pyproject.toml

[build-system]
requires = [
    "cython",
    "numpy>=1.25.0",
    "setuptools>=77.0.0",
]
build-backend = "setuptools.build_meta"

[project]
name = "bx-python"
dynamic = ["version"]
authors = [
    { name = "James Taylor", email = "james@jamestaylor.org" },
    { name = "Bob Harris" },
    { name = "David King" },
    { name = "Brent Pedersen" },
    { name = "Kanwei Li" },
    { name = "Nicola Soranzo", email = "nicola.soranzo@earlham.ac.uk" },
]
description = "Tools for manipulating biological data, particularly multiple sequence alignments"
readme = "README.md"
license = "MIT"
license-files = [
    "LICENSE",
]
classifiers = [
    "Development Status :: 5 - Production/Stable",
    "Intended Audience :: Developers",
    "Intended Audience :: Science/Research",
    "Operating System :: POSIX",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Programming Language :: Python :: 3.14",
    "Programming Language :: Python :: 3.15",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Topic :: Software Development :: Libraries :: Python Modules",
]
requires-python = ">=3.11"
dependencies = [
    "numpy",
    "pyparsing",
]

[project.urls]
Homepage = "https://github.com/bxlab/bx-python"
"Bug Tracker" = "https://github.com/bxlab/bx-python/issues"
"Source Code" = "https://github.com/bxlab/bx-python"

[tool.black]
include = '\.pyi?$'
line-length = 120

[tool.cibuildwheel]
enable = ["pypy"]
# NumPy 2.5.0 removed support for PyPy3.12, can be restored when
# https://github.com/numpy/numpy/pull/32332 is merged
skip = ["pp312-*"]
test-command = """
python -c 'import bx, bx.align, bx.align.axt, bx.align.core, bx.align.epo, \
bx.align.lav, bx.align.maf, bx.align.score, bx.align.sitemask, \
bx.align.sitemask.core, bx.align.sitemask.cpg, bx.align.sitemask.quality, \
bx.align.tools, bx.align.tools.chop, bx.align.tools.fuse, \
bx.align.tools.thread, bx.arrays, bx.arrays.array_tree, bx.arrays.bed, \
bx.arrays.wiggle, bx.bbi, bx.bbi.bbi_file, bx.bbi.bigwig_file, \
bx.bbi.bpt_file, bx.bbi.cirtree_file, bx.binned_array, bx.bitset, \
bx.bitset_builders, bx.bitset_utils, bx.cookbook, \
bx.cookbook.attribute, bx.cookbook.doc_optparse, \
bx.filter, bx.gene_reader, bx.interval_index_file, bx.intervals, \
bx.intervals.cluster, bx.intervals.intersection, bx.intervals.io, \
bx.intervals.operations, bx.intervals.operations.base_coverage, \
bx.intervals.operations.complement, bx.intervals.operations.concat, \
bx.intervals.operations.coverage, bx.intervals.operations.find_clusters, \
bx.intervals.operations.intersect, bx.intervals.operations.join, \
bx.intervals.operations.merge, bx.intervals.operations.quicksect, \
bx.intervals.operations.subtract, bx.intervals.random_intervals, \
bx.intseq, bx.intseq.ngramcount, bx.misc, bx.misc.bgzf, bx.misc.binary_file, \
bx.misc.cdb, bx.misc.filecache, bx.misc.readlengths, bx.misc.seekbzip2, \
bx.misc.seeklzop, bx.motif, bx.motif.io, bx.motif.logo, bx.motif.pwm, \
bx.phylo, bx.phylo.newick, bx.phylo.phast, bx.pwm, \
bx.pwm.bed_score_aligned_pwm, bx.pwm.bed_score_aligned_string, \
bx.pwm.maf_select_motifs, bx.pwm.position_weight_matrix, bx.pwm.pwm_score_maf, \
bx.pwm.pwm_score_motifs, bx.pwm.pwm_score_positions, bx.seq, bx.seq.core, \
bx.seq.fasta, bx.seq.nib, bx.seq.qdna, bx.seq.seq, bx.seq.twobit, \
bx.seqmapping, bx.tabular, bx.tabular.io, bx.wiggle, bx_extras, \
bx_extras.fpconst, bx_extras.lrucache, bx_extras.pstat, bx_extras.stats'
"""

[tool.cibuildwheel.linux]
before-all = """
if command -v yum; then
    yum -y install zlib-devel
elif command -v apk; then
    apk add zlib-dev
else
    apt-get -y install libz-dev
fi
"""

[tool.cibuildwheel.macos]
# If there is no wheel for numpy on macOS (e.g. for the oldest supported numpy
# for PyPy3.7), we need to build it using OpenBLAS (both before building the
# bx-python wheel and when testing it), see
# https://github.com/numpy/numpy/issues/15947#issuecomment-683355728
# The ~/.numpy-site.cfg is supported by numpy <1.26.0 , see
# https://numpy.org/doc/stable/release/1.26.0-notes.html#numpy-specific-build-customization
before-all = """
brew install openblas && cat > ~/.numpy-site.cfg <<EOF
[openblas]
libraries = openblas
library_dirs = $(brew --prefix openblas)/lib
include_dirs = $(brew --prefix openblas)/include
runtime_library_dirs = $(brew --prefix openblas)/lib
EOF
"""

[tool.darker]
isort = true

[tool.ruff.lint]
# Enable: pycodestyle errors (E), Pyflakes (F), flake8-bugbear (B),
# flake8-comprehensions (C4), flake8-logging-format (G),
# flake8-implicit-str-concat (ISC), NumPy-specific rules (NPY)
# and pyupgrade (UP)
#select = ["E", "F", "B", "C4", "G", "ISC", "NPY", "UP"]
select = ["E", "F", "C4", "G", "ISC", "NPY", "UP", "W291"]
# Exceptions:
# B9 flake8-bugbear opinionated warnings
# E501 is line length (delegated to black)
# E741 Ambiguous variable name
ignore = ["B9", "BLE001", "E501", "E741", "I001", "RET501", "SIM102", "TRY002", "TRY004"]

[tool.setuptools.dynamic]
version = {attr = "bx.__version__"}

[tool.setuptools.exclude-package-data]
"*" = ["*.c", "*.h", "*.pxd", "*.pyx"]

[tool.setuptools.package-data]
"*" = ["*.ps"]

[tool.setuptools.packages.find]
where = ["lib"]