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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,151 +1,147 @@ | ||
| [build-system] | ||
| build-backend = "hatchling.build" | ||
| requires = ["hatchling"] | ||
| requires = [ "hatchling" ] | ||
|
|
||
| [project] | ||
| name = "dso" | ||
| version = "0.8.2" | ||
| description = "Data Science Operations on top of dvc" | ||
| readme = "README.md" | ||
| requires-python = ">=3.10" | ||
| license = {file = "LICENSE"} | ||
| license = { file = "LICENSE" } | ||
| maintainers = [ | ||
| { name = "Gregor Sturm", email = "[email protected]" }, | ||
| ] | ||
| authors = [ | ||
| {name = "Gregor Sturm"}, | ||
| {name = "Thomas Schwarzl"}, | ||
| {name = "Alexander Peltzer"} | ||
| { name = "Gregor Sturm" }, | ||
| { name = "Thomas Schwarzl" }, | ||
| { name = "Alexander Peltzer" }, | ||
| ] | ||
| maintainers = [ | ||
| {name = "Gregor Sturm", email = "[email protected]"}, | ||
| requires-python = ">=3.10" | ||
| classifiers = [ | ||
| "Programming Language :: Python :: 3 :: Only", | ||
| "Programming Language :: Python :: 3.10", | ||
| "Programming Language :: Python :: 3.11", | ||
| "Programming Language :: Python :: 3.12", | ||
| ] | ||
| urls.Documentation = "https://github.com/Boehringer-Ingelheim/dso" | ||
| urls.Source = "https://github.com/Boehringer-Ingelheim/dso" | ||
| urls.Home-page = "https://github.com/Boehringer-Ingelheim/dso" | ||
| dependencies = [ | ||
| "rich-click", | ||
| "pyyaml", | ||
| "tqdm", | ||
| "platformdirs", | ||
| "Jinja2", | ||
| "pre-commit", | ||
| # "hiyapyco", # using vendored code now | ||
| "ruamel.yaml", | ||
| "dvc", | ||
| "panflute", | ||
| "pillow", | ||
| "svgutils", | ||
| "questionary" | ||
| "dvc", | ||
| "jinja2", | ||
| "panflute", | ||
| "pillow", | ||
| "platformdirs", | ||
| "pre-commit", | ||
| "pyyaml", | ||
| "questionary", | ||
| "rich-click", | ||
| # "hiyapyco", # using vendored code now | ||
| "ruamel-yaml", | ||
| "svgutils", | ||
| "tqdm", | ||
| ] | ||
|
|
||
| [project.scripts] | ||
| dso = "dso:cli" | ||
| dso_pandocfilter = "dso.pandocfilter:main" | ||
|
|
||
| [project.optional-dependencies] | ||
| dev = [ ] | ||
| doc = [ | ||
| "docutils>=0.8,!=0.18.*,!=0.19.*", | ||
| "sphinx>=4", | ||
| "sphinx-book-theme>=1.0.0", | ||
| "myst-nb>=1.1.0", | ||
| "sphinxcontrib-bibtex>=1.0.0", | ||
| "sphinx-autodoc-typehints", | ||
| "sphinxext-opengraph", | ||
| # For notebooks | ||
| "ipykernel", | ||
| "ipython", | ||
| "sphinx-copybutton", | ||
| optional-dependencies.dev = [ ] | ||
| optional-dependencies.doc = [ | ||
| "docutils>=0.8,!=0.18.*,!=0.19.*", | ||
| # For notebooks | ||
| "ipykernel", | ||
| "ipython", | ||
| "myst-nb>=1.1", | ||
| "sphinx>=4", | ||
| "sphinx-autodoc-typehints", | ||
| "sphinx-book-theme>=1", | ||
| "sphinx-copybutton", | ||
| "sphinxcontrib-bibtex>=1", | ||
| "sphinxext-opengraph", | ||
| ] | ||
| test = [ | ||
| "pytest", | ||
| "coverage", | ||
| "freezegun", | ||
| "pytest-cov", | ||
| "pytest-xdist", # for parallel testing with `pytest -n` | ||
| "pytest-asyncio", # for async tests | ||
| "quarto", | ||
| ] | ||
|
|
||
| [tool.coverage.run] | ||
| source = ["dso"] | ||
| omit = [ | ||
| "**/test_*.py", | ||
| ] | ||
|
|
||
| [tool.pytest.ini_options] | ||
| testpaths = ["tests"] | ||
| xfail_strict = true | ||
| addopts = [ | ||
| "--import-mode=importlib", # allow using test files with same name | ||
| optional-dependencies.test = [ | ||
| "coverage", | ||
| "freezegun", | ||
| "pytest", | ||
| "pytest-asyncio", # for async tests | ||
| "pytest-cov", | ||
| "pytest-xdist", # for parallel testing with `pytest -n` | ||
| "quarto", | ||
| ] | ||
| urls.Documentation = "https://github.com/Boehringer-Ingelheim/dso" | ||
| urls.Home-page = "https://github.com/Boehringer-Ingelheim/dso" | ||
| urls.Source = "https://github.com/Boehringer-Ingelheim/dso" | ||
| scripts.dso = "dso:cli" | ||
| scripts.dso_pandocfilter = "dso.pandocfilter:main" | ||
|
|
||
| [tool.ruff] | ||
| line-length = 120 | ||
| src = ["src"] | ||
| extend-include = ["*.ipynb"] | ||
| src = [ "src" ] | ||
| extend-include = [ "*.ipynb" ] | ||
| exclude = [ | ||
| "src/dso/hiyapyco.py" | ||
| "src/dso/hiyapyco.py", | ||
| ] | ||
|
|
||
| [tool.ruff.format] | ||
| docstring-code-format = true | ||
|
