auto-options-python 0.1.4__tar.gz

auto_options_python-0.1.4/.github/workflows/create_doc.yml

@@ -0,0 +1,47 @@
+name: Docs
+on:
+  push:
+    branches:
+      - main
+      - npe2
+    tags:
+      - "v*" # Push events to matching v*, i.e. v1.0, v20.15.10
+  pull_request:
+    branches:
+      - main
+      - npe2
+  workflow_dispatch:
+permissions:
+    contents: write
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+      - name: Install dependencies
+        run: |
+          pip install "napari[all]"
+          pip install numpy magicgui qtpy pyperclip 
+          pip install git+https://github.com/MontpellierRessourcesImagerie/auto-options-python.git
+          pip install sphinx sphinx_rtd_theme
+      - name: Sphinx build
+        run: |
+          pip install .
+          sphinx-apidoc -T -f -e -o docs/source/ src/autooptions
+          cd ./docs
+          make html
+          cd ..
+      - name: Deploy
+        uses: peaceiris/actions-gh-pages@v3
+        if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
+        with:
+          publish_branch: gh-pages
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: docs/build/html
+          force_orphan: true
+

auto_options_python-0.1.4/.github/workflows/test_and_deploy.yml

@@ -0,0 +1,76 @@
+# This workflows will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+name: tests
+
+on:
+  release:
+    types: [created]
+  workflow_dispatch:
+
+jobs:
+  test:
+    name: ${{ matrix.platform }} py${{ matrix.python-version }}
+    runs-on: ${{ matrix.platform }}
+    timeout-minutes: 30
+    strategy:
+      matrix:
+        platform: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ["3.10"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      # these libraries enable testing on Qt on linux
+      - uses: tlambert03/setup-qt-libs@v1
+
+
+      # note: if you need dependencies from conda, considering using
+      # setup-miniconda: https://github.com/conda-incubator/setup-miniconda
+      # and
+      # tox-conda: https://github.com/tox-dev/tox-conda
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install setuptools tox tox-gh-actions
+
+      # this runs the platform-specific tests declared in tox.ini
+      - name: Test with tox
+        uses: aganders3/headless-gui@v2
+        with:
+          run: python -m tox
+        env:
+          PLATFORM: ${{ matrix.platform }}
+
+      - name: Coverage
+        uses: codecov/codecov-action@v3
+
+  deploy:
+    # this will run when you have tagged a commit, starting with "v*"
+    # and requires that you have put your twine API key in your
+    # github secrets (see readme for details)
+    needs: [test]
+    runs-on: ubuntu-latest
+    if: contains(github.ref, 'tags')
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -U setuptools setuptools_scm wheel twine build
+      - name: Build and publish
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.TWINE_API_KEY }}
+        run: |
+          python -m build .
+          twine upload dist/*

auto_options_python-0.1.4/.gitignore

@@ -0,0 +1,213 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[codz]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+*_version.py
+
+# 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
+nosetests.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
+#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
+
+# Marimo
+marimo/_static/
+marimo/_lsp/
+__marimo__/
+
+# ide settings
+.idea
+
+

auto_options_python-0.1.4/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 Montpellier Ressources Imagerie
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

auto_options_python-0.1.4/PKG-INFO

@@ -0,0 +1,58 @@
+Metadata-Version: 2.4
+Name: auto-options-python
+Version: 0.1.4
+Summary: Mange command options in python and create QWidgets for them.
+Author: Volker Baecker
+Author-email: volker.baecker@mri.cnrs.fr
+License: MIT License
+        
+        Copyright (c) 2025 Montpellier Ressources Imagerie
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+        
+Project-URL: Bug Tracker, https://github.com/MontpellierRessourcesImagerie/auto-options-python/issues
+Project-URL: Documentation, https://montpellierressourcesimagerie.github.io/auto-options-python/
+Project-URL: Source Code, https://github.com/MontpellierRessourcesImagerie/auto-options-python
+Project-URL: User Support, https://github.com/MontpellierRessourcesImagerie/auto-options-python/issues
+Classifier: Development Status :: 4 - Beta
+Classifier: Framework :: napari
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: appdirs
+Requires-Dist: pyqt5
+Requires-Dist: qtpy
+Requires-Dist: napari
+Requires-Dist: pyperclip
+Requires-Dist: matplotlib
+Dynamic: license-file
+
+# auto-options-python
+Mange command options in python and create QWidgets for them.

auto_options_python-0.1.4/README.md

@@ -0,0 +1,2 @@
+# auto-options-python
+Mange command options in python and create QWidgets for them.

