Import tab empty in the interface

I have just installed Scipion following the guide, but there is a problem in the interface, the 'Imports tab' on the left is empty. scipion_interface_import _tab_empty

I ran the tests 'scipion tests pwem.tests.protocols.test_protocols_import_micrographs' and got the output :

Creating project at: /home/eloy/ScipionUserData/projects/TestImportMicrographs/project.sqlite

python3 /home/eloy/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/apps/pw_sync_data.py --download xmipp_tutorial Selected datasets: xmipp_tutorial Local copy of dataset xmipp_tutorial detected. Checking for updates... Regenerating local MANIFEST... Calculating md5 for local workflow.json ... DONE! Calculating md5 for local BPV_scale_filtered_windowed_64.vol ... DONE! Calculating md5 for local volume_1_iter_002.mrc ... DONE! Calculating md5 for local volume_2_iter_002.mrc ... DONE! Calculating md5 for local BPV_scale_filtered_windowed_110.vol ... DONE! Calculating md5 for local bpv64_rotated.vol ... DONE! Calculating md5 for local ali.vol ... DONE! Calculating md5 for local bpv64.vol ... DONE! Calculating md5 for local BPV_1388.pos ... DONE! Calculating md5 for local templates.stk ... DONE! Calculating md5 for local BPV_1387.pos ... DONE! Calculating md5 for local BPV_1386.pos ... DONE! Calculating md5 for local config.xmd ... DONE! Calculating md5 for local model_rotpca_model.xmd ... DONE! Calculating md5 for local templates.stk ... DONE! Calculating md5 for local BPV_1386.pos ... DONE! Calculating md5 for local model_particle_avg.xmp ... DONE! Calculating md5 for local model_training.txt ... DONE! Calculating md5 for local model_pca_model.stk ... DONE! Calculating md5 for local config.xmd ... DONE! Calculating md5 for local model_svm.txt ... DONE! Calculating md5 for local model_rotpca_model.stk ... DONE! Calculating md5 for local scipion_BPV_1386.pos ... DONE! Calculating md5 for local BPV_1388.pos ... DONE! Calculating md5 for local scipion_BPV_1387.pos ... DONE! Calculating md5 for local templates.stk ... DONE! Calculating md5 for local scipion_BPV_1388.pos ... DONE! Calculating md5 for local BPV_1387.pos ... DONE! Calculating md5 for local BPV_1386.pos ... DONE! Calculating md5 for local model_particle_avg.xmp ... DONE! Calculating md5 for local model_training.txt ... DONE! Calculating md5 for local model_pca_model.stk ... DONE! Calculating md5 for local config.xmd ... DONE! Calculating md5 for local model_svm.txt ... DONE! Calculating md5 for local model_rotpca_model.stk ... DONE! Calculating md5 for local scipion_BPV_1386.pos ... DONE! Calculating md5 for local .eman2settings.bak ... DONE! Calculating md5 for local scipion_micrographs_coordinates.json ... DONE! Calculating md5 for local .eman2settings.dat ... DONE! Calculating md5 for local .eman2settings.dir ... DONE! Calculating md5 for local .eman2log.txt ... DONE! Calculating md5 for local BPV_1388_info.json ... DONE! Calculating md5 for local BPV_1387_info.json ... DONE! Calculating md5 for local BPV_1386_info.json ... DONE! Calculating md5 for local BPV_1388.json ... DONE! Calculating md5 for local swarm_panel.json ... DONE! Calculating md5 for local BPV_1387.json ... DONE! Calculating md5 for local BPV_1386.json ... DONE! Calculating md5 for local gauss_box_DB.json ... DONE! Calculating md5 for local base.json ... DONE! Calculating md5 for local coarse_flat_image_359x377x1 ... DONE! Calculating md5 for local coarse_sigma_image_368x377x1 ... DONE! Calculating md5 for local coarse_flat_image.bdb ... DONE! Calculating md5 for local coarse_flat_image_330x385x1 ... DONE! Calculating md5 for local coarse_sigma_image_542x555x1 ... DONE! Calculating md5 for local flcf_image.bdb ... DONE! Calculating md5 for local flcf_image_330x385x1 ... DONE! Calculating md5 for local coarse_sigma_image.bdb ... DONE! Calculating md5 for local coarse_sigma_image_359x377x1 ... DONE! Calculating md5 for local coarse_sigma_image_330x385x1 ... DONE! Calculating md5 for local 00image_counts.bdb ... DONE! Calculating md5 for local coarse_flat_image_542x555x1 ... DONE! Calculating md5 for local flcf_image_368x377x1 ... DONE! Calculating md5 for local flcf_image_359x377x1 ... DONE! Calculating md5 for local flcf_image_542x555x1 ... DONE! Calculating md5 for local coarse_flat_image_368x377x1 ... DONE! Calculating md5 for local extra-BPV_1387.box ... DONE! Calculating md5 for local extra-BPV_1388.box ... DONE! Calculating md5 for local extra-BPV_1386.box ... DONE! Calculating md5 for local BPV_1387.mrc ... DONE! Calculating md5 for local BPV_1386.mrc ... DONE! Calculating md5 for local BPV_1388.mrc ... DONE! Calculating md5 for local micrographs.sqlite ... DONE! Calculating md5 for local mask.vol ... DONE! Calculating md5 for local mask2d.xmp ... DONE! Calculating md5 for local .project.sqlite ... DONE! Calculating md5 for local .project.cfg ... DONE! Calculating md5 for local import_micrographs_run_001_summary.txt ... DONE! Calculating md5 for local screen_micrographs_run_001_summary.txt ... DONE! Calculating md5 for local import_micrographs_run_001.pyc ... DONE! Calculating md5 for local screen_micrographs_run_001.pyc ... DONE! Calculating md5 for local screen_micrographs_run_001.py ... DONE! Calculating md5 for local import_micrographs_run_001.py ... DONE! Calculating md5 for local import_micrographs_run_001.log ... DONE! Calculating md5 for local import_micrographs_run_001.out ... DONE! Calculating md5 for local import_micrographs_run_001.err ... DONE! Calculating md5 for local screen_micrographs_run_001.log ... DONE! Calculating md5 for local screen_micrographs_run_001.out ... DONE! Calculating md5 for local screen_micrographs_run_001.err ... DONE! Calculating md5 for local micrographs_noMics.xmd ... DONE! Calculating md5 for local microscope.xmd ... DONE! Calculating md5 for local micrographs_empty.xmd ... DONE! Calculating md5 for local acquisition_info.xmd ... DONE! Calculating md5 for local micrographs_gold.sqlite ... DONE! Calculating md5 for local micrographs.xmd ... DONE! Calculating md5 for local xmipp_ctf_ctfmodel_halfplane.xmp ... DONE! Calculating md5 for local xmipp_ctf.ctfparam ... DONE! Calculating md5 for local xmipp_ctf_enhanced_psd.xmp ... DONE! Calculating md5 for local xmipp_ctf.xmd ... DONE! Calculating md5 for local xmipp_ctf.psd ... DONE! Calculating md5 for local xmipp_ctf_ctfmodel_quadrant.xmp ... DONE! Calculating md5 for local envelope.xmd ... DONE! Calculating md5 for local xmipp_ctf_ctfmodel_halfplane.xmp ... DONE! Calculating md5 for local xmipp_ctf.ctfparam ... DONE! Calculating md5 for local xmipp_ctf_enhanced_psd.xmp ... DONE! Calculating md5 for local xmipp_ctf.xmd ... DONE! Calculating md5 for local xmipp_ctf.psd ... DONE! Calculating md5 for local xmipp_ctf_ctfmodel_quadrant.xmp ... DONE! Calculating md5 for local envelope.xmd ... DONE! Calculating md5 for local xmipp_ctf_ctfmodel_halfplane.xmp ... DONE! Calculating md5 for local xmipp_ctf.ctfparam ... DONE! Calculating md5 for local xmipp_ctf_enhanced_psd.xmp ... DONE! Calculating md5 for local xmipp_ctf.xmd ... DONE! Calculating md5 for local xmipp_ctf.psd ... DONE! Calculating md5 for local xmipp_ctf_ctfmodel_quadrant.xmp ... DONE! Calculating md5 for local envelope.xmd ... DONE! Calculating md5 for local micrographs_gold.sqlite ... DONE! Calculating md5 for local micrographs.xmd ... DONE! Calculating md5 for local microscope.xmd ... DONE! Calculating md5 for local acquisition_info.xmd ... DONE! Calculating md5 for local BPV_1388_ptcls.hed ... DONE! Calculating md5 for local sphere_12.xmd ... DONE! Calculating md5 for local BPV_1386_ptcls.hed ... DONE! Calculating md5 for local BPV_1388.stk ... DONE! Calculating md5 for local BPV_1386.stk ... DONE! Calculating md5 for local BPV_particles_aligned.sqlite ... DONE! Calculating md5 for local BPV_1388_ptcls.img ... DONE! Calculating md5 for local BPV_1387_ptcls.hdf ... DONE! Calculating md5 for local sphere_128.stk ... DONE! Calculating md5 for local BPV_1386_ptcls.img ... DONE! Calculating md5 for local BPV_1387.stk ... DONE! Calculating md5 for local BPV_particles.sqlite ... DONE! Calculating md5 for local BPV_1387_ptcls.hed ... DONE! Calculating md5 for local sphere_128.xmd ... DONE! Calculating md5 for local BPV_1386_ptcls.hdf ... DONE! Calculating md5 for local BPV_1387_ptcls.img ... DONE! Calculating md5 for local .bshow ... DONE! Calculating md5 for local BPV_1388_ptcls.hdf ... DONE! Calculating md5 for local images200k.xmd ... DONE! Calculating md5 for local xmipp_ctf.ctfparam ... DONE! Calculating md5 for local coordinates_gold.sqlite ... DONE! Calculating md5 for local aligned_particles.sqlite.backup ... DONE! Calculating md5 for local images10.xmd ... DONE! Calculating md5 for local xmipp_ml2d_images.xmd ... DONE! Calculating md5 for local particles_lau.sqlite ... DONE! Calculating md5 for local micrographs2_gold.sqlite ... DONE! Calculating md5 for local level_classes_lau.xmd ... DONE! Calculating md5 for local aligned_particles.sqlite ... DONE! Calculating md5 for local micrographs_gold.sqlite ... DONE! Calculating md5 for local level_classes_lau.stk ... DONE! Calculating md5 for local micrographs_gold.xmd ... DONE! Calculating md5 for local BPV_1387_ctf.psd ... DONE! Calculating md5 for local BPV_1388_ctf.ctfparam ... DONE! Calculating md5 for local BPV_1386_ctf.ctfparam ... DONE! Calculating md5 for local BPV_1388_ctf.psd ... DONE! Calculating md5 for local BPV_1386_ctf.psd ... DONE! Calculating md5 for local ctfs.sqlite ... DONE! Calculating md5 for local BPV_1387_ctf.ctfparam ... DONE! Verifying MD5s... ...done. Updated files: 0 python3 /home/eloy/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/apps/pw_sync_data.py --download emx Selected datasets: emx Dataset emx not in local machine. Downloading... Fetching files of dataset "emx"... ##################################################>>>> python3 /home/eloy/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/apps/pw_sync_data.py --download hemoglobin_mda Selected datasets: hemoglobin_mda Dataset hemoglobin_mda not in local machine. Downloading... Fetching files of dataset "hemoglobin_mda"... #################################################** Running command: 'python3 /home/eloy/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/apps/pw_protocol_run.py "/home/eloy/ScipionUserData/projects/TestImportMicrographs" "Runs/000002_ProtImportMicrographs/logs/run.db" 2'

