+name = 'Blosc2'
+version = '2.6.1'
+
+homepage = 'https://www.blosc.org/'
+
+description = "Blosc, an extremely fast, multi-threaded, meta-compressor library"
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+toolchainopts = {'pic': True, 'cstd': 'c++11'}
+
+source_urls = ['https://github.com/Blosc/c-blosc2/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['514a793368093893c1a7cae030f7e31faca7f86465ae69dd576f256d8bf28c08']
+
+builddependencies = [
+    ('binutils', '2.38'),
+    ('CMake', '3.24.3'),
+]
+
+sanity_check_paths = {
+    'files': ['include/blosc2/blosc2-export.h', 'include/blosc2.h', 'lib/libblosc2.a',
+              'lib/libblosc2.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'lib'

easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022a.eb

@@ -0,0 +1,74 @@
+# http://www.pytables.org/usersguide/installation.html
+# updated: Denis Kristak (INUITS)
+
+easyblock = 'PythonBundle'
+
+name = 'PyTables'
+version = '3.8.0'
+
+homepage = 'https://www.pytables.org'
+description = """PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope
+ with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the
+ NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical
+ parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browsing,
+ processing and searching very large amounts of data. One important feature of PyTables is that it optimizes memory and 
+ disk resources so that data takes much less space (specially if on-flight compression is used) than other solutions 
+ such as relational or object oriented databases."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+toolchainopts = {'usempi': True}
+
+builddependencies = [
+    ('pkgconf', '1.8.0'),
+    ('CMake', '3.24.3'),
+    ('Ninja', '1.10.2'),
+    ('scikit-build', '0.15.0'),
+]
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),  # provides numexpr
+    ('HDF5', '1.12.2'),
+    ('LZO', '2.10'),
+    ('Blosc', '1.21.3'),
+    ('Blosc2', '2.6.1'),
+    ('py-cpuinfo', '9.0.0'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('blosc2', '2.0.0', {
+        'patches': ['blosc2-2.0.0_use-Blosc2-dep.patch'],
+        'checksums': [
+            {'blosc2-2.0.0.tar.gz': 'f19b0b3674f6c825b490f00d8264b0c540c2cdc11ec7e81178d38b83c57790a1'},
+            {'blosc2-2.0.0_use-Blosc2-dep.patch': '6a9443f378472ada3c8fe8a8a346fe16f22b01bab7d9e60c23b64b546178054b'},
+        ],
+    }),
+    ('tables', version, {
+        'patches': [
+            'PyTables-%(version)s_fix-libs.patch',
+            'PyTables-3.8.0_fix-find-blosc2-library-path.patch',
+        ],
+        'checksums': [
+            {'tables-3.8.0.tar.gz': '34f3fa2366ce20b18f1df573a77c1d27306ce1f2a41d9f9eff621b5192ea8788'},
+            {'PyTables-3.8.0_fix-libs.patch': '7a1e6fa1f9169e52293e2b433a4302fa13c5d31e7709cd4fe0e087199b9e3f8a'},
+            {'PyTables-3.8.0_fix-find-blosc2-library-path.patch':
+             'dcf6c3a16a138454296161e99cf6470620755d4c26303186a744f09a11e6013b'},
+        ],
+    }),
+]
+
+local_bins = ['pt2to3', 'ptdump', 'ptrepack', 'pttree']
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in local_bins],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+options = {'modulename': 'tables'}
+
+sanity_check_commands = ["%s --help" % x for x in local_bins]
+
+sanity_pip_check = True
+
+moduleclass = 'data'

easybuild/easyconfigs/p/PyTables/PyTables-3.8.0_fix-find-blosc2-library-path.patch

@@ -0,0 +1,44 @@
+determine location to Blosc2 library via $EBROOTBLOSC2, if defined,
+since mechanism to locate the library via blosc2-*.dist-info/RECORD doesn't work if blosc2 was not installed
+with vendored c-blosc2 library;
+author: Kenneth Hoste (HPC-UGent)
+--- tables-3.8.0/setup.py.orig	2023-01-19 20:10:15.637759755 +0100
++++ tables-3.8.0/setup.py	2023-01-19 20:11:48.590853686 +0100
+@@ -110,19 +110,25 @@
+
+ def get_blosc2_directories():
+     """Get Blosc2 directories for the C library by using wheel metadata"""
+-    try:
+-        import blosc2
+-    except ModuleNotFoundError:
+-        raise EnvironmentError("Cannot import the blosc2 requirement")
+-    version = blosc2.__version__
+-    basepath = Path(os.path.dirname(blosc2.__file__))
+-    recinfo = basepath.parent / f'blosc2-{version}.dist-info' / 'RECORD'
+     library_path = None
+-    for line in open(recinfo):
+-        if 'libblosc2' in line:
+-            library_path = Path(os.path.abspath(basepath.parent /
+-                                                Path(line[:line.find('libblosc2')])))
+-            break
++    blosc2_root = os.getenv('EBROOTBLOSC2')
++    if blosc2_root:
++        library_path = Path(os.path.join(blosc2_root, 'lib'))
++    else:
++        try:
++            import blosc2
++        except ModuleNotFoundError:
++            raise EnvironmentError("Cannot import the blosc2 requirement")
++        version = blosc2.__version__
++        basepath = Path(os.path.dirname(blosc2.__file__))
++        recinfo = basepath.parent / f'blosc2-{version}.dist-info' / 'RECORD'
++        library_path = None
++        for line in open(recinfo):
++            if 'libblosc2' in line:
++                library_path = Path(os.path.abspath(basepath.parent /
++                                                    Path(line[:line.find('libblosc2')])))
++                break
++
+     if not library_path:
+         raise NotADirectoryError("Library directory not found for blosc2!")
+

