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pyproject.toml
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[build-system]
requires = [
"setuptools >= 62.3.0",
"wheel >= 0.29.0",
]
build-backend = 'setuptools.build_meta'
[project]
name = 'ccbr_tools'
dynamic = ['version','readme']
description = "Utilities for CCBR Bioinformatics Software"
authors = [
{name = "Kelly Sovacool", email = "[email protected]"},
{name = "Vishal Koparde", email = "[email protected]"},
{name = "Skyler Kuhn"},
{name = "Mayank Tandon"},
{name = "Susan Huse"},
]
maintainers = [
{name = "CCR Collaborative Bioinformatics Resource", email = "[email protected]"},
]
license = {file = "LICENSE"}
classifiers = [
"Environment :: Console",
"Environment :: MacOS X",
"Intended Audience :: Science/Research",
"License :: OSI Approved :: MIT license",
"Natural Language :: English",
"Operating System :: POSIX :: Linux",
"Operating System :: MacOS :: MacOS X",
"Programming Language :: Python :: 3.7",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Topic :: Scientific/Engineering :: Bio-Informatics",
]
requires-python = ">3.10, <3.12"
dependencies = [
"biopython",
"cffconvert >= 2.0.0",
"Click >= 8.1.3",
"pandas",
"pyyaml >= 6.0",
"requests"
]
[project.optional-dependencies]
dev = [
"black >= 23.10.0",
"pre-commit"
]
test = [
"pytest",
"pytest-cov"
]
docs = [
"quartodoc >= v0.7.6",
"jupyter"
]
[project.scripts]
ccbr_tools = "ccbr_tools.__main__:main"
gb2gtf = "ccbr_tools.gb2gtf:main"
hf = "ccbr_tools.homologfinder.hf:main"
jobby = "ccbr_tools.jobby:main"
jobinfo = "ccbr_tools.jobinfo:main"
intersect = "ccbr_tools.intersect:main"
peek = "ccbr_tools.peek:main"
[project.urls]
Repository = "https://github.com/CCBR/Tools"
[tool.numpydoc_validation]
checks = [
"all", # report on all checks, except the below
"EX01",
"SA01",
"ES01",
]
# remember to use single quotes for regex in TOML
exclude = [ # don't report on objects that match any of these regex
'\.undocumented_method$',
'\.__repr__$',
]
override_SS05 = [ # override SS05 to allow docstrings starting with these words
'^Process ',
'^Assess ',
'^Access ',
]
[tool.setuptools.package-data]
"*" = ["LICENSE", "VERSION", "CITATION.cff", "CHANGELOG.md", "pyproject.toml"]
"ccbr_tools.templates" = ["src/ccbr_tools/templates/*"]
"ccbr_tools.extensions" = ["src/ccbr_tools/_extensions/**"]
"ccbr_tools.homologfinder" = ["src/ccbr_tools/homologfinder/*.rpt","src/ccbr_tools/homologfinder/*.txt"]
[tool.setuptools.dynamic]
version = {file = "VERSION"}
readme = {file = "README.md"}
[tool.setuptools]
script-files = [
"scripts/add_gene_name_to_count_matrix.R",
"scripts/aggregate_data_tables.R",
"scripts/argparse.bash",
"scripts/cancel_snakemake_jobs.sh",
"scripts/create_hpc_link.sh",
"scripts/extract_value_from_json.py",
"scripts/extract_value_from_yaml.py",
"scripts/filter_bam_by_readids.py",
"scripts/filter_fastq_by_readids_highmem.py",
"scripts/filter_fastq_by_readids_highmem_pe.py",
"scripts/gather_cluster_stats.sh",
"scripts/gather_cluster_stats_biowulf.sh",
"scripts/get_buyin_partition_list.bash",
"scripts/get_slurm_file_with_error.sh",
"scripts/github_milestones.sh",
"scripts/gsea_preranked.sh",
"scripts/karyoploter.R",
"scripts/make_labels_for_pipeliner.sh",
"scripts/rawcounts2normalizedcounts_DESeq2.R",
"scripts/rawcounts2normalizedcounts_limmavoom.R",
"scripts/run_jobby_on_nextflow_log",
"scripts/run_jobby_on_nextflow_log_full_format",
"scripts/run_jobby_on_snakemake_log",
"scripts/run_jobby_on_snakemake_log_full_format",
"scripts/spooker",
"scripts/which_vpn.sh"
]