RosettaX 0.0.1__tar.gz

rosettax-0.0.1/.flake8

@@ -0,0 +1,11 @@
+[flake8]
+max-line-length = 300
+exclude =
+    .git
+    docs/build
+    docs/source/gallery
+    development
+
+count = true
+per-file-ignores =
+    __init__.py: F403, F401

rosettax-0.0.1/.github/dependabot.yml

@@ -0,0 +1,11 @@
+# Specify reviewers for pull requests
+
+version: 2
+updates:
+  - package-ecosystem: "pip"
+    directory: "/"
+    target-branch: "master"
+    schedule:
+      interval: "monthly"
+      day: "sunday"
+      time: "09:00"

rosettax-0.0.1/.github/workflows/deploy_PyPi.yml

@@ -0,0 +1,20 @@
+name: Deploy to PyPi
+
+on:
+  push:
+    branches: [ "master" ]
+    tags:
+      - '*'
+  pull_request:
+    branches: [ "master" ]
+
+permissions:
+    contents: write
+
+jobs:
+  pure_package:
+    uses: MartinPdeS/MPSActions/.github/workflows/publish_pure_package_to_PyPi.yml@master
+    with:
+      python-version: "3.13"
+    secrets:
+      PYPI_API_TOKEN: ${{ secrets.PYPI_API_TOKEN }}

rosettax-0.0.1/.github/workflows/deploy_anaconda.yml

@@ -0,0 +1,21 @@
+name: Deploy Conda Packages
+
+on:
+  push:
+    branches: [ "master" ]
+    tags: '*'
+  pull_request:
+    branches: [ "master" ]
+
+permissions:
+    contents: write
+
+jobs:
+  ManyLinux_x86_64:
+    uses: MartinPdeS/MPSActions/.github/workflows/publish_compiled_package_to_anaconda.yml@master
+    with:
+      python-versions: '["3.13"]'
+      apt-package: ""
+    secrets:
+      ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_API_TOKEN }}
+

rosettax-0.0.1/.github/workflows/deploy_coverage.yml

@@ -0,0 +1,25 @@
+# Simple workflow for deploying static content to GitHub Pages
+name: Deploy coverage
+
+on:
+  push:
+    branches: [ "master" ]
+    tags: '*'
+  pull_request:
+    branches: [ "master" ]
+
+
+# Sets permissions of the  GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: write
+  pages: write
+  id-token: write
+
+jobs:
+  ManyLinux_x86_64:
+    uses: MartinPdeS/MPSActions/.github/workflows/publish_coverage.yml@master
+    with:
+      python-version: "3.13"
+      apt-package: xvfb
+    secrets:
+      _GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

rosettax-0.0.1/.github/workflows/deploy_documentation.yml

@@ -0,0 +1,24 @@
+# Simple workflow for deploying static content to GitHub Pages
+name: Documentation
+
+on:
+  push:
+    branches: [ "master" ]
+    tags: '*'
+  pull_request:
+    branches: [ "master" ]
+
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: write
+  pages: write
+  id-token: write
+
+jobs:
+  ManyLinux_x86_64:
+    uses: MartinPdeS/MPSActions/.github/workflows/publish_documentation.yml@master
+    with:
+      python-version: "3.13"
+      package-name: "RosettaX"
+      apt-package: xvfb jq

rosettax-0.0.1/.gitignore

@@ -0,0 +1,29 @@
+
+# Ignore all
+/*
+
+# Except ...
+!.github
+!RosettaX
+!development
+!docs
+!tests
+!.flake8
+!.gitignore
+!.pre-commit-config.yaml
+!LICENSE
+!meta.yaml
+!pyproject.toml
+!README.rst
+!notebook.ipynb
+!CMakeLists.txt
+
+# But ignore docs/build inside docs and code
+docs/build/
+docs/source/gallery/
+
+# Compiled files in the project
+*__pycache__*
+*.DS_Store*
+*.so*
+*.a*

rosettax-0.0.1/.pre-commit-config.yaml

@@ -0,0 +1,20 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-added-large-files
+
+  - repo: https://github.com/psf/black
+    rev: 24.4.2
+    hooks:
+      - id: black
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.6.9
+    hooks:
+      - id: ruff
+        args: [--select, I, --fix]   # import-order rules + auto-fix
+      - id: ruff-format               # optional (formatter)

rosettax-0.0.1/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2020 Martin de Sivry
+
+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.