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Logging configured. STDOUT --> Runs/000002_ProtImportMicrographs/logs/run.stdout , STDERR --> Runs/000002_ProtImportMicrographs/logs/run.stderr RUNNING PROTOCOL ----------------- Protocol starts Hostname: langlang PID: 151403 pyworkflow: 3.0.17 plugin: pwem plugin v: 3.0.13 currentDir: /home/eloy/ScipionUserData/projects/TestImportMicrographs workingDir: Runs/000002_ProtImportMicrographs runMode: Continue MPI: 1 threads: 1

error when importing from emxlib: No module named 'emxlib' File "", line 991, in _find_and_load Check the plugin manager (Configuration->Plugins in Scipion manager window) or use 'scipion installp --help --checkUpdates' in the command line to check for upgrades, it could be a versions compatibility issue.

Protocol has validation errors: Protocol validation failed. It usually happens because there are some input missing. Please check if the error message gives you any hint: Error: TypeError Description: 'NoneType' object is not callable Traceback: File "/home/eloy/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 1917, in validate childErrors = self._validate()

File "/home/eloy/anaconda3/envs/scipion3/lib/python3.8/site-packages/pwem/protocols/protocol_import/micrographs.py", line 383, in _validate ci = self.getImportClass()

File "/home/eloy/anaconda3/envs/scipion3/lib/python3.8/site-packages/pwem/protocols/protocol_import/micrographs.py", line 418, in getImportClass return EmxImport(self, self.importFilePath)

------------------- PROTOCOL FAILED (DONE 0/0)

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[ FAILED ] TestImportMicrographs.test_fromEmx

Traceback (most recent call last): File "/home/eloy/anaconda3/envs/scipion3/lib/python3.8/unittest/case.py", line 60, in testPartExecutor yield File "/home/eloy/anaconda3/envs/scipion3/lib/python3.8/unittest/case.py", line 676, in run self._callTestMethod(testMethod) File "/home/eloy/anaconda3/envs/scipion3/lib/python3.8/unittest/case.py", line 633, in _callTestMethod method() File "/home/eloy/anaconda3/envs/scipion3/lib/python3.8/site-packages/pwem/tests/protocols/test_protocols_import_micrographs.py", line 138, in test_fromEmx self.launchProtocol(protEmxImport) File "/home/eloy/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/tests/tests.py", line 113, in launchProtocol raise Exception("Protocol %s execution failed. See last log lines above for more details." % prot.getRunName()) Exception: Protocol from emx execution failed. See last log lines above for more details. Importing from sqlite: /home/eloy/scipion3/data/tests/xmipp_tutorial/micrographs/micrographs.sqlite _samplingRate -> 1.237 _acquisition._voltage -> 300.0 _acquisition._magnification -> 50000.0 Running command: 'python3 /home/eloy/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/apps/pw_protocol_run.py "/home/eloy/ScipionUserData/projects/TestImportMicrographs" "Runs/000056_ProtImportMicrographs/logs/run.db" 56' [ RUN OK ] TestImportMicrographs.test_fromScipion (0.944 secs) Running command: 'python3 /home/eloy/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/apps/pw_protocol_run.py "/home/eloy/ScipionUserData/projects/TestImportMicrographs" "Runs/000129_ProtImportMicrographs/logs/run.db" 129' Running command: 'python3 /home/eloy/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/apps/pw_protocol_run.py "/home/eloy/ScipionUserData/projects/TestImportMicrographs" "Runs/000202_ProtImportMicrographs/logs/run.db" 202' [ RUN OK ] TestImportMicrographs.test_fromXmipp (1.796 secs) Running command: 'python3 /home/eloy/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/apps/pw_protocol_run.py "/home/eloy/ScipionUserData/projects/TestImportMicrographs" "Runs/000281_ProtImportMicrographs/logs/run.db" 281' Running command: 'python3 /home/eloy/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/apps/pw_protocol_run.py "/home/eloy/ScipionUserData/projects/TestImportMicrographs" "Runs/000354_ProtImportMicrographs/logs/run.db" 354' Running command: 'python3 /home/eloy/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/apps/pw_protocol_run.py "/home/eloy/ScipionUserData/projects/TestImportMicrographs" "Runs/000427_ProtImportMicrographs/logs/run.db" 427' Running command: 'python3 /home/eloy/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/apps/pw_protocol_run.py "/home/eloy/ScipionUserData/projects/TestImportMicrographs" "Runs/000500_ProtImportMicrographs/logs/run.db" 500' Running command: 'python3 /home/eloy/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/apps/pw_protocol_run.py "/home/eloy/ScipionUserData/projects/TestImportMicrographs" "Runs/000573_ProtImportMicrographs/logs/run.db" 573'

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Logging configured. STDOUT --> Runs/000573_ProtImportMicrographs/logs/run.stdout , STDERR --> Runs/000573_ProtImportMicrographs/logs/run.stderr RUNNING PROTOCOL ----------------- Protocol starts Hostname: langlang PID: 151539 pyworkflow: 3.0.17 plugin: pwem plugin v: 3.0.13 currentDir: /home/eloy/ScipionUserData/projects/TestImportMicrographs workingDir: Runs/000573_ProtImportMicrographs runMode: Continue MPI: 1 threads: 1

error when importing from emxlib: No module named 'emxlib' File "", line 991, in _find_and_load Check the plugin manager (Configuration->Plugins in Scipion manager window) or use 'scipion installp --help --checkUpdates' in the command line to check for upgrades, it could be a versions compatibility issue.

