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pyproject.toml
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pyproject.toml
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[project]
name = "scTM"
version = "0.1.3"
description = "A toolbox for single cell topic models"
authors = [
{name = "chengwei94", email = "chengwei8@gmail.com"},
]
dependencies = [
"scanpy>=1.9.3",
"anndata>=0.9.1",
"gseapy>=1.0.4",
"pyro-ppl>=1.8.4",
#"torch-geometric>=2.3.1",
"squidpy>=1.2.2",
"torch>=2.0.1",
"torchinfo>=1.8.0",
# "torch-sparse>=0.6.17",
# "torch-scatter>=2.1.1"
"discotoolkit>=1.0.0.1",
"scikit-misc>=0.2.0",
]
requires-python = ">=3.8"
readme = "README.rst"
license = {text = "MIT"}
[build-system]
requires = ["pdm-backend"]
build-backend = "pdm.backend"
[tool.pdm.dev-dependencies]
format = [
"black>=23.3.0",
"isort>=5.12.0",
]
dev = [
"pre-commit>=3.3.3",
]
docs = [
"mkdocs-material>=9.1.14",
"mkdocs>=1.4.3",
"mkdocs-jupyter>=0.24.1",
"mkdocs-gen-files>=0.5.0",
"mkdocs-literate-nav>=0.6.0",
"mkdocstrings[python]>=0.21.2",
"pymdown-extensions>=10.0.1",
]
[tool.ruff]
exclude = [
".bzr",
".direnv",
".eggs",
".git",
".git-rewrite",
".hg",
".ipynb_checkpoints",
".mypy_cache",
".nox",
".pants.d",
".pyenv",
".pytest_cache",
".pytype",
".ruff_cache",
".svn",
".tox",
".venv",
".vscode",
"__pypackages__",
"_build",
"buck-out",
"build",
"dist",
"node_modules",
"site-packages",
"venv",
]
src = ["."]
line-length = 88
indent-width = 4
target-version = "py38"
[tool.ruff.format]
# Like Black, use double quotes for strings.
quote-style = "double"
# Like Black, indent with spaces, rather than tabs.
indent-style = "space"
# Like Black, respect magic trailing commas.
skip-magic-trailing-comma = false
# Like Black, automatically detect the appropriate line ending.
line-ending = "auto"
# Enable auto-formatting of code examples in docstrings. Markdown,
# reStructuredText code/literal blocks and doctests are all supported.
# This is currently disabled by default, but it is planned for this
# to be opt-out in the future.
docstring-code-format = false
[tool.ruff.lint]
# Enable Pyflakes (F) and a subset of the pycodestyle (E) codes by default.
# pycodestyle warnings (W)
# Activate Security Rules (S) to replace bandit
# Enable the isort rules (I) to replace isort
# flake8-bugbear (B)
# flake8-simplify (SIM)
select = ["F", "E4", "E7", "E9", "W", "S", "I", "B"]
ignore = ["E741", "B006", "B007", "B008", "B026", "S101"]
# Allow auto-fixing of all enabled rules when using the `--fix` option.
fixable = ["ALL"]
unfixable = [] # Specify rules that cannot be auto-fixed, if any.
# Define a regex pattern for allowed unused variables (typically underscore-prefixed).
dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"