rxiv-maker 1.14.3__tar.gz

rxiv_maker-1.14.3/.gitignore

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+# Build directories (contains all generated files)
+build/
+output/
+dist/
+.pybuild/
+
+# Package distribution artifacts
+apt-repo/
+*.deb
+*.buildinfo
+*.changes
+
+# Build and audit logs
+build.log
+pip-audit-report.json
+
+# Docker build logs
+src/docker/build-*.log
+
+# Generated figures (exclude generated, include source templates)
+!src/figures/Figure*_placeholder.txt
+
+# Figure generation artifacts
+scripts/figures/__pycache__/
+scripts/figures/*.pyc
+
+# LaTeX auxiliary files
+*.aux
+*.bbl
+*.blg
+*.fls
+*.fdb_latexmk
+*.log
+*.out
+*.toc
+*.fmt
+*.fot
+*.cb
+*.cb2
+.*.lb
+*.pdf
+*.zip
+
+# gptrepo
+output.txt
+
+# OS and editor files
+.DS_Store
+.vscode/
+*.swp
+*.swo
+*~
+
+# Claude Code configuration
+CLAUDE.md
+.claude
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# Python files in base directory only (not subdirectories)
+/*.py
+
+# Debug and temporary development files
+debug_*.py
+todo*.md
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+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
+.rxiv_cache/
+nosetests.xml
+coverage.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
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.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/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# 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
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+activate_venv.sh
+
+# 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/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and 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/
+
+# Abstra
+# Abstra is an AI-powered process automation framework.
+# Ignore directories containing user credentials, local state, and settings.
+# Learn more at https://abstra.io/docs
+.abstra/
+
+# Visual Studio Code
+#  Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore
+#  that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+#  and can be added to the global gitignore or merged into this file. However, if you prefer,
+#  you could uncomment the following to ignore the entire vscode folder
+# .vscode/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# Cursor
+#  Cursor is an AI-powered code editor. `.cursorignore` specifies files/directories to
+#  exclude from AI features like autocomplete and code analysis. Recommended for sensitive data
+#  refer to https://docs.cursor.com/context/ignore-files
+.cursorignore
+.cursorindexingignore
+
+# Auto-generated API documentation
+docs/api/*.md
+!docs/api/README.md
+!docs/api/index.md
+
+# Git submodules are tracked by .gitmodules
+# Individual submodule contents are managed by git submodule commands
+
+# Prevent individual submodule files from being committed
+# Submodules should only be managed via git submodule commands
+submodules/homebrew-rxiv-maker/
+submodules/scoop-rxiv-maker/
+submodules/vscode-rxiv-maker/
+
+# Repository contamination prevention
+# Prevent common files from wrong repositories being accidentally added
+
+
+# Scoop files should only be in scoop-rxiv-maker submodule
+/bucket/
+*.ps1
+scoop-*
+
+# VSCode extension files should only be in vscode-rxiv-maker submodule
+/.vscodeignore
+/language-configuration.json
+/*.tmLanguage.json
+/src/extension.ts
+/src/test/extension.test.ts
+/schemas/config-schema.json
+/esbuild.js
+/eslint.config.mjs
+
+# Prevent temporary submodule clones from being committed
+temp-*-clone/
+temp-*-fix/
+
+# Safeguard system logs and temporary files
+scripts/safeguards/*.log
+.safeguard-validation-*
+
+.gitignore
+MANUSCRIPT/2025__author_et_al__rxiv.pdf
+EXAMPLE_MANUSCRIPT/2025__Saraiva_et_al__for_arxiv.zip
+
+# Allow PDFs in FIGURES directories to be tracked
+!MANUSCRIPT/FIGURES/*.pdf
+!EXAMPLE_MANUSCRIPT/FIGURES/*.pdf
+GEMINI.md
+# Markdown files - ignore by default except important ones
+*.md
+.github/*.md
+
+# Important markdown files to keep tracked
+!README.md
+!CHANGELOG.md
+!CONTRIBUTING.md
+!CODE_OF_CONDUCT.md
+!docs/**/*.md
+!EXAMPLE_MANUSCRIPT/**/*.md
+!MANUSCRIPT/**/*.md
+!examples/**/*.md
+!test_init/**/*.md
+!src/**/*.md
+!tests/**/*.md
+!scripts/**/*.md
+!.github/**/*.md
+
+# Specific temporary/working files to ignore
+todo*.md
+DOCKER_ACCELERATION.md
+GEMINI.md
+CLAUDE.md
+output.md
+
+# Temporary analysis files
+.folder2md_ignore
+submodules/vscode-rxiv-maker/node_modules
+test-results
+plan_prompt.md
+.gha-logs
+.bandit
+bandit-report.json
+iv-maker/output.md
+lms/todo.md
+pip-audit-report.json
+coverage.json
+
+# Reports and logs (auto-generated)
+*.log
+*.xml
+*-report.json
+coverage*.xml
+coverage*.json
+*.report
+report-*.json
+*.audit
+audit-*.json
+
+# Distribution artifacts (should be generated via CI/CD)
+dist/
+*.whl
+*.tar.gz
+
+# Backup directories
+backup/
+
+# Environment files (local overrides only)
+.env
+.env.local
+.env.*.local
+
+# Tool configuration files
+.folder2md_ignore
+.bandit
+
+# MyPy cache
+.mypy_cache/
+
+# Output directories and generated files
+*/output/*.log
+*/output/*.xml
+*/output/.log
+output/
+build/
+
+# APT repository validation results (temporary files)
+validation-results/
+packaging/validation-results/
+.venv-linux
+rxivdraft/MANUSCRIPT/2025__antónio_d_brito_et_al__rxiv.pdf
+.ci_artifacts
+
+.gemini/
+.gemini-clipboard/
+gha-creds-*.json
+fatetracking/MANUSCRIPT/.rxiv_cache