Merge pull request #21694 from PetrKralCZ/20241017190952_new_pr_scTIE…

…20231205

{bio,lib,math}[foss/2023a] scTIE v20231205, POT v0.9.3, CVXOPT v1.3.2 w/ CUDA 12.1.1

easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.3.2-foss-2023a.eb

@@ -0,0 +1,49 @@
+easyblock = 'PythonPackage'
+
+name = 'CVXOPT'
+version = '1.3.2'
+
+homepage = 'https://cvxopt.org'
+description = """CVXOPT is a free software package for convex optimization based on the Python programming language.
+ Its main purpose is to make the development of software for convex optimization applications straightforward by
+ building on Python's extensive standard library and on the strengths of Python as a high-level programming language.
+"""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'pic': True}
+
+source_urls = [PYPI_LOWER_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+
+patches = ['CVXOPT-1.3.1_fix-setup-py.patch']
+
+checksums = [
+    '3461fa42c1b2240ba4da1d985ca73503914157fc4c77417327ed6d7d85acdbe6',  # cvxopt-1.3.2.tar.gz
+    '350904c0427d4652fc73b95b7e0d78a17c917cb94ed6c356dbbbfb07f2173849',  # CVXOPT-1.3.1_fix-setup-py.patch
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SuiteSparse', '7.1.0'),
+    ('GSL', '2.7'),
+]
+
+use_pip = True
+sanity_pip_check = True
+download_dep_fail = True
+
+preinstallopts = " ".join([
+    'CVXOPT_BUILD_FFTW=1',
+    'CVXOPT_BUILD_GSL=1',
+    'CVXOPT_BLAS_EXTRA_LINK_ARGS="$LIBBLAS"',
+    'CVXOPT_LAPACK_EXTRA_LINK_ARGS="$LIBLAPACK"',
+    'CVXOPT_FFTW_EXTRA_LINK_ARGS="$LIBFFT"',
+    'CVXOPT_SUITESPARSE_LIB_DIR=$EBROOTSUITESPARSE/lib',
+    'CVXOPT_SUITESPARSE_INC_DIR=$EBROOTSUITESPARSE/include',
+])
+
+installopts = ' --no-binary cvxopt'
+
+sanity_check_commands = ['cd %(builddir)s/%(namelower)s-%(version)s && python -m unittest discover -s tests']
+
+moduleclass = 'math'

easybuild/easyconfigs/p/POT/POT-0.9.3-foss-2023a-CUDA-12.1.1.eb

@@ -0,0 +1,47 @@
+easyblock = 'PythonBundle'
+
+name = 'POT'
+version = '0.9.3'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://github.com/rflamary/POT'
+description = """POT (Python Optimal Transport) is a Python library provide several solvers for optimization problems
+ related to Optimal Transport for signal, image processing and machine learning."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('matplotlib', '3.7.2'),
+    ('scikit-learn', '1.3.1'),
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('PyTorch', '2.1.2', versionsuffix),
+    ('jax', '0.4.25', versionsuffix),
+    ('CVXOPT', '1.3.2'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('autograd', '1.7.0', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['49680300f842f3a8722b060ac0d3ed7aca071d1ad4d3d38c9fdadafdcc73c30b'],
+    }),
+    ('versioneer', '0.29', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['0f1a137bb5d6811e96a79bb0486798aeae9b9c6efc24b389659cebb0ee396cb9'],
+    }),
+    ('pymanopt', '2.2.1', {
+        # Requirements forbid some versions of `scipy` which are known to have a bug but we have fixed it.
+        # see `scipy-1.11.1_vectorization_error.patch`
+        'preinstallopts': """sed -i 's/"scipy>=1.0[^"]*"/"scipy>=1.0"/g' pyproject.toml && """,
+        'checksums': ['c784929a436eb06d73371b53ae5db3cdc19c5e60280f8131553bc805cbf7a1da'],
+    }),
+    (name, version, {
+        'modulename': 'ot',
+        'checksums': ['eecf2394390a73472e727ef75f7c801fc47509039f00c40f8fc64fdeea617c86'],
+    }),
+]
+
+moduleclass = 'lib'

easybuild/easyconfigs/s/scTIE/scTIE-20231205-foss-2023a-CUDA-12.1.1.eb

@@ -0,0 +1,46 @@
+easyblock = 'Tarball'
+
+name = 'scTIE'
+version = '20231205'
+local_commit = '044d91a'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://github.com/SydneyBioX/scTIE'
+description = """scTIE (single-cell Temporal Integration and inference of multimodal Experiments)
+ is an autoencoder-based method for integrating multimodal profiling of scRNA-seq and scATAC-seq
+ data over a time course and inferring cell-type specific GRNs. scTIE projects cells from all time
+ points into a common embedding space, followed by extracting interpretable information from this
+ space to predict cell trajectories."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+github_account = 'SydneyBioX'
+source_urls = [GITHUB_SOURCE]
+sources = ['%s.tar.gz' % local_commit]
+checksums = ['bcbf7c846539d0f04e7bbf3cc6ae2fe075a4ba11e3a4388c29def943d39af53e']
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('PyTorch', '2.1.2', versionsuffix),
+    ('SciPy-bundle', '2023.07'),
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('POT', '0.9.3', versionsuffix),
+]
+
+postinstallcmds = ['cd %(installdir)s && mkdir bin && ln -r -s main.py bin/sctie && chmod a+x main.py']
+
+fix_python_shebang_for = ['main.py']
+
+modextrapaths = {
+    'PATH': '',
+    'PYTHONPATH': '',
+}
+
+sanity_check_paths = {
+    'files': ['bin/sctie'],
+    'dirs': [],
+}
+
+sanity_check_commands = ['sctie --help']
+
+moduleclass = 'bio'