File "/home/eloy/anaconda3/envs/scipion3/lib/python3.8/site-packages/pwem/protocols/protocol_import/micrographs.py", line 383, in _validate ci = self.getImportClass()

File "/home/eloy/anaconda3/envs/scipion3/lib/python3.8/site-packages/pwem/protocols/protocol_import/micrographs.py", line 418, in getImportClass return EmxImport(self, self.importFilePath)

------------------- PROTOCOL FAILED (DONE 0/0)

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[ FAILED ] TestImportMicrographs.test_pattern

[==========] run 4 tests (94.257 secs) [ FAILED ] 2 tests [ PASSED ] 2 tests

Hi! COuld you please send the output of:

scipion3 printenv

Thanks for quick reply ! scipion print env returns :

export CHIMERA_HEADLESS_HOME="software/em/chimera_headless" export CHIMERA_HOME="software/em/chimera-1.13.1" export CONDA_ACTIVATION_CMD="eval "$(/home/eloy/anaconda3/bin/conda shell.bash hook)"" export CUDA="True" export CUDA_BIN="/usr/lib/cuda/bin" export CUDA_LIB="/usr/lib/cuda/lib64" export EM_ROOT="software/em" export MAXIT_HOME="/home/eloy/scipion3/software/em/maxit-10.1" export MPI_BINDIR="/home/eloy/opt/openmpi/bin/" export MPI_INCLUDE="/home/eloy/opt/openmpi/include/" export MPI_LIBDIR="/home/eloy/opt/openmpi/lib/" export OPENCV="False" export SCIPION_CONFIG="/home/eloy/scipion3/config/scipion.conf" export SCIPION_CWD="/home/eloy/Documents/stage_reconstruction_spfluo/tests_scripts" export SCIPION_DOMAIN="pwem" export SCIPION_FONT_NAME="Helvetica" export SCIPION_GUI_REFRESH_IN_THREAD="False" export SCIPION_HOME="/home/eloy/scipion3" export SCIPION_HOSTS="/home/eloy/scipion3/config/hosts.conf" export SCIPION_LOCAL_CONFIG="/home/eloy/.config/scipion/scipion.conf" export SCIPION_LOG="/home/eloy/ScipionUserData/logs/scipion.log" export SCIPION_LOGO="scipion_logo.gif" export SCIPION_LOGS="/home/eloy/ScipionUserData/logs" export SCIPION_LOG_LEVEL="INFO" export SCIPION_NOTES_ARGS="" export SCIPION_NOTES_FILE="notes.txt" export SCIPION_NOTES_PROGRAM="" export SCIPION_NOTIFY="True" export SCIPION_PLUGIN_REPO_URL="http://scipion.i2pc.es/getplugins/" export SCIPION_PROTOCOLS="/home/eloy/scipion3/config/protocols.conf" export SCIPION_SOFTWARE="/home/eloy/scipion3/software" export SCIPION_SUPPORT_EMAIL="scipion@cnb.csic.es" export SCIPION_TESTS="/home/eloy/scipion3/data/tests" export SCIPION_TESTS_CMD="scipion3 tests" export SCIPION_TESTS_OUTPUT="/home/eloy/ScipionUserData/Tests" export SCIPION_TMP="/home/eloy/ScipionUserData/tmp" export SCIPION_URL="http://scipion.cnb.csic.es/downloads/scipion" export SCIPION_URL_SOFTWARE="http://scipion.cnb.csic.es/downloads/scipion/software" export SCIPION_URL_TESTDATA="http://scipion.cnb.csic.es/downloads/scipion/data/tests" export SCIPION_USER_DATA="/home/eloy/ScipionUserData" export SCIPION_VERSION="v3.0.9 - Eugenius" export VIEWERS="{"Volume":["pyworkflow.em.viewers.viewers_data.DataViewer"]}" export VMD_HOME="software/em/vmd" export WIZARD_MASK_COLOR="[0.125, 0.909, 0.972]" export XMIPP2_HOME="/home/eloy/scipion3/software/em/Xmipp-2.4-src" export XMIPP_HOME="/home/eloy/scipion3/software/em/xmipp"

(scipion3 command doesn't work)

umm, thanks. Have you got anything at: /home/eloy/scipion3/config/protocols.conf? (probably not)

Try these other commands:

scipion protocols

and

scipion installp --help

And send output, please.

