fixes structure

GeertvanGeest · Dec 14, 2024 · ebb7c03 · ebb7c03
1 parent f8f9b51
commit ebb7c03
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Showing 11 changed files with 14 additions and 14 deletions.
diff --git a/.github/workflows/tutorials.yaml b/.github/workflows/tutorials.yaml
@@ -22,7 +22,7 @@ jobs:
       - run: |
           cd docs
           mkdir -p _test_tutorials
-          python extract_bash_code.py -o _test_tutorials *.md
+          python extract_bash_code.py -o _test_tutorials documentation/*.md tutorials/*.md
           cd _test_tutorials
           bash installation.sh
           bash tutorial_hiv.sh
diff --git a/docs/_config.yml b/docs/_config.yml
@@ -8,12 +8,12 @@ logo: assets/images/logo-vpipe.svg
 
 # Force re-execution of notebooks on each build.
 # See https://jupyterbook.org/content/execute.html
-execute:
-  execute_notebooks: force
-  timeout: -1
-  exclude_patterns:
-    - '*.ipynb'
-    - 'documentation/vp-analysis/*'
+# execute:
+#   execute_notebooks: force
+#   timeout: -1
+#   exclude_patterns:
+#     - '*.ipynb'
+#     - 'documentation/vp-analysis/*'
 
 # Define the name of the latex output file for PDF builds
 latex:

diff --git a/docs/_toc.yml b/docs/_toc.yml
@@ -6,15 +6,15 @@ root: index
 parts:
 - caption: Documentation
   chapters:
-  - file: documentation/overview
-  - file: documentation/installation
-  - file: documentation/configuration
-  - file: documentation/running
-  - file: documentation/output
+  - file: documentation/overview.md
+  - file: documentation/installation.md
+  - file: documentation/configuration.md
+  - file: documentation/running.md
+  - file: documentation/output.md
 - caption: Tutorials
   chapters:
-  - file: tutorials/tutorial_sarscov2
-  - file: tutorials/tutorial_hiv
+  - file: tutorials/tutorial_sarscov2.md
+  - file: tutorials/tutorial_hiv.md
   - file: tutorials/tutorial_cowwid.md
 
 - caption: Bibliography

diff --git a/docs/configuration.md → docs/documentation/configuration.md b/docs/configuration.md → docs/documentation/configuration.md
diff --git a/docs/installation.md → docs/documentation/installation.md b/docs/installation.md → docs/documentation/installation.md
diff --git a/docs/output.md → docs/documentation/output.md b/docs/output.md → docs/documentation/output.md
diff --git a/docs/overview.md → docs/documentation/overview.md b/docs/overview.md → docs/documentation/overview.md
diff --git a/docs/running.md → docs/documentation/running.md b/docs/running.md → docs/documentation/running.md
diff --git a/docs/tutorial_cowwid.md → docs/tutorials/tutorial_cowwid.md b/docs/tutorial_cowwid.md → docs/tutorials/tutorial_cowwid.md
diff --git a/docs/tutorial_hiv.md → docs/tutorials/tutorial_hiv.md b/docs/tutorial_hiv.md → docs/tutorials/tutorial_hiv.md
diff --git a/docs/tutorial_sarscov2.md → docs/tutorials/tutorial_sarscov2.md b/docs/tutorial_sarscov2.md → docs/tutorials/tutorial_sarscov2.md