# Byte-compiled / optimized / DLL files
__pycache__/
*.py[codz]
*$py.class
.DS_Store
data/
/models/
docs/diary.md
/outputs/
/one_off_scripts/
/scratchpad/
# Throwaway investigations: probe scripts, progress logs and figures, one
# subfolder per run. Never part of the shipped demo surface.
/scratch/
demos/_*.py
!demos/__init__.py
docs/_*
demos/models/_*
tests/unit/_*

# C extensions
*.so

# Distribution / packaging
.Python
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
share/python-wheels/
*.egg-info/
.installed.cfg
*.egg
MANIFEST

# 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
pip-delete-this-directory.txt

# 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

# UV
#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
#   This is especially recommended for binary packages to ensure reproducibility, and is more
#   commonly ignored for libraries.
#uv.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
#poetry.toml

# pdm
#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
#   pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
#   https://pdm-project.org/en/latest/usage/project/#working-with-version-control
#pdm.lock
#pdm.toml
.pdm-python
.pdm-build/

# pixi
#   Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control.
#pixi.lock
#   Pixi creates a virtual environment in the .pixi directory, just like venv module creates one
#   in the .venv directory. It is recommended not to include this directory in version control.
.pixi

# 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
.envrc
.venv
.venv_*/
env/
venv/
ENV/
env.bak/
venv.bak/

# Vivarium work (separate venv + embedded git repo)
vivarium_work/

# 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/

# Abstra
# Abstra is an AI-powered process automation framework.
# Ignore directories containing user credentials, local state, and settings.
# Learn more at https://abstra.io/docs
.abstra/

# Visual Studio Code
#  Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore 
#  that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
#  and can be added to the global gitignore or merged into this file. However, if you prefer, 
#  you could uncomment the following to ignore the entire vscode folder
# .vscode/

# Ruff stuff:
.ruff_cache/

# PyPI configuration file
.pypirc



# Streamlit
.streamlit/secrets.toml

# images
*.png
*.jpg
*.jpeg
*.gif
*.svg
!demos/assets/*.svg
*.bmp
*.tiff

*.pkl
*.mp4

# Allow specific image
!docs/assets/hallsim_architecture.png

# Local scratch / untracked notes
/misc/

# Framework stress-test artefacts (mitochondrial-aging experiment)
/src/hallsim/models/mitochondrial_aging.py
/src/hallsim/models/sbml/kowald2006/
/src/hallsim/models/sbml/nazaret2009/
/demos/mitochondrial_aging.py
/demos/mito_bioenergetics_reduction.py
/demos/mito_clock_costs.py
/tests/unit/test_mitochondrial_aging.py

/docs/framework-report-mitochondria.md
/docs/mitochondrial-aging-model.md
/docs/performance-audit.md
# Review-panel reports: raw evidence. Findings that matter are lifted into
# docs/known-problems.md, which is what the repo carries.
docs/review-*.md
docs/dp_edison.txt
# The panel's *reports* are raw evidence and stay out; the panel itself is
# repo infrastructure — it produced known-problems.md and is the intake gate.
.claude/*
!.claude/agents/
# Working notes: design sketches, model critiques and measurement reports
# kept locally, not shipped.
docs/crossgen-suggestions.md
docs/dallepezze2014-critique.md
docs/design-model-admissibility.md
docs/design-pathway-maps.md
docs/design-fate-architecture.md
docs/design-spontaneous-endpoint.md
docs/design-stochastic-lane.md
docs/eriq-equation-revisions.md
docs/gpu-verification.md
docs/gz06-population.md
docs/jacobian-reuse.md
docs/proctor2007-comparison.md
docs/senescence-model-rebuild.md
