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Running Tests

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Jose Miguel de la Rosa Trevin edited this page Nov 16, 2015 · 9 revisions

From early stages in the development of Scipion, we have included a number of automatic tests.

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.

Table of Contents

Small tests
Medium tests
Large Tests
Procotol Tests

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

| Test | 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 |

| Test | 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 |

| Test | 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.

| Test | 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® E5540 2.53 GHz, 64 GB RAM |

| Test | 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® E5540 2.53 GHz, 64 GB RAM |

| Test | 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® Core™ i7-2640M CPU @ 2.80GHz, 8 GB RAM |

Procotol Tests

Import

| Test | 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 |

Micrographs

| Test | 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 | Brandeis | | ctf estimation | scipion tests tests.em.protocols.test_protocols_brandeis.TestBrandeisCtffind | | Input | Dataset xmipp tutorial | | Time | | | CPU | i7-2640M 2.8GHz, 8GB RAM |

Preprocessing 2D

| Test | 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 | | Screen Classes | scipion test tests.em.protocols.test_protocols_xmipp_2d.TestXmippScreenClasses | | Projection Outliers | scipion test tests.em.protocols.test_protocols_xmipp_2d.TestXmippProjectionOutliers | | 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 |

Align and Classify 2D

| Test | 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

| Test | 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 |