pyproject.toml

[project]
authors = [{ name = "Henry Webel", email = "henry.webel@sund.ku.dk" }]
description = "Imputing (MS-based prote-) omics data using self supervised deep learning models."
name = "pimms-learn"
# This means: Load the version from the package itself.
# See the section below: [tools.setuptools.dynamic]
dynamic = ["version"]
readme = "README.md"
requires-python = ">=3.9"
# These are keywords
classifiers = [
  "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
  "Intended Audience :: Healthcare Industry",
  "Intended Audience :: Science/Research",
  "Programming Language :: Python :: 3",
  "Topic :: Scientific/Engineering :: Bio-Informatics",
]
dependencies = [
  "pandas",
  "numpy",
  "torch",
  "fastai",
  "scikit-learn>=1.0",
  "seaborn",
  "matplotlib",
  "plotly", # not used in library, but workflow
  "omegaconf",
  "pingouin",
  "njab>=0.1"
]

[project.scripts]
# pimms-report-imputation-comparison
# pimms-report-diff-analysis
pimms-setup-imputation-comparison = "pimmslearn.cmd_interface.setup_imp_cp_website:main"
pimms-add-diff-comp = "pimmslearn.cmd_interface.setup_diff_analysis_website:main"

[project.urls]
"Bug Tracker" = "https://github.com/RasmussenLab/pimms/issues"
"Homepage" = "https://github.com/RasmussenLab/pimms"

[project.optional-dependencies]
docs = [
  "sphinx",
  "sphinx-book-theme",
  "myst-nb",
  "ipywidgets",
  "sphinx-new-tab-link!=0.2.2",
]

[tool.flake8]
max-line-length = 120
aggressive = 2
ignore = ["E501"]

[build-system]
build-backend = "setuptools.build_meta"
requires = ["setuptools>=64", "setuptools_scm>=8", "wheel"]

[tool.setuptools_scm]
# https://setuptools-scm.readthedocs.io/ 
# used to pick up the version from the git tags or the latest commit.

[tool.setuptools.packages.find]
include = ["pimmslearn"]