From ebb7c032d101caa3600c447aaa52bf3e6164329d Mon Sep 17 00:00:00 2001 From: Geert van Geest Date: Sat, 14 Dec 2024 16:58:15 +0100 Subject: [PATCH] fixes structure --- .github/workflows/tutorials.yaml | 2 +- docs/_config.yml | 12 ++++++------ docs/_toc.yml | 14 +++++++------- docs/{ => documentation}/configuration.md | 0 docs/{ => documentation}/installation.md | 0 docs/{ => documentation}/output.md | 0 docs/{ => documentation}/overview.md | 0 docs/{ => documentation}/running.md | 0 docs/{ => tutorials}/tutorial_cowwid.md | 0 docs/{ => tutorials}/tutorial_hiv.md | 0 docs/{ => tutorials}/tutorial_sarscov2.md | 0 11 files changed, 14 insertions(+), 14 deletions(-) rename docs/{ => documentation}/configuration.md (100%) rename docs/{ => documentation}/installation.md (100%) rename docs/{ => documentation}/output.md (100%) rename docs/{ => documentation}/overview.md (100%) rename docs/{ => documentation}/running.md (100%) rename docs/{ => tutorials}/tutorial_cowwid.md (100%) rename docs/{ => tutorials}/tutorial_hiv.md (100%) rename docs/{ => tutorials}/tutorial_sarscov2.md (100%) diff --git a/.github/workflows/tutorials.yaml b/.github/workflows/tutorials.yaml index bcb51c8b..44c910cc 100644 --- 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 \ No newline at end of file diff --git a/docs/_config.yml b/docs/_config.yml index fd999c75..29af0d6d 100644 --- 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 index 1ab4ed84..bcd61d31 100644 --- 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 b/docs/documentation/configuration.md similarity index 100% rename from docs/configuration.md rename to docs/documentation/configuration.md diff --git a/docs/installation.md b/docs/documentation/installation.md similarity index 100% rename from docs/installation.md rename to docs/documentation/installation.md diff --git a/docs/output.md b/docs/documentation/output.md similarity index 100% rename from docs/output.md rename to docs/documentation/output.md diff --git a/docs/overview.md b/docs/documentation/overview.md similarity index 100% rename from docs/overview.md rename to docs/documentation/overview.md diff --git a/docs/running.md b/docs/documentation/running.md similarity index 100% rename from docs/running.md rename to docs/documentation/running.md diff --git a/docs/tutorial_cowwid.md b/docs/tutorials/tutorial_cowwid.md similarity index 100% rename from docs/tutorial_cowwid.md rename to docs/tutorials/tutorial_cowwid.md diff --git a/docs/tutorial_hiv.md b/docs/tutorials/tutorial_hiv.md similarity index 100% rename from docs/tutorial_hiv.md rename to docs/tutorials/tutorial_hiv.md diff --git a/docs/tutorial_sarscov2.md b/docs/tutorials/tutorial_sarscov2.md similarity index 100% rename from docs/tutorial_sarscov2.md rename to docs/tutorials/tutorial_sarscov2.md