Sphinx Autostart with small changes

.gitignore

@@ -12,3 +12,7 @@ venv
 build
 # Ignore Data Folder
 Data
+# ignore Sphinx documentation output
+*docs/build
+# Ignore .DS_Store
+.DS_Store
\ No newline at end of file

Makefile

+# 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)

README.md

-# POD
+# Model Order Reduction for Stokes Flow in Microstructures
 
 [![Pipeline Status](https://git.rwth-aachen.de/janhab/pod/badges/main/pipeline.svg)](https://git.rwth-aachen.de/janhab/pod/pipelines)
 [![Documentation](https://img.shields.io/badge/docs-latest-blue)](https://janhab.pages.rwth-aachen.de/pod/)
@@ -7,7 +7,7 @@
 
 ## Seminar Thesis
 
-This repository contains the code to reproduce the results presented in the seminar thesis: PLACEHOLDER
+This repository contains the code to reproduce the results presented in the seminar thesis: Model Order Reduction for Stokes Flow in Microstructures
 
 ## Installation
 

README_files/libs/clipboard/clipboard.min.js

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README_files/libs/quarto-html/anchor.min.js

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README_files/libs/quarto-html/quarto-syntax-highlighting-e26003cea8cd680ca0c55a263523d882.css

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-  --quarto-hl-co-color: #5E5E5E;
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-  --quarto-hl-cn-color: #8f5902;
-  --quarto-hl-sc-color: #5E5E5E;
-  --quarto-hl-dv-color: #AD0000;
-  --quarto-hl-kw-color: #003B4F;
-}
-
-/* other quarto variables */
-:root {
-  --quarto-font-monospace: SFMono-Regular, Menlo, Monaco, Consolas, "Liberation Mono", "Courier New", monospace;
-}
-
-pre > code.sourceCode > span {
-  color: #003B4F;
-}
-
-code span {
-  color: #003B4F;
-}
-
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-  color: #003B4F;
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-}
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-  color: #5E5E5E;
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-  color: #00769E;
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-  color: #20794D;
-  font-style: inherit;
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-  color: #AD0000;
-  font-style: inherit;
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-  color: #AD0000;
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-  color: #5E5E5E;
-  font-style: inherit;
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-  color: #5E5E5E;
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-  color: #8f5902;
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-  color: #003B4F;
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-.prevent-inlining {
-  content: "</";
-}
-
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README_files/libs/quarto-html/tippy.css

-.tippy-box[data-animation=fade][data-state=hidden]{opacity:0}[data-tippy-root]{max-width:calc(100vw - 10px)}.tippy-box{position:relative;background-color:#333;color:#fff;border-radius:4px;font-size:14px;line-height:1.4;white-space:normal;outline:0;transition-property:transform,visibility,opacity}.tippy-box[data-placement^=top]>.tippy-arrow{bottom:0}.tippy-box[data-placement^=top]>.tippy-arrow:before{bottom:-7px;left:0;border-width:8px 8px 0;border-top-color:initial;transform-origin:center top}.tippy-box[data-placement^=bottom]>.tippy-arrow{top:0}.tippy-box[data-placement^=bottom]>.tippy-arrow:before{top:-7px;left:0;border-width:0 8px 8px;border-bottom-color:initial;transform-origin:center bottom}.tippy-box[data-placement^=left]>.tippy-arrow{right:0}.tippy-box[data-placement^=left]>.tippy-arrow:before{border-width:8px 0 8px 8px;border-left-color:initial;right:-7px;transform-origin:center left}.tippy-box[data-placement^=right]>.tippy-arrow{left:0}.tippy-box[data-placement^=right]>.tippy-arrow:before{left:-7px;border-width:8px 8px 8px 0;border-right-color:initial;transform-origin:center right}.tippy-box[data-inertia][data-state=visible]{transition-timing-function:cubic-bezier(.54,1.5,.38,1.11)}.tippy-arrow{width:16px;height:16px;color:#333}.tippy-arrow:before{content:"";position:absolute;border-color:transparent;border-style:solid}.tippy-content{position:relative;padding:5px 9px;z-index:1}
\ No newline at end of file