I have something at '/home/eloy/scipion3/config/protocols.conf' Content of file 'protocol.conf ' [PROTOCOLS] Protocols SPA = [ {"tag": "section", "text": "Imports", "icon": "bookmark.gif", "children": [ {"tag": "section", "text": "more", "openItem": "False", "children": [ ]} ]}, {"tag": "section", "text": "Movies", "openItem": "False", "children": []}, {"tag": "section", "text": "Micrographs", "children": [ {"tag": "protocol_group", "text": "CTF estimation", "openItem": "False", "children": [ {"tag": "section", "text": "more", "openItem": "False", "children": []} ]} ]}, {"tag": "section", "text": "Particles", "children": [ {"tag": "protocol_group", "text": "Picking", "openItem": "False", "children": []}, {"tag": "protocol_group", "text": "Extract", "openItem": "False", "children": [ {"tag": "section", "text": "more", "openItem": "False", "children": []} ]}, {"tag": "protocol_group", "text": "Preprocess", "openItem": "False", "children": []}, {"tag": "protocol_group", "text": "Filter", "openItem": "False", "children": []}, {"tag": "protocol_group", "text": "Mask", "openItem": "False", "children": []} ]}, {"tag": "section", "text": "2D", "children": [ {"tag": "protocol_group", "text": "Align", "openItem": "False", "children": [ {"tag": "section", "text": "more", "openItem": "False", "children": []} ]}, {"tag": "protocol_group", "text": "Classify", "openItem": "False", "children": [ {"tag": "section", "text": "more", "openItem": "False", "children": []} ]} ]}, {"tag": "section", "text": "3D", "children": [ {"tag": "protocol_group", "text": "Initial volume", "openItem": "False", "children": [ {"tag": "section", "text": "more", "openItem": "False", "children": []} ]}, {"tag": "protocol_group", "text": "Preprocess", "openItem": "False", "children": [ {"tag": "section", "text": "more", "openItem": "False", "children": []} ]}, {"tag": "protocol_group", "text": "Classify", "openItem": "False", "children": []}, {"tag": "protocol_group", "text": "Refine", "openItem": "False", "children": [ {"tag": "section", "text": "more", "openItem": "False", "children": []} ]}, {"tag": "protocol_group", "text": "Postprocess", "openItem": "False", "children": []}, {"tag": "protocol_group", "text": "Analysis", "openItem": "False", "children": [ {"tag": "section", "text": "Heterogeneity", "openItem": "False", "children": []}, {"tag": "section", "text": "Validation", "openItem": "False", "children": []}, {"tag": "section", "text": "Resolution", "openItem": "False", "children": []}, {"tag": "section", "text": "more", "openItem": "False", "children": []} ]}, {"tag": "protocol_group", "text": "Reconstruct", "openItem": "False", "children": []} ]}, {"tag": "section", "text": "Tools", "openItem": "False", "children": [ {"tag": "protocol_group", "text": "Sets", "openItem": "False", "children": [ ]} ]}, {"tag": "section", "text": "Exports", "openItem": "False", "children": [] }] Model building = [ {"tag": "section", "text": "Imports", "icon": "bookmark.gif", "children": []}, {"tag": "section", "text": "Preprocess map", "icon": "bookmark.gif", "children": []}, {"tag": "section", "text": "Initial model", "icon": "bookmark.gif", "children": []}, {"tag": "section", "text": "Rigid fitting", "icon": "bookmark.gif", "children": []}, {"tag": "section", "text": "Flexible fitting", "icon": "bookmark.gif", "children": []}, {"tag": "section", "text": "Validation", "icon": "bookmark.gif", "children": []}, {"tag": "section", "text": "Tools-Calculators", "icon": "bookmark.gif", "children": []}, {"tag": "section", "text": "Others", "icon": "bookmark.gif", "children": []}, {"tag": "section", "text": "Exports", "icon": "bookmark.gif", "children": []}

Output of scipion protocols :

