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pyproject.toml
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pyproject.toml
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[build-system]
build-backend = "hatchling.build"
requires = ["hatchling"]
[project]
authors = [
{name = "daniele arosio", email = "daniele.arosio@cnr.it"}
]
classifiers = [
"Environment :: Console",
"Operating System :: OS Independent",
"Programming Language :: Python :: 3 :: Only",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"Programming Language :: Unix Shell",
"Intended Audience :: Science/Research",
"Topic :: Scientific/Engineering",
"Development Status :: 3 - Alpha"
]
dependencies = [
'arviz <= 0.18.0',
'click <= 8.1.7',
'corner <= 2.2.2',
'emcee <= 3.1.6',
'lmfit <= 1.3.1',
'matplotlib <= 3.9.0',
'numpy <= 1.26.4',
'openpyxl <= 3.1.3',
'pandas <= 2.2.2',
'scipy <= 1.13.1',
'seaborn <= 0.13.2',
'sympy <= 1.12.1',
'tqdm <= 4.66.4',
'xlrd <= 2.0.1'
]
description = "Cli for fitting macromolecule pH titration or binding assays data e.g. fluorescence spectra."
keywords = [
"svd",
"ClopHensor",
"data fitting",
"pH",
"macromolecule binding"
]
license = "BSD-3-Clause"
name = "clophfit"
readme = "README.md"
requires-python = ">=3.10"
version = "0.10.7"
[project.optional-dependencies]
dev = [
"commitizen <= 3.27.0",
"ipykernel",
"jupyter",
"jupyterlab",
"ruff <= 0.4.7",
"pre-commit <= 3.7.1",
"pylsp-mypy",
"ruff-lsp"
]
docs = [
"autodocsumm <= 0.2.12",
"nbsphinx <= 0.9.4",
"pydata-sphinx-theme <= 0.15.3",
"Sphinx <= 7.3.7",
"sphinx-click <= 6.0.0",
"sphinx_autodoc_typehints <= 2.1.1",
"sphinxcontrib-plantuml <= 0.30",
"pymc",
"graphviz"
]
tests = [
"coverage[toml] <= 7.5.3",
"mypy <= 1.10.0",
"pandas-stubs <= 2.2.2.240603",
"Pygments <= 2.18.0",
"pytest <= 8.2.1",
"types-click <= 7.1.8",
"xdoctest <= 1.1.4"
]
[project.scripts]
"clop" = "clophfit.__main__:clop"
"fit-titration" = "clophfit.__main__:fit_titration"
"note_to_csv" = "clophfit.__main__:note2csv"
"ppr" = "clophfit.__main__:ppr"
[project.urls]
"Bug Tracker" = "https://github.com/darosio/ClopHfit/issues"
Changelog = "https://github.com/darosio/ClopHfit/blob/main/CHANGELOG.md"
# Discussions = "https://github.com/darosio/ClopHfit/discussions"
Documentation = "https://clophfit.readthedocs.io"
"Github releases" = "https://github.com/darosio/ClopHfit/releases"
Homepage = "https://github.com/darosio/ClopHfit"
[tool.bandit]
# skips = ["B101", "B603"]
exclude_dirs = ["*/test_*.py"]
[tool.codespell]
count = ''
ignore-words-list = "whis,nd"
quiet-level = 3
[tool.commitizen]
name = "cz_customize"
tag_format = "v$version"
version = "0.10.7"
version_files = [
"pyproject.toml:version",
"docs/conf.py:release",
"README.md:Version"
]
[tool.commitizen.customize]
bump_map = {"^.+!:" = "MAJOR", "BREAKING CHANGE" = "MAJOR", "feat" = "MINOR", "fix" = "PATCH", "perf" = "PATCH", "refactor" = "PATCH"}
bump_pattern = "^(BREAKING CHANGE|feat|fix|perf|refactor)"
change_type_map = {"feat" = "Feat", "fix" = "Fix", "docs" = "Docs", "build" = "Build", "style" = "Style", "refactor" = "Refactor", "perf" = "Perf", "test" = "Test", "ci" = "CI/CD"}
change_type_order = ["BREAKING CHANGE", "Feat", "Fix", "Docs", "Style", "Perf", "Test", "Build", "CI/CD"]
changelog_pattern = "^(feat|fix|docs|style|refactor|perf|test|build|ci)?(\\(.*\\))?(!)?"