rosettax-0.0.1/PKG-INFO

@@ -0,0 +1,60 @@
+Metadata-Version: 2.4
+Name: RosettaX
+Version: 0.0.1
+Summary: A package for Flow-cytometer calibration.
+Author-email: Martin  / Victor / Edwin <martin.poinsinet.de.sivry@gmail.com>
+License: MIT License
+        
+        Copyright (c) 2020 Martin de Sivry
+        
+        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: Homepage, https://github.com/MartinPdeS/RosettaX
+Project-URL: Documentation, https://martinpdes.github.io/RosettaX/
+Project-URL: Repository, https://github.com/MartinPdeS/RosettaX.git
+Keywords: flow-cytometre,calibration,physics,data-analysis
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: Implementation :: CPython
+Classifier: Development Status :: 3 - Alpha
+Classifier: Topic :: Scientific/Engineering :: Physics
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Intended Audience :: Science/Research
+Requires-Python: >=3.10
+Description-Content-Type: text/x-rst
+License-File: LICENSE
+Requires-Dist: PyMieSim
+Requires-Dist: pydantic
+Requires-Dist: numpy
+Requires-Dist: MPSPlots
+Provides-Extra: testing
+Requires-Dist: pytest<9.0,>=7.4; extra == "testing"
+Requires-Dist: pytest-cov<7,>=2; extra == "testing"
+Requires-Dist: pytest-json-report~=1.5; extra == "testing"
+Requires-Dist: coverage~=7.6; extra == "testing"
+Provides-Extra: documentation
+Requires-Dist: numpydoc~=1.8; extra == "documentation"
+Requires-Dist: sphinx>=6; extra == "documentation"
+Requires-Dist: sphinx-gallery~=0.17; extra == "documentation"
+Requires-Dist: sphinx-rtd-theme~=3.0; extra == "documentation"
+Requires-Dist: pydata-sphinx-theme~=0.15; extra == "documentation"
+Provides-Extra: dev
+Requires-Dist: flake8==7.2.0; extra == "dev"
+Dynamic: license-file

rosettax-0.0.1/RosettaX/__init__.py

@@ -0,0 +1,11 @@
+"""
+PyMieSim package initialization.
+"""
+
+try:
+    from ._version import version as __version__
+
+except ImportError:
+    __version__ = "0.0.0"
+
+debug_mode = False

rosettax-0.0.1/RosettaX/_version.py

@@ -0,0 +1,34 @@
+# file generated by setuptools-scm
+# don't change, don't track in version control
+
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "version",
+    "version_tuple",
+    "__commit_id__",
+    "commit_id",
+]
+
+TYPE_CHECKING = False
+if TYPE_CHECKING:
+    from typing import Tuple
+    from typing import Union
+
+    VERSION_TUPLE = Tuple[Union[int, str], ...]
+    COMMIT_ID = Union[str, None]
+else:
+    VERSION_TUPLE = object
+    COMMIT_ID = object
+
+version: str
+__version__: str
+__version_tuple__: VERSION_TUPLE
+version_tuple: VERSION_TUPLE
+commit_id: COMMIT_ID
+__commit_id__: COMMIT_ID
+
+__version__ = version = '0.0.1'
+__version_tuple__ = version_tuple = (0, 0, 1)
+
+__commit_id__ = commit_id = 'g73b999451'