auto_options_python-0.1.4/docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

auto_options_python-0.1.4/docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

auto_options_python-0.1.4/docs/source/auto-options-python.rst

@@ -0,0 +1,22 @@
+autooptions package
+===================
+
+Submodules
+----------
+
+.. toctree::
+    :maxdepth: 4
+
+    autooptions.array_util
+    autooptions.napari_util
+    autooptions.options
+    autooptions.qtutil
+    autooptions.widget
+
+Module contents
+---------------
+
+.. automodule:: autooptions
+   :members:
+   :undoc-members:
+   :show-inheritance:

auto_options_python-0.1.4/docs/source/autooptions.array_util.rst

@@ -0,0 +1,4 @@
+.. automodule:: napari_bigfish.array_util
+   :members:
+   :undoc-members:
+   :show-inheritance:

auto_options_python-0.1.4/docs/source/autooptions.napari_util.rst

@@ -0,0 +1,4 @@
+.. automodule:: autooptions.napari_util
+   :members:
+   :undoc-members:
+   :show-inheritance:

auto_options_python-0.1.4/docs/source/autooptions.options.rst

@@ -0,0 +1,4 @@
+.. automodule:: autooptions.options
+   :members:
+   :undoc-members:
+   :show-inheritance:

auto_options_python-0.1.4/docs/source/autooptions.qtutil.rst

@@ -0,0 +1,4 @@
+.. automodule:: autooptions.qtutil
+   :members:
+   :undoc-members:
+   :show-inheritance:

auto_options_python-0.1.4/docs/source/autooptions.widget.rst

@@ -0,0 +1,4 @@
+.. automodule:: autooptions.widget
+   :members:
+   :undoc-members:
+   :show-inheritance:

auto_options_python-0.1.4/docs/source/conf.py

@@ -0,0 +1,85 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import os
+import sys
+sys.path.insert(0, os.path.abspath('../../src'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'napari-autooptions'
+copyright = '2026, INSERM'
+author = 'Volker Baecker, Clement Benedetti'
+
+# The full version, including alpha/beta/rc tags
+release = 'v0.1'
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+	'sphinx.ext.autodoc',
+	'sphinx.ext.linkcode'
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = []
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+#html_theme = 'alabaster'
+html_theme = "sphinx_rtd_theme"
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+# Options for the linkcode extension
+# ----------------------------------
+# Resolve function
+# This function is used to populate the (source) links in the API
+def linkcode_resolve(domain, info):
+    def find_source():
+        # try to find the file and line number, based on code from numpy:
+        # https://github.com/numpy/numpy/blob/master/doc/source/conf.py#L286
+        obj = sys.modules[info['module']]
+        for part in info['fullname'].split('.'):
+            obj = getattr(obj, part)
+        import inspect
+        import os
+        fn = inspect.getsourcefile(obj)
+        fn = os.path.relpath(fn, start=os.path.abspath('..'))
+        source, lineno = inspect.getsourcelines(obj)
+        return fn, lineno, lineno + len(source) - 1
+
+    if domain != 'py' or not info['module']:
+        return None
+    try:
+        filename = '%s#L%d-L%d' % find_source()
+    except Exception:
+        filename = info['module'].replace('.', '/') + '.py'
+    return "https://github.com/MontpellierRessourcesImagerie/auto-options-python/blob/main/%s" % (filename)
+

auto_options_python-0.1.4/docs/source/index.rst

@@ -0,0 +1,10 @@
+Documentation of `auto-options-python <https://github.com/MontpellierRessourcesImagerie/auto-options-python/>`_
+===============================
+
+.. toctree::
+   :maxdepth: 4
+
+   user/user_documentation
+   modules
+   
+

auto_options_python-0.1.4/docs/source/modules.rst

@@ -0,0 +1,7 @@
+API-Documentation
+=================
+
+.. toctree::
+   :maxdepth: 4
+
+   auto-options-python

auto_options_python-0.1.4/docs/source/user/installation.rst

@@ -0,0 +1,6 @@
+Installation
+============
+
+You can install autooptions via pip:
+
+	pip install auto-options-python

auto_options_python-0.1.4/docs/source/user/introduction.rst

@@ -0,0 +1,47 @@
+Introduction
+============
+.. figure:: https://dev.mri.cnrs.fr/attachments/download/4544/autooptions_conv.png
+    :width: 250
+    :align: center
+    :alt: the napari-bigfish plugin
+
+    Fig. 1.1 - A simple dialog created with autooptions
+
+Autooptions allows to create options for operations in napari, in a simple way. Autooptions automatically saves and
+loads non transient options. It can create a dialog from the options, in which the user can change the values of the
+options. It updates combo-boxes containing layers of a given type when layers of that type are added or removed in
+napari. The user can provide callbacks that are called when the value of an option changes.
+
+The option types currently supported are:
+
+- Image
+- FFT (specific to 3D-toolbox)
+- Labels
+- Points
+- Int
+- Float
+- Choice
+- String
+- Boolean
+
+The layer types (FFT, Labels, Points and Image) and Choice will be represented via combo-boxes in the dialog. Boolean
+is using a checkbox and the others are using input fields.
+
+The code to create the options-dialog in Fig.1.1 is:
+
+.. code-block:: python
+
+   import napari
+   from autooptions.options import Options
+   from autooptions.widget import OptionsWidget
+
+   options = Options("3D Toolbox", "Convolution")
+   options.addImage()
+   option.addImage(name="kernel")
+   options.addChoice("mode", choices=["same", "valid", "full"])
+   options.addChoice("method", choices=["auto", "direct", "fft"])
+   options.load()
+   widget = OptionsWidget(self.viewer, self.options, self)
+   widget.addApplyButton(None)
+   viewer = napari.Viewer()
+   viewer.window.add_dock_widget(widget, name=options.optionsName)