PACKAGE PROTOCOL xmipp3 ProtMovieAlignment xmipp3 XmippMetaProtCreateOutput xmipp3 XmippMetaProtCreateSubset xmipp3 XmippMetaProtDiscrete xmipp3 XmippMetaProtGoldenHighRes xmipp3 XmippParticlePickingAutomatic xmipp3 XmippProtAddNoiseParticles xmipp3 XmippProtAddNoiseVolumes xmipp3 XmippProtAlignVolume xmipp3 XmippProtAlignVolumeForWeb xmipp3 XmippProtAlignVolumeParticles xmipp3 XmippProtAnalyzeLocalCTF xmipp3 XmippProtAngBreakSymmetry xmipp3 XmippProtAngularAlignmentZernike3D xmipp3 XmippProtApplyAlignment xmipp3 XmippProtApplyTransformationMatrix xmipp3 XmippProtAssignmentTiltPair xmipp3 XmippProtCL2D xmipp3 XmippProtCL2DAlign xmipp3 XmippProtCTFConsensus xmipp3 XmippProtCTFCorrectWiener2D xmipp3 XmippProtCTFDefocusGroup xmipp3 XmippProtCTFMicrographs xmipp3 XmippProtCenterParticles xmipp3 XmippProtCompareAngles xmipp3 XmippProtCompareReprojections xmipp3 XmippProtConsensusClasses3D xmipp3 XmippProtConsensusLocalCTF xmipp3 XmippProtConsensusPicking xmipp3 XmippProtConvertPdb xmipp3 XmippProtCreateGallery xmipp3 XmippProtCreateMask2D xmipp3 XmippProtCreateMask3D xmipp3 XmippProtCropResizeParticles xmipp3 XmippProtCropResizeVolumes xmipp3 XmippProtDeepDenoising xmipp3 XmippProtDeepMicrographScreen xmipp3 XmippProtDeepRes xmipp3 XmippProtDeepVolPostProc xmipp3 XmippProtDeformPDBZernike3D xmipp3 XmippProtDenoiseParticles xmipp3 XmippProtEliminateEmptyClasses xmipp3 XmippProtEliminateEmptyParticles xmipp3 XmippProtEnrich xmipp3 XmippProtExtractMovieParticles xmipp3 XmippProtExtractParticles xmipp3 XmippProtExtractParticlesPairs xmipp3 XmippProtExtractUnit xmipp3 XmippProtFSO xmipp3 XmippProtFilterParticles xmipp3 XmippProtFilterVolumes xmipp3 XmippProtGenerateReprojections xmipp3 XmippProtGpuCrrCL2D xmipp3 XmippProtHelicalParameters xmipp3 XmippProtImageOperateParticles xmipp3 XmippProtImageOperateVolumes xmipp3 XmippProtKerdensom xmipp3 XmippProtKmeansClassif2D xmipp3 XmippProtLocSharp xmipp3 XmippProtLocalCTF xmipp3 XmippProtML2D xmipp3 XmippProtMaskParticles xmipp3 XmippProtMaskVolumes xmipp3 XmippProtMonoDir xmipp3 XmippProtMonoRes xmipp3 XmippProtMovieAverage xmipp3 XmippProtMovieCorr xmipp3 XmippProtMovieGain xmipp3 XmippProtMovieMaxShift xmipp3 XmippProtMovieResize xmipp3 XmippProtMultiRefAlignability xmipp3 XmippProtMultipleFSCs xmipp3 XmippProtNormalizeStrain xmipp3 XmippProtOFAlignment xmipp3 XmippProtParticleBoxsize xmipp3 XmippProtParticlePicking xmipp3 XmippProtParticlePickingPairs xmipp3 XmippProtPickNoise xmipp3 XmippProtPickingRemoveDuplicates xmipp3 XmippProtPreprocessMicrographs xmipp3 XmippProtPreprocessParticles xmipp3 XmippProtPreprocessVolumes xmipp3 XmippProtProjMatch xmipp3 XmippProtRCT xmipp3 XmippProtRansac xmipp3 XmippProtReconstructFourier xmipp3 XmippProtReconstructHeterogeneous xmipp3 XmippProtReconstructHighRes xmipp3 XmippProtReconstructSignificant xmipp3 XmippProtReconstructSwarm xmipp3 XmippProtResolution3D xmipp3 XmippProtRotSpectra xmipp3 XmippProtRotationalSymmetry xmipp3 XmippProtScreenDeepConsensus xmipp3 XmippProtScreenDeepLearning xmipp3 XmippProtScreenParticles xmipp3 XmippProtShiftParticles xmipp3 XmippProtSimulateCTF xmipp3 XmippProtSolidAngles xmipp3 XmippProtSplitFrames xmipp3 XmippProtSplitVolumeHierarchical xmipp3 XmippProtSplitvolume xmipp3 XmippProtStrGpuCrrCL2D xmipp3 XmippProtStrGpuCrrSimple xmipp3 XmippProtStructureMap xmipp3 XmippProtStructureMapZernike3D xmipp3 XmippProtTriggerData xmipp3 XmippProtValFit xmipp3 XmippProtValidateNonTilt xmipp3 XmippProtValidateOverfitting xmipp3 XmippProtVolAdjust xmipp3 XmippProtVolConsensus xmipp3 XmippProtVolSubtraction xmipp3 XmippProtVolumeDeformZernike3D xmipp3 XmippProtVolumeStrain xmipp3 XmippProtbfactorResolution pwem ProtAlignmentAssign pwem ProtAlignmentInvertHand pwem ProtAverageFrames pwem ProtCTFAssign pwem ProtClassesConsensus pwem ProtCreateStreamData pwem ProtExportDataBases pwem ProtExtractCoords pwem ProtImportAverages pwem ProtImportCTF pwem ProtImportCoordinates pwem ProtImportCoordinatesPairs pwem ProtImportMask pwem ProtImportMicrographs pwem ProtImportMicrographsTiltPairs pwem ProtImportMovies pwem ProtImportParticles pwem ProtImportPdb pwem ProtImportSequence pwem ProtImportVolumes pwem ProtMovieAssignGain pwem ProtMovieEraser pwem ProtOrigSampling pwem ProtPDFReport pwem ProtPickingDifference pwem ProtSetEditor pwem ProtSetFilter pwem ProtSplitSet pwem ProtStress pwem ProtSubSet pwem ProtSubSetByCoord pwem ProtSubSetByMic pwem ProtTestParallel pwem ProtUnionSet tomo ProtAlignmentAssignSubtomo tomo ProtAssignTomo2Subtomo tomo ProtAssignTransformat tomo ProtConsensusClassesSubtomo tomo ProtImportCoordinates3D tomo ProtImportSubTomograms tomo ProtImportTomograms tomo ProtImportTs tomo ProtImportTsMovies tomo ProtSplitEvenOddTomoSet tomo ProtTomoExtractCoords tomo ProtTsAverage pyworkflowtests ProtOutputTest xmipp2 Xmipp2ProtMLTomo LABEL
