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Running Tests

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Laura edited this page Sep 4, 2018 · 9 revisions
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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://heisenberg.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. You will also find how to launch the tests from the command line.

Small tests

Classes and functions

Software

 
Scipion

Command

 
scipion tests model.test_object
scipion tests model.test_mappers
scipion tests em.data.test_data
scipion tests em.data.test_convert_xmipp

Spider MDA Workflow

Software

 
SPIDER

Command

 
scipion tests em.workflows.test_workflow_spiderMDA

Input

 
Fake dataset of Worm Hemogoblin with 76 images

Time

 
 ~50 sec

EMX import

Software

 
Scipion

Command

 
scipion tests tests.em.protocols.test_protocols_emx

Input

 
The different data sets used in http://i2pc.cnb.csic.es/emx

Time

 
 ~10 sec

CTF Discrepancy

Software

 
Xmipp

Command

 
scipion tests tests.em.workflows.test_workflow_xmipp_ctf_discrepancy

Input

 
CTF obtained from micrograph of PcV (http://dx.doi.org/doi:10.1073/pnas.1404330111)

Time

 
 ~10 sec

Medium tests

Xmipp Workflow

Software

 
 Xmipp

Command

 
 `scipion tests em.workflows.test_workflow_xmipp`

Input

 
 Dataset with 3 micrographs of the Bovino Papiloma Virus (BPV)

Time

 
 ~300 sec

CPU

 
 i7-2640M 2.8GHz, 8GB RAM

Mixed Workflow 3D Reconstruction

Software

 
 Xmipp, CTFfind, EMAN, Frealign

Command

 
 `scipion 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

Software

 
 Xmipp, CTFfind, EMAN

Command

 
`scipion 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

Software

 
 Xmipp, CTFfind, EMAN, Relion

Command

 
 `scipion tests em.workflows.test_workflow_mixed_large.TestMixedRelionTutorial`

Input

 
 Dataset with 20 micrographs of the Ribosome.

Time

 
 ~3*h*

CPU

 
 16 CPUs. Xeon(R) E5540 2.53 GHz, 64 GB RAM

Mixed Workflow Frealign 3D classification

Software

 
 Xmipp, CTFfind, EMAN, Frealign

Command

 
 `scipion 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

Software

 
 Xmipp

Command

 
 `scipion 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

Software

 
 Scipion

Import micrographs

 
 `scipion tests tests.em.protocols.test_protocols_import_micrographs`

Import particles

 
 `scipion tests tests.em.protocols.test_protocols_import_particles`

Import volumes

 
 `scipion tests tests.em.protocols.test_protocols_import_volumes`

Input

 
 From different datasets

Time

 








CPU


 i7-2640M 2.8GHz, 8GB RAM













Processing micrographs













Software


 Xmipp






preprocess


 `scipion tests tests.em.protocols.test_protocols_xmipp_mics.TestXmippPreprocessMicrographs`






ctf estimation


 `scipion tests tests.em.protocols.test_protocols_xmipp_mics.TestXmippCTFEstimation`






Extract Particles


 `scipion tests tests.em.protocols.test_protocols_xmipp_mics.TestXmippExtractParticles`






Software


 Grigoriefflab






ctf estimation


 `scipion tests tests.em.protocols.test_protocols_grigoriefflab.TestBrandeisCtffind`






Input


 Dataset xmipp tutorial








Time















Preprocessing 2D













Software


 Xmipp






Create Mask 2D


 `scipion test tests.em.protocols.test_protocols_xmipp_2d.TestXmippCreateMask2D`






Apply Mask 2D


 `scipion test tests.em.protocols.test_protocols_xmipp_2d.TestXmippApplyMask2D`






Filter Particles


 `scipion test tests.em.protocols.test_protocols_xmipp_2d.TestXmippFilterParticles`






Preprocess Particles


 `scipion test tests.em.protocols.test_protocols_xmipp_2d.TestXmippPreprocessParticles`






Software


 Relion






Preprocess Particles


 `scipion test tests.em.protocols.test_protocols_relion.TestRelionPreprocess`






Input


 From different datasets






Time


 ~400 sec








CPU


 i7-2640M 2.8GHz, 8GB RAM













Particles alignment and classification













Software


 Xmipp






ML2D


 `scipion test tests.em.protocols.test_protocols_xmipp_2d.TestXmippML2D`






CL2D


 `scipion test tests.em.protocols.test_protocols_xmipp_2d.TestXmippCL2D`






CL2D Align


 `scipion test tests.em.protocols.test_protocols_xmipp_2d.TestXmippProtCL2DAlign`






Apply Alignment


 `scipion test tests.em.protocols.test_protocols_xmipp_2d.TestXmippApplyAlignment`






Rotational Spectra


 `scipion test tests.em.protocols.test_protocols_xmipp_2d.TestXmippRotSpectra`






Kerdensom


 `scipion test tests.em.protocols.test_protocols_xmipp_2d.TestXmippKerdensom`






Software


 Relion






Classify 2D


 `scipion test tests.em.protocols.test_protocols_relion.TestRelionClassify2D`






Input


 Mda dataset






Time










CPU


 i7-2640M 2.8GHz, 8GB RAM













Preprocessing 3D













Software


 Xmipp






Create Mask 3D


 `scipion test tests.em.protocols.test_protocols_xmipp_3d.TestXmippCreateMask3D`






Apply Mask 3D


 `scipion test tests.em.protocols.test_protocols_xmipp_3d.TestXmippApplyMask3D`






Filter Volumes


 `scipion test tests.em.protocols.test_protocols_xmipp_3d.TestXmippFilterVolumes`






Preprocess Volumes


 `scipion test tests.em.protocols.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


 `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 3D


 `scipion test tests.em.protocols.test_protocols_relion.TestRelionClassify3D`






Input


 MDA data.






Time


 ~200 sec








CPU


 i7-2640M 2.8GHz, 8GB RAM










              


          



  
          

            

              

                

                  

                    
                  

                

              


            
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