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pyproject.toml
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pyproject.toml
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[project]
name = "mgnify_pipelines_toolkit"
version = "0.1.8"
readme = "README.md"
license = {text = "Apache Software License 2.0"}
authors = [
{ name = "MGnify team", email = "[email protected]" },
]
keywords = ["bioinformatics", "pipelines", "metagenomics"]
description = "Collection of scripts and tools for MGnify pipelines"
requires-python = ">=3.9"
classifiers = [
"Programming Language :: Python :: 3",
"License :: OSI Approved :: Apache Software License",
"Operating System :: OS Independent",
]
dependencies = [
"biopython==1.82",
"numpy==1.26.0",
"pandas==2.0.2",
"regex==2023.12.25",
"requests==2.32.3"
]
[build-system]
requires = ["setuptools>=61.0"]
build-backend = "setuptools.build_meta"
[tool.setuptools]
packages = ["mgnify_pipelines_toolkit",
"mgnify_pipelines_toolkit.analysis",
"mgnify_pipelines_toolkit.constants",
"mgnify_pipelines_toolkit.utils",
"mgnify_pipelines_toolkit.analysis.shared",
"mgnify_pipelines_toolkit.analysis.amplicon",
"mgnify_pipelines_toolkit.analysis.assembly",
]
[project.scripts]
# analysis.shared
get_subunits = "mgnify_pipelines_toolkit.analysis.shared.get_subunits:main"
get_subunits_coords = "mgnify_pipelines_toolkit.analysis.shared.get_subunits_coords:main"
mapseq2biom = "mgnify_pipelines_toolkit.analysis.shared.mapseq2biom:main"
fastq_suffix_header_check = "mgnify_pipelines_toolkit.analysis.shared.fastq_suffix_header_check:main"
library_strategy_check = "mgnify_pipelines_toolkit.analysis.shared.library_strategy_check:main"
# analysis.amplicon
are_there_primers = "mgnify_pipelines_toolkit.analysis.amplicon.are_there_primers:main"
assess_inflection_point_mcp = "mgnify_pipelines_toolkit.analysis.amplicon.assess_inflection_point_mcp:main"
assess_mcp_proportions = "mgnify_pipelines_toolkit.analysis.amplicon.assess_mcp_proportions:main"
classify_var_regions = "mgnify_pipelines_toolkit.analysis.amplicon.classify_var_regions:main"
find_mcp_inflection_points = "mgnify_pipelines_toolkit.analysis.amplicon.find_mcp_inflection_points:main"
make_asv_count_table = "mgnify_pipelines_toolkit.analysis.amplicon.make_asv_count_table:main"
remove_ambiguous_reads = "mgnify_pipelines_toolkit.analysis.amplicon.remove_ambiguous_reads:main"
rev_comp_se_primers = "mgnify_pipelines_toolkit.analysis.amplicon.rev_comp_se_primers:main"
standard_primer_matching = "mgnify_pipelines_toolkit.analysis.amplicon.standard_primer_matching:main"
mapseq_to_asv_table = "mgnify_pipelines_toolkit.analysis.amplicon.mapseq_to_asv_table:main"
primer_val_classification = "mgnify_pipelines_toolkit.analysis.amplicon.primer_val_classification:main"
# analysis.assembly
add_rhea_chebi_annotation = "mgnify_pipelines_toolkit.analysis.assembly.add_rhea_chebi_annotation:main"
# utils
fasta_to_delimited = "mgnify_pipelines_toolkit.utils.fasta_to_delimited:main"
get_mpt_version = "mgnify_pipelines_toolkit.utils.get_mpt_version:main"
[project.optional-dependencies]
tests = [
"pytest==7.4.0",
"pytest-md==0.2.0",
"pytest-workflow==2.0.1",
"biopython==1.82",
"pandas==2.0.2",
"numpy==1.26.0",
"regex==2023.12.25",
"requests==2.32.3"
]
dev = [
"mgnify_pipelines_toolkit[tests]",
"pre-commit==3.8.0",
"black==24.8.0",
"flake8==7.1.1",
"pep8-naming==0.14.1"
]