scenicplus-1.0.0-foss-2022b.eb

easyblock = 'PythonBundle'

name = 'scenicplus'
version = '1.0.0'

homepage = 'https://scenicplus.readthedocs.io/'
description = """SCENIC+ is a python package to build enhancer driven gene regulatory networks
 (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell
 chromatin accessibility (scATAC-seq) data."""

toolchain = {'name': 'foss', 'version': '2022b'}

builddependencies = [
    ('Rust', '1.65.0'),
    ('nodejs', '18.12.1'),
    ('CMake', '3.24.3'),
]

dependencies = [
    ('Python', '3.10.8'),
    ('SciPy-bundle', '2023.02'),
    ('pySCENIC', '0.12.1'),
    ('Biopython', '1.81'),
    ('pycisTarget', '1.0.2'),
    ('matplotlib', '3.7.0'),
    ('MACS2', '2.2.9.1'),
    ('h5py', '3.8.0'),
    ('plotly.py', '5.13.1'),
    ('lxml', '4.9.2'),
    ('pyBigWig', '0.3.22'),
    ('Seaborn', '0.12.2'),
    ('scanpy', '1.9.3'),
    ('jupyter-server', '2.7.0'),
    ('meson-python', '0.11.0'),
    ('Ray-project', '2.6.2'),
    ('BeautifulSoup', '4.11.1'),
    ('scikit-build', '0.17.2'), # for Levenshtein
]

use_pip = True
sanity_pip_check = False

local_preinstallopts = ' sed -i -e "s/setup(/setup(version=\'%(version)s\',/" setup.py && '
local_preinstallopts += ' sed -i -e "s/use_scm_version=True/use_scm_version=False/" setup.py && '

exts_list = [
    ('pyproject-metadata', '0.7.1'),
    ('kaleido', '0.2.1', {
        #https://files.pythonhosted.org/packages/ae/b3/a0f0f4faac229b0011d8c4a7ee6da7c2dca0b6fd08039c95920846f23ca4/kaleido-0.2.1-py2.py3-none-manylinux1_x86_64.whl
        'source_tmpl': '%(name)s-%(version)s-py2.py3-none-manylinux1_x86_64.whl',
    }),
    ('click', '8.1.6'), #  from loompy
    ('numpy_groupies', '0.9.22'), #  from loompy
    ('loompy', '3.0.7'),
    ('mypy_extensions', '1.0.0'),
    ('typing_inspect', '0.9.0'),
    ('marshmallow', '3.20.1'),
    ('dataclasses_json', '0.5.14'),
    ('loomxpy', '0.4.2'),
    ('mudata', '0.2.3'),
    ('arboreto', '0.1.6', {
        # the source on PyPI is missing 'requirements.txt', fetching from github instead
        'source_urls': ['https://github.com/aertslab/arboreto/archive/refs/tags/'],
        'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}],
        'checksums': ['f94c0bc084ca61422e8b74ecdb80585a45b168ac682f18dd3c52c9097ee29caa'],
    }),
    ('gseapy', '0.10.8'),
    ('ctxcore', '0.2.0', {
        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
    }),
    ('adjustText', '0.8', {
        'modulename': 'adjustText',
    }),
    ('nodeenv', '1.8.0'),
    ('sphinx-theme-builder', '0.2.0b2', {
        'modulename': 'sphinx_theme_builder',
    }),
    ('certifi', '2023.7.22'),
    ('nbsphinx', '0.9.2'),
    ('nbsphinx-link', '1.3.0', {
        'modulename': 'nbsphinx_link',
    }),
    ('tzdata', '2023.3'),
    ('mizani', '0.10.0'),  # from plotnine
    ('patsy', '0.5.3'), # from plotnine
    ('statsmodels', '0.14.0'), # from plotnine
    ('plotnine', '0.12.2'),
    ('python-utils', '3.7.0', {
        'modulename': 'python_utils',
    }),
    ('progressbar2', '4.2.0', { #  from pygam
        'modulename': 'progressbar',
    }),
    ('pygam', '0.9.0'),
    ('autopaths', '1.6.0'),
    ('retry', '0.9.2'), #  from plumbing
    ('plumbing', '2.11.2'),
    ('sh', '2.0.6'),
    ('fasta', '2.3.2'),
    ('pyfaidx', '0.7.2.1'),
    ('lda', '2.0.0'),
    ('globre', '0.1.5'), #  from tmtoolkit
    ('et_xmlfile', '1.1.0'), #  from openpyxl
    ('openpyxl', '3.1.2'), #  from tmtoolkit
    ('bidict', '0.22.1'), #  from tmtoolkit
    ('tmtoolkit', '0.12.0'), # from pycistopic
    ('named', '1.3.0'), #  from Levenshtein
    ('Levenshtein', '0.21.1'), # from pycistopic
    ('pycisTopic', '1.0.2', {
        'modulename': 'pycisTopic',
        'preinstallopts': local_preinstallopts,
        'source_urls': ['https://github.com/aertslab/pycisTopic/archive/refs/tags'],
        'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}],
    }),
    #('pycistarget', '1.0.2', {
    #    'preinstall_opts': local_preinstallopts,
    #    'source_urls': ['https://github.com/aertslab/pycistarget/archive/refs/tags'],
    #    'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}],
    #}),
    ('tspex', '0.6.3'),
    (name, version, {
        'preinstallopts': local_preinstallopts,
        'source_tmpl': 'v%(version)s.tar.gz',
        'source_urls': ['https://github.com/aertslab/scenicplus/archive/refs/tags'],
    }),
]

sanity_check_paths = {
    'files': [],
    'dirs': ['lib/python%(pyshortver)s/site-packages'],
}

moduleclass = 'bio'