nutmeg

nutmeg is a regression test framework for the MCell simulator (www.mcell.org).

Installation

The nutmeg test framework is written in go. If you don't already use go, you'll probably need to set your GOPATH, which you can do like this:

export GOPATH=$HOME/go

Note: feel free to use some other path than $HOME/go.

To pull in nutmeg's dependencies, change into the top-level nutmeg directory and type this:

go get -u all

Finally, to build nutmeg, enter this:

go build

Production versions of nutmeg will be shipped with precompiled binaries for Linux, Mac OSX, and Windows.

nutmeg expects a config file in TOML format called nutmeg.conf in the directory where the binary is located. Currently, this file only contains information on the path of the MCell executable and the location of the tests/ directory. A sample nutmeg.conf is available in the share/ subdirectory.

Usage

nutmeg [option]

Here [option] can be one of

  -c
    clean temporary test data

  -d test_selection
    show description for selected tests

  -l
    show available test cases

  -L
    show available test categories

  -m
    number of concurrent test jobs (default: 2)

  -n
    number of concurrent simulation jobs (default: 2)

  -r test_selection
    run specified tests (i, i:j, 'all')

  -R test_category
    run all the tests in a given category (e.g. reactions, parser)

Here, test_selection is a comma separated lists of test cases specified either by their numeric test ID or their name (as returned by nutmeg -l). It is also possible to specify numeric ranges via i:j with lower and upper limits i and j, respectively. The keyword all triggers testing of all available cases. Please note that the comma separated list of test_selections may not contain spaces unless the whole expression is enclosed in double quotes. Concurrent simulation jobs will each run as separate MCell processes. Thus, to optimize throughput n should be chosen as large as possible but not exceed the physical number of cores on the test machine.

Examples

Run all the tests:

./nutmeg -r all

Run the count_enclosed and all_enclosed test:

./nutmeg -r count_enclosed,all_enclosed

Run tests eighty through eighty-four (the numbers correspond to those shown by nutmeg -l):

./nutmeg -r 80:85

Run all the dynamic geometry tests:

./nutmeg -R "dynamic geometry"

Adding New Test Cases

To add a new test case, simply create a new and descriptively named subdirectory in tests/. All files pertaining to this test (including any test output) are contained in this directory. At a minumum, a test case consists of an MCell test input file in MDL format and a file called test_description.toml, containing the description of this particular test case in TOML format. A sample test description file is available in share/ and can be modified to fit the specific needs of new test cases (more details on how to add new tests will follow soon).

Author

(C) Markus Dittrich, 2014 National Center for Multiscale Modeling of Biological Systems.