AutoDoc is a GAP package which is meant to aid GAP package authors in creating and maintaining the documentation of their packages. In this capacity it builds upon the GAPDoc package (see https://www.gap-system.org/Packages/gapdoc.html). As such, it is not a replacement for GAPDoc, but rather complements it.
In this chapter we describe how to get started using AutoDoc for your package. First, we explain in Section 1.1 how to write a new package manual from scratch.
Then we show in Section 1.3 how you might benefit from AutoDoc even if you already have a complete manual written using GAPDoc.
In Section 1.4, we explain how you may use AutoDoc to generate a title page and the main XML file for your manual.
Finally, Section 1.5, explains what AutoDoc worksheets are and how to use them.
Suppose your package is already up and running, but so far has no manual. Then you can rapidly generate a "scaffold" for a package manual using the AutoDoc (4.1-1) command like this, while running GAP from within your package's directory (the one containing the PackageInfo.g file):
LoadPackage( "AutoDoc" ); AutoDoc( rec( scaffold := true ) );
This first reads the PackageInfo.g file from the current directory. It extracts information about package from it (such as its name and version, see Section 1.4-1). It then creates two XML files doc/NAME_OF_YOUR_PACKAGE.xml and doc/title.xml inside the package directory. Finally, it runs GAPDoc on them to produce a nice initial PDF and HTML version of your fresh manual.
To ensure that the GAP help system picks up your package manual, you should also add something like the following to your PackageInfo.g:
PackageDoc := rec( BookName := ~.PackageName, ArchiveURLSubset := ["doc"], HTMLStart := "doc/chap0.html", PDFFile := "doc/manual.pdf", SixFile := "doc/manual.six", LongTitle := ~.Subtitle, ),
Congratulations, your package now has a minimal working manual. Of course it will be mostly empty for now, but it already should contain some useful information, based on the data in your PackageInfo.g. This includes your package's name, version and description as well as information about its authors. And if you ever change the package data, (e.g. because your email address changed), just re-run the above command to regenerate the two main XML files with the latest information.
Next of course you need to provide actual content (unfortunately, we were not yet able to automate that for you, more research on artificial intelligence is required). To add more content, you have several options: You could add further GAPDoc XML files containing extra chapters, sections and so on. Or you could use classic GAPDoc source comments. For details on either, please refer to GAPDoc: Distributing a Document into Several Files, as well as Section 1.3 of this manual on how to teach the AutoDoc (4.1-1) command to include this extra documentation. Or you could use the special documentation facilities AutoDoc provides (see Section 1.2).
You will probably want to re-run the AutoDoc (4.1-1) command frequently, e.g. whenever you modified your documentation or your PackageInfo.g. To make this more convenient and reproducible, we recommend putting its invocation into a file makedoc.g in your package directory, with content based on the following example:
LoadPackage( "AutoDoc" ); AutoDoc( rec( autodoc := true ) ); QUIT;
Then you can regenerate the package manual from the command line with the following command, executed from within in the package directory:
gap makedoc.g
To get one of your global functions, operations, attributes etc. to appear in the package manual, simply insert an AutoDoc comment of the form #! directly in front of it. For example:
#! DeclareOperation( "ToricVariety", [ IsConvexObject ] );
This tiny change is already sufficient to ensure that the operation appears in the manual. In general, you will want to add further information about the operation, such as in the following example:
#! @Arguments conv #! @Returns a toric variety #! @Description #! Creates a toric variety out #! of the convex object <A>conv</A>. DeclareOperation( "ToricVariety", [ IsConvexObject ] );
For a thorough description of what you can do with AutoDoc documentation comments, please refer to chapter 2.
Suppose you have not been using GAPDoc before but instead used the process described in section 1.1 to create your manual. Then the following GAP command will regenerate the manual and automatically include all newly documented functions, operations etc.:
LoadPackage( "AutoDoc" );
AutoDoc( rec( scaffold := true,
autodoc := true ) );
If you are not using the scaffolding feature, e.g. because you already have an existing GAPDoc based manual, then you can still use AutoDoc documentation comments. Just make sure to first edit the main XML file of your documentation, and insert the line
<#Include SYSTEM "_AutoDocMainFile.xml">
in a suitable place. This means that you can mix AutoDoc documentation comment freely with your existing documentation; you can even still make use of any existing GAPDoc documentation comments in your code. The following command should be useful for you in this case; it still scans the package code for AutoDoc documentation comments and the runs GAPDoc to produce HTML and PDF output, but does not touch your documentation XML files otherwise.
