Merge pull request opencobra#2226 from pavan-kumar-s/gh-pages

Update README.md
rxpavan · Feb 19, 2024 · f65aadc · f65aadc
2 parents 22aac36 + 3393c05
commit f65aadc
Show file tree

Hide file tree

Showing 2 changed files with 34 additions and 3 deletions.
diff --git 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 <br>
+       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.

diff --git a/latest/index.html b/latest/index.html
@@ -3,7 +3,7 @@
 
 <!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
 <!--[if gt IE 8]><!--> <html class="no-js" lang="en"> <!--<![endif]-->
-<head>
+<head> 
 <meta charset="utf-8"/>
 <meta content="width=device-width, initial-scale=1.0" name="viewport"/>
 <title>Home Page — The COBRA Toolbox</title>
@@ -247,4 +247,4 @@ <h2>Cite the COBRA Toolbox v3.0</h2>
     gtag('config', 'G-TRCMZL1FKK');
   </script>
 </body>
-</html>
+</html>