Merge pull request #186 from matthiaskoenig/sbmlsim2

documentation and sensitivity

Author: matthiaskoenig

.gitignore

@@ -1,3 +1,4 @@
+
 .vscode
 workspace.code-workspace
 .venv
@@ -45,3 +46,6 @@ src/sbmlsim/combine/results
 src/sbmlsim/combine/examples/l1v4/sbmlsim/
 
 src/sbmlsim/comparison/amicitesting/icg_sd/
+
+/.quarto/
+**/*.quarto_ipynb

.nojekyll

@@ -0,0 +1,4 @@
+tests/
+release_notes/
+build/
+**/__pycache__/

.quartoignore

@@ -1,4 +1,4 @@
-![sbmlsim logo](https://github.com/matthiaskoenig/sbmlsim/raw/develop/docs/images/favicon/sbmlsim-100x100-300dpi.png)
+![](https://github.com/matthiaskoenig/sbmlsim/raw/develop/docs/images/favicon/sbmlsim-100x100-300dpi.png)
 
 
 # sbmlsim: SBML simulation made easy
@@ -37,7 +37,7 @@ pip install git+https://github.com/matthiaskoenig/sbmlsim.git@develop
 ```
 
 ## How to cite
-[![DOI](https://zenodo.org/badge/55952847.svg)](https://zenodo.org/badge/latestdoi/55952847)
+[![](https://zenodo.org/badge/55952847.svg)](https://zenodo.org/badge/latestdoi/55952847)
 
 
 ## License
@@ -53,4 +53,32 @@ A Systems Medicine Approach)" by grant number 436883643 and by grant number
 Matthias König was supported by the Federal Ministry of Education and Research (BMBF, Germany)
 within the research network Systems Medicine of the Liver (LiSyM, grant number 031L0054).
 
+## Development
+### Install dev dependencies:
+To setup everything for the develop environment use
+```bash
+# install core dependencies
+uv sync
+# install dev dependencies
+uv pip install -r pyproject.toml --extra dev
+uv tool install tox --with tox-uv
+uv pip install pre-commit
+pre-commit install
+pre-commit run
+```
+
+### Testing
+Testing is performed with tox
+Run single tox target
+```bash
+tox r -e py314
+```
+Run all tests in parallel
+```bash
+tox run-parallel
+```
+
+## Documentation
+If you haven’t already, you’ll need to [install Quarto](https://quarto.org/docs/get-started/).
+
 © 2019-2026 Matthias König

README.md

@@ -0,0 +1,22 @@
+/*
+This file generated automatically by quartodoc version 0.11.1.
+Modifications may be overwritten by quartodoc build. If you want to
+customize styles, create a new .css file to avoid losing changes.
+*/
+
+
+/* styles for parameter tables, etc.. ----
+*/
+
+.doc-section dt code {
+    background: none;
+}
+
+.doc-section dt {
+    /* background-color: lightyellow; */
+    display: block;
+}
+
+.doc-section dl dd {
+    margin-left: 3rem;
+}