Merge pull request #20116 from pavelToman/20240314150352_new_pr_Singl…

…e-cell-python-bundle202402

{bio}[foss/2023a] Single-cell-python-bundle v2024.02

easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-12.3.0.eb

@@ -0,0 +1,39 @@
+# Updated to MesonNinja as the autogen.sh complained.
+# Author: J. Sassmannshausen (Imperial College London)
+
+easyblock = 'MesonNinja'
+
+name = 'cairomm'
+version = '1.16.2'
+
+homepage = 'http://cairographics.org'
+description = "The Cairomm package provides a C++ interface to Cairo."
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+
+source_urls = ['http://cairographics.org/releases/']
+sources = [SOURCE_TAR_XZ]
+checksums = ['6a63bf98a97dda2b0f55e34d1b5f3fb909ef8b70f9b8d382cb1ff3978e7dc13f']
+
+builddependencies = [
+    ('Meson', '1.1.1'),
+    ('Ninja', '1.11.1'),
+    ('Doxygen', '1.9.7'),
+    ('M4', '1.4.19'),
+]
+
+dependencies = [
+    ('cairo', '1.17.8'),
+    ('libsigc++', '3.6.0'),
+    ('mm-common', '1.0.6'),
+    ('Boost', '1.82.0'),
+]
+
+runtest = 'ninja test'
+
+sanity_check_paths = {
+    'files': ['lib/libcairomm-1.16.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'vis'

easybuild/easyconfigs/g/gawk/gawk-5.3.0-GCC-12.3.0.eb

@@ -0,0 +1,23 @@
+easyblock = 'ConfigureMake'
+
+name = 'gawk'
+version = '5.3.0'
+
+homepage = 'https://www.gnu.org/software/gawk'
+description = """The awk utility interprets a special-purpose programming language that makes it possible to handle
+simple data-reformatting jobs with just a few lines of code."""
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCE_TAR_GZ]
+checksums = ['378f8864ec21cfceaa048f7e1869ac9b4597b449087caf1eb55e440d30273336']
+
+sanity_check_paths = {
+    'files': ['bin/gawk'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["gawk --help"]
+
+moduleclass = 'tools'

easybuild/easyconfigs/g/graph-tool/graph-tool-2.59-foss-2023a.eb

@@ -0,0 +1,62 @@
+# Author: J. Sassmannshausen (Imperial College London/UK)
+# Update: Pavel Tománek (Inuits)
+
+easyblock = 'ConfigureMake'
+
+name = 'graph-tool'
+version = '2.59'
+
+homepage = 'https://graph-tool.skewed.de/'
+description = """Graph-tool is an efficient Python module for manipulation and
+ statistical analysis of graphs (a.k.a. networks). Contrary to
+ most other python modules with similar functionality, the core
+ data structures and algorithms are implemented in C++, making
+ extensive use of template metaprogramming, based heavily on
+ the Boost Graph Library. This confers it a level of
+ performance that is comparable (both in memory usage and
+ computation time) to that of a pure C/C++ library."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'cstd': 'c++17', 'openmp': True}
+
+source_urls = ['https://downloads.skewed.de/%(name)s/']
+sources = [SOURCE_TAR_BZ2]
+checksums = ['cde479c0a7254b72f6e795d03b0273b0a7d81611a6a3364ba649c2c85c99acae']
+
+builddependencies = [
+    ('gawk', '5.3.0'),
+    ('pkgconf', '1.9.5'),
+    ('expat', '2.5.0'),
+    ('CGAL', '5.6'),
+    ('GMP', '6.2.1'),
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Boost.Python', '1.82.0'),
+    ('sparsehash', '2.0.4'),
+    ('matplotlib', '3.7.2'),
+    ('PyCairo', '1.25.0'),
+    ('cairomm', '1.16.2'),
+    ('PyGObject', '3.46.0'),
+    ('GTK3', '3.24.37'),
+]
+
+configopts = '--enable-openmp --with-cgal=$EBROOTCGAL --with-boost=$EBROOTBOOST '
+configopts += '--with-boost-python=boost_python311  '
+configopts += '--with-python-module-path=%(installdir)s/lib/python%(pyshortver)s/site-packages '
+
+
+sanity_check_paths = {
+    'files': ['lib/python%(pyshortver)s/site-packages/graph_tool/all.py'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/graph_tool/include', 'share'],
+}
+
+sanity_check_commands = [
+    "python -c 'from graph_tool.all import Graph, BlockState'",
+    "python -c 'import graph_tool.inference'",
+]
+
+modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
+
+moduleclass = 'math'

easybuild/easyconfigs/p/Pyomo/Pyomo-6.7.3-foss-2023a.eb

@@ -0,0 +1,34 @@
+easyblock = 'PythonBundle'
+
+name = 'Pyomo'
+version = '6.7.3'
+
+homepage = 'https://www.pyomo.org/'
+description = """ Pyomo is a Python-based open-source software package that supports a diverse set of optimization
+ capabilities for formulating and analyzing optimization models. """
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('mpi4py', '3.1.4'),
+    ('PLY', '3.11'),
+]
+
+exts_list = [
+    ('PyUtilib', '6.0.0', {
+        'preinstallopts': """sed -i "s/'nose',//g" setup.py && """,
+        'checksums': ['d3c14f8ed9028a831b2bf51b8ab7776eba87e66cfc58a06b99c359aaa640f040'],
+    }),
+    (name, version, {
+        'checksums': ['b7f0441c405af4f42f38527ae38826a5c0a4984dd7bea1fe07172789d8594770'],
+    }),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+sanity_check_commands = ['pyomo -h']
+
+moduleclass = 'math'