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Add env- and lamin-setup dropdown to all chapters with make dropdown (#348)
* python script and md for inserting dropdowns * make works with python script * add anchors to every chapter * correct Makefile * rename yml files * take section yml if local one does not exist * also go through markdown * adding anchors to markdown * stop printing * add preprocessing.yml * clean up code * only one file for build env * Update scripts/insert_yml.py Co-authored-by: Lukas Heumos <lukas.heumos@posteo.net> * add make dropdown to the CI * improvements to my code * get_index_in_cell error resolved * added all comments from Lukas (raising error, private function, ...) * also process lamin anchors * adding lamin setup dropdown bug fixed and rename python script * adding lamin anchors to pseudotemporal * add changelog * delete content between env-setup anchors * final improvements of coding style --------- Co-authored-by: Luis <ge34lah@mytum.de> Co-authored-by: Lukas Heumos <lukas.heumos@posteo.net>
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‎.github/workflows/build_book.yml‎

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v1-${{ github.ref }}
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- name: Insert env-setup dropdown to all chapters
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run: make dropdown
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- name: Build the JupyterBook
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run: make
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‎.github/workflows/build_environments.yml‎

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environments:
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"jupyter-book/introduction/analysis_tools.yml",
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"jupyter-book/preprocessing_visualization/preprocessing.yml",
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"jupyter-book/preprocessing_visualization/preprocessing_visualization.yml",
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"jupyter-book/cellular_structure/clustering.yml",
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‎Makefile‎

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build:
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jupyter-book build $(JUPYTER_BOOK_DIR)
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dropdown:
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python3 scripts/insert_dropdown.py
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clean:
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jupyter-book clean --all $(JUPYTER_BOOK_DIR)
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‎changelog.d/348.added.md‎

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Add env- and lamin-setup dropdown with `make dropdown`

‎jupyter-book/air_repertoire/clonotype.ipynb‎

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"``````{dropdown} <i class=\"fa-solid fa-gear\"></i>&nbsp;&nbsp;&nbsp;Environment setup\n",
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‎jupyter-book/air_repertoire/ir_profiling.ipynb‎

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‎jupyter-book/air_repertoire/multimodal_integration.ipynb‎

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‎jupyter-book/air_repertoire/specificity.ipynb‎

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‎jupyter-book/cellular_structure/annotation.ipynb‎

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‎jupyter-book/cellular_structure/clustering.ipynb‎

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