Merge pull request #188 from matthiaskoenig/sbmlsim2

updated docs

Author: matthiaskoenig

README.md

@@ -1,4 +1,4 @@
-![](https://github.com/matthiaskoenig/sbmlsim/raw/develop/docs/images/favicon/sbmlsim-100x100-300dpi.png)
+![](./_docs/images/favicon/sbmlsim-100x100-300dpi.png)
 
 
 # sbmlsim: SBML simulation made easy
@@ -21,6 +21,7 @@ Features include among others
 - parameter fitting
 - sensitivity analysis
 
+Documentation is available from [https://matthiaskoenig.github.io/sbmlsim/](https://matthiaskoenig.github.io/sbmlsim/).
 If you have any questions or issues please [open an issue](https://github.com/matthiaskoenig/sbmlsim/issues).
 
 ## Installation
@@ -78,7 +79,4 @@ Run all tests in parallel
 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

_docs/release.md RELEASE.md_docs/release.md renamed to RELEASE.md

@@ -4,6 +4,7 @@
 * update release notes in `release-notes` with commit
 * make sure all tests run (`tox -p`)
 * check formating and linting (`ruff check`)
+* build documentation
 * test bump version (`uvx bump-my-version bump [major|minor|patch] --dry-run -vv`)
 * bump version (`uvx bump-my-version bump [major|minor|patch]`)
 * `git push --tags` (triggers release)

_docs/_quarto.yml

@@ -19,8 +19,11 @@ website:
   bread-crumbs: true
   repo-url: https://github.com/matthiaskoenig/sbmlsim
   repo-branch: develop
+  repo-subdir: _docs
   repo-link-target: _blank
   repo-actions: [ edit, source, issue ]
+
+
   sidebar:
     # title: sbmlsim
     # logo: images/favicon/sbmlsim-100x100-300dpi.png

_docs/index.qmd

@@ -1,5 +1,4 @@
-![](https://github.com/matthiaskoenig/sbmlsim/raw/develop/docs/images/favicon/sbmlsim-100x100-300dpi.png)
-
+![](./images/favicon/sbmlsim-100x100-300dpi.png)
 
 # sbmlsim: SBML simulation made easy
 [![GitHub Actions CI/CD Status](https://github.com/matthiaskoenig/sbmlsim/workflows/CI-CD/badge.svg)](https://github.com/matthiaskoenig/sbmlsim/actions/workflows/main.yml)
@@ -21,6 +20,7 @@ Features include among others
 - parameter fitting
 - sensitivity analysis
 
+Documentation is available from [https://matthiaskoenig.github.io/sbmlsim/](https://matthiaskoenig.github.io/sbmlsim/).
 If you have any questions or issues please [open an issue](https://github.com/matthiaskoenig/sbmlsim/issues).
 
 ## Installation

docs/api/index.html

@@ -222,7 +222,7 @@ <h2 id="toc-title">On this page</h2>
   <li><a href="#api-sensitivity" id="toc-api-sensitivity" class="nav-link" data-scroll-target="#api-sensitivity">API sensitivity</a></li>
   </ul></li>
   </ul>
-<div class="toc-actions"><ul><li><a href="https://github.com/matthiaskoenig/sbmlsim/edit/develop/api/index.qmd" target="_blank" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/matthiaskoenig/sbmlsim/blob/develop/api/index.qmd" target="_blank" class="toc-action"><i class="bi empty"></i>View source</a></li><li><a href="https://github.com/matthiaskoenig/sbmlsim/issues/new" target="_blank" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
+<div class="toc-actions"><ul><li><a href="https://github.com/matthiaskoenig/sbmlsim/edit/develop/_docs/api/index.qmd" target="_blank" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/matthiaskoenig/sbmlsim/blob/develop/_docs/api/index.qmd" target="_blank" class="toc-action"><i class="bi empty"></i>View source</a></li><li><a href="https://github.com/matthiaskoenig/sbmlsim/issues/new" target="_blank" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
     </div>
 <!-- main -->
 <main class="content" id="quarto-document-content"><header id="title-block-header" class="quarto-title-block"><nav class="quarto-page-breadcrumbs quarto-title-breadcrumbs d-none d-lg-block" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="../api/index.html">API</a></li><li class="breadcrumb-item"><a href="../api/index.html">Sensitivity</a></li></ol></nav></header>
@@ -857,7 +857,7 @@ <h2 class="anchored" data-anchor-id="api-sensitivity">API sensitivity</h2>
 </div>
     <div class="nav-footer-center">
       &nbsp;
-    <div class="toc-actions d-sm-block d-md-none"><ul><li><a href="https://github.com/matthiaskoenig/sbmlsim/edit/develop/api/index.qmd" target="_blank" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/matthiaskoenig/sbmlsim/blob/develop/api/index.qmd" target="_blank" class="toc-action"><i class="bi empty"></i>View source</a></li><li><a href="https://github.com/matthiaskoenig/sbmlsim/issues/new" target="_blank" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></div>
+    <div class="toc-actions d-sm-block d-md-none"><ul><li><a href="https://github.com/matthiaskoenig/sbmlsim/edit/develop/_docs/api/index.qmd" target="_blank" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/matthiaskoenig/sbmlsim/blob/develop/_docs/api/index.qmd" target="_blank" class="toc-action"><i class="bi empty"></i>View source</a></li><li><a href="https://github.com/matthiaskoenig/sbmlsim/issues/new" target="_blank" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></div>
     <div class="nav-footer-right">
       <ul class="footer-items list-unstyled">
     <li class="nav-item compact">

