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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

Basic tests

Plugins Core, Xmipp, Relion
  scipion tests pyworkflowtests.tests.test_object.TestObject
  scipion tests pyworkflowtests.tests.test_mappers
  scipion tests
  scipion tests xmipp3.tests.test_convert_xmipp
  scipion tests relion.tests.test_convert_relion

Spider MDA Workflow

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

EMX import

Plugins emxlib
Command scipion tests emxlib.tests.test_protocols_emx.TestEmxBase
Input The different data sets used in
Time ~10 sec

CTF Discrepancy

Plugins Xmipp, Cistem
Command scipion tests pwem.tests.workflows.test_workflow_xmipp_ctf_consensus.TestCtfConsensus
Input CTF obtained from micrograph of PcV (
Time ~10 sec

Medium tests

Xmipp Workflow

Plugins Xmipp
Command scipion tests pwem.tests.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 tests pwem.tests.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 tests pwem.tests.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, Cistem, EMAN, Relion
Command scipion tests pwem.tests.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

Random Conical Tilt reconstruction

Plugins Xmipp
Command scipion tests pwem.tests.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 tests pwem.tests.protocols.test_protocols_import_micrographs
Import particles scipion tests pwem.tests.protocols.test_protocols_import_particles
Import volumes scipion tests pwem.tests.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 tests xmipp3.tests.test_protocols_xmipp_mics.TestXmippPreprocessMicrographs
ctf estimation scipion tests xmipp3.tests.test_protocols_xmipp_mics.TestXmippCTFEstimation
Extract Particles scipion tests xmipp3.tests.test_protocols_xmipp_mics.TestXmippExtractParticles
Software Cistem
ctf estimation scipion tests cistem.tests.test_protocols_cistem.TestCtffind4
Input Dataset xmipp tutorial
CPU i7-2640M 2.8GHz, 8GB RAM

Preprocessing 2D

Software Xmipp
Create Mask 2D scipion tests xmipp3.tests.test_protocols_xmipp_2d.TestXmippCreateMask2D
Apply Mask 2D scipion tests xmipp3.tests.test_protocols_xmipp_2d.TestXmippApplyMask2D
Filter Particles scipion tests xmipp3.tests.test_protocols_xmipp_2d.TestXmippFilterParticles
Software Relion
Preprocess Particles scipion tests relion.tests.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 tests xmipp3.tests.test_protocols_xmipp_2d.TestXmippML2D
CL2D scipion tests xmipp3.tests.test_protocols_xmipp_2d.TestXmippCL2D
CL2D Align scipion tests xmipp3.tests.test_protocols_xmipp_2d.TestXmippProtCL2DAlign
Apply Alignment scipion tests xmipp3.tests.test_protocols_xmipp_2d.TestXmippApplyAlignment
Rotational Spectra scipion tests xmipp3.tests.test_protocols_xmipp_2d.TestXmippRotSpectra
Kerdensom scipion tests xmipp3.tests.test_protocols_xmipp_2d.TestXmippKerdensom
Software Relion
Classify 2D scipion tests relion.tests.test_protocols_relion.TestRelionClassify2D
Input Mda dataset
CPU i7-2640M 2.8GHz, 8GB RAM

Preprocessing 3D

Software Xmipp
Create Mask 3D scipion tests xmipp3.tests.test_protocols_xmipp_3d.TestXmippCreateMask3D
Apply Mask 3D scipion tests xmipp3.tests.test_protocols_xmipp_3d.TestXmippApplyMask3D
Filter Volumes scipion tests xmipp3.tests.test_protocols_xmipp_3d.TestXmippFilterVolumes
Preprocess Volumes scipion tests 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

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

Classify 3D

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