commit_parser = "^(?P<change_type>feat|fix|docs|style|refactor|perf|test|build|ci|chore|revert)(?:\\((?P<scope>[^()\r\n]*)\\)|\\()?(?P<breaking>!)?:\\s(?P<message>.*)?"
example = """fix(parser): correct minor typos in code\n
see the issue for details on the typos fixed\n
closes issue #12
"""
info_path = "cz_customize_info.txt"
message_template = "{{change_type}}:{% if show_message %} {{message}}{% endif %}"
schema = """
<type>(<scope>): <subject>
<BLANK LINE>
<body>
<BLANK LINE>
(BREAKING CHANGE: )<footer>
"""
schema_pattern = "^(feat|fix|docs|style|refactor|perf|test|build|ci|chore|revert|bump)(?:\\(([^()\r\n]*)\\)|\\()?(!)?:\\s(.*)?"
[[tool.commitizen.customize.questions]]
choices = [
{value = "feat", name = "feat: A new feature. Correlates with MINOR in SemVer"},
{value = "fix", name = "fix: A bug fix. Correlates with PATCH in SemVer"},
{value = "perf", name = "perf: A code change that improves performance. Correlates with PATCH in SemVer"},
{value = "docs", name = "docs: Documentation only changes"},
{value = "style", name = "style: Changes that do not affect the meaning of the code (white-space, formatting, missing semi-colons, etc)"},
{value = "refactor", name = "refactor: A code change that neither fixes a bug nor adds a feature"},
{value = "test", name = "test: Adding missing or correcting existing tests"},
{value = "build", name = "build: Changes that update the build system, development tools or external dependencies"},
{value = "ci", name = "ci: Changes to our CI configuration files and scripts (example scopes: GitLabCI)"},
{value = "revert", name = "revert: Reverting to previous commit(s)."}
]
message = "Select the type of change you are committing"
name = "change_type"
type = "list"
[[tool.commitizen.customize.questions]]
message = "Body."
name = "message"
type = "input"
[[tool.commitizen.customize.questions]]
message = "Do you want to add body message in commit?"
name = "show_message"
type = "confirm"
[tool.coverage.paths]
source = ["src", "*/site-packages"]
tests = ["tests", "*/tests"]
[tool.coverage.report]
# fail_under = 100
exclude_lines = [
"pragma: no cover"
]
show_missing = true
[tool.coverage.run]
branch = true
omit = ["*__init__.py", "*/old/*"]
source = ["clophfit", "tests"]
[tool.hatch.envs.default]
features = ["dev", "tests", "docs"]
[tool.hatch.envs.default.scripts]
bump = [
"cz bump --major-version-zero -ch {args}", # e.g. "--increment PATCH"
"hatch build",
"hatch publish -r test -u __token__"
]
ch = "cz ch --incremental --unreleased-version HEAD"
clean = "rm -rf ./build .coverage ./__pycache__ ./.mypy_cache ./.pytest_cache ./docs/_build ./tests/__pycache__ ./dist ./src/clophfit/__pycache__"
docs = "sphinx-build docs docs/_build"
docserve = "python -m http.server 8000 -d docs/_build"
init = [
"pre-commit --version",
"pre-commit install",
"pre-commit install --hook-type commit-msg --hook-type pre-push"
]
lint = [
"pre-commit --version",
"pre-commit run --all-files --hook-stage=manual --show-diff-on-failure {args}"
]
[tool.hatch.envs.tests]
features = ["tests"]
template = "tests"
[[tool.hatch.envs.tests.matrix]]
python = ["3.12", "3.11", "3.10"] # reverse order to ensure the presence in older python of module included in newer versions
[tool.hatch.envs.tests.scripts]
all = ["test", "type", "xdoc", "cov"]
cov = [
"coverage combine",
"coverage report",
"coverage xml"
]
test = "coverage run -p -m pytest"
type = "mypy src tests docs/conf.py"