LoadPackage( "AutoDoc" ); AutoDoc( rec( autodoc := true ) );
Even if you already have an existing GAPDoc manual, it might be interesting for you to use AutoDoc for two purposes:
First off, with AutoDoc is very convenient to regenerate your documentation.
Secondly, the scaffolding feature which generates a title page with all the metadata of your package in a uniform way is very handy. The somewhat tedious process of keeping your title page in sync with your PackageInfo.g is fully automated this way (including the correct version, release data, author information and so on).
There are various examples of packages using AutoDoc for only this purpose, e.g. io and orb.
Suppose you already have a complete XML manual, with some main and title XML files and some documentation for operations distributed over all your .g, .gd, and .gi files. Suppose the main XML file is named PACKAGENAME.xml and is in the /doc subdirectory of your package. Then you can rebuild your manual by executing the following two GAP commands from a GAP sessions started started in the root directory of your package:
LoadPackage( "AutoDoc" ); AutoDoc( );
In contrast, the RingsForHomalg currently uses essentially the following code in its makedoc.g file to achieve the same result
LoadPackage( "GAPDoc" );
SetGapDocLaTeXOptions( "utf8" );
bib := ParseBibFiles( "doc/RingsForHomalg.bib" );
WriteBibXMLextFile( "doc/RingsForHomalgBib.xml", bib );
list := [
"../gap/RingsForHomalg.gd",
"../gap/RingsForHomalg.gi",
"../gap/Singular.gi",
"../gap/SingularBasic.gi",
"../examples/RingConstructionsExternalGAP.g",
"../examples/RingConstructionsSingular.g",
"../examples/RingConstructionsMAGMA.g",
"../examples/RingConstructionsMacaulay2.g",
"../examples/RingConstructionsSage.g",
"../examples/RingConstructionsMaple.g",
];
MakeGAPDocDoc( "doc", "RingsForHomalg", list, "RingsForHomalg" );
GAPDocManualLab( "RingsForHomalg" );
Note that in particular, you do not have to worry about keeping a list of your implementation files up-to-date.
But there is more. AutoDoc can create .tst files from the examples in your manual to test your package. This can be achieved via
LoadPackage( "AutoDoc" ); AutoDoc( rec( extract_examples := true ) );
Now files PACKAGENAME01.tst, PACKAGENAME02.tst and so appear in the tst/ subdirectory of your package, and can be tested as usual using Test (Reference: Test) respectively TestDirectory (Reference: TestDirectory).
Sometimes, the default values for the GAPDoc command used by AutoDoc may not be suitable for your manual.
Suppose your main XML file is not named PACKAGENAME.xml, but rather something else, e.g. main.xml. Then you can tell AutoDoc to use this file as the main XML file via
LoadPackage( "AutoDoc" ); AutoDoc( rec( gapdoc := rec( main := "main" ) ) );
As explained above, by default AutoDoc scans all .g, .gd and .gi files it can find inside of your package root directory, and in the subdirectories gap, lib, examples and examples/doc as well. If you keep source files with documentation in other directories, you can adjust the list of directories AutoDoc scans via the scan_dirs option. The following example illustrates this by instructing AutoDoc to only search in the subdirectory package_sources of the packages root directory.
LoadPackage( "AutoDoc" ); AutoDoc( rec( gapdoc := rec( scan_dirs := [ "package_sources" ] ) ) );
You can also specify an explicit list of files containing documentation, which will be searched in addition to any files located within the scan directories:
LoadPackage( "AutoDoc" ); AutoDoc( rec( gapdoc := rec( files := [ "path/to/some/hidden/file.gds" ] ) ) );
Giving such a file does not prevent the standard scan_dirs from being scanned for other files.
