# Ignore SNID Fortran sources (covers snid-5 and snid-5.0 at repo root)
/snid-5*/

# Ignore local scripts directory at repo root
/scripts/

# Ignore external NGSF source tree at repo root
/NGSF-main/

# SNID SAGE - .gitignore
# Prevent sensitive data and development artifacts from being committed

# ===== SECURITY & SENSITIVE FILES =====
# API Keys and credentials - CRITICAL SECURITY
my_API_key_OPENROUTER.txt
**/api_key*.txt
**/*_key*.txt
**/*_API_*.txt
.env
.env.local
.env.production
*.pem
*.key

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

# Generated version file (setuptools_scm)
*/_version.py

# C extensions
*.so

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

# Virtual environments
venv/
env/
ENV/
env.bak/
venv.bak/
venv_wsl/

# ===== IDE & EDITOR FILES =====
# VS Code
.vscode/

# Cursor IDE
.cursor/

# PyCharm
.idea/

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

# ===== TESTING & TEMPORARY FILES =====
# Test outputs and temporary results - CLEANUP FOR PRODUCTION
temp_test_results/
snid_test_output/
*.tmp
*.temp

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

# ===== OS GENERATED FILES =====
# macOS
.DS_Store
.AppleDouble
.LSOverride

# Windows
Thumbs.db
ehthumbs.db
Desktop.ini
$RECYCLE.BIN/

# Linux
*~

# ===== LOG FILES =====
*.log
logs/

# ===== RESULTS & USER DATA =====
# User-generated results (empty directories are OK)
results/*
!results/.gitkeep
!results/README.md

# Custom user templates (if they contain personal data)
# Uncomment if you want to exclude user templates:
# custom_templates/*
# !custom_templates/README.md

# ===== DOCUMENTATION BUILD =====
docs/_build/
site/
# Note: site/ is excluded during development but will be built by GitHub Actions
# for deployment to GitHub Pages

# ===== DOCUMENTATION SUBDIRECTORIES =====
# Keep all documentation tracked; only ignore build output

# ===== JUPYTER NOTEBOOKS =====
.ipynb_checkpoints

# ===== BACKUP FILES =====
*.bak
*.backup
*~

# ===== BUILD & DISTRIBUTION =====
# Build artifacts for production
build/
dist/
*.wheel
*.tar.gz

# PyInstaller
*.manifest
*.spec

# ===== DOCUMENTATION MANAGEMENT =====
# Main README is now included in version control 

# ===== ADDITIONAL PATTERNS FOR SNID SAGE =====

# ===== TEMPORARY & GENERATED FILES =====
# Git status output files (typo files)
tatus
status

# Game/entertainment files
space_debris_highscore.txt
*_highscore.txt
*_score.txt

# ===== ANALYSIS & VALIDATION RESULTS =====
# Large analysis result directories
# Analysis/results/validation/
# Analysis/clustering_analysis_results/
# Analysis/*.png
# Analysis/*.csv
# Analysis/*.json

# SNID output directories (generated during analysis)
**/snid_output_*/
**/synthetic_*_*.dat
**/synthetic_*_*.flattened
**/synthetic_*_*.png

# Validation and test results
**/validation_summary.json
**/detailed_validation_results.csv
**/validation_analysis_plots.png
**/synthetic_spectrum_diagnostic.png

# ===== DATA FILES =====
# Large data files that shouldn't be in version control
# Ignore the entire data directory
data/

# ===== TEMPLATE FILES =====
# Individual template files (large binary files) - exclude the entire folder
templates/Individual_templates/

# ===== PLOT & VISUALIZATION FILES =====
# Generated plot files
plots/*.pdf
plots/*.png
plots/*.jpg
plots/*.jpeg
plots/*.svg

# ===== SPECTRAL LINE DATA =====
# Large spectral line files
spectral_lines/*.csv

# ===== WINDOWS SPECIFIC =====
# Windows batch files (development convenience)
*.bat

# ===== DEVELOPMENT & DEBUGGING =====
# Debug output files
debug_*.txt
debug_*.log
*_debug.*
*_error.*
*_warning.*

# Performance profiling
*.prof
*.profile
*_profile.*

# Memory dumps
*.dump
*.dmp

# ===== LARGE BINARY FILES =====
# Large binary files that shouldn't be in git
*.h5
*.hdf
*.fits
*.fits.gz
*.fz

# ===== TEMPORARY WORK FILES =====
# Temporary work files
work_*
temp_*
tmp_*
*_temp.*
*_tmp.*

# ===== BACKUP & VERSION FILES =====
# Backup files with various extensions
*~
*.orig
*.rej
*.swp
*.swo
*#

# ===== PACKAGING & DEPLOYMENT =====
# Package files
*.tar
*.tar.gz
*.zip
*.rar
*.7z

# ===== MONITORING & METRICS =====
# Performance monitoring files
*.perf
*_metrics.txt
*_metrics.csv
*_metrics.json
*_metrics.log
*_stats.txt
*_stats.csv
*_stats.json
*_stats.log
performance_*
metrics_*
stats_*

# ===== CACHE & TEMPORARY DIRECTORIES =====
# Cache directories
.cache/
cache/
tmp/
temp/

# ===== LARGE TEXT FILES =====
# Large text files that might be generated
large_*.txt
*_large.*
*_bulk.*
bulk_*

# ===== TEST DATA =====
# Test data files
test_data/
test_*.dat
test_*.csv
test_*.json
test_*.txt

# ===== BENCHMARK FILES =====
# Benchmark results
benchmark_*
*_benchmark.*
*_bench.*

# ===== VALIDATION FILES =====
# Validation output files
validation_*
*_validation.*
*_valid.*

# ===== QUALITY ASSESSMENT FILES =====
# Quality assessment outputs
quality_*
*_quality.*
*_qa.*

# ===== CORRELATION & STATISTICS FILES =====
# Statistical analysis outputs
correlation_*
*_correlation.*
*_corr.*
statistics_*
*_stats.*
*_stat.*

# ===== PROJECT FOLDERS TO IGNORE =====
.vscode/
examples/
spectral_lines/
wise_spectra/
OLD_ICONS/

# ===== MARKDOWN FILES =====
# Track markdown files (remove previous global ignore). No entries here on purpose.