{bio}foss/2022a] CellRank v2.0.2, scVelo v0.2.5, slepc4py v3.17.2, petsc4py v3.17.4

easybuild/easyconfigs/c/CellRank/CellRank-2.0.2-foss-2022a.eb

@@ -0,0 +1,67 @@
+easyblock = 'PythonBundle'
+
+name = 'CellRank'
+version = '2.0.2'
+
+homepage = 'https://cellrank.readthedocs.io/en/stable/'
+description = """CellRank is a toolkit to uncover cellular dynamics based on
+ Markov state modeling of single-cell data.  It contains two main modules:
+kernels compute cell-cell transition probabilities and estimators generate
+hypothesis based on these. """
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('petsc4py', '3.17.4'),
+    ('slepc4py', '3.17.2'),
+    ('scikit-learn', '1.1.2'),
+    ('scVelo', '0.2.5'),
+    ('scanpy', '1.9.1'),  # also provides anndata
+    ('numba', '0.56.4'),
+    ('networkx', '2.8.4'),
+    ('matplotlib', '3.5.2'),
+    ('Seaborn', '0.12.1'),
+    ('wrapt', '1.15.0'),
+]
+
+use_pip = True
+
+_preinstallopts_pygam = """sed -i -e 's/numpy = .*/numpy = "^1.22.3"/g' """
+_preinstallopts_pygam += """-e 's/scipy = .*/scipy = "^1.8.1"/g' pyproject.toml && """
+
+exts_list = [
+    ('docrep', '0.3.2', {
+        'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'],
+    }),
+    ('python-utils', '3.8.1', {
+        'checksums': ['ec3a672465efb6c673845a43afcfafaa23d2594c24324a40ec18a0c59478dc0b'],
+    }),
+    ('progressbar2', '4.3.2', {
+        'modulename': 'progressbar',
+        'checksums': ['c37e6e1b4e57ab43f95c3d0e8d90061bec140e4fed56b8343183db3aa1e19a52'],
+    }),
+    ('pygam', '0.9.0', {
+        'patches': ['pygam-0.9.0_fix-poetry.patch'],
+        'checksums': [
+            {'pygam-0.9.0.tar.gz': 'dba62285a275cdd15a6adf764f6717b3cd077502f01cf1bcee5ce7cbda221956'},
+            {'pygam-0.9.0_fix-poetry.patch': '90460a5416167f146f5bf2c55e46c23d1e7a8f864652e24665354a1b39d7e3d0'},
+        ],
+        'preinstallopts': _preinstallopts_pygam,
+    }),
+    ('pygpcca', '1.0.4', {
+        'checksums': ['5e3b49279abc62d25133811daeee050715f995ff02042c46e2a2034331d090d1'],
+        'preinstallopts': "sed -i 's/jinja2==/jinja2>=/g' requirements.txt && ",
+    }),
+    ('cellrank', version, {
+        'checksums': ['47c1d2e953ac91f572937d816142b4ac5f0c876174c60f857562de76a9f8aa61'],
+        # strip away too strict version requirements for pandas + anndata
+        'preinstallopts': "sed -i -e 's/pandas>=1.5.0/pandas/g' -e 's/anndata>=0.9/anndata/g' pyproject.toml && ",
+    }),
+]
+
+sanity_pip_check = True
+
+sanity_check_commands = ["python -c 'import cellrank as cr'"]
+
+moduleclass = 'bio'

easybuild/easyconfigs/c/CellRank/pygam-0.9.0_fix-poetry.patch

@@ -0,0 +1,26 @@
+workaround for:
+  RuntimeError: The Poetry configuration is invalid:
+    - Additional properties are not allowed ('group' was unexpected)
+author: Kenneth Hoste (HPC-UGent)
+--- pygam-0.9.0/pyproject.toml.orig	2024-01-05 22:13:47.399107878 +0100
++++ pygam-0.9.0/pyproject.toml	2024-01-05 22:13:52.323119792 +0100
+@@ -12,19 +12,6 @@
+ scipy = "^1.10.1"
+ progressbar2 = "^4.2.0"
+
+-[tool.poetry.group.dev.dependencies]
+-pytest = "^7.2.2"
+-flake8 = "^6.0.0"
+-codecov = "^2.1.12"
+-pytest-cov = "^4.0.0"
+-mock = "^5.0.1"
+-nbsphinx = "^0.9.0"
+-sphinx-rtd-theme = "^1.2.0"
+-sphinxcontrib-napoleon = "^0.7"
+-ipython = "^8.11.0"
+-pandas = "^1.5.3"
+-black = "^23.1.0"
+-
+ [tool.black]
+ line-length = 88
+ skip-string-normalization = true

easybuild/easyconfigs/p/petsc4py/petsc4py-3.17.4-foss-2022a.eb

@@ -0,0 +1,26 @@
+easyblock = 'PythonPackage'
+
+name = 'petsc4py'
+version = '3.17.4'
+
+homepage = 'https://bitbucket.org/petsc/petsc4py'
+description = "petsc4py are Python bindings for PETSc, the Portable, Extensible Toolchain for Scientific Computation."
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['216c3da074557946615d37d0826bc89f1f2e599323e2dacbdc45326d78bd50c6']
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('PETSc', version),
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+sanity_check_commands = ["python -c 'from petsc4py import PETSc'"]
+
+moduleclass = 'tools'

easybuild/easyconfigs/s/scVelo/scVelo-0.2.5-foss-2022a.eb

@@ -0,0 +1,47 @@
+easyblock = 'PythonBundle'
+
+name = 'scVelo'
+version = '0.2.5'
+
+homepage = "https://scvelo.org"
+description = """scVelo is a scalable toolkit for estimating and analyzing RNA velocities in single cells using
+ dynamical modeling."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+builddependencies = [
+    ('pkgconf', '1.8.0'),
+]
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('scikit-learn', '1.1.2'),
+    ('h5py', '3.7.0'),
+    ('matplotlib', '3.5.2'),
+    ('networkx', '2.8.4'),
+    ('numba', '0.56.4'),
+    ('PyTables', '3.8.0'),
+    ('statsmodels', '0.13.1'),
+    ('libpng', '1.6.37'),
+    ('freetype', '2.12.1'),
+    ('Tkinter', '%(pyver)s'),
+    ('tqdm', '4.64.0'),
+    ('scanpy', '1.9.1'),  # also provides anndata
+    ('Seaborn', '0.12.1'),
+    ('loompy', '3.0.7'),  # also provides numpy-groupies
+    ('umap-learn', '0.5.3'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    (name, version, {
+        'modulename': 'scvelo',
+        'source_tmpl': '%(namelower)s-%(version)s.tar.gz',
+        'checksums': ['7e32d9e34245971330d69c12f4339cebe0acebb61e59a8b1aca9b369078b5207'],
+    }),
+]
+
+moduleclass = 'bio'

easybuild/easyconfigs/s/slepc4py/slepc4py-3.17.2-foss-2022a.eb

@@ -0,0 +1,26 @@
+easyblock = 'PythonPackage'
+
+name = 'slepc4py'
+version = '3.17.2'
+
+homepage = 'https://bitbucket.org/slepc/slepc4py'
+description = "Python bindings for SLEPc, the Scalable Library for Eigenvalue Problem Computations."
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['e5b235486b6901cd4ff0d94083f0e5eeacaef3a2893e1714769717ad488a3885']
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SLEPc', version),
+    ('petsc4py', '3.17.4'),
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+sanity_check_commands = ["python -c 'from slepc4py import SLEPc'"]
+
+moduleclass = 'tools'