# =============================================================================
# Python
# =============================================================================

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

# 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

# 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/

# =============================================================================
# IDEs and Editors
# =============================================================================

# VSCode
.vscode/
*.code-workspace

# PyCharm
#  JetBrains specific template is maintained in a separate JetBrains.gitignore that 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/

# Vim
*.swp
*.swo
*~

# Emacs
*~
\#*\#
/.emacs.desktop
/.emacs.desktop.lock
*.elc
auto-save-list
tramp
.\#*

# Sublime Text
*.sublime-project
*.sublime-workspace

# =============================================================================
# Operating System
# =============================================================================

# macOS
.DS_Store
.AppleDouble
.LSOverride
Icon?
._*
.DocumentRevisions-V100
.fseventsd
.Spotlight-V100
.TemporaryItems
.Trashes
.VolumeIcon.icns
.com.apple.timemachine.donotpresent
.AppleDB
.AppleDesktop
Network Trash Folder
Temporary Items
.apdisk

# Windows
Thumbs.db
Thumbs.db:encryptable
ehthumbs.db
ehthumbs_vista.db
*.tmp
*.temp
Desktop.ini
$RECYCLE.BIN/
*.cab
*.msi
*.msix
*.msm
*.msp
*.lnk

# Linux
*~
.fuse_hidden*
.directory
.Trash-*
.nfs*

# =============================================================================
# Project Specific - Bioinformatics
# =============================================================================

# Sample data files (potentially large)
samples/
sample_data/
test_data/
data/

# FASTQ files (can be very large)
*.fastq
*.fastq.gz
*.fq
*.fq.gz

# FASTA files
*.fasta
*.fas
*.fa
*.fna
*.ffn
*.frn

# SAM/BAM files (alignment files, usually large)
*.sam
*.bam
*.bai

# VCF files (variant call format)
*.vcf
*.vcf.gz

# BED files
*.bed

# GFF/GTF files
*.gff
*.gff3
*.gtf

# Common bioinformatics output formats
*.blast
*.hmm
*.aln
*.tree
*.nwk
*.phy

# =============================================================================
# Project Specific - CSV/Data Files
# =============================================================================

# Test input files (keep sample files but ignore real data)
input.csv
metadata.csv
output.csv
results.csv
*_results.csv
*_metadata.csv

# Excel files
*.xlsx
*.xls

# TSV files
*.tsv
*.tab

# =============================================================================
# Logs and Temporary Files
# =============================================================================

# Log files
*.log
logs/

# Temporary files
tmp/
temp/
*.tmp
*.temp

# Backup files
*.bak
*.backup
*~

# =============================================================================
# Documentation Build
# =============================================================================

# Sphinx
_build/
_static/
_templates/

# MkDocs
site/

# =============================================================================
# CI/CD
# =============================================================================

# GitHub Actions
# (Keep workflow files but ignore artifacts)

# Coverage reports
.coverage*
htmlcov/
coverage.xml

# =============================================================================
# Package Distribution
# =============================================================================

# Keep build artifacts out of version control
dist/
build/
*.egg-info/

# =============================================================================
# Configuration Files (sensitive)
# =============================================================================

# API keys and secrets
.env
.env.local
.env.*.local
secrets.json
config.ini

# Authentication tokens
.pypirc

# =============================================================================
# Performance Profiling
# =============================================================================

# Python profiling
*.prof
*.profile

# Memory profiling
*.memprof

# =============================================================================
# Other Tools
# =============================================================================

# Rope
.ropeproject

# Black
.black

# Ruff
.ruff_cache/

# Pre-commit
.pre-commit-config.yaml.bak