docs/api/sensitivity.html

@@ -220,7 +220,7 @@ <h2 id="toc-title">On this page</h2>
   <ul>
   <li><a href="#sbmlsim.sensitivity" id="toc-sbmlsim.sensitivity" class="nav-link active" data-scroll-target="#sbmlsim.sensitivity">sensitivity</a></li>
   </ul>
-<div class="toc-actions"><ul><li><a href="https://github.com/matthiaskoenig/sbmlsim/edit/develop/api/sensitivity.qmd" target="_blank" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/matthiaskoenig/sbmlsim/blob/develop/api/sensitivity.qmd" target="_blank" class="toc-action"><i class="bi empty"></i>View source</a></li><li><a href="https://github.com/matthiaskoenig/sbmlsim/issues/new" target="_blank" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
+<div class="toc-actions"><ul><li><a href="https://github.com/matthiaskoenig/sbmlsim/edit/develop/_docs/api/sensitivity.qmd" target="_blank" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/matthiaskoenig/sbmlsim/blob/develop/_docs/api/sensitivity.qmd" target="_blank" class="toc-action"><i class="bi empty"></i>View source</a></li><li><a href="https://github.com/matthiaskoenig/sbmlsim/issues/new" target="_blank" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
     </div>
 <!-- main -->
 <main class="content" id="quarto-document-content"><header id="title-block-header" class="quarto-title-block"><nav class="quarto-page-breadcrumbs quarto-title-breadcrumbs d-none d-lg-block" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="../api/index.html">API</a></li><li class="breadcrumb-item"><a href="../api/sensitivity.html"><code>sensitivity</code></a></li></ol></nav></header>
@@ -826,7 +826,7 @@ <h1>sensitivity</h1>
 </div>
     <div class="nav-footer-center">
       &nbsp;
-    <div class="toc-actions d-sm-block d-md-none"><ul><li><a href="https://github.com/matthiaskoenig/sbmlsim/edit/develop/api/sensitivity.qmd" target="_blank" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/matthiaskoenig/sbmlsim/blob/develop/api/sensitivity.qmd" target="_blank" class="toc-action"><i class="bi empty"></i>View source</a></li><li><a href="https://github.com/matthiaskoenig/sbmlsim/issues/new" target="_blank" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></div>
+    <div class="toc-actions d-sm-block d-md-none"><ul><li><a href="https://github.com/matthiaskoenig/sbmlsim/edit/develop/_docs/api/sensitivity.qmd" target="_blank" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/matthiaskoenig/sbmlsim/blob/develop/_docs/api/sensitivity.qmd" target="_blank" class="toc-action"><i class="bi empty"></i>View source</a></li><li><a href="https://github.com/matthiaskoenig/sbmlsim/issues/new" target="_blank" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></div>
     <div class="nav-footer-right">
       <ul class="footer-items list-unstyled">
     <li class="nav-item compact">

