setup.py

#!/usr/bin/env python3
# mypy: ignore-errors
import os
import re

import setuptools_scm  # noqa
from setuptools import find_packages, setup

LINK_PATTERN = r"(\[.*?\]\()([^http][^)]*)\)"
IMAGE_SRC_PATTERN = r'(<img\s+[^>]*src=")([^"]*)(")'
BASE_URL = "https://github.com/bioinform/somaticseq"


# Read __version__ from the _version.py file
version_file = os.path.join("somaticseq", "_version.py")
with open(version_file) as f:
    exec(f.read())  # This will define __version__


def modify_markdown_for_3rd_party(base_markdown: str) -> str:
    def _replace_link(match: re.Match) -> str:
        # Replace relative links in .md from [text](RELATIVE/LINK) into
        # [text]({BASE_URL}/blob/TAG/RELATIVE/LINK)
        text = match.group(1)
        url = match.group(2)
        return f"{text}{BASE_URL}/blob/v{__version__}/{url})"  # noqa

    def _replace_src(match: re.Match) -> str:
        # Replace relative image links
        prefix = match.group(1)  # part before the url
        url = match.group(2)  # original url
        suffix = match.group(3)  # part after the url
        return f"{prefix}{BASE_URL}/raw/v{__version__}/{url}{suffix}"  # noqa

    with_abs_url = re.sub(LINK_PATTERN, _replace_link, base_markdown)
    with_abs_img_src = re.sub(IMAGE_SRC_PATTERN, _replace_src, with_abs_url)
    return with_abs_img_src


with open("README.md") as fn:
    long_description = fn.read()
    description_for_3rd_party = modify_markdown_for_3rd_party(long_description)


setup(
    name="somaticseq",
    description=(
        "SomaticSeq: "
        "An ensemble approach to accurately detect somatic mutations using SomaticSeq"
    ),
    version=__version__,  # noqa
    long_description=description_for_3rd_party,
    long_description_content_type="text/markdown",
    author="Li Tai Fang",
    author_email="ltfang@gmail.com",
    url="https://github.com/bioinform/somaticseq",
    packages=find_packages(),
    package_data={"": ["*.R"]},
    python_requires=">=3.11.0",
    setup_requires=["setuptools>=42", "setuptools_scm"],
    install_requires=[  # pyproject.toml overrides them
        "pysam",
        "numpy",
        "scipy",
        "pandas",
        "xgboost>=1.4",
        "pydantic>=2.0.0,<3.0",
    ],
    scripts=[
        "somaticseq/somaticseq_parallel.py",
        "somaticseq/run_somaticseq.py",
        "somaticseq/single_sample_vcf2tsv.py",
        "somaticseq/somatic_vcf2tsv.py",
        "somaticseq/somatic_xgboost.py",
        "somaticseq/somatic_tsv2vcf.py",
        "somaticseq/genomic_file_parsers/concat.py",
        "somaticseq/utilities/linguistic_sequence_complexity.py",
        "somaticseq/utilities/lociCounterWithLabels.py",
        "somaticseq/utilities/paired_end_bam2fastq.py",
        "somaticseq/utilities/remove_callers_from_somaticseq_tsv.py",
        "somaticseq/utilities/split_bed_into_equal_regions.py",
        "somaticseq/utilities/tally_variants_from_multiple_vcfs.py",
        "somaticseq/utilities/variant_annotation.py",
        "somaticseq/utilities/vcfsorter.pl",
        "somaticseq/utilities/dockered_pipelines/makeAlignmentScripts.py",
        "somaticseq/utilities/dockered_pipelines/makeSomaticScripts.py",
        "somaticseq/utilities/dockered_pipelines/run_workflows.py",
        "somaticseq/vcf_modifier/split_vcf.py",
        "r_scripts/ada_model_builder_ntChange.R",
        "r_scripts/ada_model_predictor.R",
    ],
)