Simplify Colab notebook links

Author: hiyama341

docs/colab_notebooks.rst

@@ -5,55 +5,7 @@ These notebooks capture the larger, end-to-end strictosidine case study workflow
 ``teemi``. They are the best starting point if you want to run the published DBTL examples in
 Google Colab with as little setup as possible.
 
-Each notebook includes a direct Colab launch badge plus a GitHub source link.
-
-.. |colab00| image:: https://colab.research.google.com/assets/colab-badge.svg
-   :alt: Open notebook 00 in Google Colab
-   :target: https://colab.research.google.com/github/hiyama341/teemi/blob/main/colab_notebooks/00_1_DESIGN_Homologs.ipynb
-
-.. |colab01| image:: https://colab.research.google.com/assets/colab-badge.svg
-   :alt: Open notebook 01 in Google Colab
-   :target: https://colab.research.google.com/github/hiyama341/teemi/blob/main/colab_notebooks/01_1_DESIGN_Promoters.ipynb
-
-.. |colab02| image:: https://colab.research.google.com/assets/colab-badge.svg
-   :alt: Open notebook 02 in Google Colab
-   :target: https://colab.research.google.com/github/hiyama341/teemi/blob/main/colab_notebooks/02_1_DESIGN_Combinatorial_library.ipynb
-
-.. |colab03| image:: https://colab.research.google.com/assets/colab-badge.svg
-   :alt: Open notebook 03 in Google Colab
-   :target: https://colab.research.google.com/github/hiyama341/teemi/blob/main/colab_notebooks/03_1_BUILD_gRNA_plasmid.ipynb
-
-.. |colab04| image:: https://colab.research.google.com/assets/colab-badge.svg
-   :alt: Open notebook 04 in Google Colab
-   :target: https://colab.research.google.com/github/hiyama341/teemi/blob/main/colab_notebooks/04_1_BUILD_Background_strain.ipynb
-
-.. |colab05| image:: https://colab.research.google.com/assets/colab-badge.svg
-   :alt: Open notebook 05 in Google Colab
-   :target: https://colab.research.google.com/github/hiyama341/teemi/blob/main/colab_notebooks/05_1_BUILD_Combinatorial_library.ipynb
-
-.. |colab06| image:: https://colab.research.google.com/assets/colab-badge.svg
-   :alt: Open notebook 06 in Google Colab
-   :target: https://colab.research.google.com/github/hiyama341/teemi/blob/main/colab_notebooks/06_1_TEST_Library_characterisation.ipynb
-
-.. |colab07| image:: https://colab.research.google.com/assets/colab-badge.svg
-   :alt: Open notebook 07 in Google Colab
-   :target: https://colab.research.google.com/github/hiyama341/teemi/blob/main/colab_notebooks/07_1_LEARN_Modelling_and_predictions.ipynb
-
-.. |colab08| image:: https://colab.research.google.com/assets/colab-badge.svg
-   :alt: Open notebook 08 in Google Colab
-   :target: https://colab.research.google.com/github/hiyama341/teemi/blob/main/colab_notebooks/08_2_DESIGN_Model_recommended_combinatiorial_library.ipynb
-
-.. |colab09| image:: https://colab.research.google.com/assets/colab-badge.svg
-   :alt: Open notebook 09 in Google Colab
-   :target: https://colab.research.google.com/github/hiyama341/teemi/blob/main/colab_notebooks/09_2_BUILD_Combinatorial_library.ipynb
-
-.. |colab10| image:: https://colab.research.google.com/assets/colab-badge.svg
-   :alt: Open notebook 10 in Google Colab
-   :target: https://colab.research.google.com/github/hiyama341/teemi/blob/main/colab_notebooks/10_2_TEST_Library_characterization.ipynb
-
-.. |colab11| image:: https://colab.research.google.com/assets/colab-badge.svg
-   :alt: Open notebook 11 in Google Colab
-   :target: https://colab.research.google.com/github/hiyama341/teemi/blob/main/colab_notebooks/11_2_LEARN_Modelling_and_predictions.ipynb
+Each notebook links to both Google Colab and the GitHub source file.
 