docs/api/sensitivity.sensitivity_fast.html

@@ -262,7 +262,7 @@ <h2 id="toc-title">On this page</h2>
   </ul></li>
   </ul></li>
   </ul>
-<div class="toc-actions"><ul><li><a href="https://github.com/matthiaskoenig/sbmlsim/edit/develop/api/sensitivity.sensitivity_fast.qmd" target="_blank" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/matthiaskoenig/sbmlsim/blob/develop/api/sensitivity.sensitivity_fast.qmd" target="_blank" class="toc-action"><i class="bi empty"></i>View source</a></li><li><a href="https://github.com/matthiaskoenig/sbmlsim/issues/new" target="_blank" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
+<div class="toc-actions"><ul><li><a href="https://github.com/matthiaskoenig/sbmlsim/edit/develop/_docs/api/sensitivity.sensitivity_fast.qmd" target="_blank" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/matthiaskoenig/sbmlsim/blob/develop/_docs/api/sensitivity.sensitivity_fast.qmd" target="_blank" class="toc-action"><i class="bi empty"></i>View source</a></li><li><a href="https://github.com/matthiaskoenig/sbmlsim/issues/new" target="_blank" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
     </div>
 <!-- main -->
 <main class="content" id="quarto-document-content"><header id="title-block-header" class="quarto-title-block"><nav class="quarto-page-breadcrumbs quarto-title-breadcrumbs d-none d-lg-block" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="../api/index.html">API</a></li><li class="breadcrumb-item"><a href="../api/sensitivity.sensitivity_fast.html"><code>sensitivity_fast</code></a></li></ol></nav></header>
@@ -943,7 +943,7 @@ <h5 class="anchored" data-anchor-id="sbmlsim.sensitivity.sensitivity_fast.FASTSe
 </div>
     <div class="nav-footer-center">
       &nbsp;
-    <div class="toc-actions d-sm-block d-md-none"><ul><li><a href="https://github.com/matthiaskoenig/sbmlsim/edit/develop/api/sensitivity.sensitivity_fast.qmd" target="_blank" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/matthiaskoenig/sbmlsim/blob/develop/api/sensitivity.sensitivity_fast.qmd" target="_blank" class="toc-action"><i class="bi empty"></i>View source</a></li><li><a href="https://github.com/matthiaskoenig/sbmlsim/issues/new" target="_blank" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></div>
+    <div class="toc-actions d-sm-block d-md-none"><ul><li><a href="https://github.com/matthiaskoenig/sbmlsim/edit/develop/_docs/api/sensitivity.sensitivity_fast.qmd" target="_blank" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/matthiaskoenig/sbmlsim/blob/develop/_docs/api/sensitivity.sensitivity_fast.qmd" target="_blank" class="toc-action"><i class="bi empty"></i>View source</a></li><li><a href="https://github.com/matthiaskoenig/sbmlsim/issues/new" target="_blank" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></div>
     <div class="nav-footer-right">
       <ul class="footer-items list-unstyled">
     <li class="nav-item compact">

docs/api/sensitivity.sensitivity_local.html

@@ -262,7 +262,7 @@ <h2 id="toc-title">On this page</h2>
   </ul></li>
   </ul></li>
   </ul>
-<div class="toc-actions"><ul><li><a href="https://github.com/matthiaskoenig/sbmlsim/edit/develop/api/sensitivity.sensitivity_local.qmd" target="_blank" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/matthiaskoenig/sbmlsim/blob/develop/api/sensitivity.sensitivity_local.qmd" target="_blank" class="toc-action"><i class="bi empty"></i>View source</a></li><li><a href="https://github.com/matthiaskoenig/sbmlsim/issues/new" target="_blank" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
+<div class="toc-actions"><ul><li><a href="https://github.com/matthiaskoenig/sbmlsim/edit/develop/_docs/api/sensitivity.sensitivity_local.qmd" target="_blank" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/matthiaskoenig/sbmlsim/blob/develop/_docs/api/sensitivity.sensitivity_local.qmd" target="_blank" class="toc-action"><i class="bi empty"></i>View source</a></li><li><a href="https://github.com/matthiaskoenig/sbmlsim/issues/new" target="_blank" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
     </div>
 <!-- main -->
 <main class="content" id="quarto-document-content"><header id="title-block-header" class="quarto-title-block"><nav class="quarto-page-breadcrumbs quarto-title-breadcrumbs d-none d-lg-block" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="../api/index.html">API</a></li><li class="breadcrumb-item"><a href="../api/sensitivity.sensitivity_local.html"><code>sensitivity_local</code></a></li></ol></nav></header>
@@ -1005,7 +1005,7 @@ <h5 class="anchored" data-anchor-id="sbmlsim.sensitivity.sensitivity_local.Local
 </div>
     <div class="nav-footer-center">
       &nbsp;
-    <div class="toc-actions d-sm-block d-md-none"><ul><li><a href="https://github.com/matthiaskoenig/sbmlsim/edit/develop/api/sensitivity.sensitivity_local.qmd" target="_blank" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/matthiaskoenig/sbmlsim/blob/develop/api/sensitivity.sensitivity_local.qmd" target="_blank" class="toc-action"><i class="bi empty"></i>View source</a></li><li><a href="https://github.com/matthiaskoenig/sbmlsim/issues/new" target="_blank" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></div>
+    <div class="toc-actions d-sm-block d-md-none"><ul><li><a href="https://github.com/matthiaskoenig/sbmlsim/edit/develop/_docs/api/sensitivity.sensitivity_local.qmd" target="_blank" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/matthiaskoenig/sbmlsim/blob/develop/_docs/api/sensitivity.sensitivity_local.qmd" target="_blank" class="toc-action"><i class="bi empty"></i>View source</a></li><li><a href="https://github.com/matthiaskoenig/sbmlsim/issues/new" target="_blank" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></div>
     <div class="nav-footer-right">
       <ul class="footer-items list-unstyled">
     <li class="nav-item compact">