rosettax-0.0.1/RosettaX/directories.py

@@ -0,0 +1,25 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+from pathlib import Path
+import RosettaX
+
+__all__ = ["root_path", "doc_path", "logo_path", "doc_css_path"]
+
+root_path = Path(RosettaX.__path__[0])
+
+project_path = root_path.parents[0]
+
+doc_path = root_path.parents[0].joinpath("docs")
+
+logo_path = doc_path.joinpath("images/logo.png")
+
+doc_css_path = doc_path.joinpath("source/_static/default.css")
+
+if __name__ == "__main__":
+    for path_name in __all__:
+        path = locals()[path_name]
+        print(path)
+        assert path.exists(), f"Path {path_name} do not exists"
+
+# -

rosettax-0.0.1/RosettaX.egg-info/PKG-INFO

@@ -0,0 +1,60 @@
+Metadata-Version: 2.4
+Name: RosettaX
+Version: 0.0.1
+Summary: A package for Flow-cytometer calibration.
+Author-email: Martin  / Victor / Edwin <martin.poinsinet.de.sivry@gmail.com>
+License: MIT License
+        
+        Copyright (c) 2020 Martin de Sivry
+        
+        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: Homepage, https://github.com/MartinPdeS/RosettaX
+Project-URL: Documentation, https://martinpdes.github.io/RosettaX/
+Project-URL: Repository, https://github.com/MartinPdeS/RosettaX.git
+Keywords: flow-cytometre,calibration,physics,data-analysis
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: Implementation :: CPython
+Classifier: Development Status :: 3 - Alpha
+Classifier: Topic :: Scientific/Engineering :: Physics
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Intended Audience :: Science/Research
+Requires-Python: >=3.10
+Description-Content-Type: text/x-rst
+License-File: LICENSE
+Requires-Dist: PyMieSim
+Requires-Dist: pydantic
+Requires-Dist: numpy
+Requires-Dist: MPSPlots
+Provides-Extra: testing
+Requires-Dist: pytest<9.0,>=7.4; extra == "testing"
+Requires-Dist: pytest-cov<7,>=2; extra == "testing"
+Requires-Dist: pytest-json-report~=1.5; extra == "testing"
+Requires-Dist: coverage~=7.6; extra == "testing"
+Provides-Extra: documentation
+Requires-Dist: numpydoc~=1.8; extra == "documentation"
+Requires-Dist: sphinx>=6; extra == "documentation"
+Requires-Dist: sphinx-gallery~=0.17; extra == "documentation"
+Requires-Dist: sphinx-rtd-theme~=3.0; extra == "documentation"
+Requires-Dist: pydata-sphinx-theme~=0.15; extra == "documentation"
+Provides-Extra: dev
+Requires-Dist: flake8==7.2.0; extra == "dev"
+Dynamic: license-file

rosettax-0.0.1/RosettaX.egg-info/SOURCES.txt

@@ -0,0 +1,34 @@
+.flake8
+.gitignore
+.pre-commit-config.yaml
+LICENSE
+pyproject.toml
+.github/dependabot.yml
+.github/workflows/deploy_PyPi.yml
+.github/workflows/deploy_anaconda.yml
+.github/workflows/deploy_coverage.yml
+.github/workflows/deploy_documentation.yml
+RosettaX/__init__.py
+RosettaX/_version.py
+RosettaX/directories.py
+RosettaX/utils.py
+RosettaX.egg-info/PKG-INFO
+RosettaX.egg-info/SOURCES.txt
+RosettaX.egg-info/dependency_links.txt
+RosettaX.egg-info/requires.txt
+RosettaX.egg-info/top_level.txt
+docs/Makefile
+docs/make.bat
+docs/examples/README.rst
+docs/examples/workflow/README.rst
+docs/examples/workflow/workflow.py
+docs/images/logo.png
+docs/source/code.rst
+docs/source/conf.py
+docs/source/index.rst
+docs/source/references.rst
+docs/source/sg_execution_times.rst
+docs/source/theory.rst
+docs/source/_static/default.css
+tests/__init__.py
+tests/test_loader.py

