pyproject.toml

[tool.poetry]
name = "make_prg"
version = "0.5.0"
description = "Code to create a PRG from a Multiple Sequence Alignment file"
authors = ["Michael Hall <michael@mbh.sh>", "Leandro Ishi <leandro@ebi.ac.uk>", "Brice Letcher <bletcher@ebi.ac.uk>",
           "Rachel Colquhoun <rachel.colquhoun@ed.ac.uk>"]
license = "MIT"
readme = "README.md"
homepage = "https://github.com/iqbal-lab-org/make_prg"
repository = "https://github.com/iqbal-lab-org/make_prg"
documentation = "https://github.com/iqbal-lab-org/make_prg"
packages = [{include = "make_prg"}]
keywords = ["python", "reference-graph", "genome-graph", "bioinformatics"]

[tool.poetry.scripts]
make_prg = 'make_prg.__main__:main'

[tool.poetry.dependencies]
python = ">=3.8,<=3.11"
setuptools = "^65"
biopython = "1.79"
loguru = "^0.6.0"
numpy = "^1.24.4"
scikit-learn = "^1.3.0"
intervaltree = "^3.1.0"
pygraphviz = { version = "1.7", optional = true }
networkx = { version = "^2.6.3", optional = true }
matplotlib = { version = "^3.5.0", optional = true }
pyinstaller = {version = "^5.6", optional = true}

[tool.poetry.group.dev.dependencies]
pytest = "^7.4.0"
pytest-cov = "^4.1.0"
pytest-forked = "^1.6.0"
pytest-xdist = "^3.3.1"
pytest-ordering = "^0.6"
hypothesis = "^6.24.5"
black = "^22.10.0"
isort = "^5.10.1"
flake8 = "^5.0.4"

[tool.black]
line-length = 88
include = '\.pyi?$'
exclude = '''
(
  /(
      \.eggs         # exclude a few common directories in the
    | \.git          # root of the project
    | \.hg
    | \.mypy_cache
    | \.tox
    | \.venv
    | venv
    | _build
    | buck-out
    | build
    | dist
  )/
)
'''

[tool.isort]
profile = "black"

[build-system]
requires = ["poetry-core"]
build-backend = "poetry.core.masonry.api"

[tool.poetry.extras]
debug_graphs = ["pygraphviz", "networkx", "matplotlib"]
precompiled_binary = ["pygraphviz", "networkx", "matplotlib", "pyinstaller"]

# Note: to make breakpoints work when running tests through pycharm IDE, comment out section [tool.pytest.ini_options]
# See https://intellij-support.jetbrains.com/hc/en-us/community/posts/360008107400-PyCharm-2020-1-not-stopping-on-breakpoints-anymore
# Note: to make pycharm IDE able to collect coverage statistics, comment out sections
# [tool.pytest.ini_options], [tool.coverage.run], [tool.coverage.report]

[tool.pytest.ini_options]
addopts = "--cov --cov-report term --cov-report xml --cov-fail-under=98 --forked -n 4"
testpaths = ["tests"]

[tool.coverage.run]
omit = [
    "make_prg/utils/recursive_tree_drawer.py",  # this source file is never executed by users, just for internal debugging
    "make_prg/subcommands/from_msa.py",         # CLI source file, ignored in coverage
    "make_prg/subcommands/update.py",           # CLI source file, ignored in coverage
    "tests/**"                                  # test source dir, ignored in coverage, as it can bring the percentage up
]

[tool.coverage.report]
exclude_lines = [
    "def __repr__",
    "@abstractmethod",
    "raise NotImplementedError",
    "logger.*"
]