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Running Tests

From early stages in the development of Scipion, we have included a number of automatic tests. There is an automatic tool (buildbot) that executes periodically those tests and those executions can be examined in http://scipion-test.cnb.csic.es:9980/#/

Some of these tests run very quick. Their main goal is to validate the behavior of some important classes and functions (in the spirit of unit tests).

Other tests are more focused on the execution of protocols and complete workflows. They usually take more time to execute, and require some input data (which should be downloaded automatically on demand).

In the following sections you will find a brief explanation about the more important tests, and their input data. All of them must be executed from the command line using the specified commands.

Small tests

Classes and functions

Plugins Eman2 2.3
  scipion test pyworkflow.tests.model.test_object
Command scipion test pyworkflow.tests.model.test_mappers
  scipion test pyworkflow.tests.em.data.test_data
  scipion tests xmipp3.tests.test_convert_xmipp

Spider MDA Workflow

Plugins Spider
Command scipion test spider.tests.test_workflow_spiderMDA
Input Fake dataset of Worm Hemogoblin with 76 images
Time ~50 sec

EMX import

Plugins emxlib
Command scipion test emxlib.tests.test_protocols_emx
Input The different data sets used in http://i2pc.cnb.csic.es/emx
Time ~10 sec

CTF Discrepancy

Plugins Xmipp, grigoriefflab
Command scipion test pyworkflow.tests.em.workflows.test_workflow_xmipp_ctf_consensus
Input CTF obtained from micrograph of PcV (http://dx.doi.org/doi:10.1073/pnas.1404330111)
Time ~10 sec

Medium tests

Xmipp Workflow

Plugins Xmipp
Command scipion tests pyworkflow.tests.em.workflows.test_workflow_xmipp
Input Same data as in Xmipp Workflow. A refined volume generated with Frealign is obtained
Time ~300 sec
CPU i7-2640M 2.8GHz, 8GB RAM

Mixed Workflow 3D Reconstruction

Plugins Xmipp, EMAN
Command scipion test pyworkflow.tests.em.workflows.test_workflow_mixed.TestMixedBPV
Input Same data as in Xmipp Workflow. A refined volume generated with Frealign is obtained
Time ~150 sec
CPU i7-2640M 2.8GHz, 8GB RAM

Mixed Workflow Initial Volume

Plugins Xmipp, EMAN
Command scipion test pyworkflow.tests.em.workflows.test_workflow_mixed.TestMixedBPV2
Input Same data as in Xmipp Workflow. An initial volume generated with EMAN is obtained
Time ~200 sec
CPU i7-2640M 2.8GHz, 8GB RAM

Large Tests

[WARNING] The following tests must be run on computers with enough processing power.

Mixed Workflow Relion 2D classification

Plugins Xmipp, CTFfind, EMAN, Relion
Command scipion test pyworkflow.tests.em.workflows.test_workflow_mixed_large.TestMixedRelionTutorial
Input Dataset with 20 micrographs of the Ribosome.
Time ~3*h* sec
CPU 16 CPUs. Xeon(R) E5540 2.53 GHz, 64 GB RAM

Mixed Workflow Frealign 3D classification

Plugins Xmipp, CTFfind, EMAN, Frealign
Command scipion test pyworkflow.tests.em.workflows.test_workflow_mixed_large.TestMixedFrealignClassify
Input Same data as in Mixed Workflow Relion 2D classification.
Time ~30 min
CPU 16 CPUs. Xeon(R) E5540 2.53 GHz, 64 GB RAM

Random Conical Tilt reconstruction

Plugins Xmipp
Command scipion test pyworkflow.tests.em.workflows.test_workflow_xmipp_rct
Input Dataset with 6 pairs of untilted-tilted micrographs.
Time ~15 min
CPU 4 CPUs. Intel(R) Core(TM) i7-2640M CPU @ 2.80GHz, 8 GB RAM

