From 4caf475c61ea2a4071e621fdc27b7ee882b42458 Mon Sep 17 00:00:00 2001
From: pavan-kumar-s <138394293+pavan-kumar-s@users.noreply.github.com>
Date: Mon, 12 Feb 2024 16:15:05 +0530
Subject: [PATCH 1/2] Update README.md
Update details about CI for modules page
---
README.md | 33 ++++++++++++++++++++++++++++++++-
1 file changed, 32 insertions(+), 1 deletion(-)
diff --git a/README.md b/README.md
index 205e782129..baf2cdc50f 100644
--- a/README.md
+++ b/README.md
@@ -11,7 +11,38 @@ Here are the following steps taken in the tutorial CI pipeline:
3. This then triggers a [seperate Github actions workflow](https://github.com/opencobra/cobratoolbox/blob/gh-pages/.github/workflows/main.yml) on the cobratoolbox gh-pages branch. This workflow reconfigures the various files and directories so that the html tutorial can be integrated into the website
## Continuous Integration of Functions
-to be added ...
+Each accepted pull request triggers two workflows (W1 and W2) to generate documentation for functions,
+contributors and citations.
+
+### W1 (.github/workflows/UpdateFunctionDocs.yml)
+This workflow does the following:
+1) Install python 3.10
+2) Install required packages defined in /docs/requirements.txt
+3) Run Python code (/docs/source/sphinxext/GenerateCitationsRST.py) to generate './docs/source/citations.rst' file
+4) Run Python code (/docs/source/sphinxext/copy_files.py) to adapt the installed packages for Matlab functions. Files required to run this:
+ 1) 'docs/source/sphinxext/linkcode.py'
+ 2) 'docs/source/sphinxext/tabs.css'
+5) Run python code (/docs/source/modules/GetRSTfiles.py) to generate all the .rst files required for documenting all the functions in '/src/'
+6) Generate documentation using 'make HTML'. Files required to run this:
+ 1) 'docs/createModulesPage.sh'
+ 2) 'docs/generateJSONList.py'
+ 3) 'docs/source/sphinxext/CitationStyle.py'
+ 4) 'docs/COBRA.bib'.
+COBRA.bib file has to be updated manually each month. Currently the .bib file is retrieved from [web of science](https://www.webofscience.com/wos/woscc/summary/d043671b-cd33-418b-9781-a92c21471897-bec2b3ea/relevance/1(overlay:export/exbt))
+7) Deploying to gh-pages in the latest folder (Only files in /latest/modules/ folder and /latest/citations.html will get updated). This requires 'docs/source/Citations/citations.html'
+
+### W2 (.github/workflows/UpdateContributors.yml)
+This workflow does the following:
+1) Install python 3.10
+2) Install required packages defined in /docs/source/Contributions/requirements.txt
+3) Run Python code files:
+ 1) /docs/source/Contributions/UpdateContributorsList.py
+ 2) /docs/source/Contributions/GenerateContributorsHTML.py
+ This code requires:
+ 1) '/docs/source/Contributions/AllContributors.csv'
+ 2) '/docs/source/Contributions/contributorsTemp.html'
+ 3) '/docs/source/Contributions/contributors/contributors.html'
+4) Deploying to gh-pages (/latest/contributors.html)
## Running Matlab Tests on Pull Requests
The testing workflow is defined in the main.yml file. This workflow is triggered on every push to the repository and runs the MATLAB tests using the GitHub Actions runner.
From 3393c059307b2acca9334647844e79df307c33d3 Mon Sep 17 00:00:00 2001
From: pavan-kumar-s <138394293+pavan-kumar-s@users.noreply.github.com>
Date: Mon, 12 Feb 2024 17:14:28 +0530
Subject: [PATCH 2/2] Update index.html
---
latest/index.html | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/latest/index.html b/latest/index.html
index 476aca87f0..06fe23f04e 100755
--- a/latest/index.html
+++ b/latest/index.html
@@ -3,7 +3,7 @@
-
+
Home Page — The COBRA Toolbox
@@ -247,4 +247,4 @@ Cite the COBRA Toolbox v3.0
gtag('config', 'G-TRCMZL1FKK');
-
\ No newline at end of file
+