Update .gitignore template and review all rules

Fix #234

Author: PierreRaybaut

.gitignore

@@ -1,41 +1,56 @@
-winpython.env
-.spyderproject
+# ---------------------------- Specific to this project --------------------------------
+
+# DataLab project specific
+resources/*.png
 doc.zip
+releases/
+/tutorialnotes*.md
+doc/contributing/changelog.md
+scenario_*.h5
+
+# Windows specific
 Thumbs.db
-doctmp/
-.vs/
+
+# Microsoft Visual Studio
 *.pyproj
 *.sln
-releases/
+
+# Sphinx documentation
+doctmp/
 .doctrees/
 doc/install_requires.txt
 doc/extras_require-dev.txt
 doc/extras_require-doc.txt
-*.bak
-/tutorialnotes*.md
 doc/locale/pot/_sphinx_design_static/
-doc/contributing/changelog.md
 
-# Visual Studio Code
-.venv
-.env
+# Backup files (e.g. created during merge conflicts)
+*.bak
+
+# WiX files
+.wix/
+wix/DataLab-*.wxs
+wix/bin/
+wix/obj/
+wix/*.bmp
+*.wixpdb
+*.msi
+
+# ------------------ Template `Python.gitignore` from gitignore.io ---------------------
 
 # Created by https://www.gitignore.io/api/python
 
 ### Python ###
 # Byte-compiled / optimized / DLL files
 __pycache__/
-*.py[cod]
+*.py[codz]
 *$py.class
 
 # C extensions
 *.so
 
 # Distribution / packaging
 .Python
-env/
 build/
-_build/
 develop-eggs/
 dist/
 downloads/
@@ -46,13 +61,16 @@ 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 info into it.
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
 *.manifest
 # *.spec
 
@@ -63,38 +81,169 @@ pip-delete-this-directory.txt
 # Unit test / coverage reports
 htmlcov/
 .tox/
+.nox/
 .coverage
 .coverage.*
 .cache
 nosetests.xml
 coverage.xml
-*,cover
+*.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/
-cdl/data/doc/
 
 # PyBuilder
+.pybuilder/
 target/
 
-# Files related to WiX
-.wix/
-wix/DataLab-*.wxs
-wix/bin/
-wix/obj/
-wix/*.bmp
-*.wixpdb
-*.msi
+# Jupyter Notebook
+.ipynb_checkpoints
 
-# Files generated by tests
-scenario_*.h5
+# 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
+#poetry.toml
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#   pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
+#   https://pdm-project.org/en/latest/usage/project/#working-with-version-control
+#pdm.lock
+#pdm.toml
+.pdm-python
+.pdm-build/
+
+# pixi
+#   Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control.
+#pixi.lock
+#   Pixi creates a virtual environment in the .pixi directory, just like venv module creates one
+#   in the .venv directory. It is recommended not to include this directory in version control.
+.pixi
+
+# 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
+.env
+.envrc
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# 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
 
-# Image resources
-resources/*.png
+# Marimo
+marimo/_static/
+marimo/_lsp/
+__marimo__/