| [build-system] | |
| requires = ["setuptools>=42", "wheel"] | |
| build-backend = "setuptools.build_meta" | |
| [project] | |
| name = "dgeb" | |
| version = "0.1.0" | |
| description = "Diverse Genomic Embedding Benchmark" | |
| readme = "README.md" | |
| license = { file = "LICENSE" } | |
| keywords = [ | |
| "scientific software", | |
| "genomic embeddings", | |
| "machine learning", | |
| "benchmark", | |
| ] | |
| classifiers = [ | |
| "Development Status :: 2 - Pre-Alpha", | |
| "Environment :: Console", | |
| "Intended Audience :: Developers", | |
| "Intended Audience :: Information Technology", | |
| "Intended Audience :: Science/Research", | |
| "License :: OSI Approved :: Apache Software License", | |
| "Operating System :: OS Independent", | |
| "Programming Language :: Python", | |
| ] | |
| dependencies = [ | |
| "datasets>=2.20.0", | |
| "matplotlib>=3.9.0", | |
| "numpy>=2.0.0", | |
| "pandas>=2.2.2", | |
| "pydantic>=2.7.4", | |
| "pytrec_eval_terrier>=0.5", | |
| "rich>=13.7.1", | |
| "scikit_learn>=1.5.0", | |
| "scipy>=1.13.1", | |
| "seaborn>=0.13.2", | |
| "torch>=2.3.1", | |
| "tqdm>=4.66.4", | |
| "transformers>=4.41.2", | |
| ] | |
| [project.urls] | |
| homepage = "https://github.com/TattaBio/DGEB" | |
| "Huggingface Organization" = "https://huggingface.co/tattabio" | |
| "Source Code" = "https://github.com/TattaBio/DGEB" | |
| [project.scripts] | |
| dgeb = "dgeb.cli:main" | |
| [project.optional-dependencies] | |
| dev = ["ruff>=0.0.254", "pytest", "pytest-xdist"] | |
| [tool.setuptools.packages.find] | |
| exclude = ["tests", "results", "leaderboard", "Dockerfile"] | |
| [tool.setuptools.package-data] | |
| "*" = ["*.json"] | |
| [tool.ruff] | |
| target-version = "py38" | |
| exclude = [".venv", "build/"] | |
| line-length = 88 | |
| indent-width = 4 | |
| [tool.semantic_release] | |
| version_toml = ["pyproject.toml:project.version"] | |
| build_command = "python -m pip install build; python -m build" | |
| commit_message = "{version}\n\nAutomatically generated by python-semantic-release [skip ci]" | |
| logging_use_named_masks = false | |
| major_on_zero = true | |
| allow_zero_version = true | |
| no_git_verify = false | |
| tag_format = "v{version}" | |
| [tool.semantic_release.branches.main] | |
| match = "(main|master)" | |
| prerelease_token = "rc" | |
| prerelease = false | |
| [tool.semantic_release.changelog] | |
| template_dir = "templates" | |
| changelog_file = "CHANGELOG.md" | |
| exclude_commit_patterns = [] | |
| [tool.semantic_release.changelog.environment] | |
| block_start_string = "{%" | |
| block_end_string = "%}" | |
| variable_start_string = "{{" | |
| variable_end_string = "}}" | |
| comment_start_string = "{#" | |
| comment_end_string = "#}" | |
| trim_blocks = false | |
| lstrip_blocks = false | |
| newline_sequence = "\n" | |
| keep_trailing_newline = false | |
| extensions = [] | |
| autoescape = true | |
| [tool.semantic_release.commit_author] | |
| env = "GIT_COMMIT_AUTHOR" | |
| default = "semantic-release <semantic-release>" | |
| [tool.semantic_release.commit_parser_options] | |
| allowed_tags = [ | |
| "build", | |
| "chore", | |
| "ci", | |
| "docs", | |
| "feat", | |
| "fix", | |
| "perf", | |
| "style", | |
| "refactor", | |
| "test", | |
| ] | |
| minor_tags = ["feat"] | |
| patch_tags = ["fix", "perf"] | |
| default_bump_level = 0 | |
| [tool.semantic_release.remote] | |
| name = "origin" | |
| type = "github" | |
| ignore_token_for_push = false | |
| insecure = false | |
| [tool.semantic_release.publish] | |
| dist_glob_patterns = ["dist/*"] | |
| upload_to_vcs_release = true | |