Documentation

PSI4’s documentation is generated by Sphinx and lives in psi4/doc/sphinxman.

Installing Sphinx

Installing Sphinx is only necessary to build the documentation yourself, locally. Ultimately, the docs will be served, either from trac or psicode, so most users/developers won’t need Sphinx installed. Nevertheless, installation is easy.

On Mac:

>>> easy_install sphinx

On Linux:

• Download

  >>> curl -O http://pypi.python.org/packages/source/S/Sphinx/Sphinx-1.1.3.tar.gz
  

• Unpack, etc.

• Build and Install

  >>> python setup.py build
  >>> sudo python setup.py install
  

• Check the path

  >>> which sphinx-build
  >>> which latex
  >>> which dvipng
  

• LaTeX and dvipng are needed to render math. If the latter is missing, the following may work.

  >>> sudo yum install dvipng-1.14-1.fc15.x86_64
  

Documentation Structure

Sphinx has nice capabilities for extracting docstrings from python files, presenting both auto generated and explicitly composed documentation in the same format, hyperlinking within and to trac/external websites, and generating documentation in different formats from the same source. PSI4’s documentation is a unified document covering information for both users and programmers, with different portions served up depending on the target audience. To this end, one can navigate to $(OBJDIR)/doc/sphinxman and build the following targets.:

>>> make help  # to see options
>>> make       # to build html

>>> make html
>>> make html-user
>>> make html-prog
>>> make latexpdf-user
>>> make latexpdf-prog

This will build the following files, respectively.

build/html/index.html
build/html-user/index.html
build/html-prog/index.html
build/latex-prog/psi4_userman.pdf
build/latex-prog/psi4_progman.pdf

Much of the documentation is auto-generated from the source. At present, this covers:

• Physical Constants: psi4/include/physconst.h
• Python Driver: docstrings from *.py files in psi4/lib/python
• Databases: docstrings from *.py files in psi4/lib/databases
• Basis Sets: *.gbs files in psi4/lib/basis
• C++ Keywords: psi4/src/bin/psi4/read_options.cc
• Sample Inputs: input.dat files in psi4/samples
• PSI Variables: Process::environment.globals lines and comments in the C++ code
• Plugins: doc.rst text, *.py modules, and C++ keywords in psi4/tests/plugin_* plugin directories

Some documentation is even extracted from Psi4 objects at runtime.

• PsiMod: docstrings for the PsiMod built-in module constructed in psi4/src/bin/psi4
• DFT: functional availibility and characteristics as encoded in psi4/lib/python/functional.py

Run make help to see choices for cleaning various stages of the build. Running make realclean clears out the built documentation. Building all the documentation takes ~10 minutes. There is now good dependency structure built into the psi4/doc/sphinxman/Makefile.in , so very long builds should be infrequent (unless you’re touching psi4/src/bin/psi4/read_options.cc. Note that not all dependencies are encoded (PSI variables, for instance, depend on every .cc file in the source tree), so for a definitive doc build, run make realclean and start from scratch.

reStructuredText

Sphinx files are written in reStructuredText (*.rst). In the html documentation, source code is available from the sidebar. Here’re a few resources on Sphinx formatting.

• reStructuredText
• rendered test document vs. source test document
• Another reStructuredText
• A third reStructuredText and Sphinx
• LaTeX that Sphinx can handle
• Sphinx Docs

Math in the Codebase

It is often useful to have mathematical expressions in docstrings or comments in the code that are auto-documented into the manual. Such locations include the #! comment comments at the top of test case input files, the /*- comment -*/ comments in psi4/src/bin/psi4/read_options.cc, and the """ comment """ docstrings in python modules. For the two former, math has traditionally been written in LaTeX (with the special substitution @@ for subscripting underscore). The autodoc script has been trained to convert inline LaTeX math to reST math, provided the expression within dollar signs is offset from other text. That is, expressions of the form ^ $latex math$[., ]$ (pseudo-regex) are good, while H$_2$O and LaTeX tables are not translated correctly. Python docstrings are absorbed as-is, so please use reST math formatting (essentially $latex math$ :math:`latex math`).