pyproject.toml

[build-system]
requires = [
    "cython",
    "numpy>=1.25.0; python_version>='3.9'",
    "oldest-supported-numpy; python_version<'3.9'",
    "setuptools",
]
build-backend = "setuptools.build_meta"

[tool.black]
include = '\.pyi?$'
line-length = 120
target-version = ['py38']

[tool.cibuildwheel]
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]
target-version = "py38"

[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"]
# Exceptions:
# B9 flake8-bugbear opinionated warnings
# E501 is line length (delegated to black)
# E741 Ambiguous variable name
ignore = ["B9", "E501", "E741"]