 Strictosidine Case: First DBTL Cycle
 ------------------------------------
@@ -62,81 +14,69 @@ Design
 ~~~~~~
 
 .. list-table::
-   :widths: 7 43 25 25
+   :widths: 7 53 40
    :header-rows: 1
 
    * - ID
      - Focus
-     - Launch
-     - Source
+     - Links
    * - 00
      - Automatically fetch homologs from NCBI in a standardizable and repeatable way.
-     - |colab00|
-     - `GitHub <https://github.com/hiyama341/teemi/blob/main/colab_notebooks/00_1_DESIGN_Homologs.ipynb>`__
+     - `Open in Colab <https://colab.research.google.com/github/hiyama341/teemi/blob/main/colab_notebooks/00_1_DESIGN_Homologs.ipynb>`__ | `GitHub <https://github.com/hiyama341/teemi/blob/main/colab_notebooks/00_1_DESIGN_Homologs.ipynb>`__
    * - 01
      - Select promoters from RNA-seq data and fetch them from online databases with quality checks.
-     - |colab01|
-     - `GitHub <https://github.com/hiyama341/teemi/blob/main/colab_notebooks/01_1_DESIGN_Promoters.ipynb>`__
+     - `Open in Colab <https://colab.research.google.com/github/hiyama341/teemi/blob/main/colab_notebooks/01_1_DESIGN_Promoters.ipynb>`__ | `GitHub <https://github.com/hiyama341/teemi/blob/main/colab_notebooks/01_1_DESIGN_Promoters.ipynb>`__
    * - 02
      - Generate a combinatorial library with ``DesignAssembly`` and prepare it for downstream build planning.
-     - |colab02|
-     - `GitHub <https://github.com/hiyama341/teemi/blob/main/colab_notebooks/02_1_DESIGN_Combinatorial_library.ipynb>`__
+     - `Open in Colab <https://colab.research.google.com/github/hiyama341/teemi/blob/main/colab_notebooks/02_1_DESIGN_Combinatorial_library.ipynb>`__ | `GitHub <https://github.com/hiyama341/teemi/blob/main/colab_notebooks/02_1_DESIGN_Combinatorial_library.ipynb>`__
 
 Build
 ~~~~~
 
 .. list-table::
-   :widths: 7 43 25 25
+   :widths: 7 53 40
    :header-rows: 1
 
    * - ID
      - Focus
-     - Launch
-     - Source
+     - Links
    * - 03
      - Assemble a CRISPR plasmid with USER cloning.
-     - |colab03|
-     - `GitHub <https://github.com/hiyama341/teemi/blob/main/colab_notebooks/03_1_BUILD_gRNA_plasmid.ipynb>`__
+     - `Open in Colab <https://colab.research.google.com/github/hiyama341/teemi/blob/main/colab_notebooks/03_1_BUILD_gRNA_plasmid.ipynb>`__ | `GitHub <https://github.com/hiyama341/teemi/blob/main/colab_notebooks/03_1_BUILD_gRNA_plasmid.ipynb>`__
    * - 04
      - Construct the background strain by knocking out G8H and CPR.
-     - |colab04|
-     - `GitHub <https://github.com/hiyama341/teemi/blob/main/colab_notebooks/04_1_BUILD_Background_strain.ipynb>`__
+     - `Open in Colab <https://colab.research.google.com/github/hiyama341/teemi/blob/main/colab_notebooks/04_1_BUILD_Background_strain.ipynb>`__ | `GitHub <https://github.com/hiyama341/teemi/blob/main/colab_notebooks/04_1_BUILD_Background_strain.ipynb>`__
    * - 05
      - Generate the first combinatorial library covering 1280 possible combinations.
-     - |colab05|
-     - `GitHub <https://github.com/hiyama341/teemi/blob/main/colab_notebooks/05_1_BUILD_Combinatorial_library.ipynb>`__
+     - `Open in Colab <https://colab.research.google.com/github/hiyama341/teemi/blob/main/colab_notebooks/05_1_BUILD_Combinatorial_library.ipynb>`__ | `GitHub <https://github.com/hiyama341/teemi/blob/main/colab_notebooks/05_1_BUILD_Combinatorial_library.ipynb>`__
 
 Test
 ~~~~
 
 .. list-table::
-   :widths: 7 43 25 25
+   :widths: 7 53 40
    :header-rows: 1
 
    * - ID
      - Focus
-     - Launch
-     - Source
+     - Links
    * - 06
      - Process LC-MS data and genotype the generated strains.
-     - |colab06|
-     - `GitHub <https://github.com/hiyama341/teemi/blob/main/colab_notebooks/06_1_TEST_Library_characterisation.ipynb>`__
+     - `Open in Colab <https://colab.research.google.com/github/hiyama341/teemi/blob/main/colab_notebooks/06_1_TEST_Library_characterisation.ipynb>`__ | `GitHub <https://github.com/hiyama341/teemi/blob/main/colab_notebooks/06_1_TEST_Library_characterisation.ipynb>`__
 
 Learn
 ~~~~~
 