rosettax-0.0.1/RosettaX.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

rosettax-0.0.1/RosettaX.egg-info/requires.txt

@@ -0,0 +1,20 @@
+PyMieSim
+pydantic
+numpy
+MPSPlots
+
+[dev]
+flake8==7.2.0
+
+[documentation]
+numpydoc~=1.8
+sphinx>=6
+sphinx-gallery~=0.17
+sphinx-rtd-theme~=3.0
+pydata-sphinx-theme~=0.15
+
+[testing]
+pytest<9.0,>=7.4
+pytest-cov<7,>=2
+pytest-json-report~=1.5
+coverage~=7.6

rosettax-0.0.1/RosettaX.egg-info/top_level.txt

@@ -0,0 +1 @@
+RosettaX

rosettax-0.0.1/docs/Makefile

@@ -0,0 +1,19 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+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)

rosettax-0.0.1/docs/examples/README.rst

@@ -0,0 +1,6 @@
+.. _examples_gallery:
+
+Examples
+========
+
+A gallery of examples and that showcase how RosettaX can be used. Some examples demonstrate the use of the API in general and some demonstrate specific applications in tutorial form.

rosettax-0.0.1/docs/examples/workflow/README.rst

@@ -0,0 +1,4 @@
+.. _examples_workflow_gallery:
+
+Workflow
+========

rosettax-0.0.1/docs/examples/workflow/workflow.py

@@ -0,0 +1,9 @@
+"""
+Workflow example
+================
+
+Just a dummy example to illustrate the workflow examples gallery.
+
+"""
+
+print("Hello, World!")

rosettax-0.0.1/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
+
+if "%1" == "" goto help
+
+%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.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+
+:end
+popd

rosettax-0.0.1/docs/source/_static/default.css

@@ -0,0 +1,19 @@
+/* Additional styling for the PyData Sphinx theme. */
+
+/* Use hyperlink color for grid-item-cards.
+TODO find a way to only apply this to grid-item-cards that link somewhere */
+.sd-card-title {
+    color: var(--pst-color-link);
+}
+
+/* Use text base color for hyperlinks in code cells. Pygments "default" theme
+doesn't seem to set this color, so the default light blue link color is applied
+which has a very low contrast with the background. */
+div.highlight a {
+    color: var(--pst-color-text-base);
+}
+
+/* Stack components in footer vertically. */
+.bd-footer .footer-items__end, .bd-footer .footer-items__start {
+  flex-direction: row;
+}

