cytoscape-manual

This project contains the complete user manual for Cytoscape 3. There are versions of the manual based on specific versions of Cytoscape. There is also a "stable" version that links to the latest tagged release of the manual. A "latest" link refers to the master branch. The versions are automatically built at ReadTheDocs.org from tags of this repo, for example 3.8.2. Access to ReadTheDocs.org is restricted, Barry and Kristina have the credentials.

Latest Cytoscape version link: http://manual.cytoscape.org/en/stable

Version-specific link: http://manual.cytoscape.org/en/3.8.2/

Master branch version: http://manual.cytoscape.org/en/latest

A new tag is necessary for every Cytoscape point release, otherwise the manual links from Cytoscape fail.

Rebuilding the Manual

The manual is automatically rebuilt by ReadTheDocs when the GitHub repository is updated. (This is courtesy of a WebHook that Barry installed per http://docs.readthedocs.org/en/latest/webhooks.html). A build at ReadTheDocs can take anywhere from 3 minutes to 10 minutes, depending on how busy the build server is. It's always best to verify recent changes by viewing them in the built document. A note on timing: Since the "stable" version at ReadTheDocs is the latest tagged release (as described above), it is best to wait to produce a release/tag until right before (1 day) a scheduled release. Otherwise stable links (from the website for example) will go to the unreleased version.

Process for updating the manual content, pre-release

1. Make a new branch at GitHub corresponding to the new version of Cytoscape, for example 3.9.1. Make sure to mirror the exact version number that is being developed (refer to code.cytoscape.org); the format should be "X.Y.Z".
2. Any changes to the manual content should be done on the new branch. ReadTheDocs will create a build as soon as a branch is created. To review content throughout the update period, go to the branch-specific version of the manual, for example http://manual.cytoscape.org/en/3.9.1/.
3. Review updates to docs and images at GitHub.
4. Add any new manual sections to index.rst and update Copyright year (if applicable).
5. Update version number and Copyright year (if applicable) in conf.py
6. Double-check the manual at ReadTheDocs here: http://manual.cytoscape.org/en/3.9.1/.

⚠️ When you're checking a new version of the manual, be sure to clear your browser's cache ... otherwise, you'll be looking at an obsolete version, which will quickly become confusing.

Process for releasing the new manual content for a new CS release

Do this as late as possible before a new Cytoscape release

1. Go to the latest branch, and open a pull request for the master branch. This will update the master branch, which will trigger a build for the "latest" version of the manual.
2. Create a new release with the relevant release number, for example 3.8.0. This will automatically trigger a build at ReadTheDocs for this release. Leave "binary attachments" empty. Do not add the "v" in front of the version number as suggested by GitHub (i.e., use 3.9.0 instead of v3.9.0).
3. After 3-10 minutes, verify that all ReadTheDocs links work:

• http://manual.cytoscape.org/en/3.9.1/
• http://manual.cytoscape.org/en/latest
• http://manual.cytoscape.org/en/stable

Troubleshooting

If a problem with a new tagged release (and the corresponding ReadTheDocs build) is discovered, the tag at GitHub has to both be removed and recreated in order to fix the ReadTheDocs build.

1. Delete the relevant release via the github.com UI. Go to tags (https://github.com/cytoscape/cytoscape-manual/tags), click on the title of the tag you want to delete, then click the "Delete" button in upper right.
2. Log into ReadTheDocs. Under "Builds", select the appropriate build number, for example 3.8.1, in the drop-down and then click the "Build" button.

Note: If the build you are looking for does not appear in the drop-down even though it should be there (i.e. there is a tag at GitHub), it is possible that the build is just "inactive". Go to the "Versions" page and scroll down to the list at the bottom. Locate the build there, for example 3.8.1, and click "Activate".

Editing the Manual

To edit manual text, you must first check out this repository and use a text editor on your workstation. For small edits, you can use GitHub's native Markdown editor.

• All document components are in the "docs" directory. Each chapter is contained in its own file, and the files are assembled as a complete document by naming them in the "docs/index.rst" file.
• Images are stored in the "docs/_static/images" directory, organized into subdirectories by chapter. For high quality images, vector graphic files produce best results (e.g., .png).
• Simple tables can be represented in Markdown, but high quality formatting requires direct HTML coding. By convention, we encode tables as HTML-tagged data, but do not specify visual attributes and layout inline. Instead, we use preset table styles contained in "docs/_static/css" for formatting -- we do not use Markdown's table formatting. Note that additional CSS files can be added, but must be accounted for in "_templates/layout.html" and "conf.py". Note that while the tables appear in the HTML document, they do not appear in the PDF version -- we're working on this.

Note that the GitHub file viewer displays Markdown files reasonably well. However, it only approximates the look of tables created via HTML. For an accurate view of a table, you must look at a document rendered by ReadTheDocs.

Note that a full (browsable) link to a location has the form: "http://manual.cytoscape.org/en/stable/Launching_Cytoscape.html#mylink" where "http://manual.cytoscape.org/en/stable/" is the full URL, "Launching_Cytoscape" is the root name of the file containing the target link, and "mylink" is a named section (e.g., System requirements). A link between chapters in the document has the form My Link, and a link within the same chapter can have the form My Link. For intra-document references, it is best to use the Launching_Cytoscape.html#mylink form, as ReadTheDocs will append the full URL appropriate for the build (e.g., "stable", "latest", "3.3", etc).

How the manual works

While the manual sources are maintained in GitHub, the document is actually assembled, formatted, and staged by the ReadTheDocs.org site. ReadTheDocs presents online and PDF versions.

ReadTheDocs can present versions of the manual for each Cytoscape release, as identified by GitHub tags. For example, given a tag of 3.3, ReadTheDocs will produce a document containing the repository files as they were for Cytoscape 3.3, and will make it available at http://manual.cytoscape.org/en/3.3. ReadTheDocs will make a "stable" version of the manual available at http://manual.cytoscape.org/en/stable ... it will resolve to the latest tagged version (ignoring beta versions such as 3.4b1). The "latest" version of the manual will be available at http://manual.cytoscape.org/en/latest, and will contain all of the latest GitHub content, irrespective of tagging.

Note that for a manual under developement, "latest" has been configured as non-public (configurable in ReadTheDocs) so it isn't indexed by Google.

For anyone interested in how ReadTheDocs works, see their documentation.