Fix and update wiki pages

[zhucaoxiang]

We are now using the GitHub pages (https://princetonuniversity.github.io/STELLOPT/) as the official site for hosting all the wikis and documentation.

I have converted all the wikis into markdown format, but most of them need to be minorly fixed. Incompatibilities are found such as,

• Tables, code snippets, etc need revisions
• Equations should be fixed.
• Table of Contents needs to be inserted.
• Links are broken and other issues.

Besides, some contents need to be updated, such as compiling instructions.

All the markdown source files are stored in the branch gh-pages. I have created a project at fix the wikis to track the progress.

Everyone is welcome to contribute. For more information, please view README.md.

[zhucaoxiang]

@lazersos I have updated the STELLOPT page and use this page as the landing page of STELLOPT on DOECODE. Please check if any revisions are needed, especially for the namelist.

[zhucaoxiang]

@jonathanschilling
I revised the Toroidal Coordinates. Please view the generated page(https://princetonuniversity.github.io/STELLOPT/Toroidal%20Coordinates).

Here is a way to show the differences (ignore Sam's change with FIELDLINES).
https://github.com/PrincetonUniversity/STELLOPT/compare/5fd627e..38142dd

We should probably create some automatic tools, like awk, to do the most of revisions.

[jonathanschilling]

@zhucaoxiang
Thanks for that. How does one generate the actual webpage?
I tried editing the *.md files on the gh-pages branch, but the website seemed not to change.

[zhucaoxiang]

@jonathanschilling It seems GitHub is generating the website automatically. Of course, with some latency, like about one minute.

The annoying part with MathJax is that we cannot preview the changes. That is why I always have to make multiple commits incrementally.

[zhucaoxiang]

Just remember to use raw LaTex equations included with $$ ... $$ for inline,

\$$ ...  $$

for equations in separate lines (break lines before and after).

[jonathanschilling]

@zhucaoxiang

It seems that one can manually trigger the gh-pages rebuild using a local bash script.
See this StackOverFlow answer for details.

Let's see if it works... I just received

{
  "status": "queued",
  "url": "https://api.github.com/repositories/200653423/pages/builds/latest"
}

after execution.

Edit:
gh-pages are automatically rebuilt after each commit to the respective branch.
Looking at the build log, the last few builds each took about 20s.

[zhucaoxiang]

@jonathanschilling 20s after the commit is not too bad.

[zhucaoxiang]

A simple python script was added fix_format.py to automatically convert some characters into markdown words. To use it, just type python fix_format.py FIELDLINES.md. An executable of gh-md-toc is required to insert the table of contents.

Additional manual correction is still necessary.

[zhucaoxiang]

It seems using some template/theme could simplify our format fixing. For example, right now we don't have to put { include head.html } in the head of each page to enable MathJax. Also, the table of contents is now automatically generated as the sidebar. But the style is a little bit too colourful.

[cdfantasy]

Excuse me,I have see the [DESCUR] code and the [NMORPH] code in VMEC wiki,but there are neither in the release version.how cloud i use those 2 code.also,there are some code appear in github,but not in the VMEC wiki.

[zhucaoxiang]

@lazersos might know the history.

[lazersos]

Much of the wiki precedes the existence of the git repository. NMORPH is maintained by Michael Drevlak at IPP. If you wish to use that code please contact him.

DESCUR can be found in the DESCUR branch, but it no longer part of the public release of STELLOPT because it uses routines which are not technically open source.

[cdfantasy]

ok，thank you very much。