rosettax-0.0.1/docs/source/code.rst

@@ -0,0 +1,5 @@
+.. _source_code:
+
+Source code
+===========
+

rosettax-0.0.1/docs/source/conf.py

@@ -0,0 +1,169 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import sys
+from sphinx_gallery.sorting import FileNameSortKey
+from MPSPlots.styles import use_mpsplots_style
+import RosettaX
+
+from RosettaX.directories import project_path, doc_css_path
+
+
+sys.path.insert(0, project_path)
+sys.path.insert(0, project_path.joinpath('Rosetta'))
+
+
+def setup(app):
+    app.add_css_file(str(doc_css_path))
+
+
+autodoc_mock_imports = [
+    'numpy',
+    'matplotlib',
+    'scipy',
+    'numpydoc',
+]
+
+
+project = 'Rosetta'
+copyright = '2023, Martin Poinsinet de Sivry-Houle'
+author = 'Martin Poinsinet de Sivry-Houle'
+
+
+version = RosettaX.__version__
+
+
+extensions = [
+    'sphinx.ext.mathjax',
+    'sphinx_gallery.gen_gallery',
+    'sphinx.ext.autodoc',
+    'sphinx.ext.napoleon',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.autosectionlabel',
+    'sphinx.ext.intersphinx',
+]
+
+# Napoleon settings for docstrings
+napoleon_google_docstring = False
+napoleon_numpy_docstring = True
+
+
+def reset_mpl(gallery_conf, fname):
+    use_mpsplots_style()
+
+
+examples_files = [
+    'workflow'
+]
+
+
+sphinx_gallery_conf = {
+    "examples_dirs": ['../examples/' + f for f in examples_files],
+    "gallery_dirs": ['gallery/' + f for f in examples_files],
+    'image_scrapers': ('matplotlib'),
+    'filename_pattern': '',
+    'ignore_pattern': '/__',
+    'plot_gallery': True,
+    'thumbnail_size': [600, 600],
+    'download_all_examples': False,
+    'reset_modules': reset_mpl,
+    'line_numbers': False,
+    'remove_config_comments': True,
+    'within_subsection_order': FileNameSortKey,
+    'capture_repr': ('_repr_html_', '__repr__'),
+    'nested_sections': True,
+}
+
+
+autodoc_default_options = {
+    'members': False,
+    'members-order': 'bysource',
+    'undoc-members': False,
+    'show-inheritance': True,
+}
+
+autosectionlabel_prefix_document = True
+numpydoc_show_class_members = False
+add_module_names = False
+
+source_suffix = '.rst'
+master_doc = 'index'
+language = 'en'
+highlight_language = 'python3'
+html_theme = "pydata_sphinx_theme"
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+exclude_trees = []
+# default_role = "autolink"
+pygments_style = "sphinx"
+
+# -- Sphinx-gallery configuration --------------------------------------------
+major, minor = version[:2]
+binder_branch = f"v{major}.{minor}.x"
+
+html_theme_options = {
+    # Navigation bar
+    "logo": {
+        "alt_text": "RosettaX's logo",
+        "text": "RosettaX",
+        "link": "https://rosetta.readthedocs.io/en/master/",
+    },
+    "icon_links": [
+        {
+            "name": "GitHub",
+            "url": "https://github.com/MartinPdeS/RosettaX",
+            "icon": "fa-brands fa-github",
+        },
+        {
+            "name": "PyPI",
+            "url": "https://pypi.org/project/rosettax/",
+            "icon": "fa-solid fa-box",
+        },
+        {
+            "name": "Anaconda",
+            "url": "https://anaconda.org/MartinPdeS/rosettax",
+            "icon": "fa-brands fa-python",
+        },
+    ],
+    "navbar_align": "left",
+    "navbar_end": ["version-switcher", "navbar-icon-links"],
+    "show_prev_next": False,
+    "show_version_warning_banner": True,
+    # Footer
+    "footer_start": ["copyright"],
+    "footer_end": ["sphinx-version", "theme-version"],
+    # Other
+    "pygment_light_style": "default",
+    "pygment_dark_style": "github-dark",
+}
+
+htmlhelp_basename = 'RosettaXdoc'
+
+latex_elements = {}
+
+
+latex_documents = [
+    (master_doc, 'RosettaX.tex', 'RosettaX Documentation',
+     'Martin Poinsinet de Sivry-Houle', 'manual'),
+]
+
+man_pages = [
+    (master_doc, 'supymode', 'RosettaX Documentation',
+     [author], 1)
+]
+
+texinfo_documents = [
+    (master_doc, 'RosettaX', 'RosettaX Documentation',
+     author, 'RosettaX', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+epub_title = project
+
+html_static_path = ['_static']
+templates_path = ['_templates']
+html_css_files = ['default.css']
+epub_exclude_files = ['search.html']
+
+# -

rosettax-0.0.1/docs/source/index.rst

@@ -0,0 +1,14 @@
+**Date**: |today|, **Version**: |version|
+
+
+.. include:: ../../README.rst
+    :start-line: 0
+
+.. toctree::
+    :maxdepth: 2
+    :hidden:
+
+    theory
+    code
+    gallery/index.rst
+    references

