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Running Tests

Scipion discovers all tests using the following command:

./scipion3 tests

This command creates a list with Scipion’s own tests as well as the tests of the installed plugins:

    >>>> cistem
 scipion3 tests cistem.tests.test_protocols_cistem_movies
   scipion3 tests cistem.tests.test_protocols_cistem_movies.TestUnblur
 scipion3 tests cistem.tests.test_protocols_cistem
   scipion3 tests cistem.tests.test_protocols_cistem.TestRefine2D
   scipion3 tests cistem.tests.test_protocols_cistem.TestFindParticles
   scipion3 tests cistem.tests.test_protocols_cistem.TestCtffind4
>>>> relion
 scipion3 tests relion.tests.test_workflow_relion3
   scipion3 tests relion.tests.test_workflow_relion3.TestWorkflowRelion3Betagal
 scipion3 tests relion.tests.test_protocols_relion3
   scipion3 tests relion.tests.test_protocols_relion3.TestRelion31ImportParticles
   scipion3 tests relion.tests.test_protocols_relion3.Relion3TestMultiBody
   scipion3 tests relion.tests.test_protocols_relion3.Relion3TestMotioncor
   scipion3 tests relion.tests.test_protocols_relion3.Relion3TestAssignOptics

This command shows all tests with the following order: <module_name>.<tests_folder>.<test_file>.<test_class_derived_from_BaseTest>

To list the tests filtering by a pattern we can use the following command:

./scipion3 tests --grep <pattern>


./scipion3 test --grep cryosparc

 scipion3 tests cryosparc2.tests.test_utils
   scipion3 tests cryosparc2.tests.test_utils.TestUtils
 scipion3 tests cryosparc2.tests.test_protocols_cryosparc2
   scipion3 tests cryosparc2.tests.test_protocols_cryosparc2.TestCryosparcSharppening
   scipion3 tests cryosparc2.tests.test_protocols_cryosparc2.TestCryosparcParticlesSubtract
   scipion3 tests cryosparc2.tests.test_protocols_cryosparc2.TestCryosparcNonUniformRefine3D
   scipion3 tests cryosparc2.tests.test_protocols_cryosparc2.TestCryosparcLocalRefine
   scipion3 tests cryosparc2.tests.test_protocols_cryosparc2.TestCryosparcLocalCtfRefinement
   scipion3 tests cryosparc2.tests.test_protocols_cryosparc2.TestCryosparcGlobalCtfRefinement
   scipion3 tests cryosparc2.tests.test_protocols_cryosparc2.TestCryosparcClassify2D
   scipion3 tests cryosparc2.tests.test_protocols_cryosparc2.TestCryosparc3DRefinement
   scipion3 tests cryosparc2.tests.test_protocols_cryosparc2.TestCryosparc3DInitialModel
   scipion3 tests cryosparc2.tests.test_protocols_cryosparc2.TestCryosparc3DClassification

The shortest, simplest way of running the test suite is the following command from the Scipion directory:

$ ./scipion3 tests <test>

test case from string identifier (module, class or callable)

for example:

./scipion3 tests cryosparc2.tests.test_utils
./scipion3 tests cryosparc2.tests.test_utils.TestUtils
./scipion3 tests cryosparc2.test.test_utils.TestUtils.testSamplingRateConvertion

the last script produces the following output:

Running tests....
[ RUN   OK ] TestUtils.testSamplingRateConvertion (0.000 secs)

[==========] run 1 tests (0.000 secs)
[  PASSED  ] 1 tests

The other commands that can be used are shown below:

usage: ./scipion3 test [-h] [--run | --show] [--pattern PATTERN]
                        [--grep GREP [GREP ...]] [--skip SKIP [SKIP ...]]
                        [--log [LOG]] [--mode {modules,classes,onlyclasses,all}]
                        [TEST [TEST ...]]

Run or show the selected tests. Tests can be selected by giving the "case", or
by giving the paths and file pattern to use for searching them.

positional arguments:
  TEST                  test case from string identifier (module, class or

optional arguments:
  -h, --help            show this help message and exit
  --run                 run the selected tests
  --show                show available tests
  --pattern PATTERN     pattern for the files that will be used in the tests
  --grep GREP [GREP ...]
                        only show/run tests containing the provided words
  --skip SKIP [SKIP ...]
                        skip tests that contains these words
  --log [LOG]           Generate logs files with the output of each test.
  --mode {modules,classes,onlyclasses,all}
                        how much detail to give in show mode

We can also combine the parameters of this command to run more than one test, for example:

./scipion3 test --grep cryosparc --run

and all the tests that match the pattern “cryosparc” will be executed automatically.