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Contributor FAQ

The following contains answers to typical questions from contributors about OpenMS.

General

The following section provides general information to new contributors.

I am new to OpenMS. What should I do first?

What is the difference between an OpenMS tool and util?

A tool starts its lifecycle in UTILS and may exist without being thoroughly tested. Tools may be promoted from UTILS to TOOLS if they are stable enough, are fully tested, fully documented, and a test workflow exists.

I have written a class for OpenMS. What should I do?

Follow the OpenMS coding conventions.

Coding style (brackets, variable names, etc.) must conform to the conventions.

  • The class and all the members must be documented thoroughly.
  • Check your code with the tool tools/checker.php. Call php tools/checker.php for detailed instructions.

Please open a pull request and follow the pull request guidelines.

Troubleshooting

The following section provides information about how to troubleshoot common OpenMS issues.

OpenMS complains about boost not being found

CMake got confused. Set up a new build directory and try again. Build from source, deleting the CMakeCache.txt and cmake directory might help.

Build System

The following questions are related to the build system.

What is CMake?

CMake builds BuildSystems for different platforms, e.g. VisualStudio Solutions on Windows, Makefiles on Linux etc. This allows us to define in one central location (namely CMakeLists.txt) how OpenMS is build and have the platform specific stuff handled by CMake. View the cmake website for more information.

How do I use CMake?

See Installation instructions for your platform. In general, call CMake(.exe) with some parameters to create the native build-system. Afterwards, (but usually) don't have to edit the current configuration using a GUI named ccmake (or CMake-GUI in Windows), which ships with CMake).

Whenever `ccmake` is mentioned in this document, substitute this by `CMake-GUI` if your OS is Windows. Edit
the `CMakeCache.txt` file directly.

How do I generate a build-system for Eclipse, KDevelop, CodeBlocks etc?

Type cmake into a console. This will list the available code generators available on your platform, pass them to CMake using the -G option.

How do I add a new class to the build system?

  1. Create the new class in the corresponding sub-folder of the sub-project. The header has to be created in src/<sub-project>/include/OpenMS and the cpp file in src/<sub-project>/source, e.g., src/openms/include/OpenMS/FORMAT/NewFileFormat.h and src/openms/source/FORMAT/NewFileFormat.cpp.
  2. Add both to the respective sources.cmake file in the same directory (e.g., src/openms/source/FORMAT/ and src/openms/include/OpenMS/FORMAT/).
  3. Add the corresponding class test to src/tests/class_tests/<sub-project>/ (e.g., src/tests/class_tests/openms/source/NewFileFormat_test.cpp).
  4. Add the test to the executables.cmake file in the test folder (e.g., src/tests/class_tests/openms/executables.cmake).
  5. Add them to git by using the command git add.

How do I add a new directory to the build system?

  1. Create two new sources.cmake files (one for src/<sub-project>/include/OpenMS/MYDIR, one for src/<sub-project>/source/MYDIR), using existing sources.cmake files as template.
  2. Add the new sources.cmake files to src/<sub-project>/includes.cmake
  3. If you created a new directory directly under src/openms/source, then have a look at src/tests/class_tests/openms/executables.cmake.
  4. Add a new section that makes the unit testing system aware of the new (upcoming) tests.
  5. Look at the very bottom and augment TEST_executables.
  6. Add a new group target to src/tests/class_tests/openms/CMakeLists.txt.

Debugging

The following section provides information about how to debug your code.

How do I run a single test?

Execute an OpenMS class test using the CTest regular expressions:

$ ctest -V -R "^<class>_test"

# To build a class test, call the respective make target in ./source/TEST:

$ make <class>_test

To run a TOPP test, use:

$ ctest -V -R "TOPP_<tool>"

To build the tool, use:

$ make <tool>

How do I debug uncaught exceptions?

Dump a core if an uncaught exception occurs, by setting the environment variable OPENMS_DUMP_CORE.

Each time an uncaught exception occurs, the OPENMS_DUMP_CORE variable is checked and a segmentation fault is caused, if it is set.

(Linux) How can I set breakpoints in gdb to debug OpenMS?

Debug the TOPPView application to stop at line 341 of SpectrumMDIWindow.C.

  1. Enter the following in your terminal:
Run gdb:
shell> gdb TOPPView
  1. Start the application (and close it):
gdb> run [arguments]
  1. Set the breakpoint:
gdb> break SpectrumMDIWindow.C:341
  1. Start the application again (with the same arguments):
gdb> run

Doxygen Documentation

Where can I find the definition of the main page?

Find a definition of the main page here.

Where can I add a new module?

Add a new module here.

How is the command line documentation for TOPP/UTILS tools created?

The program OpenMS/doc/doxygen/parameters/TOPPDocumenter.cpp creates the command line documentation for all classes that are included in the static ToolHandler.cpp tools list. It can be included in the documentation using the following doxygen command:

@verbinclude TOPP_<tool name>.cli

Test if everything worked by calling make doc_param_internal. The command line documentation is written to OpenMS/doc/doxygen/parameters/output/.

What are the important files for adding a new tutorial section?

View the following OpenMS tutorials:

  • OpenMS/doc/OpenMS_tutorial/refman_overwrite.tex.in (for PDF tutorials)
  • OpenMS/doc/doxygen/public/OpenMS_Tutorial_html.doxygen (for html tutorials)

View the following TOPP and TOPPView tutorials:

  • OpenMS/doc/TOPP_tutorial/refman_overwrite.tex.in (for PDF tutorials)
  • OpenMS/doc/doxygen/public/TOPP_Tutorial_html.doxygen (for html tutorials)

Bug Fixes

How do I contribute to a bug fix?

To contribute to a bug fix:

  1. Submit the bug as a GitHub issue.
  2. Create a feature branch (e.g. feature/fix_missing_filename_issue_615) from your (up-to-date) develop branch in your fork of OpenMS.
  3. Fix the bug and add a test.
  4. Create a pull request for your branch.
  5. After approval and merge make sure the issue is closed.