xdoc = "python -m xdoctest clophfit all"
[tool.isort]
combine_as_imports = true
force_single_line = false
include_trailing_comma = true
known_first_party = "clophfit"
line_length = 88 # to match black's default line length
multi_line_output = 3
profile = "black"
[tool.mypy]
# enable_error_code = ["ignore-without-code", "redundant-expr", "truthy-bool"]
enable_error_code = ["redundant-expr", "truthy-bool"]
exclude = "src/clophfit/old"
plugins = ["numpy.typing.mypy_plugin"]
pretty = true
show_column_numbers = true
show_error_codes = true
show_error_context = true
strict = true
warn_unreachable = true
warn_unused_configs = true
[tool.pylint]
[tool.pylint.master]
ignore-paths = ["src/clophfit/_version.py", "src/clophfit/old"]
py-version = "3.12"
[tool.pylint.messages_control]
disable = [
"invalid-name",
"design",
"line-too-long",
"too-many-lines",
"inconsistent-return-statements",
"import-error",
"fixme",
# "consider-using-f-string",
# "unnecessary-pass",
# "unspecified-encoding",
# "unused-argument",
# "raise-missing-from",
# "use-a-generator",
# "consider-using-generator",
# "no-else-raise",
# "protected-access",
# "unidiomatic-typecheck",
# "attribute-defined-outside-init",
# # "all",
# # https://pylint.pycqa.org/en/latest/user_guide/checkers/features.html
# # for tests
# "pointless-string-statement",
# "consider-using-with",
# "comparison-with-itself",
# "comparison-of-constants",
# "consider-using-with",
# "use-maxsplit-arg",
"unnecessary-dunder-call"
]
[tool.pylint.reports]
output-format = "colorized"
[tool.pylint.similarities]
ignore-imports = "yes"
[tool.pylsp-mypy]
dmypy = false
enabled = true
live_mode = true
strict = true
[tool.pytest.ini_options]
addopts = ["-ra", "--showlocals", "--strict-markers", "--strict-config"]
# xfail_strict = true
# filterwarnings = ["ignore::DeprecationWarning", "ignore:OVER"]
filterwarnings = ["ignore::DeprecationWarning"]
log_cli_level = "INFO"
minversion = "6.0"
testpaths = [
"tests"
]
[tool.ruff]
extend-exclude = ["src/clophfit/old/"]
force-exclude = true
line-length = 88
target-version = "py312"
[tool.ruff.format]
docstring-code-format = true
[tool.ruff.lint]
ignore = ["ANN101", "ANN102", "ANN201", "E501", "ISC001"]
select = [
"A", # builtins
"ANN", # typing annotation
"ARG", # unused arguments
"B", # bugbear
"C",
"C4", # comprehensions
"C90", # mccabe
"D", # pydocstyle
"DTZ", # dates
"E", # pycodestyle
"TRY", # exceptions
"EM", # exceptions
"ERA", # eradicate
"F", # pyflakes
# "FBT", # boolean-trap
"I", # isort
"ICN", # import conventions (opinionated)
"ISC", # implicit-str-concat
"N", # pep8-naming
"PD", # pandas-vet
# "PGH", # pygrep WAIT
"PL", # pylint see PLR2004...
"PT", # pytest-style
"PTH", # use-pathlib
"Q", # quotes
"RUF", # Ruff
"S", # bandit XXX
"SIM", # simplify
"TID", # tidy-imports
"UP", # pyupgrade
"YTT", # 2020
"W" # pycodestyle
]
isort.combine-as-imports = true
isort.force-single-line = false
isort.known-first-party = ["clophfit"]
isort.split-on-trailing-comma = true
mccabe.max-complexity = 12
[tool.ruff.lint.per-file-ignores]
"*.ipynb" = [
"ERA",
"N802",
"N803",
"N806",
"N816",
"ANN001",
"ANN002",
"ANN003",
"ANN202",
"D103",
"ICN001",
"PD901",
"PLR0913",
"PLR2004"
]
"__init__.py" = ["I002"] # don't need annotations
"src/clophfit/__main__.py" = [
"ANN001" # params are annotated using click
]
"tests/*" = [
"PLR2004",
"S101"
]
[tool.ruff.lint.pydocstyle]
convention = "numpy"