xmipp3 - optical alignment
xmipp3 - metaprotocol heterogeneity output xmipp3 - metaprotocol heterogeneity subset HeterogeneityScheduler xmipp3 - metaprotocol heterogeneity xmipp3 - metaprotocol golden highres xmipp3 - auto-picking (step 2)
xmipp3 - add noise particles
xmipp3 - add noise volume/s
xmipp3 - align volume
xmipp3 - align volume web
xmipp3 - align volume and particles xmipp3 - analyze local defocus
xmipp3 - break symmetry
xmipp3 - angular align - Zernike3D xmipp3 - apply alignment 2d
xmipp3 - apply transformation matrix xmipp3 - assign tiltpairs
xmipp3 - cl2d
xmipp3 - align with cl2d
xmipp3 - ctf consensus
xmipp3 - ctf_correct_wiener2d
xmipp3 - defocus group
xmipp3 - ctf estimation
xmipp3 - center particles
xmipp3 - compare angles
xmipp3 - compare reprojections
xmipp3 - consensus classes 3D
xmipp3 - consensus local defocus
xmipp3 - picking consensus
xmipp3 - convert a PDB
xmipp3 - create gallery
xmipp3 - create 2d mask
xmipp3 - create 3d mask
xmipp3 - crop/resize particles
xmipp3 - crop/resize volumes
xmipp3 - deep denoising
xmipp3 - deep micrograph cleaner
xmipp3 - local deepRes
xmipp3 - deepEMhancer
xmipp3 - deform pdb - Zernike3D
xmipp3 - denoise particles
xmipp3 - eliminate empty classes
xmipp3 - eliminate empty particles xmipp3 - enrich
xmipp3 - extract movie particles
xmipp3 - extract particles
xmipp3 - extract particle pairs
xmipp3 - extract asymmetric unit
xmipp3 - resolution fso
xmipp3 - filter particles
xmipp3 - filter volumes
xmipp3 - generate reprojections
xmipp3 - gl2d
xmipp3 - helical symmetry
xmipp3 - operate particles
xmipp3 - operate volumes
xmipp3 - kerdensom
xmipp3 - 2D kmeans clustering
xmipp3 - localdeblur sharpening
xmipp3 - estimate local defocus
xmipp3 - ml2d
xmipp3 - apply 2d mask
xmipp3 - apply 3d mask
xmipp3 - directional resolution MonoDir xmipp3 - local MonoRes
xmipp3 - movie average
xmipp3 - FlexAlign
xmipp3 - movie gain
xmipp3 - movie maxshift
xmipp3 - movie resize
xmipp3 - multireference alignability xmipp3 - multiple fscs
xmipp3 - normalize strain
xmipp3 - optical alignment
xmipp3 - particle boxsize
xmipp3 - manual-picking (step 1)
xmipp3 - tilt pairs particle picking xmipp3 - pick noise
xmipp3 - remove duplicates
xmipp3 - preprocess micrographs
xmipp3 - preprocess particles
xmipp3 - preprocess volumes
xmipp3 - projection matching
xmipp3 - random conical tilt
xmipp3 - ransac
xmipp3 - reconstruct fourier
xmipp3 - significant heterogeneity xmipp3 - highres
xmipp3 - reconstruct significant
xmipp3 - swarm consensus
xmipp3 - resolution 3D
xmipp3 - rotational spectra
xmipp3 - rotational symmetry
xmipp3 - deep consensus picking
xmipp3 - screen deep learning
xmipp3 - screen particles
xmipp3 - shift particles
xmipp3 - simulate ctf
xmipp3 - solid angles
xmipp3 - split frames
xmipp3 - split volume hierarchical xmipp3 - split volume
xmipp3 - gl2d streaming
xmipp3 - gl2d static
xmipp3 - struct map
xmipp3 - struct map - Zernike3D
xmipp3 - trigger data
xmipp3 - validate fsc-q
xmipp3 - validate_nontilt
xmipp3 - validate overfitting
xmipp3 - volumes adjust
xmipp3 - volume consensus
xmipp3 - volumes subtraction
xmipp3 - volume deform - Zernike3D xmipp3 - calculate strain
xmipp3 - local resolution/local bfactor pwem - assign alignment
pwem - invert hand
pwem - average frames
pwem - assign ctf
pwem - classes consensus
pwem - create stream data
pwem - export emdb/pdb
pwem - extract coordinates
pwem - import averages
pwem - import ctf
pwem - import coordinates
pwem - import coordinate pairs
pwem - import mask
pwem - import micrographs
pwem - import tilted micrographs
pwem - import movies
pwem - import particles
pwem - import atomic structure
pwem - import sequence
pwem - import volumes
pwem - assign gain to movies
pwem - movie eraser
pwem - assign Orig & Sampling
pwem - pdf report
pwem - picking difference
pwem - edit set
pwem - filter set
pwem - split sets
pwem - stress
pwem - subset
pwem - particles subset by coordinates pwem - particles subset by micrograph pwem - parallel test
pwem - join sets
tomo - assign alignment
tomo - assign tomos to subtomos
ionMatrixTiltSeries tomo - Tilt-series assign alignment tomo - consensus classes subtomo
tomo - import set of coordinates 3D tomo - import subtomograms
tomo - import tomograms
tomo - import tilt-series
tomo - import tilt-series movies
tomo - split even/odd tomos/subtomos tomo - extract 3D coordinates
tomo - average tilt-series movies
pyworkflowtests - test output
xmipp2 - mltomo