docs/Makefile

+# 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)

docs/make.bat

+@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

docs/source/conf.py

+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = 'Model Order Reduction for Stokes Flow in Microstructures'
+copyright = '2025, Jan Habscheid'
+author = 'Jan Habscheid'
+release = '1.0'
+
+# Add src folder to path
+import os
+import sys
+sys.path.insert(0, os.path.abspath(os.path.join("..", "../src")))
+sys.path.insert(0, os.path.abspath('../gismo'))
+sys.path.insert(0, os.path.abspath('../miscellaneous'))
+sys.path.insert(0, os.path.abspath('../models'))
+sys.path.insert(0, os.path.abspath('../'))
+
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    'sphinx.ext.napoleon',
+    'sphinx.ext.autodoc', 
+    'myst_parser',
+    'sphinx_copybutton',
+    'sphinx.ext.coverage',
+    'sphinx.ext.autosectionlabel',
+]
+
+templates_path = ['_templates']
+exclude_patterns = []
+
+source_suffix = {
+    '.rst': 'restructuredtext',
+    '.txt': 'markdown',
+    '.md': 'markdown',
+}
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+# html_theme = 'alabaster'
+html_theme = 'sphinx_rtd_theme'
+html_static_path = ['_static']

docs/source/index.rst

+.. Model Order Reduction for Stokes Flow in Microstructures documentation master file, created by
+   sphinx-quickstart on Tue Feb 25 21:24:19 2025.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Model Order Reduction for Stokes Flow in Microstructures documentation
+======================================================================
+
+.. image:: https://git.rwth-aachen.de/janhab/pod/badges/main/pipeline.svg
+   :target: https://git.rwth-aachen.de/JanHab/pod/pipelines
+.. image:: https://img.shields.io/badge/docs-latest-blue
+   :target: https://janhab.pages.rwth-aachen.de/pod/
+.. image:: https://img.shields.io/badge/version-1.0-blue.svg
+   :target: https://git.rwth-aachen.de/janhab/pod/-/tags
+
+Seminar Thesis
+==============
+
+| This repository contains the code to reproduce the results presented in the seminar thesis: **Model Order Reduction for Stokes Flow in Microstructures**
+
+Installation
+============
+
+| Use **`Python=3.12.7`** and run:
+
+.. code-block:: 
+
+   pip install -r requirements.txt
+
+Simulation: use `gismo`
+========================
+
+| For the CFD simulation **Isogeometric Analysis** is utilized.
+| For this a fork from the `gismo` package is used.
+
+.. code-block:: 
+
+   git clone git@github.com:markriegler/gismo.git -b starter-stokes
+   cd gismo
+   make
+   cd build
+   ./bin/gsView
+
+| The used program is the `stokes_example` in `build/bin`.
+| The executable (compiled with clang on macOS and gcc on Ubuntu) was moved to this package.
+| Be careful: Some errors occured with the Ubuntu version.
+
+Contact
+=======
+
+**Author**
+
+- Jan Habscheid
+- Jan.Habscheid@rwth-aachen.de
+
+**Supervisor**
+
+- Mark Riegler
+- Computational Analysis of Technical Systems
+- RWTH Aachen University
+- riegler@cats.rwth-aachen.de
+
+
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+

make.bat

+@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

requirements.txt

@@ -12,4 +12,8 @@ scikit-learn==1.5.2
 scipy==1.14.1
 splinepy==0.1.3
 tensorflow==2.18.0
-vedo==2024.5.2
+vedo==2024.5.2
\ No newline at end of file
+sphinx==8.2.1
+myst-parser==4.0.1
+sphinx-copybutton==0.5.2
+sphinx-rtd-theme==3.0.2
\ No newline at end of file