Procotol Tests

Import different type of objects

Plugins Scipion
Import micrographs scipion test pyworkflow.tests.em.protocols.test_protocols_import_micrographs
Import particles scipion test pyworkflow.tests.em.protocols.test_protocols_import_particles
Import volumes scipion test pyworkflow.tests.em.protocols.test_protocols_import_volumes
Input From different datasets
Time ~15 min
CPU i7-2640M 2.8GHz, 8GB RAM

Processing micrographs

Plugins Xmipp
preprocess scipion test xmipp3.tests.test_protocols_xmipp_mics.TestXmippPreprocessMicrographs
ctf estimation scipion test xmipp3.tests.test_protocols_xmipp_mics.TestXmippCTFEstimation
Extract Particles scipion test xmipp3.tests.test_protocols_xmipp_mics.TestXmippExtractParticles
Software Grigoriefflab
ctf estimation scipion test grigoriefflab.tests.test_protocols_grigoriefflab.TestCtffind4
Input Dataset xmipp tutorial
Time  
CPU i7-2640M 2.8GHz, 8GB RAM

Preprocessing 2D

Plugins Xmipp
Create Mask 2D scipion test xmipp3.tests.test_protocols_xmipp_2d.TestXmippCreateMask2D
Apply Mask 2D scipion test xmipp3.tests.test_protocols_xmipp_2d.TestXmippApplyMask2D
Filter Particles scipion test xmipp3.tests.test_protocols_xmipp_2d.TestXmippFilterParticles
Software Relion
Preprocess Particles scipion test relion.tests.test_protocols_relion.TestRelionPreprocess
Input From different datasets
Time ~400 sec
CPU i7-2640M 2.8GHz, 8GB RAM

Particles alignment and classification

Plugins Xmipp
ML2D scipion test xmipp3.tests.test_protocols_xmipp_2d.TestXmippML2D
CL2D scipion test xmipp3.tests.test_protocols_xmipp_2d.TestXmippCL2D
CL2D Align scipion test xmipp3.tests.test_protocols_xmipp_2d.TestXmippProtCL2DAlign
Apply Alignment scipion test xmipp3.tests.test_protocols_xmipp_2d.TestXmippApplyAlignment
Rotational Spectra | scipion test xmipp3.tests.test_protocols_xmipp_2d.TestXmippRotSpectra
Kerdensom scipion test xmipp3.tests.test_protocols_xmipp_2d.TestXmippKerdensom
Software Relion
Classify 2D scipion test relion.tests.test_protocols_relion.TestRelionClassify2D
Input Mda dataset
Time scipion test relion.tests.test_protocols_relion.TestRelionClassify2D
CPU i7-2640M 2.8GHz, 8GB RAM

Preprocessing 3D

Software Xmipp
Create Mask 3D scipion test xmipp3.tests.test_protocols_xmipp_3d.TestXmippCreateMask3D
Apply Mask 3D scipion test xmipp3.tests.test_protocols_xmipp_3d.TestXmippApplyMask3D
Filter Volumes scipion test xmipp3.tests.test_protocols_xmipp_3d.TestXmippFilterVolumes
Preprocess Volumes scipion test xmipp3.tests.test_protocols_xmipp_3d.TestXmippPreprocessVolumes
Input Same data as in Xmipp Workflow.
Time ~400 sec
CPU i7-2640M 2.8GHz, 8GB RAM

Initial volume

Test Significant
Software Xmipp
Reconstruct significant scipion test pyworkflow.tests.em.workflows.test_workflow_initialvolume.TestSignificant
Input Groel data
Time ~27 min
CPU 4 CPUs on Asimov

Classify 3D

Test Classify 3D
Software Relion
Relion Classify 3D scipion test relion.tests.test_protocols_relion.TestRelionClassify3D
Input MDA data
Time ~200 sec
CPU i7-2640M 2.8GHz, 8GB RAM