docs/api/sensitivity.sensitivity_morris.html

@@ -265,7 +265,7 @@ <h2 id="toc-title">On this page</h2>
   </ul></li>
   </ul></li>
   </ul>
-<div class="toc-actions"><ul><li><a href="https://github.com/matthiaskoenig/sbmlsim/edit/develop/api/sensitivity.sensitivity_morris.qmd" target="_blank" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/matthiaskoenig/sbmlsim/blob/develop/api/sensitivity.sensitivity_morris.qmd" target="_blank" class="toc-action"><i class="bi empty"></i>View source</a></li><li><a href="https://github.com/matthiaskoenig/sbmlsim/issues/new" target="_blank" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
+<div class="toc-actions"><ul><li><a href="https://github.com/matthiaskoenig/sbmlsim/edit/develop/_docs/api/sensitivity.sensitivity_morris.qmd" target="_blank" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/matthiaskoenig/sbmlsim/blob/develop/_docs/api/sensitivity.sensitivity_morris.qmd" target="_blank" class="toc-action"><i class="bi empty"></i>View source</a></li><li><a href="https://github.com/matthiaskoenig/sbmlsim/issues/new" target="_blank" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
     </div>
 <!-- main -->
 <main class="content" id="quarto-document-content"><header id="title-block-header" class="quarto-title-block"><nav class="quarto-page-breadcrumbs quarto-title-breadcrumbs d-none d-lg-block" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="../api/index.html">API</a></li><li class="breadcrumb-item"><a href="../api/sensitivity.sensitivity_morris.html"><code>sensitivity_morris</code></a></li></ol></nav></header>
@@ -984,7 +984,7 @@ <h3 class="anchored" data-anchor-id="sbmlsim.sensitivity.sensitivity_morris.plot
 </div>
     <div class="nav-footer-center">
       &nbsp;
-    <div class="toc-actions d-sm-block d-md-none"><ul><li><a href="https://github.com/matthiaskoenig/sbmlsim/edit/develop/api/sensitivity.sensitivity_morris.qmd" target="_blank" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/matthiaskoenig/sbmlsim/blob/develop/api/sensitivity.sensitivity_morris.qmd" target="_blank" class="toc-action"><i class="bi empty"></i>View source</a></li><li><a href="https://github.com/matthiaskoenig/sbmlsim/issues/new" target="_blank" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></div>
+    <div class="toc-actions d-sm-block d-md-none"><ul><li><a href="https://github.com/matthiaskoenig/sbmlsim/edit/develop/_docs/api/sensitivity.sensitivity_morris.qmd" target="_blank" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/matthiaskoenig/sbmlsim/blob/develop/_docs/api/sensitivity.sensitivity_morris.qmd" target="_blank" class="toc-action"><i class="bi empty"></i>View source</a></li><li><a href="https://github.com/matthiaskoenig/sbmlsim/issues/new" target="_blank" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></div>
     <div class="nav-footer-right">
       <ul class="footer-items list-unstyled">
     <li class="nav-item compact">