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Fix existing tests, add new, make coverage reports and mutation testing (#118)
* fix: naming issues in pipelines and tests * fix: naming issues in pipelines and tests * chore: move some tests to correct dir * fix: doc map test * fix: test for gh2bt map * test: maps for both sides * chore: add inits where needed * fix: handler tests * fix: gh ingestor tests * fix: upd gh provider tests * fix: handler arg validation tests * test: add pmc tests and make pmc safer * test: spdx ingestor * test: policy for gh to bt * test: upd license * test: shared version, fix regex * fix: version test * test: add more test cases for mapping version * fix: fix map test bt to gh * fix: expand bt dummy * fix: doc map * fix: revert * chore: cleanup * test: topics map * test: make coverage report * test: configure cosmic-rays * chore: upd cosmic-ray setup * chore: remove unncecessary installs from ci * test: badges util * test: cleaning utils + pydantic warnings * test: comparisons utils * test: conversions utils * test: files utils * test: templating utils * test: shared publications * test: biotools id map * test: name map * test: upd biotools * test: map language * test: homepage map * test: maturity map + homepage fix * test: publication map * test: description map * test: policy over * test: policy on top * test: description * test: homepage * test: name map * test: license map * test: upd topics map * test: version map * test: readme map + actual func * test: citation map * chore: rename map tests * test: map main gh2bt * test: map main bt2gh * test: fix mismatch in map tests * fix: test files utils * test: none prop protocol * test: map protocol * test: gh transformer + actual bug * test: bt transformer * test: pmc transformer * test: spdx transformer * test: spdx composer * test: gh composer * test: pmc composer * test: biotools composer * chore: separated black config * chore: separated ruff config * chore: separated pytest config * chore: separated coverage config * chore: cleanup * chore: narrowed coverage report * chore: update cr config * chore: tighten checks further * fix: correct python version in ci * fix: patch tokens in tests * fix: patch tokens in tests correctly
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‎.coveragerc‎

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[run]
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source = bridge
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branch = True
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parallel = True
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[report]
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skip_covered = False
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show_missing = True
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omit =
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*/tests/*
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*/__init__.py
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*/core/*
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*/bridge/config.py
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*/bridge/logging.py
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exclude_lines =
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pragma: no cover
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if TYPE_CHECKING:
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raise NotImplementedError
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@abstractmethod
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def __repr__
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def __str__
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if __name__ == .__main__.:
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if logger\.isEnabledFor
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^\s*\.\.\.\s*$

‎.github/workflows/tests.yml‎

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uses: actions/checkout@v4
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- name: Setup Python
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uses: actions/setup-python@v4
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uses: actions/setup-python@v5
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with:
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python-version: '3.11'
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python-version: '3.12'
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- name: Cache pip and poetry
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uses: actions/cache@v4
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python -m pip install --upgrade pip
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pip install poetry
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poetry config virtualenvs.create false --local
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poetry install --no-interaction --no-ansi
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poetry install --no-interaction --no-ansi --with docs
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- name: Run unit tests
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env:

‎.gitignore‎

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# VSCode
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.vscode
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# Tests
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.coverage
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htmlcov/
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cosmic-ray.sqlite
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cosmic-ray-report.html

‎black.toml‎

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[tool.black]
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line-length = 120
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target-version = ["py312"]
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force-exclude = '''
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(
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(^|/)src/bridge/core/biotools\\.py
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| (^|/)src/bridge/core/github_repo\\.py
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| (^|/)src/bridge/core/github_latest_release\\.py
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| (^|/)src/bridge/core/github_languages\\.py
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| (^|/)src/bridge/core/license\\.py
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| (^|/)docs/
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| (^|/)tests/
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)
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"""
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'''

‎cosmic-ray.ci.toml‎

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[cosmic-ray]
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module-path = "src"
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timeout = 45
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test-command = "python -m pytest -q"
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excluded-modules = [
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"bridge.core",
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"bridge.logging",
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"bridge.config",
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]
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[[cosmic-ray.targets]]
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module = "bridge"
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[cosmic-ray.distributor]
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name = "local"

