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pyproject.toml
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[build-system]
requires = ["setuptools>=61.0", "wheel"]
build-backend = "setuptools.build_meta"
[project]
name = "rpbp"
description = "Rp-Bp: Ribosome Profiling with Bayesian Predictions"
readme = "README.md"
license = { text = "MIT" }
authors = [{ name = "Brandon Malone" }]
maintainers = [
{ name = "Etienne Boileau", email = "boileau@uni-heidelberg.de" }
]
keywords = [
"bioinformatics",
"riboseq",
"open reading frame discovery",
"translation"
]
# See https://pypi.python.org/pypi?%3Aaction=list_classifiers
classifiers = [
"Development Status :: 4 - Beta",
"Intended Audience :: Science/Research",
"Topic :: Scientific/Engineering :: Bio-Informatics",
"License :: OSI Approved :: MIT License",
"Operating System :: MacOS :: MacOS X",
"Operating System :: POSIX :: Linux",
"Programming Language :: Python :: 3 :: Only",
"Programming Language :: Python :: 3.7",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
]
dynamic = ["version"]
requires-python = ">=3.7,<3.11"
dependencies = [
"pbiotools>=4.0.2",
"appdirs",
"biopython",
"cmdstanpy",
"dash",
"dash-bio",
"dash-bootstrap-components",
"statsmodels",
]
[project.scripts]
# preprocessing
extract-orf-coordinates = "rpbp.reference_preprocessing.extract_orf_coordinates:main"
label-orfs = "rpbp.reference_preprocessing.label_orfs:main"
prepare-rpbp-genome = "rpbp.reference_preprocessing.prepare_rpbp_genome:main"
# pipeline
run-rpbp-pipeline = "rpbp.run_rpbp_pipeline:main"
run-all-rpbp-instances = "rpbp.run_all_rpbp_instances:main"
# profile construction
create-orf-profiles = "rpbp.orf_profile_construction.create_orf_profiles:main"
create-base-genome-profile = "rpbp.orf_profile_construction.create_base_genome_profile:main"
extract-orf-profiles = "rpbp.orf_profile_construction.extract_orf_profiles:main"
merge-replicate-orf-profiles = "rpbp.translation_prediction.merge_replicate_orf_profiles:main"
extract-metagene-profiles = "rpbp.orf_profile_construction.extract_metagene_profiles:main"
estimate-metagene-profile-bayes-factors = "rpbp.orf_profile_construction.estimate_metagene_profile_bayes_factors:main"
select-periodic-offsets = "rpbp.orf_profile_construction.select_periodic_offsets:main"
# translation prediction
predict-translated-orfs = "rpbp.translation_prediction.predict_translated_orfs:main"
estimate-orf-bayes-factors = "rpbp.translation_prediction.estimate_orf_bayes_factors:main"
select-final-prediction-set = "rpbp.translation_prediction.select_final_prediction_set:main"
# profile construction quality control and dashboard
summarize-rpbp-profile-construction = "rpbp.analysis.profile_construction.summarize_rpbp_profile_construction:main"
visualize-metagene-profile-bayes-factor = "rpbp.analysis.profile_construction.visualize_metagene_profile_bayes_factor:main"
get-all-read-filtering-counts = "rpbp.analysis.profile_construction.get_all_read_filtering_counts:main"
rpbp-profile-construction-dashboard = "rpbp.analysis.profile_construction.dashboard.rpbp_profile_construction_dashboard:main"
# predictions and dashboard
summarize-rpbp-predictions = "rpbp.analysis.rpbp_predictions.summarize_rpbp_predictions:main"
visualize-orf-type-metagene-profiles = "rpbp.analysis.rpbp_predictions.visualize_orf_type_metagene_profiles:main"
rpbp-predictions-dashboard = "rpbp.analysis.rpbp_predictions.dashboard.rpbp_predictions_dashboard:main"
# proteomics
get-orf-peptide-matches = "rpbp.analysis.proteomics.get_orf_peptide_matches:main"
get-all-orf-peptide-matches = "rpbp.analysis.proteomics.get_all_orf_peptide_matches:main"
filter-nonunique-peptide-matches = "rpbp.analysis.proteomics.filter_nonunique_peptide_matches:main"
# other
compile-rpbp-models = "rpbp.ribo_utils.compile_rpbp_models:main"
create-read-length-orf-profiles = "rpbp.analysis.profile_construction.create_read_length_orf_profiles:main"
collect-read-length-orf-profiles = "rpbp.analysis.profile_construction.collect_read_length_orf_profiles:main"
[project.urls]
Github = "https://github.com/dieterich-lab/rp-bp"
Issues = "https://github.com/dieterich-lab/rp-bp/issues"
[project.optional-dependencies]
tests = ["pytest", "pytest-cov", "pytest-depends"]
docs = [
"ipykernel",
"matplotlib",
"nbsphinx",
"pandoc",
"sphinx>=4.5.0",
"sphinx_rtd_theme>=1.0.0",
"furo",
"sphinx-argparse",
"sphinx-copybutton"
]
[tool.setuptools.dynamic]
version = { attr = "rpbp.__version__" }
[tool.setuptools.packages.find]
where = ["src"]
[tool.pytest.ini_options]
testpaths = ["tests"]
log_cli = true
log_cli_level = "INFO"