OpenMS · timosachsenberg · Mar 25, 2026 · Mar 25, 2026
diff --git a/.github/workflows/build-push-notebooks.yaml b/.github/workflows/build-push-notebooks.yaml
diff --git a/.github/workflows/test-notebooks.yml b/.github/workflows/test-notebooks.yml
diff --git a/.github/workflows/test-pr.yaml b/.github/workflows/test-pr.yaml
diff --git a/README.md b/README.md
@@ -1,6 +1,4 @@
 [![Documentation Status](https://readthedocs.org/projects/pyopenms/badge/?version=latest)](https://pyopenms.readthedocs.io/en/latest/?badge=latest)
-[![Build notebooks from master and push to master+ipynb](https://github.com/OpenMS/pyopenms-docs/actions/workflows/build-push-notebooks.yaml/badge.svg)](https://github.com/OpenMS/pyopenms-docs/actions/workflows/build-push-notebooks.yaml)
-[![Test code in notebooks](https://github.com/OpenMS/pyopenms-docs/actions/workflows/test-notebooks.yml/badge.svg)](https://github.com/OpenMS/pyopenms-docs/actions/workflows/test-notebooks.yml)
 
 pyOpenMS Documentation
 ======================
@@ -27,11 +25,3 @@ Documentation
 The readthedocs pyOpenMS documentation is generated from the master branch of this repository, see [docs/README.md](docs/README.md)
 
 The generated documentation is available here: https://pyopenms.readthedocs.io/en/latest/
-
-Jupyter Notebooks
-=============
-Are created by CI and stored in master+ipynb to not clutter the master branch.
-
-Binder integration
-=============
-Binder uses the Jupyter Notebooks in master+ipynb. The conda environment is described in environment.yml, the post-build event installs the nightly pyopenms wheel. Currently, only environment.yml is used by binder. Note: You can test a branch "jpfeuffer-patch-6" using https://notebooks.gesis.org/binder/v2/gh/OpenMS/pyopenms-docs/jpfeuffer-patch-6 
diff --git a/docs/Makefile b/docs/Makefile
@@ -12,9 +12,6 @@ BUILDDIR      = build
 help:
 	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
-doc:
-	cd source ;bash generate_ipynb.sh
-
 .PHONY: help Makefile
 
 # Catch-all target: route all unknown targets to Sphinx using the new

diff --git a/docs/pandoc_filters/admonitionfilter.py b/docs/pandoc_filters/admonitionfilter.py
diff --git a/docs/pandoc_filters/code_pandocfilter.py b/docs/pandoc_filters/code_pandocfilter.py
diff --git a/docs/pandoc_filters/ignore_pandocfilter.py b/docs/pandoc_filters/ignore_pandocfilter.py
diff --git a/docs/pandoc_filters/transformlinks_pandocfilter.py b/docs/pandoc_filters/transformlinks_pandocfilter.py
diff --git a/docs/pandoc_filters/transformreferences_pandocfilter.py b/docs/pandoc_filters/transformreferences_pandocfilter.py
diff --git a/docs/source/_templates/navbar-run-binder.html b/docs/source/_templates/navbar-run-binder.html