pyproject.toml

# Build system backend to create package to upload on pypi
[build-system]
build-backend = "setuptools.build_meta"
requires = [
    "setuptools>=42",
    "setuptools_scm[toml]>=6.2"
]

# configuration of setuptools_scm to use tag version autoincrementation
[tool.setuptools_scm]
write_to = "rattleSNP/_version.py"
version_scheme = "release-branch-semver"
tag_regex = "^(\\d.\\d.\\d)-*\\w*\\d*$"       # allow value like 0.0.1-rc0
local_scheme = "no-local-version"

# define Project settings
[project]
name = "rattleSNP"
dynamic = ["version"]
description = "RattleSNP is mapping workflow!!!!!"
authors = [
    { name = "Ravel Sebastien (CIRAD)", email = "sebastien.ravel@cirad.fr" },
]
dependencies = ["PyYAML", "click>=8.0.3", "pandas", "matplotlib", "tabulate", "biopython", "numpy", "argparse", "snakemake", "tqdm", "cookiecutter", "docutils", "snakecdysis"]
requires-python = ">=3.8"
readme = "README.rst"
license = { file = "LICENCE" }
keywords = ["snakemake", "SNP calling", "workflow"]
classifiers = [
    "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
    'License :: CeCILL-C Free Software License Agreement (CECILL-C)',
    'License :: Free for non-commercial use',
    'Development Status :: 5 - Production/Stable',
    'Intended Audience :: Developers',
    'Intended Audience :: End Users/Desktop',
    'Operating System :: POSIX :: Linux',
    'Programming Language :: Python :: 3.8',
    'Programming Language :: Python :: 3.9',
    'Programming Language :: R',
    'Natural Language :: English',
    'Topic :: Scientific/Engineering',
    'Topic :: Scientific/Engineering :: Bio-Informatics'
]

[project.urls]
Homepage = "https://forge.ird.fr/phim/sravel/RattleSNP"
Documentation = "https://rattlesnp.readthedocs.io/en/latest/"
repository = "https://forge.ird.fr/phim/sravel/RattleSNP.git"
"Bug Tracker" = "https://forge.ird.fr/phim/sravel/RattleSNP/issues"
"Source Code" = "https://forge.ird.fr/phim/sravel/RattleSNP"

[project.optional-dependencies]
docs = [
    "sphinx",
    "sphinx_click",
    "sphinx_copybutton",
    "sphinx_rtd_theme",
    "tox",
]

# setup scripts links
[project.scripts]
vcf2geno = "rattleSNP.scripts.vcf2geno:main"
vcf2phylip = "rattleSNP.scripts.vcf2phylip:main"
rattleSNP = "rattleSNP.main:main"

# setup library entry-points
[project.entry-points.rattleSNP]
rattleSNP = "__init__"

# Try to link sphinx to file
[tool.sphinx]
source-dir = "docs/source"
build-dir = "docs/build"
config-dir = "docs/source"

#######
# tox test to mv on gitlab-ci.yaml
[tool.tox]
legacy_tox_ini = """
[tox]
envlist = py{38,39}
skip_missing_interpreters = True
skipsdist=False

[gh-actions]
python = 3.8: py38

[testenv:py{38,39}]
description = Run the install in Python 3.8
skip_install = False
changedir={envdir}
whitelist_externals =
    bash
    echo
envdir =
    py38: {toxworkdir}/py38
    py39: {toxworkdir}/py39
commands =
    rattleSNP --help
    bash -ec 'echo `pwd`'
    bash -ec 'CPDIR="./lib/python3.8/site-packages/rattleSNP/containers/"; DIR="/usr/local/rattleSNP/Containers"; if [[ -d $DIR ]]; then ls $DIR;  echo "copy Containers files in $DIR to $CPDIR"; ln -sf $DIR/* $CPDIR; fi'
    rattleSNP install_local


[run]
description = Run Installation rattleSNP install_local
changedir={envdir}
whitelist_externals =
    bash
    echo
    mkdir
skipsdist=True
skip_install=True
commands =
    mkdir -p data_test_mapping
    bash -ec 'CPFILE="./data_test_mapping/data_test_rattleSNP.zip"; FILE="/usr/local/rattleSNP/data_test_mapping/data_test_rattleSNP.zip"; if [[ -f "$FILE" ]]; then ls $FILE;  echo "copy data_test files in $FILE to $CPFILE"; ln -sf $FILE $CPFILE; fi'
    rattleSNP test_install -d data_test_mapping
    rattleSNP run_local --threads 8 --config {posargs} --singularity-args '--bind /builds:/builds'


[testenv:py38-run]
description = Run workflow pass on args to rattleSNP
envdir =
    py38: {toxworkdir}/py38
    py39: {toxworkdir}/py39
changedir={envdir}
whitelist_externals =
    bash
    echo
    mkdir
skipsdist=True
skip_install=True
commands = {[run]commands}

"""