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pyproject.toml
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pyproject.toml
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# See the NOTICE file distributed with this work for additional information
# regarding copyright ownership.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
# pyproject.toml -- Ensembl GenomIO project configuration
## Generic configuration
[project]
name = "ensembl-genomio"
dynamic = [
"version",
]
requires-python = ">= 3.10"
description = "Ensembl GenomIO -- pipelines to convert basic genomic data into Ensembl cores and back to flatfile"
readme = "README.md"
authors = [
{name = "Ensembl", email = "[email protected]"},
]
license = {text = "Apache License 2.0"}
keywords = [
"genome_io",
"ensembl",
"bioinformatics",
"annotation",
"setup",
]
classifiers = [
"Development Status :: 4 - Beta",
"Environment :: Console",
"Intended Audience :: Science/Research",
"License :: OSI Approved :: Apache Software License",
"Operating System :: OS Independent",
"Programming Language :: Python",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3 :: Only",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Topic :: Scientific/Engineering :: Bio-Informatics",
"Topic :: Software Development :: Libraries :: Python Modules",
]
dependencies = [
"bcbio-gff == 0.7.1",
"biopython >= 1.81",
"ensembl-py >= 2.1.0",
"ensembl-utils >= 0.4.1",
"jsonschema >= 4.6.0",
"intervaltree >= 3.1.0",
"mysql-connector-python >= 8.0.29",
"python-redmine >= 2.3.0",
"requests >= 2.28.0",
"spython >= 0.3.13",
]
[project.optional-dependencies]
build = [
"build",
"setuptools",
"setuptools-scm",
"wheel",
]
cicd = [
"black >= 23.11.0",
"coverage >= 7.3.2",
"deepdiff >= 6.7.1",
"genbadge[coverage]",
"mypy >= 1.2.0",
"pylint >= 3.0.2",
"pytest >= 7.4.3",
"pytest-dependency",
"pytest-mock",
"pytest-workflow >= 2.1.0",
"types-requests",
]
docs = [
"mkdocs >= 1.5.3",
"mkdocs-autorefs",
"mkdocs-gen-files",
"mkdocs-literate-nav",
"mkdocs-material",
"mkdocs-material-extensions",
"mkdocs-section-index",
"mkdocstrings",
"mkdocstrings-python",
]
# Database dependencies
mysql = [
"ensembl-utils[mysql]",
]
[project.urls]
homepage = "https://www.ensembl.org"
repository = "https://github.com/Ensembl/ensembl-genomio"
documentation = "https://ensembl.github.io/ensembl-genomio"
[project.scripts]
# Assembly
assembly_download = "ensembl.io.genomio.assembly.download:main"
assembly_tracker = "ensembl.io.genomio.assembly.status:main"
# Database
database_factory = "ensembl.io.genomio.database.factory:main"
# Events
events_dump = "ensembl.io.genomio.events.dump:main"
events_load = "ensembl.io.genomio.events.load:main"
events_format = "ensembl.io.genomio.events.format:main"
# Fasta
fasta_chunk = "ensembl.io.genomio.fasta.chunk:main"
fasta_process = "ensembl.io.genomio.fasta.process:main"
# GenBank
genbank_download = "ensembl.io.genomio.genbank.download:main"
genbank_extract_data = "ensembl.io.genomio.genbank.extract_data:main"
# Genome metadata
genome_metadata_dump = "ensembl.io.genomio.genome_metadata.dump:main"
genome_metadata_extend = "ensembl.io.genomio.genome_metadata.extend:main"
genome_metadata_prepare = "ensembl.io.genomio.genome_metadata.prepare:main"
# Genome statistics
genome_stats_compare = "ensembl.io.genomio.genome_stats.compare:main"
genome_stats_dump = "ensembl.io.genomio.genome_stats.dump:main"
# GFF3
gff3_process = "ensembl.io.genomio.gff3.process:main"
# annotation
annotation_update_description = "ensembl.io.genomio.annotation.update_description:main"
# Manifest
manifest_check_integrity = "ensembl.io.genomio.manifest.check_integrity:main"
manifest_compute_stats = "ensembl.io.genomio.manifest.compute_stats:main"
manifest_generate = "ensembl.io.genomio.manifest.generate:main"
# Schemas
schemas_json_factory = "ensembl.io.genomio.schemas.json.factory:main"
schemas_json_validate = "ensembl.io.genomio.schemas.json.validate:main"
# Sequence region
seq_region_dump = "ensembl.io.genomio.seq_region.dump:main"
seq_region_prepare = "ensembl.io.genomio.seq_region.prepare:main"
seq_region_rename = "ensembl.io.genomio.seq_region.rename:main"
[tool.setuptools]
package-dir = {"" = "src/python"}
[tool.setuptools.dynamic]
version = {attr = "ensembl.io.genomio.__version__"}
[tool.setuptools.packages.find]
where = ["src/python"] # list of folders that contain the packages (["."] by default)
# For additional information on `setuptools` configuration see:
# https://setuptools.pypa.io/en/latest/userguide/quickstart.html
# https://setuptools.pypa.io/en/latest/userguide/pyproject_config.html
# https://packaging.python.org/en/latest/specifications/declaring-project-metadata/
[build-system]
requires = [
"setuptools",
"setuptools-scm",
"wheel"
]
build-backend = "setuptools.build_meta"
[tool.black]
line-length = 110
[tool.pylint.main]
max-line-length = 110
disable = [
"invalid-name",
"logging-fstring-interpolation",
"similarities",
"too-few-public-methods",
"too-many-arguments",
"too-many-locals",
"too-many-statements",
"unspecified-encoding",
"wildcard-import",
]
max-attributes = 12
max-branches = 15
[tool.ruff]
line-length = 110
show-fixes = true
[tool.ruff.format]
docstring-code-format = true
[tool.ruff.lint.per-file-ignores]
# Ignore `F403` (unable to detect undefined names) in all `__init__.py` files
"__init__.py" = ["F403"]
[tool.mypy]
mypy_path = "src/python"
disallow_untyped_defs = true
explicit_package_bases = true
ignore_missing_imports = true
show_error_codes = true
warn_unused_configs = true
[tool.pytest.ini_options]
addopts = [
"--import-mode=importlib",
"--tb=native",
]
testpaths = ["src/python/tests"]
norecursedirs = ["data", "docs", "*.egg_info"]
[tool.coverage.run]
branch = true
source = [
"ensembl.io.genomio",
]
[tool.coverage.report]
exclude_lines = [
# Do not complain about missing debug-only code
"def __repr__",
"if self\\.debug",
# Do not complain if tests do not hit defensive assertion code
"raise AssertionError",
"raise NotImplementedError",
# Do not complain if non-runnable code is not run
"if __name__ == .__main__.:",
"def main",
# Do not complain about abstract methods, they are not run
"@(abc\\.)?abstractmethod",
]