Output of scipion installp --help usage: scipion installp [-h] [--noBin] [-p pluginName [pipVersion ...]]

optional arguments: -h, --help show help --noBin Optional flag to install plugins only as a python module, without installing the plugin binaries. This will affect all plugins specified in the command. --checkUpdates Optional flag to check which plugins have new releases. -p pluginName [pluginVersion ...], --plugin pluginName [pluginVersion ...]

pluginName: the name of the plugin to install from the list of available plugins shown below.
pluginVersion: (optional) pip version to install. If not specified, will install the latest compatible with current Scipion. --devel Optional flag to indicate that we will pass install sources instead of pip names. Sources might be local paths or git urls. With local paths, will do pip install -e (editable mode). It is expected to find the plugin name in the basename of the path or in the repo name. (i.e. it needs to match the one specified in setup.py). E.g: scipion installp -p path/to/pluginName --devel scipion installp -p https://github.com/someOrg/pluginName.git --devel -j j Number of CPUs to use for compilation

Example: scipion installp -p scipion-em-motioncorr 1.0.6 -p scipion-em-relion -p scipion-em-eman2

Available plugins: ([ ] not installed, [X] seems already installed)

scipion-em-appion [ ] scipion-em-aretomo [ ] scipion-em-atomstructutils [ ] scipion-em-atsas [ ] scipion-em-bamfordlab [ ] scipion-em-bsoft [ ] scipion-em-ccp4 [ ] scipion-em-chimera [ ] scipion-em-cistem [ ] scipion-em-continuousflex [ ] scipion-em-cryoassess [ ] scipion-em-cryodrgn [ ] scipion-em-cryoef [ ] scipion-em-cryosparc2 [ ] scipion-em-eman2 [ ] scipion-em-empiar [ ] scipion-em-emxlib [ ] scipion-em-facilities [ ] scipion-em-fsc3d [ ] scipion-em-gautomatch [ ] scipion-em-gctf [ ] scipion-em-imagic [ ] scipion-em-localrec [ ] scipion-em-locscale [ ] scipion-em-motioncorr [ ] scipion-em-phenix [ ] scipion-em-relion [ ] scipion-em-resmap [ ] scipion-em-sidesplitter [ ] scipion-em-sphire [ ] scipion-em-spider [ ] scipion-em-topaz [ ] scipion-em-xmipp 21.9.0 [X] scipion-em-xmipp2 3.0.1 [X]

Try to:

