.gitignore

### Julia ###
# Files generated by invoking Julia with --code-coverage
*.jl.cov
*.jl.*.cov

# Files generated by invoking Julia with --track-allocation
*.jl.mem

# System-specific files and directories generated by the BinaryProvider and BinDeps packages
# They contain absolute paths specific to the host computer, and so should not be committed
deps/deps.jl
deps/build.log
deps/downloads/
deps/usr/
deps/src/

# Build artifacts for creating documentation generated by the Documenter package
docs/build/
docs/site/

# Manifest.toml is committed for reproducibility (this is an application, not a library)

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

# C extensions and the Julia sysimage (MetaManifold.so / .dylib / .dll)
*.so
*.dylib
*.dll

# 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
lcov.info
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/

### Python Patch ###
# Poetry local configuration file - https://python-poetry.org/docs/configuration/#local-configuration
poetry.toml

# ruff
.ruff_cache/

# LSP config files
pyrightconfig.json

### R ###
# renv project library and caches: large, machine-specific, and reproducible
# from renv.lock. Commit only the lockfile, the activation script, and renv
# settings; leave the installed packages on disk untracked.
renv/library/
renv/local/
renv/staging/
renv/lock/
renv/python/
renv/sandbox/

# History files
.Rhistory
.Rapp.history

# Session Data files
.RData
.RDataTmp

# User-specific files
.Ruserdata

# Example code in package build process
*-Ex.R

# Output files from R CMD build
/*.tar.gz

# Output files from R CMD check
/*.Rcheck/

# RStudio files
.Rproj.user/

# produced vignettes
vignettes/*.html
vignettes/*.pdf

# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
.httr-oauth

# knitr and R markdown default cache directories
*_cache/
/cache/

# Temporary files created by R markdown
*.utf8.md
*.knit.md

# R Environment Variables
.Renviron

## Documentation kept local except published release, cladistics, format, statistics, and schema notes
docs/*
!docs/release-notes/
!docs/cladistics/
!docs/format-migration.md
!docs/statistics/
!docs/schemas/

# translation temp files

# Local Julia precompile trace used for sysimage generation
generate_precompile_trace.jl
po/*~

# RStudio Connect folder
rsconnect/

### R.Bookdown Stack
# R package: bookdown caching files
/*_files/

# vscode
.vscode

### Other
# Things with ambiguous intellectual property
internal
data/*
# MiSeq SOP integration test dataset (3-sample subset, public domain)
!data/MiSeq_SOP/
data/MiSeq_SOP/*
!data/MiSeq_SOP/pipeline.yml
!data/MiSeq_SOP/run_A/
data/MiSeq_SOP/run_A/*
!data/MiSeq_SOP/run_A/*.fastq.gz
!data/MiSeq_SOP/run_B/
data/MiSeq_SOP/run_B/*
!data/MiSeq_SOP/run_B/*.fastq.gz

### Frontend
node_modules/

### Lock files
.~lock.*
.csv#

### Tool paths, downloaded binaries and databases
bin/
databases/

# Machine-level config: generated from config/defaults/ on first run
# (new_project) and edited in place; never committed.
config/tools.yml
config/pipeline.yml
config/databases.yml
config/primers.yml
config/composition.yml

# Filter presets saved from the Tables view at runtime (see routes/results.jl
# _presets_dir): your own saved table filters, not shipped defaults. Distinct
# from the composition library. Machine data; never committed.
config/presets/

# Migration backups written by scripts/migrate_composition.jl
config/backup-*/

### Bits I don't want to share yet
hide.*
projects/
pipelinesteps.txt
archive/
.*

### Exceptions
!.github
!.github/**
!.editorconfig
!.gitleaks.toml
!.Rprofile

# Brainstorming visual-companion scratch (mock-ups, server state)
.superpowers/

# Reference tree library (machine data)
reference_trees/

# Per-machine Julia preferences, e.g. skipping the precompile workload while developing
LocalPreferences.toml

# Development server log (dev/dev.sh)
dev/server.log

# Agda interface files (proofs/agda)
proofs/agda/_build/

# Occupancy proof dependencies and reproduction logs
/_build/

# Fork governance: the gitbot-fleet enrolment manifest, report-backs, and K9 contractiles are tracked.
!.gitbot-fleet/
!.gitbot-fleet/**
!.machine_readable/
!.machine_readable/**