rosettax-0.0.1/docs/source/references.rst

@@ -0,0 +1,8 @@
+:orphan:
+
+.. _references:
+
+References
+===========
+
+

rosettax-0.0.1/docs/source/sg_execution_times.rst

@@ -0,0 +1,37 @@
+
+:orphan:
+
+.. _sphx_glr_sg_execution_times:
+
+
+Computation times
+=================
+**00:00.035** total execution time for 1 file **from all galleries**:
+
+.. container::
+
+  .. raw:: html
+
+    <style scoped>
+    <link href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/5.3.0/css/bootstrap.min.css" rel="stylesheet" />
+    <link href="https://cdn.datatables.net/1.13.6/css/dataTables.bootstrap5.min.css" rel="stylesheet" />
+    </style>
+    <script src="https://code.jquery.com/jquery-3.7.0.js"></script>
+    <script src="https://cdn.datatables.net/1.13.6/js/jquery.dataTables.min.js"></script>
+    <script src="https://cdn.datatables.net/1.13.6/js/dataTables.bootstrap5.min.js"></script>
+    <script type="text/javascript" class="init">
+    $(document).ready( function () {
+        $('table.sg-datatable').DataTable({order: [[1, 'desc']]});
+    } );
+    </script>
+
+  .. list-table::
+   :header-rows: 1
+   :class: table table-striped sg-datatable
+
+   * - Example
+     - Time
+     - Mem (MB)
+   * - :ref:`sphx_glr_gallery_workflow_workflow.py` (``../examples/workflow/workflow.py``)
+     - 00:00.035
+     - 0.0

rosettax-0.0.1/docs/source/theory.rst

@@ -0,0 +1,7 @@
+:orphan:
+
+.. _theory:
+
+Theoretical background
+======================
+

rosettax-0.0.1/pyproject.toml

@@ -0,0 +1,85 @@
+[build-system]
+requires = ["setuptools>=40.8.0", "wheel", "setuptools_scm[toml]>=8.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "RosettaX"
+dynamic = ["version"]
+description = "A package for Flow-cytometer calibration."
+license = {file = "LICENSE"}
+readme = "README.rst"
+requires-python = ">=3.10"
+authors = [{ name="Martin  / Victor / Edwin", email="martin.poinsinet.de.sivry@gmail.com"}]
+classifiers = [
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: Implementation :: CPython",
+    "Development Status :: 3 - Alpha",
+    "Topic :: Scientific/Engineering :: Physics",
+    "License :: OSI Approved :: MIT License",
+    "Intended Audience :: Science/Research"
+]
+
+keywords = ["flow-cytometre", "calibration", "physics", "data-analysis"]
+
+dependencies = [
+    "PyMieSim",
+    "pydantic",
+    "numpy",
+    "MPSPlots",
+]
+
+[project.urls]
+Homepage = "https://github.com/MartinPdeS/RosettaX"
+Documentation = "https://martinpdes.github.io/RosettaX/"
+Repository = "https://github.com/MartinPdeS/RosettaX.git"
+
+[tool.setuptools_scm]
+write_to = "RosettaX/_version.py"
+version_scheme = "only-version"
+local_scheme = "no-local-version"
+
+[project.optional-dependencies]
+testing = [
+    "pytest >=7.4,<9.0",
+    "pytest-cov >=2,<7",
+    "pytest-json-report ~=1.5",
+    "coverage ~=7.6"
+]
+
+documentation = [
+    "numpydoc ~=1.8",
+    "sphinx >=6",
+    "sphinx-gallery ~=0.17",
+    "sphinx-rtd-theme ~=3.0",
+    "pydata-sphinx-theme ~=0.15"
+]
+
+dev = [
+    "flake8 ==7.2.0",
+]
+
+[tool.pytest.ini_options]
+minversion = "6.0"
+xfail_strict = true
+log_cli_level = "INFO"
+testpaths = ["tests/"]
+addopts = [
+    "-v",
+    "-rA",
+    "-rw",
+    "--cov=RosettaX",
+    "--cov-report=html",
+    "--cov-report=term"
+]
+
+[tool.coverage.run]
+source = ["RosettaX"]
+omit = [
+    "*/__init__.py",
+    "*/_version.py",
+    "*/directories.py"
+]
+branch = true
+relative_files = true

rosettax-0.0.1/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

rosettax-0.0.1/tests/test_loader.py

@@ -0,0 +1,9 @@
+import pytest
+
+def test_dummy():
+    assert True
+
+
+
+if __name__ == "__main__":
+    pytest.main(["-W error", __file__])