pyproject.toml

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# 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.

## Generic configuration
[project]
name = "ensembl-rnaseq-registry"
dynamic = [
    "version",
]
requires-python = ">= 3.8"
description = "EnsEMBL RNA-Seq registry, store metadata for a selection of RNA-Seq datasets and their samples."
readme = "README.md"
authors = [
    {name = "Ensembl", email = "dev@ensembl.org"},
]
license = {text = "Apache License 2.0"}
keywords = [
    "rnaseq",
    "ensembl",
    "bioinformatics",
]
classifiers = [
    "Development Status :: 3 - Alpha",
    "Environment :: Console",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: Apache Software License",
    "Natural Language :: English",
    "Programming Language :: Python :: 3 :: Only",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Topic :: Software Development :: Libraries :: Python Modules",
]
dependencies = [
    "argschema >= 3.0.4",
    "jsonschema >= 4.6.0",
    "sqlalchemy >= 2.0",
]

[project.optional-dependencies]
dev = [
    "black >= 23.11.0",
    "coverage >= 7.3.2",
    "mypy >= 1.2.0",
    "pylint >= 3.0.2",
    "pytest >= 7.4.3",
    "pytest-dependency",
    "pytest >= 7.4.3",
    "types-requests",
]

[project.scripts]
rnaseq_registry = "ensembl.rnaseq.registry.cli:main"

[tool.setuptools]
package-dir = {"" = "src"}

[tool.setuptools.dynamic]
version = {attr = "ensembl.rnaseq.registry.__version__"}

[tool.setuptools.packages.find]
where = ["src"]  # 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 = 16

[tool.mypy]
mypy_path = "src"
explicit_package_bases = true
namespace_packages = true
ignore_missing_imports = true
show_error_codes = true
warn_unused_configs = true

[tool.pytest.ini_options]
addopts = "-v"
testpaths = ["tests"]
norecursedirs = ["data", "docs", "*.egg_info"]
filterwarnings = [
    "ignore::DeprecationWarning:argschema",
]

[tool.coverage.run]
branch = true
source = [
    "ensembl.rnaseq.registry",
]