Task #867

Update Doxygen documentation for C++ code

Added by Teemu Murtola almost 9 years ago. Updated over 4 years ago.

In Progress
Target version:


In particular the transition to use exceptions throughout the C++ code left some obsolete Doxygen comments in different places in the code. While going through the code, I identified some additional refactoring needs, but now quite a few of those have been addressed. It would be useful to go through Doxygen comments in particular in the following directories:
  • src/gromacs/analysisdata/
  • src/gromacs/selection/
  • src/gromacs/trajectoryanalysis/
Things to pay particular attention to:
  • Are Doxygen comments up-to-date with the current behavior?
  • Document exception behavior where applicable.
  • In src/gromacs/selection/, files converted from earlier C framework still contain comments that are in a different style than adopted for C++. Relevant parts, and in particular the separate pages (e.g., selection parsing and compilation) should be linked to the new documentation hierarchy. Converting documentation for intramodule functions isn't a high priority.
  • Check that relevant output is produced for each level of documentation (i.e., with each Doxyfile generated at the build tree root).
  • Anything else that seems to be poorly documented.

src/gromacs/options/ should be quite well up-to-date. fatalerror/ and utility/ contain a limited amount of code, which should be quite fast to check at the same time.

Will link other existing Doxygen documentation tasks as children or related tasks to this issue to have them better organized.


Task #641: Add and document a template for using the new analysis frameworkClosedTeemu Murtola
Task #640: Add/update Doxygen documentation for src/gromacs/trajectoryanalysis/ClosedTeemu Murtola

Related issues

Related to GROMACS - Task #662: Reformat existing Doxygen commentsClosed01/12/2011
Related to GROMACS - Task #638: Doxygen supportClosed01/08/2011

Associated revisions

Revision c7a6de98 (diff)
Added by Teemu Murtola almost 9 years ago

More comments for analysisdata.

- Added, updated and/or made more uniform Doxygen comments within the
analysisdata subdirectory.
- Small source code change in analysisdata.* to allow using all features
of the underlying implementation.
- Removed one plain pointer use from datastorage.cpp (a trivial change).

Part of issue #867.

Change-Id: If351e70988ca753f62c4e8c829bf80c2e5463c12

Revision 881a24c2 (diff)
Added by Teemu Murtola almost 9 years ago

More comments for trajectoryanalysis.

- Added/updated/made more uniform Doxygen comments for general classes
in the trajectoryanalysis subdirectory.
- Removed an unnecessary method to avoid copying documentation for it.
- Removed some commented-out code.

Part of issue #640 (child of #867).

Change-Id: I2fb4a03a2054ba0e63581b3815ad6f7176ce57a2

Revision 16f6aef1 (diff)
Added by Teemu Murtola almost 9 years ago

Clean-up selection poscalc implementation.

- Replace gmx_ana_poscalc_coll_t and related functions with a C++ class.
This resolves a few exception-related TODOs, and makes the C++ code
somewhat cleaner.
- Replace gmx_ana_poscalc_get_type_enum() with a static array, as the
current uses no longer need to modify the returned array.
- Remove possibility to provide an external position calculation
collection for selections; it was not used, and the code is simpler
- Updated Doxygen comments.

Related to #867; it's easier to document the code when it behaves

Change-Id: Ia8d5ba4ad22272b14bdcd521793636892821b140

Revision f37593f8 (diff)
Added by Teemu Murtola almost 9 years ago

Updated Doxygen comments for selections.

- Updated the list of installed selection headers to a more consistent
- Added/updated/made more uniform Doxygen comments for public classes in
the selection library.
- Small source code adjustments, mainly for improved exception behavior.

Part of issue #867.

Change-Id: I289660ffc7326f810d2df5dbf6060416fdd38e45


#1 Updated by Teemu Murtola almost 9 years ago

  • Description updated (diff)

#2 Updated by Teemu Murtola almost 9 years ago

  • Status changed from New to In Progress
  • Assignee set to Teemu Murtola

Started to slowly work on this.

#3 Updated by Teemu Murtola almost 9 years ago

  • Target version set to 5.0

#4 Updated by Erik Lindahl over 6 years ago

  • Target version changed from 5.0 to 5.x

#5 Updated by Teemu Murtola over 6 years ago

  • Project changed from Next-generation analysis tools to GROMACS
  • Category set to documentation

#6 Updated by Mark Abraham over 4 years ago

  • Target version deleted (5.x)

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