‎cosmic-ray.local.toml‎

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[cosmic-ray]
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module-path = "src"
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timeout = 45
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test-command = "python -m pytest -q"
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excluded-modules = [
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"bridge.core",
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"bridge.logging",
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"bridge.config",
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]
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[[cosmic-ray.targets]]
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module = "bridge"
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[cosmic-ray.distributor]
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name = "local"
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# [cosmic-ray.distributor]
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# name = "http"
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# [cosmic-ray.distributor.http]
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# worker-urls = [
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# "http://localhost:9876",
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# "http://localhost:9877",
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# "http://localhost:9878",
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# "http://localhost:9879",
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# "http://localhost:9880",
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# "http://localhost:9881",
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# "http://localhost:9882",
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# ]

‎poetry.lock‎

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‎pyproject.toml‎

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pytest = "^8.4.2"
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pytest-asyncio = "^1.2.0"
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pytest-httpx = "^0.35.0"
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pytest-cov = "^7.0.0"
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cosmic-ray = "^8.4.3"
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[tool.poetry.group.docs.dependencies]
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sphinx = "^8.2.3"
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requires = ["poetry-core>=2.0.0,<3.0.0"]
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build-backend = "poetry.core.masonry.api"
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[tool.black]
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line-length = 120
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target-version = ["py312"]
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force-exclude = '''
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(
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(^|/)src/bridge/core/biotools\\.py
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| (^|/)src/bridge/core/github_repo\\.py
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| (^|/)src/bridge/core/github_latest_release\\.py
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| (^|/)src/bridge/core/github_languages\\.py
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| (^|/)src/bridge/core/license\\.py
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| (^|/)docs/
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)
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"""
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'''
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[tool.ruff]
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target-version = "py312"
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line-length = 120
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extend-exclude = [
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"docs",
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"src/bridge/core/biotools.py",
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"src/bridge/core/github_repo.py",
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"src/bridge/core/github_latest_release.py",
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"src/bridge/core/github_languages.py",
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"src/bridge/core/license.py",
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]
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[tool.ruff.lint]
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select = ["F", "E", "W", "I", "B", "C4", "UP", "N", "D"]
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ignore = [
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"D105", # magic methods
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"D107", # __init__
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"D200", # one-line docstring must be single line
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"D205", # blank line after summary
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"D400", # first line ends with period
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]
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per-file-ignores = { "**/__init__.py" = ["F401"] }
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[tool.ruff.lint.isort]
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known-first-party = ["bridge"]
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combine-as-imports = true
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[tool.ruff.lint.pydocstyle]
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convention = "numpy"
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[tool.pytest.ini_options]
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asyncio_mode = "auto"
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testpaths = [
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"tests",
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]
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[tool.poetry]
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packages = [{ include = "bridge", from = "src" }]
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[tool.poetry.scripts]
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lint = "scripts.quality:lint"
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fmt = "scripts.quality:fmt"
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coverage-report = "scripts.quality:coverage_report"
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cosmic-ray-report = "scripts.quality:cosmic_ray_report"
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gen-biotools-models = "scripts.gen_models:generate_biotools_models"
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gen-github-models = "scripts.gen_models:generate_github_models"
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gen-docs = "scripts.gen_docs:main"

‎pytest.ini‎

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[pytest]
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asyncio_mode = auto
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testpaths =
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tests

‎ruff.toml‎

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target-version = "py312"
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line-length = 120
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extend-exclude = [
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"docs",
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"tests",
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"src/bridge/core/biotools.py",
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"src/bridge/core/github_repo.py",
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"src/bridge/core/github_latest_release.py",
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"src/bridge/core/github_languages.py",
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"src/bridge/core/license.py",
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]
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[lint]
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select = ["F", "E", "W", "I", "B", "C4", "UP", "N", "D"]
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ignore = [
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"D105", # magic methods
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"D107", # __init__
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"D200", # one-line docstring must be single line
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"D205", # blank line after summary
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"D400", # first line ends with period
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]
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per-file-ignores = { "**/__init__.py" = ["F401"] }
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[lint.isort]
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known-first-party = ["bridge"]
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combine-as-imports = true
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[lint.pydocstyle]
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convention = "numpy"

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