Next, GAPDoc supports the documentation to be built with relative paths. This means, links to manuals of other packages or the GAP library will not be absolute, but relative from your documentation. This can be particularly useful if you want to build a release tarball or move your GAP installation around later. Suppose you are starting GAP in the root path of your package as always, and the standard call of AutoDoc (4.1-1) will then build the documentation in the doc subdirectory of your package. From this directory, the gap root directory has the relative path ../../... Then you can enable the relative paths by
LoadPackage( "AutoDoc" ); AutoDoc( rec( gapdoc := rec( gap_root_relative_path := "../../.." ) ) );
or, since ../../.. is the standard option for gap_root_relative_path, by
LoadPackage( "AutoDoc" ); AutoDoc( rec( gapdoc := rec( gap_root_relative_path := true ) ) );
Here is a checklist for authors of a package PackageName, which already has a GAPDoc based manual, who wish to use AutoDoc to build the manual from now on. We assume that the manual is currently built by reading a file makedoc.g and that the main .xml file is named manual.xml.
The files PackageInfo.g, makedoc.g, doc/title.xml and doc/PackageName.xml (if it exists) will be altered by this procedure, so it may be wise to keep backup copies.
You should have copies of the AutoDoc files PackageInfo.g and makedoc.g to hand when reading these instructions.
Copy AutoDoc/makedoc.g to PackageName/makedoc.g.
Edit PackageName/makedoc.g as follows.
Change the header comment to match other files in your package.
After LoadPackage("AutoDoc"); add LoadPackage("PackageName");.
In the AutoDoc record delete autodoc := true;.
In the scaffold record change the includes list to be the list of your .xml files that are contained in manual.xml.
If you do not have a bibliography you may delete the bib := "bib.xml", field in the scaffold. Otherwise, edit the file name if you have a different file. If you only have a .bib file (manual.bib or bib.xml.bib say) you should rename this file PackageName.bib.
In the LaTeXOptions record, which is in the gapdoc record, enter any LaTeX newcommands previously in manual.xml. (If there are none you may safely delete this record.) To illustrate this option, the AutoDoc file makedoc.g defines the command \bbZ by \newcommand{\bbZ}{\mathbb{Z}}, which may be used to produce the LaTeX formula f : bbZ^2 -> bbZ.
In the entities record enter any entities previously stored in manual.xml. (Again, if you have none, you may safely delete this record.) To illustrate this option the AutoDoc file makedoc.g defines entities for the names of packages io and PackageName.
Now edit PackageName/PackageInfo.g as follows.
Delete any PKGVERSIONDATA chunk that may be there. One reason for converting your manual to use AutoDoc is to stop using entities such as PACKAGENAMEVERSION.
Copy the AutoDoc record from AutoDoc/PackageInfo.g to the end of your file (just before the final "));".
Replace the Copyright, Abstract and Acknowledgements fields of the TitlePage record with the corresponding material from your manual.xml. (If you do not have an abstract, then delete the Abstract field, etc.) For other introductory components, such as Colophon, consult the file gap/Magic.gd.
If you are using a GitHub repository, as well as running "git add" on files makedoc.g, PackageInfo.g and doc/PackageName.bib, you should run "git rm -f" on files doc/manual.xml, and doc/title.xml.
You should now be ready to run GAP and Read("makedoc.g"); in your package root directory.
For most (if not all) GAP packages, the title page of the package manual lists information such as the release date, version, names and contact details of the authors, and so on. All this data is also contained in your PackageInfo.g, and whenever you make a change to that file, there is a risk that you forget to update your manual to match. And even if you don't forget it, you of course have to spend some time to adjust the manual. GAPDoc can help to a degree with this via entities. Thus, you will sometimes see code like this in PackageInfo.g files:
Version := "1.2.3", Date := "20/01/2015", ## <#GAPDoc Label="PKGVERSIONDATA"> ## <!ENTITY VERSION "1.2.3"> ## <!ENTITY RELEASEDATE "20 January 2015"> ## <!ENTITY RELEASEYEAR "2015"> ## <#/GAPDoc>
However, it is still easy to forget both of these versions. And it doesn't solve the problem of updating package authors addresses. Neither of these is a big issue, of course, but there have been plenty examples in the past where people forget either of these two things, and it can be slightly embarrassing. It may even require you to make a new release just to fix the issue, which in our opinion is a sad waste of your valuable time.
