.ruff_cache/
sigma2/*/__pycache__
*/data
# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
*$py.class


# C extensions
*.so
test.csv
test.py
# Distribution / packaging
.Python
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
# Anchored: the unanchored `lib/` from the packaging template also matched
# sigma2/lib/, which is package source, not a build artefact. That kept those
# modules out of version control and out of the sdist while maturin's
# "sigma2/**/*.py" still put them in the wheel.
/lib/
/lib64/
parts/
sdist/

ANALYSIS_REPORT.md
uv.lock

!Cargo.lock


!/sigma2/test.py
/sigma2/var/*
!sigma2/var/sysdata.rda
!sigma2/var/gbm_models_mmrd.rda
!sigma2/var/inter_tt_suppl.pkl
!/sigma2/api/test.py
!/sigma2/var/sysdata/data.h5

!/sigma2/var/gbm_models_mmrd.rda
!/sigma2/var/inter_tt_suppl.pkl
!/sigma2/var/sysdata.rda
!/sigma2/var/TUNER_README.md

# SigMA v1 classifiers ported out of the .rda files (see sigma2/legacy.py).
# 3.8 MB, versus the 82 MB of R blobs they replace.
!/sigma2/var/legacy_models.npz
!/sigma2/var/legacy_cutoffs.csv

# Bundled panel regions, moved in from examples/bed_files so they survive a
# pip install. Gzipped: 23 MB of BED text -> 5.2 MB.
!/sigma2/var/panels/
!/sigma2/var/panels/*.bed.gz

# Manifest of downloadable assets (checksums + URLs); the assets themselves
# live in a release, not the repo.
!/sigma2/var/registry.json
/examples/*
!/examples/1_basic.ipynb
!/examples/2_mmrd.ipynb
!/examples/3_simulation.ipynb
!/examples/4_hrd.ipynb
!/examples/5_tune.ipynb
!/examples/germline/

test.sh
test.md
wheels/
share/python-wheels/
*.egg-info/
.installed.cfg
*.egg
MANIFEST
test.ipynb
# PyInstaller
#  Usually these files are written by a python script from a template
#  before PyInstaller builds the exe, so as to inject date/other infos into it.
*.manifest
*.spec

# Installer logs
pip-log.txt
W

# Unit test / coverage reports
htmlcov/
.tox/
.nox/
.coverage
.coverage.*
.cache
nosetests.xml
coverage.xml
*.cover
*.py,cover
.hypothesis/
.pytest_cache/
cover/

# Translations
*.mo
*.pot

# Django stuff:
*.log
local_settings.py
db.sqlite3
db.sqlite3-journal

# Flask stuff:
instance/
.webassets-cache

# Scrapy stuff:
.scrapy

# Sphinx documentation
docs/_build/

# PyBuilder
.pybuilder/
target/

# Jupyter Notebook
.ipynb_checkpoints

# IPython
profile_default/
ipython_config.py

# pyenv
#   For a library or package, you might want to ignore these files since the code is
#   intended to run in multiple environments; otherwise, check them in:
# .python-version

# pipenv
#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
#   However, in case of collaboration, if having platform-specific dependencies or dependencies
#   having no cross-platform support, pipenv may install dependencies that don't work, or not
#   install all needed dependencies.
#Pipfile.lock

# poetry
#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
#   This is especially recommended for binary packages to ensure reproducibility, and is more
#   commonly ignored for libraries.
#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
#poetry.lock

# pdm
#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
#pdm.lock
#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
#   in version control.
#   https://pdm.fming.dev/#use-with-ide
.pdm.toml

# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
__pypackages__/

# Celery stuff
celerybeat-schedule
celerybeat.pid

# SageMath parsed files
*.sage.py

# Environments
.env
.venv
env/
venv/
ENV/
env.bak/
venv.bak/

# Spyder project settings
.spyderproject
.spyproject

# Rope project settings
.ropeproject

# mkdocs documentation
/site

# mypy
.mypy_cache/
.dmypy.json
dmypy.json

# Pyre type checker
.pyre/

# pytype static type analyzer
.pytype/

# Cython debug symbols
cython_debug/

# PyCharm
#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
#  and can be added to the global gitignore or merged into this file.  For a more nuclear
#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
#.idea/

# rever
rever/

# Reproduction of examples/breast_gel_filtered_1_2_1_2_results with current
# code (24 models, verified bit-identical). Regenerable from repro_1_2_1_2.py;
# 40+ MB of training artefacts do not belong in the repository.
repro_breast_gel_filtered_1_2_1_2_results/
repro_run.log
pytest_after_fix.log
pytest_final.log

# Editor/agent workspace, machine-local.
.claude/

# Reproduction outputs and test logs. The procedure itself is committed as
# tools/reproduce_run.py; its 50+ MB of training artefacts are not.
repro_*_results/
pytest_*.log
