From 04cf772725a868091b263d51387eb27b84701a63 Mon Sep 17 00:00:00 2001 From: "vinay.srinivas.bharadhwaj" Date: Mon, 18 Mar 2024 14:48:27 +0100 Subject: [PATCH] Bump version: 0.03-dev -> 0.0.3 --- .bumpversion.cfg | 2 +- docs/source/conf.py | 2 +- pyproject.toml | 69 ++++++++++++++++++++++++++++ setup.cfg | 107 -------------------------------------------- setup.py | 8 ---- 5 files changed, 71 insertions(+), 117 deletions(-) create mode 100644 pyproject.toml delete mode 100644 setup.cfg delete mode 100644 setup.py diff --git a/.bumpversion.cfg b/.bumpversion.cfg index 7f79b56..4e0054e 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 0.0.3-dev +current_version = 0.0.3 commit = True tag = False parse = (?P\d+)\.(?P\d+)\.(?P\d+)(?:-(?P[0-9A-Za-z-]+(?:\.[0-9A-Za-z-]+)*))?(?:\+(?P[0-9A-Za-z-]+(?:\.[0-9A-Za-z-]+)*))? diff --git a/docs/source/conf.py b/docs/source/conf.py index 2e2313d..807485e 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -21,7 +21,7 @@ copyright = '2019-2020, Vinay Bharadhwaj, Daniel Domingo-Fernández and Charles Tapley Hoyt' author = 'Vinay Bharadhwaj, Daniel Domingo-Fernández and Charles Tapley Hoyt' -release = '0.0.3-dev' +release = '0.0.3' parsed_version = re.match( '(?P\d+)\.(?P\d+)\.(?P\d+)(?:-(?P[0-9A-Za-z-]+(?:\.[0-9A-Za-z-]+)*))?(?:\+(?P[0-9A-Za-z-]+(?:\.[0-9A-Za-z-]+)*))?', diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..e324cc8 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,69 @@ +[project] +name = "clep" +version = "0.0.3" +description = "A Hybrid Data and Knowledge Driven Framework for Generating Patient Representations" +readme = "README.md" +requires-python = ">=3.7" +keywords = [ + "Bioinformatics", + "Machine Learning", + "Prediction Models", + "Embeddings", +] +license = { file = "LICENSE" } +authors = [ + { name = "Vinay Bharadhwaj", email = "vinay.srinivas.bharadhwaj@scai.fraunhofer.de" }, +] +classifiers = [ + "Development Status :: 4 - Beta", + "Environment :: Console", + "Intended Audience :: Developers", + "Intended Audience :: Science/Research", + "License :: OSI Approved :: Apache Software License", + "Operating System :: OS Independent", + "Programming Language :: Python", + "Programming Language :: Python :: 3.7", + "Programming Language :: Python :: 3.12", + "Programming Language :: Python :: 3 :: Only", + "Topic :: Scientific/Engineering :: Bio-Informatics", +] +dependencies = [ + "click", + "pandas", + "rpy2", + "statsmodels", + "scikit-learn", + "seaborn", + "gseapy", + "cffi", + "pycairo", + "networkx", + "xgboost", + "tqdm", + "scikit-optimize", + "pykeen", +] + +[tool.setuptools.packages.find] +where = ["src"] + +[project.optional-dependencies] +docs = [ + "sphinx", + "sphinx-rtd-theme", + "sphinx-click", + "sphinx-autodoc-typehints", +] + +[project.scripts] +"clep" = "clep.cli:main" + +[tool.doc8] +max-line-length = 120 + +[tool.coverage.run] +branch = true +source = "clep" + +[tool.coverage.report] +exclude_lines = ["def __repr__", "def __str__"] diff --git a/setup.cfg b/setup.cfg deleted file mode 100644 index 7d6eb8c..0000000 --- a/setup.cfg +++ /dev/null @@ -1,107 +0,0 @@ -########################## -# Setup.py Configuration # -########################## -[metadata] -name = clep -version = 0.0.3-dev -description = A Hybrid Data and Knowledge Driven Framework for Generating Patient Representations -long_description = file: README.md -long_description_content_type = text/markdown - -# URLs associated with the project -url = https://github.com/hybrid-kg/clep -project_urls = - Bug Tracker = https://github.com/hybrid-kg/clep/issues - Source Code = https://github.com/hybrid-kg/clep - Documentation = https://clep.readthedocs.io/en/latest/ - -# Author information -author = Vinay Bharadhwaj -author_email = vinay.srinivas.bharadhwaj@scai.fraunhofer.de -maintainer = Vinay Bharadhwaj -maintainer_email = vinay.srinivas.bharadhwaj@scai.fraunhofer.de - -# License Information -license = See LICENSE file -license_file = LICENSE - -# Search tags -classifiers = - Development Status :: 4 - Beta - Environment :: Console - Intended Audience :: Developers - Intended Audience :: Science/Research - License :: OSI Approved :: Apache Software License - Operating System :: OS Independent - Programming Language :: Python - Programming Language :: Python :: 3.7 - Programming Language :: Python :: 3.8 - Programming Language :: Python :: 3 :: Only - Topic :: Scientific/Engineering :: Bio-Informatics - -keywords = Bioinformatics, Machine Learning, Prediction Models, Embeddings - - -[options] -install_requires = - click==7.0 - pandas==1.0.2 - rpy2==3.3.5 - statsmodels==0.11.1 - scikit-learn==0.23.1 - seaborn==0.9.0 - gseapy==0.9.15 - cffi==1.12.3 - pycairo==1.19.1 - networkx==2.4 - xgboost==1.0.2 - tqdm==4.43.0 - scikit-optimize==0.7.4 - pykeen==1.0.2 - scipy==1.5.1 - numpy==1.19.0 - -# Random options -zip_safe = false -include_package_data = True -python_requires = >=3.6 - -# Where is my code -packages = find: -package_dir = - = src - -[options.packages.find] -where = src - -[options.extras_require] -docs = - sphinx - sphinx-rtd-theme - sphinx-click - sphinx-autodoc-typehints - -[options.entry_points] -console_scripts = - clep = clep.cli:main - -###################### -# Doc8 Configuration # -# (doc8.ini) # -###################### -[doc8] -max-line-length = 120 - -########################## -# Coverage Configuration # -# (.coveragerc) # -########################## -[coverage:run] -branch = True -source = clep - -[coverage:report] -show_missing = True -exclude_lines = - def __str__ - def __repr__ diff --git a/setup.py b/setup.py deleted file mode 100644 index a78fbfd..0000000 --- a/setup.py +++ /dev/null @@ -1,8 +0,0 @@ -# -*- coding: utf-8 -*- - -"""Setup module.""" - -import setuptools - -if __name__ == '__main__': - setuptools.setup()