0.5

.gitignore

@@ -3,13 +3,39 @@ reference/
 
 # Rust build artifacts
 target/
-Cargo.lock
-**/*.rs.bk
+/target/
 debug/
 release/
 *.rlib
+**/*.rs.bk
+Cargo.lock
 
 # Python build artifacts
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+*.whl
+wheelhouse/
+
+# Python project-specific build artifacts
 python/__pycache__/
 python/*.pyc
 python/*.pyo
@@ -24,36 +50,41 @@ python/.venv
 python/venv
 python/.mypy_cache
 python/.tox
+python/rustkmer/*.so
+python/rustkmer/*.cpython-*.so
 
 # IDE files
-.idea/
 .vscode/
+.idea/
 *.swp
 *.swo
 *~
 
 # OS files
 .DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+ehthumbs.db
 Thumbs.db
 
-# Environment variables
+# Environment files
 .env
 .env.local
 .env.*.local
+.env*
+!.env.example
 
 # Logs
 *.log
 npm-debug.log*
 yarn-debug.log*
 yarn-error.log*
-*.prof*
-*.d
-*.pdb
 
 # Output files
 *.jf
 *.rk
-*.txt
 *.rkdb
 
 # Except test data files that should be tracked
@@ -65,27 +96,12 @@ examples/output/
 examples/data/*.fa
 examples/data/*.fa.gz
 !examples/data/small_dataset.fa
+examples/marimo/__marimo__/
 
-# Test and temporary files (stored in /Users/forrest/Temp/demodata/)
+# Test and temporary files
 test_output/
 temp_files/
-
-# IDE files
-.vscode/
-.idea/
-*.swp
-*.swo
-
-# OS files
-.DS_Store
-Thumbs.db
-
-# Logs
-*.log
-
-# Environment files
-.env*
-!.env.example
+tmp/
 
 # Benchmark results
 benches/
@@ -97,51 +113,18 @@ coverage/
 coverage.xml
 *.xml
 
-# Added by cargo
-
-/target
-
-# Rust build artifacts
-/target/
-**/*.rs.bk
-Cargo.lock
-
-# Python cache and temp files
-__pycache__/
-*.py[cod]
-*$py.class
-*.so
-.Python
-build/
-develop-eggs/
-dist/
-downloads/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-wheels/
-*.egg-info/
-.installed.cfg
-*.egg
-MANIFEST
-
-# Python compiled modules (including rustkmer)
-python/rustkmer/*.so
-python/rustkmer/*.cpython-*.so
-#
-.claude/
-.serena/
-.spekrit/
-.specify/
+# Performance profiling files
+*.prof
+*.prof*
+*.profraw
 
 # Documentation build
 site/
 docs/venv/
 docs/_build/
+docs/.doctrees/
+*.doctree
+mkdocs.yml.local
 
 # Temporary scripts
 check_rustkmer_methods.py
@@ -152,66 +135,19 @@ IMPLEMENTATION_STATUS.md
 tests/python/fixtures/large_scale/sequence_xlarge.fa
 tests/python/fixtures/large_scale/rnaseq_reads.fq.gz
 
-# Benchmarks directory (removed due to non-compliant code)
-benches/
-
-# IDE files
-.vscode/
-.idea/
-*.swp
-*.swo
-*~
-
-# OS generated files
-.DS_Store
-.DS_Store?
-._*
-.Spotlight-V100
-.Trashes
-ehthumbs.db
-Thumbs.db
-
-# Performance profiling files
-*.prof
-*.profraw
-
-# Backup files
-*.bak
-*.backup
-*.old
-*.orig
-*.tmp
-*.temp
-
-# Documentation build
-site/
-docs/.doctrees/
-*.doctree
-
-# MkDocs build output
-mkdocs.yml.local
-
-# Python wheel builds
-*.whl
-wheelhouse/
-
-.venv/
-examples/marimo/__marimo__/
-
-tmp/
-
-
-
-# Tool-specific cache files (can be large)
+# Tool-specific cache files
+.claude/
 .serena/
+.spekrit/
+.specify/
 .venv/
-
 .venv*/
 
-# Hypothesis testing cache (property-based testing)
+# Hypothesis testing cache
 .hypothesis/
-.pytest_cache/
-# Test databases
+
+# Test reports and databases
+tests/**/test_reports/
 *.rkd
 *.rkb
 
@@ -225,4 +161,17 @@ external_sort_*
 
 # Debug files
 *.tmp
+*.temp
+*.bak
+*.backup
+*.old
+*.orig
 merged_test*.rkd
+
+# Database files
+*.d
+*.pdb
+
+# OpenCode and Sisyphus directories
+.opencode/
+.sisyphus/