Running Tests

Pablo Conesa edited this page Sep 24, 2018 · 8 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

Command

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

Software

Scipion

Spider MDA Workflow

Time

 ~50 sec

Software

SPIDER

Command

scipion tests em.workflows.test_workflow_spiderMDA

Input

Fake dataset of Worm Hemogoblin with 76 images

EMX import

Time

 ~10 sec

Software

Scipion

Command

scipion tests tests.em.protocols.test_protocols_emx

Input

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

CTF Discrepancy

Time

 ~10 sec

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)

Medium tests

Xmipp Workflow

CPU

 i7-2640M 2.8GHz, 8GB RAM

Software

 Xmipp

Command

 `scipion tests em.workflows.test_workflow_xmipp`

Input

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

Time

 ~300 sec

Mixed Workflow 3D Reconstruction

CPU

 i7-2640M 2.8GHz, 8GB RAM

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

Mixed Workflow Initial Volume

CPU

 i7-2640M 2.8GHz, 8GB RAM

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

Large Tests

Warning
The following tests must be run on computers with enough processing power.

Mixed Workflow Relion 2D classification

CPU

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

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*

Mixed Workflow Frealign 3D classification

CPU

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

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

Random Conical Tilt reconstruction

CPU

 4 CPUs. Intel(R) Core(TM) i7-2640M CPU @ 2.80GHz, 8 GB RAM

Software

 Xmipp

Command

 `scipion tests em.workflows.test_workflow_xmipp_rct`

Input

 Dataset with 6 pairs of untilted-tilted micrographs.

Time

 ~15 min

Procotol Tests

Import different type of objects

CPU

 i7-2640M 2.8GHz, 8GB RAM

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

Processing micrographs

Time

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

Preprocessing 2D

CPU

 i7-2640M 2.8GHz, 8GB RAM

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

Particles alignment and classification

CPU

 i7-2640M 2.8GHz, 8GB RAM

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

Preprocessing 3D

CPU

 i7-2640M 2.8GHz, 8GB RAM

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

Initial volume

CPU

 4 CPUs on Asimov

Test

 *Significant*

Software

 Xmipp

Reconstruct significant

 `scipion test tests.em.workflows.test_workflow_initialvolume.TestSignificant`

Input

 Groel data.

Time

 ~27 min

Classify 3D

CPU

 i7-2640M 2.8GHz, 8GB RAM

Test

 *Classify 3D*

Software

 Relion

Relion Classify 3D 3D

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

Input

 MDA data.

Time

 ~200 sec
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