easybuild/easyconfigs/p/PyTables/PyTables-3.8.0_fix-libs.patch

@@ -0,0 +1,15 @@
+# pyTables expects that LIBS is a list of library names and will add
+# a -l by itself.
+# original patch by ward.poelmans@ugent.be, ported to newer PyTables version by Kenneth Hoste (HPC-UGent)
+--- PyTables-3.8.0/setup.py.orig	2023-01-11 19:14:27.160064110 +0100
++++ PyTables-3.8.0/setup.py	2023-01-11 19:21:48.460252182 +0100
+@@ -576,6 +576,9 @@
+     # is not a good idea.
+     CFLAGS = os.environ.get("CFLAGS", "").split()
+     LIBS = os.environ.get("LIBS", "").split()
++    for idx, lib in enumerate(LIBS):
++        if lib.startswith("-l"):
++            LIBS[idx] = lib.replace("-l", "")
+     CONDA_PREFIX = os.environ.get("CONDA_PREFIX", "")
+     # We start using pkg-config since some distributions are putting HDF5
+     # (and possibly other libraries) in exotic locations.  See issue #442.

easybuild/easyconfigs/p/PyTables/blosc2-2.0.0_use-Blosc2-dep.patch

@@ -0,0 +1,24 @@
+make blosc2 use provided Blosc2 dependency, rather than letting it build its own vendored copy of c-blosc2
+author: Kenneth Hoste (HPC-UGent)
+--- blosc2-2.0.0/blosc2/CMakeLists.txt.orig	2023-01-19 13:20:38.055582814 +0100
++++ blosc2-2.0.0/blosc2/CMakeLists.txt	2023-01-19 13:21:03.808615093 +0100
+@@ -7,17 +7,14 @@
+ set(BUILD_FUZZERS OFF CACHE BOOL "Build C-Blosc2 fuzzers")
+
+ set(CMAKE_POSITION_INDEPENDENT_CODE ON)
+-# we want the binaries of the C-Blosc2 library to go into the wheels
+-set(BLOSC_INSTALL ON)
+-add_subdirectory(c-blosc2)
+-include_directories("${CMAKE_CURRENT_SOURCE_DIR}/c-blosc2/include")
++include_directories("$ENV{EBROOTBLOSC2}/include")
+ include_directories("${Python_NumPy_INCLUDE_DIRS}")
+
+
+ add_cython_target(blosc2_ext blosc2_ext.pyx)
+ add_library(blosc2_ext MODULE ${blosc2_ext})
+
+-target_link_libraries(blosc2_ext blosc2_static)
++target_link_libraries(blosc2_ext $ENV{EBROOTBLOSC2}/lib/libblosc2.a)
+
+ python_extension_module(blosc2_ext)
+

easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-9.0.0-GCCcore-11.3.0.eb

@@ -0,0 +1,39 @@
+easyblock = 'PythonPackage'
+
+name = 'py-cpuinfo'
+version = '9.0.0'
+
+homepage = 'https://github.com/workhorsy/py-cpuinfo'
+description = "py-cpuinfo gets CPU info with pure Python."
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['3cdbbf3fac90dc6f118bfd64384f309edeadd902d7c8fb17f02ffa1fc3f49690']
+
+builddependencies = [
+    ('binutils', '2.38'),
+]
+
+dependencies = [
+    ('Python', '3.10.4'),
+]
+
+download_dep_fail = True
+use_pip = True
+
+sanity_check_paths = {
+    'files': ['bin/cpuinfo'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = [
+    "cpuinfo",
+    "python -m cpuinfo",
+]
+
+options = {'modulename': 'cpuinfo'}
+
+sanity_pip_check = True
+
+moduleclass = 'tools'