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Commit 5c1fd9d5 authored by Martin Larralde's avatar Martin Larralde
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Remove outdated `setuptools` configuration files

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include README.md
include CHANGELOG.md
include CITATION.cff
include COPYING
include pyproject.toml
recursive-include include *.pxd
recursive-include pyhmmer *.h *.pxd *.pxi *.py *.pyi *.pyx py.typed
recursive-include pyhmmer/tests *
recursive-include vendor *
recursive-exclude vendor/hmmer *.ai
recursive-exclude vendor *.pl
prune vendor/easel/demotic
prune vendor/easel/documentation
prune vendor/easel/esl_msa_testfiles
prune vendor/easel/miniapps
prune vendor/easel/testsuite
prune vendor/hmmer/autobuild
prune vendor/hmmer/documentation
prune vendor/hmmer/contrib
prune vendor/hmmer/profmark
prune vendor/hmmer/testsuite
prune vendor/hmmer/test-speed
prune vendor/hmmer/tutorial
# https://gist.github.com/althonos/6914b896789d3f2078d1e6237642c35c
# --- Setuptools metadata ---------------------------------------------------
[metadata]
name = pyhmmer
version = attr: pyhmmer.__version__
author = Martin Larralde
author_email = martin.larralde@embl.de
url = https://github.com/althonos/pyhmmer
description = Cython bindings and Python interface to HMMER3.
long_description = file: README.md
long_description_content_type = text/markdown
license = MIT
platform = posix
keywords = bioinformatics, profile, HMM, sequence, pfam
classifier =
Development Status :: 4 - Beta
Intended Audience :: Developers
Intended Audience :: Science/Research
License :: OSI Approved :: MIT License
Operating System :: POSIX
Programming Language :: C
Programming Language :: Cython
Programming Language :: Python :: 3.6
Programming Language :: Python :: 3.7
Programming Language :: Python :: 3.8
Programming Language :: Python :: 3.9
Programming Language :: Python :: 3.10
Programming Language :: Python :: 3.11
Programming Language :: Python :: 3.12
Programming Language :: Python :: Implementation :: CPython
Programming Language :: Python :: Implementation :: PyPy
Topic :: Scientific/Engineering :: Bio-Informatics
Topic :: Scientific/Engineering :: Medical Science Apps.
Typing :: Typed
project_urls =
Documentation = https://pyhmmer.readthedocs.io/en/stable/
Bug Tracker = https://github.com/althonos/pyhmmer/issues
Changelog = https://github.com/althonos/pyhmmer/blob/master/CHANGELOG.md
Coverage = https://codecov.io/gh/althonos/pyhmmer/
Builds = https://github.com/althonos/pyhmmer/actions
Paper = https://doi.org/10.1093/bioinformatics/btad214
PyPI = https://pypi.org/project/pyhmmer
[options]
zip_safe = false
packages = find:
python_requires = >=3.6
test_suite = tests
include_package_data = true
setup_requires =
setuptools >=46.4
cython ~=3.0
install_requires =
psutil ~=5.8
tests_require =
importlib-resources ~=5.0 ; python_version < '3.9'
[options.package_data]
pyhmmer = py.typed, *.pyi
# --- C libraries configuration ---------------------------------------------
[configure.divsufsort]
filename = divsufsort.h
copy = vendor/hmmer/libdivsufsort/divsufsort.h.in
[configure.easel]
filename = esl_config.h
constants =
EASEL_DATE = "Aug 2023"
EASEL_COPYRIGHT = "Copyright (C) 2023 Howard Hughes Medical Institute"
EASEL_LICENSE = "Freely distributed under the BSD open source license."
EASEL_VERSION = "0.49"
EASEL_URL = "http://bioeasel.org/"
headers =
stdio.h
stdlib.h
string.h
inttypes.h
stdint.h
strings.h
sys/stat.h
sys/types.h
unistd.h
endian.h
netinet/in.h
sys/param.h
sys/sysctl.h
functions =
aligned_alloc
erfc
getpid
_mm_malloc
popen
posix_memalign
strcasecmp
strsep
sysconf
sysctl
times
fseeko
[configure.hmmer]
filename = p7_config.h
constants =
HMMER_VERSION = "3.4"
HMMER_DATE = "Aug 2023"
HMMER_LICENSE = "Freely distributed under the BSD open source license."
HMMER_URL = "http://hmmer.org/"
HMMER_COPYRIGHT = "Copyright (C) 2023 Howard Hughes Medical Institute."
p7_RAMLIMIT = 32
p7_NCPU = "2"
p7_ALILENGTH = 50
p7_ETARGET_AMINO = 0.59
p7_ETARGET_DNA = 0.62
p7_ETARGET_OTHER = 1.0
p7_SEQDBENV = "BLASTDB"
p7_HMMDBENV = "PFAMDB"
p7_MAXABET = 20
p7_MAXCODE = 29
p7_MAX_SC_TXTLEN = 11
p7_MAXDCHLET = 20
headers =
endian.h
inttypes.h
stdint.h
unistd.h
sys/types.h
netinet/in.h
sys/param.h
sys/sysctl.h
functions =
mkstemp
popen
putenv
strcasecmp
strsep
times
getpid
sysctl
sysconf
getcwd
chmod
stat
fstat
erfc
# --- Python tools configuration --------------------------------------------
[coverage:run]
plugins = Cython.Coverage
[coverage:report]
include =
pyhmmer/*.py
pyhmmer/*.pyx
show_missing = true
exclude_lines =
pragma: no cover
if typing.TYPE_CHECKING:
@abc.abstractmethod
@abc.abstractproperty
raise NotImplementedError
return NotImplemented
raise UnexpectedError
raise AllocationError
[mypy]
disallow_any_decorated = true
disallow_any_generics = true
disallow_any_unimported = false
disallow_subclassing_any = false
disallow_untyped_calls = true
disallow_untyped_defs = true
ignore_missing_imports = true
warn_unused_ignores = true
warn_return_any = true
[mypy-pyhmmer.tests.*]
ignore_errors = True
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