 .. list-table::
-   :widths: 7 43 25 25
+   :widths: 7 53 40
    :header-rows: 1
 
    * - ID
      - Focus
-     - Launch
-     - Source
+     - Links
    * - 07
      - Use AutoML to predict the best combinations for a targeted second round of library construction.
-     - |colab07|
-     - `GitHub <https://github.com/hiyama341/teemi/blob/main/colab_notebooks/07_1_LEARN_Modelling_and_predictions.ipynb>`__
+     - `Open in Colab <https://colab.research.google.com/github/hiyama341/teemi/blob/main/colab_notebooks/07_1_LEARN_Modelling_and_predictions.ipynb>`__ | `GitHub <https://github.com/hiyama341/teemi/blob/main/colab_notebooks/07_1_LEARN_Modelling_and_predictions.ipynb>`__
 
 Strictosidine Case: Second DBTL Cycle
 -------------------------------------
@@ -145,65 +85,57 @@ Design
 ~~~~~~
 
 .. list-table::
-   :widths: 7 43 25 25
+   :widths: 7 53 40
    :header-rows: 1
 
    * - ID
      - Focus
-     - Launch
-     - Source
+     - Links
    * - 08
      - Translate machine-learning results into a targeted library of strains.
-     - |colab08|
-     - `GitHub <https://github.com/hiyama341/teemi/blob/main/colab_notebooks/08_2_DESIGN_Model_recommended_combinatiorial_library.ipynb>`__
+     - `Open in Colab <https://colab.research.google.com/github/hiyama341/teemi/blob/main/colab_notebooks/08_2_DESIGN_Model_recommended_combinatiorial_library.ipynb>`__ | `GitHub <https://github.com/hiyama341/teemi/blob/main/colab_notebooks/08_2_DESIGN_Model_recommended_combinatiorial_library.ipynb>`__
 
 Build
 ~~~~~
 
 .. list-table::
-   :widths: 7 43 25 25
+   :widths: 7 53 40
    :header-rows: 1
 
    * - ID
      - Focus
-     - Launch
-     - Source
+     - Links
    * - 09
      - Construct the targeted second-round library of strains.
-     - |colab09|
-     - `GitHub <https://github.com/hiyama341/teemi/blob/main/colab_notebooks/09_2_BUILD_Combinatorial_library.ipynb>`__
+     - `Open in Colab <https://colab.research.google.com/github/hiyama341/teemi/blob/main/colab_notebooks/09_2_BUILD_Combinatorial_library.ipynb>`__ | `GitHub <https://github.com/hiyama341/teemi/blob/main/colab_notebooks/09_2_BUILD_Combinatorial_library.ipynb>`__
 
 Test
 ~~~~
 
 .. list-table::
-   :widths: 7 43 25 25
+   :widths: 7 53 40
    :header-rows: 1
 
    * - ID
      - Focus
-     - Launch
-     - Source
+     - Links
    * - 10
      - Process second-cycle LC-MS characterization data.
-     - |colab10|
-     - `GitHub <https://github.com/hiyama341/teemi/blob/main/colab_notebooks/10_2_TEST_Library_characterization.ipynb>`__
+     - `Open in Colab <https://colab.research.google.com/github/hiyama341/teemi/blob/main/colab_notebooks/10_2_TEST_Library_characterization.ipynb>`__ | `GitHub <https://github.com/hiyama341/teemi/blob/main/colab_notebooks/10_2_TEST_Library_characterization.ipynb>`__
 
 Learn
 ~~~~~
 
 .. list-table::
-   :widths: 7 43 25 25
+   :widths: 7 53 40
    :header-rows: 1
 
    * - ID
      - Focus
-     - Launch
-     - Source
+     - Links
    * - 11
      - Run the second ML cycle and inspect improved performance and saturation of top strains.
-     - |colab11|
-     - `GitHub <https://github.com/hiyama341/teemi/blob/main/colab_notebooks/11_2_LEARN_Modelling_and_predictions.ipynb>`__
+     - `Open in Colab <https://colab.research.google.com/github/hiyama341/teemi/blob/main/colab_notebooks/11_2_LEARN_Modelling_and_predictions.ipynb>`__ | `GitHub <https://github.com/hiyama341/teemi/blob/main/colab_notebooks/11_2_LEARN_Modelling_and_predictions.ipynb>`__
 
 Publication
 -----------