So instead of worrying about manually synchronising these things, you can instruct AutoDoc to generate a title page for your manual based on the information in your PackageInfo.g. The following commands do just that (in addition to building your manual), by generating a file called doc/title.xml.
LoadPackage( "AutoDoc" ); AutoDoc( rec( scaffold := rec( MainPage := false ) ) );
Note that this only outputs doc/title.xml but does not touch any other files of your documentation. In particular, you need to explicitly include doc/title.xml from your main XML file.
However, you can also tell AutoDoc to maintain the main XML file for you, in which case this is automatic. In fact, this is the default if you enable scaffolding; the above example command explicitly told AutoDoc not to generate a main page.
The following generates a main XML file for your documentation in addition to the title page. The main XML file includes the title page by default, as well as any documentation generated from AutoDoc documentation comments.
LoadPackage( "AutoDoc" ); AutoDoc( rec( scaffold := true ) );
You can instruct AutoDoc to include additional XML files by giving it a list of filenames, as in the following example:
LoadPackage( "AutoDoc" );
AutoDoc(rec(
scaffold := rec(
includes := [ "somefile.xml", "anotherfile.xml" ]
)
));
For more information, please consult the documentation of the AutoDoc (4.1-1) function.
PackageInfo.g?AutoDoc can use data from PackageInfo.g in order to generate a title page. Specifically, the following components of the package info record are taken into account:
This is used to set the <Title> element of the title page.
This is used to set the <Subtitle> element of the title page.
This is used to set the <Version> element of the title page, with the string "Version " prepended.
This is used to set the <Date> element of the title page.
This is used to generate <Author> elements in the generated title page.
This is a record (or a list of records) which is used to tell the GAP help system about the package manual. Currently AutoDoc extracts the value of the PackageDoc.BookName component and then passes that on to GAPDoc when creating the HTML, PDF and text versions of the manual.
This is a record which can be used to control the scaffolding performed by AutoDoc, specifically to provide extra information for the title page. For example, you can set AutoDoc.TitlePage.Copyright to a string which will then be inserted on the generated title page. Using this method you can customize the following title page elements: TitleComment, Abstract, Copyright, Acknowledgements and Colophon.
Note that AutoDoc.TitlePage behaves exactly the same as the scaffold.TitlePage parameter of the AutoDoc (4.1-1) function.
AutoDoc worksheets can be used to create HTML and PDF documents using AutoDoc syntax and possibly including GAP examples and implementations without having them associated to a package. A file for a worksheet could look like this:
#! @Title My first worksheet #! @Author Charlie Brown #! @Chapter Some groups #! @BeginExample S3 := SymmetricGroup( 3 );; S4 := SymmetricGroup( 4 );; #! @EndExample
Now, one can create a PDF and HTML document, like a package documentation out of it. Suppose the document above is saved as worksheet.g. Then, when GAP is started in the directory of this file, the command
AutoDocWorksheet( "worksheet.g" );
will create a subdirectory called doc of the current directory in which it will create the documentation. There are several options to configure the output of the worksheet command, which are identical to the options of the AutoDoc (4.1-1) command. It is even possible to test the examples in the worksheet using the extract_examples option of the AutoDoc (4.1-1) command.
Since the worksheets do not have a PackageInfo.g to extract information, all possible tags that GAPDoc supports for the title page can be set into the document. A fully typed title page can look like this:
#! @Title My first worksheet #! @Subtitle Some small examples #! @Author Charlie Brown #! @Version 0.1 #! @TitleComment Some worksheet #! @Date 01/01/2016 #! @Address TU Kaiserslautern #! @Abstract #! A worksheet showing some small examples about groups. #! @Copyright 2016 Charlie Brown #! @Acknowledgements Woodstock #! @Colophon Some colophon #! @Chapter Some groups #! @BeginExample S3 := SymmetricGroup( 3 );; S4 := SymmetricGroup( 4 );; #! @EndExample
generated by GAPDoc2HTML