|
||
| [tool.ruff.lint] | ||
| select = [ | ||
| "F", # Errors detected by Pyflakes | ||
| "E", # Error detected by Pycodestyle | ||
| "W", # Warning detected by Pycodestyle | ||
| "I", # isort | ||
| "D", # pydocstyle | ||
| "B", # flake8-bugbear | ||
| "TID", # flake8-tidy-imports | ||
| "C4", # flake8-comprehensions | ||
| "BLE", # flake8-blind-except | ||
| "UP", # pyupgrade | ||
| "RUF100", # Report unused noqa directives | ||
| format.docstring-code-format = true | ||
| lint.select = [ | ||
| "B", # flake8-bugbear | ||
| "BLE", # flake8-blind-except | ||
| "C4", # flake8-comprehensions | ||
| "D", # pydocstyle | ||
| "E", # Error detected by Pycodestyle | ||
| "F", # Errors detected by Pyflakes | ||
| "I", # isort | ||
| "RUF100", # Report unused noqa directives | ||
| "TID", # flake8-tidy-imports | ||
| "UP", # pyupgrade | ||
| "W", # Warning detected by Pycodestyle | ||
| ] | ||
| ignore = [ | ||
| # line too long -> we accept long comment lines; formatter gets rid of long code lines | ||
| "E501", | ||
| # Do not assign a lambda expression, use a def -> lambda expression assignments are convenient | ||
| "E731", | ||
| # allow I, O, l as variable names -> I is the identity matrix | ||
| "E741", | ||
| # Missing docstring in public package | ||
| "D104", | ||
| # Missing docstring in public module | ||
| "D100", | ||
| # Missing docstring in __init__ | ||
| "D107", | ||
| # Errors from function calls in argument defaults. These are fine when the result is immutable. | ||
| "B008", | ||
| # __magic__ methods are often self-explanatory, allow missing docstrings | ||
| "D105", | ||
| # first line should end with a period [Bug: doesn't work with single-line docstrings] | ||
| "D400", | ||
| # First line should be in imperative mood; try rephrasing | ||
| "D401", | ||
| ## Disable one in each pair of mutually incompatible rules | ||
| # We don’t want a blank line before a class docstring | ||
| "D203", | ||
| # We want docstrings to start immediately after the opening triple quote | ||
| "D213", | ||
| lint.ignore = [ | ||
| # Errors from function calls in argument defaults. These are fine when the result is immutable. | ||
| "B008", | ||
| # Missing docstring in public module | ||
| "D100", | ||
| # Missing docstring in public package | ||
| "D104", | ||
| # __magic__ methods are often self-explanatory, allow missing docstrings | ||
| "D105", | ||
| # Missing docstring in __init__ | ||
| "D107", | ||
| ## Disable one in each pair of mutually incompatible rules | ||
| # We don’t want a blank line before a class docstring | ||
| "D203", | ||
| # We want docstrings to start immediately after the opening triple quote | ||
| "D213", | ||
| # first line should end with a period [Bug: doesn't work with single-line docstrings] | ||
| "D400", | ||
| # First line should be in imperative mood; try rephrasing | ||
| "D401", | ||
| # line too long -> we accept long comment lines; formatter gets rid of long code lines | ||
| "E501", | ||
| # Do not assign a lambda expression, use a def -> lambda expression assignments are convenient | ||
| "E731", | ||
| # allow I, O, l as variable names -> I is the identity matrix | ||
| "E741", | ||
| ] | ||
| lint.per-file-ignores."docs/*" = [ "I" ] | ||
| lint.per-file-ignores."tests/*" = [ "D" ] | ||
| lint.pydocstyle.convention = "numpy" | ||
|
|
||
| [tool.ruff.lint.pydocstyle] | ||
| convention = "numpy" | ||
| [tool.pytest.ini_options] | ||
| testpaths = [ "tests" ] | ||
| xfail_strict = true | ||
| addopts = [ | ||
| "--import-mode=importlib", # allow using test files with same name | ||
| ] | ||
|
|
||
| [tool.ruff.lint.per-file-ignores] | ||
| "docs/*" = ["I"] | ||
| "tests/*" = ["D"] | ||
| [tool.coverage.run] | ||
| source = [ "dso" ] | ||
| omit = [ | ||
| "**/test_*.py", | ||
| ] | ||
|
|
||
| [tool.cruft] | ||
| skip = [ | ||
| "tests", | ||
| "src/**/__init__.py", | ||
| "src/**/basic.py", | ||
| "docs/api.md", | ||
| "docs/changelog.md", | ||
| "docs/references.bib", | ||
| "docs/references.md", | ||
| "docs/notebooks/example.ipynb", | ||
| "tests", | ||
| "src/**/__init__.py", | ||
| "src/**/basic.py", | ||
| "docs/api.md", | ||
| "docs/changelog.md", | ||
| "docs/references.bib", | ||
| "docs/references.md", | ||
| "docs/notebooks/example.ipynb", | ||
| ] |