217 lines
2.7 KiB
Plaintext
Executable File
217 lines
2.7 KiB
Plaintext
Executable File
# BBAV20311 Open Source .gitignore
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# Strategy: Only Agent system is open-sourced
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# ============================================================================
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# CLOSED-SOURCE COMPONENTS - DO NOT COMMIT
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# ============================================================================
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# Analysis scripts (based on course materials)
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apps/cli/
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scripts/
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gfa_core/tools/
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# Local data directories
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input/
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workspace/
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output/
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logs/
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*.log
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# Bioinformatics data files
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*.fa
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*.fasta
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*.fna
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*.faa
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*.gff
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*.gff3
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*.gtf
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*.bed
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*.vcf
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*.bam
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*.sam
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*.cram
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# HMM and BLAST databases
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*.hmm
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*.h3f
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*.h3i
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*.h3m
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*.h3p
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*.phr
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*.pin
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*.pog
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*.psd
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*.psi
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*.psq
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*.ptf
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*.pto
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# ============================================================================
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# PYTHON
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# ============================================================================
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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]
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*$py.class
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*.so
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.Python
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# Distribution / packaging
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build/
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develop-eggs/
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dist/
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downloads/
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eggs/
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.eggs/
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lib/
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lib64/
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parts/
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sdist/
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var/
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wheels/
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*.egg-info/
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.installed.cfg
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*.egg
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# PyInstaller
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*.manifest
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*.spec
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# Installer logs
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pip-log.txt
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pip-delete-this-directory.txt
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# Unit test / coverage reports
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htmlcov/
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.tox/
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.nox/
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.coverage
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.coverage.*
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.cache
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nosetests.xml
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coverage.xml
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*.cover
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.hypothesis/
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.pytest_cache/
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# Jupyter Notebook
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.ipynb_checkpoints
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# IPython
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profile_default/
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ipython_config.py
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# pyenv
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.python-version
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# Environments
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.env
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.venv
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env/
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venv/
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ENV/
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env.bak/
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venv.bak/
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# Spyder project settings
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.spyderproject
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.spyproject
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# Rope project settings
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.ropeproject
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# mkdocs documentation
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/site
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# mypy
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.mypy_cache/
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.dmypy.json
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dmypy.json
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# Pyre type checker
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.pyre/
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# ============================================================================
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# IDE
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# ============================================================================
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# PyCharm
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.idea/
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*.iml
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*.iws
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*.ipr
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# VSCode
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.vscode/
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*.code-workspace
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# Sublime Text
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*.sublime-project
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*.sublime-workspace
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# Vim
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*.swp
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*.swo
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*~
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# Emacs
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*~
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\#*\#
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.\#*
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# ============================================================================
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# OS
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# ============================================================================
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# macOS
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.DS_Store
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.AppleDouble
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.LSOverride
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# Windows
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Thumbs.db
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ehthumbs.db
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Desktop.ini
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$RECYCLE.BIN/
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# Linux
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*~
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.nfs*
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# ============================================================================
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# PROJECT SPECIFIC
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# ============================================================================
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# Configuration with sensitive data
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config/api_keys.yaml
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config/secrets.yaml
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# Database
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*.db
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*.sqlite
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*.sqlite3
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# Temporary files
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tmp/
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temp/
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*.tmp
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# Large files
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*.tar.gz
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*.zip
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*.rar
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*.7z
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# Model files
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*.pkl
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*.pth
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*.h5
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*.onnx
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*.pb
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# Documentation builds
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docs/_build/
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docs/_static/
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docs/_templates/
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