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pyproject.toml
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pyproject.toml
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[build-system]
requires = ["hatchling", "hatch-vcs"]
build-backend = "hatchling.build"
[project]
name = "simreaduntil"
# version = "0.0.1"
authors = [
{ name="Maximilian Mordig", email="[email protected]" },
]
description = "Simulator for ONT devices"
keywords = [
"ont",
"simulator"
]
readme = "README.md"
requires-python = ">=3.8"
classifiers = [
"Programming Language :: Python :: 3",
# "License :: OSI Approved :: MIT License",
"Operating System :: OS Independent",
]
license-files = { paths = ["LICENSE"] }
dependencies = [
"matplotlib",
"pandas",
"seaborn",
"numpy",
"pysam",
"pyfastx", # sometimes more convenient than pysam
"biopython",
"google-api-python-client", # needed for grpc
"grpcio",
"scipy", # for parameter estimation
"dill", # for serializing the gap sampler function
"joblib", # for parallelization
"more-itertools",
"tqdm",
"intervaltree",
"ipykernel",
"jupyter",
"notebook",
"jupyterlab",
"toml"
]
dynamic = [
"version", # not updated correctly during editable installs, only once built
]
[project.optional-dependencies]
# for development
dev = [
"ipdb",
"tox",
"grpcio-tools", # for building the python wrappers from the protobuf spec
"docutils", "pydoctor", # for documentation
"black",
"scalene", # for profiling
]
test = [
"pytest>=6",
"pytest-helpers-namespace", # for utility functions in tests
"pytest-datadir", # for datafiles in tests
"pytest-mock",
"pytest-xdist", # for parallelism with "pytest -n auto"
"pytest-cov",
]
readfish = [
"ont-pyguppy-client-lib",
"read-until @ git+https://github.com/nanoporetech/[email protected]",
"readfish @ {root:uri}/external/ont_readfish",
]
rawsignal = [
"pyslow5",
]
[project.scripts]
plot_seqsum = "simreaduntil.seqsum_tools.seqsum_plotting:main"
simfasta_to_seqsum = "simreaduntil.simulator.simfasta_to_seqsum:main"
simulator_with_readfish = "simreaduntil.usecase_helpers.simulator_with_readfish:main"
normalize_fasta = "simreaduntil.usecase_helpers.utils:normalize_fasta_cmd"
# helpers for the usecase
usecase_generate_random_reads = "simreaduntil.usecase_helpers.cli_usecase.generate_random_reads:main"
simulator_server_cli = "simreaduntil.usecase_helpers.cli_usecase.simulator_server_cli:main"
usecase_simulator_client_cli = "simreaduntil.usecase_helpers.cli_usecase.simulator_client_cli:main"
sim_plots_cli = "simreaduntil.usecase_helpers.cli_usecase.sim_plots_cli:main"
usecase_make_html_report = "simreaduntil.usecase_helpers.cli_usecase.make_html_report:main"
[project.urls]
"Homepage" = "https://github.com/ratschlab/sim_read_until"
"Documentation" = "https://ratschlab.github.io/sim_read_until"
"Bug Tracker" = "https://github.com/ratschlab/sim_read_until/issues"
[tool.hatch.version]
source = "vcs"
fallback-version = "0.0.0.7999" # dummy version to recognize it
[tool.hatch.metadata]
# to install from git
allow-direct-references = true
[tool.hatch.build.sources]
"src/simreaduntil" = "simreaduntil"
[tool.black]
line-length = 120
extend-exclude = """
# A regex preceded with ^/ will apply only to files and directories
# in the root of the project.
^/external/
"""
[tool.pydoctor]
# add-package = ["src/simreaduntil"]
intersphinx = ["https://docs.python.org/3/objects.inv"]
# "https://twistedmatrix.com/documents/current/api/objects.inv"
docformat = "google"
make-html = true
html-output = "./apidocs"
verbose = 1
warnings-as-errors = true
# privacy = ["HIDDEN:pydoctor.test",
# "PUBLIC:pydoctor._configparser",]
[tool.pytest.ini_options]
log_cli = true
log_cli_level = "INFO"
log_cli_format = "%(asctime)s,%(msecs)03d - %(message)s --- %(filename)s:%(lineno)d (%(funcName)s) %(levelname)s ##"
log_cli_date_format = "%Y-%m-%d %H:%M:%S" # not supported: milliseconds '%Y-%m-%d %H:%M:%S,uuu', see https://stackoverflow.com/questions/63782079/log-milliseconds-with-pytest
# addopts="-n 4" # to run in parallel