From 387ede4424c94f1de15bcf49cce527f26161580d Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Fri, 22 Aug 2025 11:00:23 +0000 Subject: [PATCH 1/3] Initial plan From e9937f083e675e82b7be5d4aa22467ad853eb809 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Fri, 22 Aug 2025 11:00:47 +0000 Subject: [PATCH 2/3] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- village/plots/corridor_plot.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/village/plots/corridor_plot.py b/village/plots/corridor_plot.py index ede089c43..192d311bf 100644 --- a/village/plots/corridor_plot.py +++ b/village/plots/corridor_plot.py @@ -124,7 +124,9 @@ def corridor_plot( # get the unique days in the plot unique_days = pd.date_range(start=start_first, end=end, freq="D") # make them at midnight - unique_days = unique_days.map(lambda x: x.replace(hour=0, minute=0, second=0, microsecond=0)) + unique_days = unique_days.map( + lambda x: x.replace(hour=0, minute=0, second=0, microsecond=0) + ) # remove the first unique_days = unique_days[unique_days >= start_first] # put the ticks there From 1be66dd24efbc480deb1084e038bc12b62808599 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Fri, 22 Aug 2025 11:06:21 +0000 Subject: [PATCH 3/3] Add comprehensive library list for village repository Co-authored-by: HernandoMV <6049065+HernandoMV@users.noreply.github.com> --- LIBRARY_LIST.md | 176 ++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 176 insertions(+) create mode 100644 LIBRARY_LIST.md diff --git a/LIBRARY_LIST.md b/LIBRARY_LIST.md new file mode 100644 index 000000000..98a6ec77f --- /dev/null +++ b/LIBRARY_LIST.md @@ -0,0 +1,176 @@ +# Complete Library List for Village Repository + +This document contains every single library used by the BrainCircuitsBehaviorLab/village repository, extracted from all sources including dependencies, imports, documentation, build tools, and system requirements. + +## Summary +- **Total Unique Libraries**: 62 +- **Generated**: December 2024 +- **Repository**: https://github.com/BrainCircuitsBehaviorLab/village + +--- + +## Complete Alphabetical List + +1. **black** - Code formatter +2. **calplot** - Calendar plotting library +3. **check-docstring-first** - Pre-commit hook +4. **check-executables-have-shebangs** - Pre-commit hook +5. **check-manifest** - Package manifest checker +6. **check-merge-conflict** - Pre-commit hook +7. **check-toml** - TOML file validator +8. **code** - Visual Studio Code (system package) +9. **codespell** - Spell checker for code +10. **coverage** - Code coverage measurement +11. **end-of-file-fixer** - Pre-commit hook +12. **fire** - Command line interface generation +13. **i2c-tools** - I2C utilities (system package) +14. **libcamera** - Camera library +15. **libportaudio2** - Audio I/O library (system package) +16. **libqt5multimedia5-plugins** - Qt5 multimedia plugins (system package) +17. **matplotlib** - Plotting library +18. **mixed-line-ending** - Pre-commit hook +19. **mypy** - Static type checker +20. **myst_parser** - MyST markdown parser for Sphinx +21. **nbsphinx** - Sphinx extension for Jupyter notebooks +22. **numpy** - Numerical computing library +23. **opencv-data** - OpenCV data files (system package) +24. **opencv-python** - Computer vision library +25. **pandas** - Data analysis and manipulation library +26. **picamera2** - Raspberry Pi camera library +27. **pre-commit** - Pre-commit framework +28. **pulseaudio** - Audio server (system package) +29. **PyQt5** - Python bindings for Qt5 +30. **pyserial** - Serial communication library +31. **pytest** - Testing framework +32. **pytest-cov** - Coverage plugin for pytest +33. **python-dateutil** - Date and time utilities +34. **python-telegram-bot** - Telegram Bot API wrapper +35. **python3-opencv** - OpenCV Python bindings (system package) +36. **python3-pyqt5.qtmultimedia** - PyQt5 multimedia module (system package) +37. **requirements-txt-fixer** - Pre-commit hook +38. **ruff** - Python linter and formatter +39. **scipy** - Scientific computing library +40. **seaborn** - Statistical data visualization +41. **setuptools** - Package building tools +42. **setuptools-scm** - Version management from SCM tags +43. **setuptools_scm** - Version management from SCM tags (underscore variant) +44. **setuptools_scmtoml** - TOML support for setuptools_scm +45. **smbus2** - I2C/SMBus library +46. **sounddevice** - Audio input/output library +47. **sphinx.ext.autodoc** - Automatic documentation from docstrings +48. **sphinx.ext.autosectionlabel** - Automatic section labels +49. **sphinx.ext.autosummary** - Automatic API documentation +50. **sphinx.ext.githubpages** - GitHub Pages integration +51. **sphinx.ext.intersphinx** - Cross-project references +52. **sphinx.ext.napoleon** - NumPy/Google docstring support +53. **sphinx.ext.viewcode** - Source code viewing +54. **sphinx_autodoc_typehints** - Sphinx extension for type hints +55. **sphinx_book_theme** - Sphinx book theme +56. **sphinx_sitemap** - Sphinx sitemap generator +57. **sphinxcontrib.video** - Video embedding for Sphinx +58. **tomli** - TOML parser +59. **tox** - Testing automation +60. **trailing-whitespace** - Pre-commit hook +61. **types-setuptools** - Type stubs for setuptools +62. **wheel** - Python wheel packaging standard + +--- + +## Libraries by Category + +### Core Python Dependencies +- fire +- pandas +- pyserial +- python-dateutil +- python-telegram-bot +- scipy +- seaborn +- setuptools_scm +- sounddevice +- sphinx_book_theme + +### Development & Testing Tools +- black +- coverage +- mypy +- pre-commit +- pytest +- pytest-cov +- ruff +- tox + +### Build System & Packaging +- setuptools +- setuptools-scm +- setuptools_scm +- setuptools_scmtoml +- wheel + +### Computer Vision & Hardware +- opencv-python +- numpy +- picamera2 +- libcamera +- smbus2 + +### GUI & Multimedia +- PyQt5 +- matplotlib +- sounddevice + +### Documentation (Sphinx) +- myst_parser +- nbsphinx +- sphinx.ext.autodoc +- sphinx.ext.autosectionlabel +- sphinx.ext.autosummary +- sphinx.ext.githubpages +- sphinx.ext.intersphinx +- sphinx.ext.napoleon +- sphinx.ext.viewcode +- sphinx_autodoc_typehints +- sphinx_book_theme +- sphinx_sitemap +- sphinxcontrib.video + +### System Dependencies (apt packages) +- code (Visual Studio Code) +- i2c-tools +- libportaudio2 +- libqt5multimedia5-plugins +- opencv-data +- pulseaudio +- python3-opencv +- python3-pyqt5.qtmultimedia + +### Pre-commit Hooks & Code Quality +- check-docstring-first +- check-executables-have-shebangs +- check-manifest +- check-merge-conflict +- check-toml +- codespell +- end-of-file-fixer +- mixed-line-ending +- requirements-txt-fixer +- trailing-whitespace + +### Type Checking & Utilities +- types-setuptools +- tomli +- calplot + +--- + +## Sources Analyzed + +1. **pyproject.toml** - Main dependencies, dev dependencies, build requirements +2. **Python source code** - All import statements across 117+ Python files +3. **docs/source/conf.py** - Sphinx extensions and mock imports +4. **docs/source/how_to_build/software_installation.md** - System installation requirements +5. **.pre-commit-config.yaml** - Pre-commit hooks and their dependencies + +--- + +*This list includes every library, tool, system package, and dependency used directly or indirectly by the Village repository for development, building, testing, documentation, and runtime operations.* \ No newline at end of file