1.- rename that protocols.conf 2.- send output of scipion run pip list

Output of scipion 'run pip list' bibtexparser 1.2.0 biopython 1.76 certifi 2021.10.8 chardet 4.0.0 configparser 5.0.2 cycler 0.11.0 future 0.18.2 idna 2.10 joblib 1.1.0 kiwisolver 1.3.2 littleutils 0.2.2 matplotlib 3.2.2 mpi4py 3.0.3 mrcfile 1.3.0 numpy 1.18.4 outdated 0.2.0 peppercorn 0.6 Pillow 8.2.0 pip 21.2.4 plotter 1.3.19 psutil 5.8.0 pyparsing 3.0.6 python-dateutil 2.8.2 PyWavelets 1.2.0 requests 2.25.1 scikit-learn 0.22.1 scipion-app 3.0.9 scipion-em 3.0.13 scipion-em-tomo 3.0.11 scipion-em-xmipp 21.9.0 scipion-em-xmipp2 3.0.1 scipion-pyworkflow 3.0.17 scipy 1.7.3 SCons 4.3.0 setuptools 58.0.4 six 1.16.0 tifffile 2021.11.2 tkcolorpicker 2.1.3 urllib3 1.26.7 wheel 0.37.0

The name of the file was already 'protocols.conf', I made a typo in my last message

Thanks all looks good!

Regarding protocols.conf y want you yo rename it, or move it away. It is optional.

El dom., 19 dic. 2021 10:03, thibaut1998e @.***> escribió:

Output of scipion 'run pip list' bibtexparser 1.2.0 biopython 1.76 certifi 2021.10.8 chardet 4.0.0 configparser 5.0.2 cycler 0.11.0 future 0.18.2 idna 2.10 joblib 1.1.0 kiwisolver 1.3.2 littleutils 0.2.2 matplotlib 3.2.2 mpi4py 3.0.3 mrcfile 1.3.0 numpy 1.18.4 outdated 0.2.0 peppercorn 0.6 Pillow 8.2.0 pip 21.2.4 plotter 1.3.19 psutil 5.8.0 pyparsing 3.0.6 python-dateutil 2.8.2 PyWavelets 1.2.0 requests 2.25.1 scikit-learn 0.22.1 scipion-app 3.0.9 scipion-em 3.0.13 scipion-em-tomo 3.0.11 scipion-em-xmipp 21.9.0 scipion-em-xmipp2 3.0.1 scipion-pyworkflow 3.0.17 scipy 1.7.3 SCons 4.3.0 setuptools 58.0.4 six 1.16.0 tifffile 2021.11.2 tkcolorpicker 2.1.3 urllib3 1.26.7 wheel 0.37.0

The name of the file was already 'protocols.conf', I made a typo in my last message

— Reply to this email directly, view it on GitHub https://github.com/scipion-em/scipion-pyworkflow/issues/319#issuecomment-997353494, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAF7ZYIZ2DUZRUM27GNSUMLURWNURANCNFSM5KFVMSSQ . You are receiving this because you commented.Message ID: @.***>

Ok, thanks. Why is the import tab empty if eveything is good ? I wont be able to use Scipion if I can't import micrographs

Hi,

I don't know what is happening with the menu and I hope you can get this fixed with the help of Pablo or other people from the team.

Anyway, you can still use any protocol without the menu. Just use the search dialog (open it with Ctrl + F) and then type some words of the protocol name...for example: import....and then you should have a list of options.

At least a workaround while the menu issue is solved. I tend to use more the search dialog than the menu.

Hope this helps, Best, Jose Miguel

On Mon, Dec 20, 2021 at 10:03 AM thibaut1998e @.***> wrote:

Ok, thanks. Why is the import tab empty if eveything is good ? I wont be able to use Scipion if I can't import micrographs

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I think I got it!

Have you removed the protocols.conf?

If I place your content of protocols.conf locally I got those same empty sections.

Forget it! But try to remove your protocols.conf and see.

Hi, I am back from holidays. Removing protocols.conf didn't work, but I can use the imports protocols using the search menu as suggested by Jose Miguel

Hi there, I met the same issue with empty import tab. And I run some basic tests. All other is good except with the command "scipion3 tests pwem.tests.data.test_data" in which 1 tests failed and 31 tests passed. Here is the running log below. Does anyone know how to fix that?

bwang@pagoda$ scipion3 tests pyworkflowtests.tests.test_object.TestObject Scipion v3.0.10 - Eugenius Running tests.... [ RUN OK ] TestObject.testWithPointer (0.000 secs) [ RUN OK ] TestObject.test_Dict (0.000 secs) [ RUN OK ] TestObject.test_Object (0.000 secs) [ RUN OK ] TestObject.test_ObjectsDict (0.000 secs) ERROR: Name collision (SetOfCoordinates) detected while discovering pwem.objects. It conflicts with pyworkflowtests [ RUN OK ] TestObject.test_Pointer (0.172 secs) Writing to sqlite: /data1/bwang/cryoem/ScipionUserData/Tests/TestObject/test_images2.sqlite Checking set iteration with limit:2 and skipRows: None Checking set iteration with limit:3 and skipRows: 2 Connection open for /data1/bwang/cryoem/ScipionUserData/Tests/TestObject/test_images2.sqlite Connection closed for /data1/bwang/cryoem/ScipionUserData/Tests/TestObject/test_images2.sqlite Connection closed for /data1/bwang/cryoem/ScipionUserData/Tests/TestObject/test_images2.sqlite [ RUN OK ] TestObject.test_Sets (1.236 secs) [ RUN OK ] TestObject.test_String (0.003 secs) [ RUN OK ] TestObject.test_copyAttributes (0.000 secs) [ RUN OK ] TestObject.test_equalAttributes (0.000 secs) [ RUN OK ] TestObject.test_formatString (0.000 secs) ('object.id', 1), ('object.label', 'test micrograph'), ('object.comment', 'Testing store and retrieve from dict.'), ('_index', 0), ('_filename', 'my_movie.mrc'), ('_samplingRate', 1.6), ('_acquisition', None), ('_acquisition._magnification', 50000.0), ('_acquisition._voltage', 200.0), ('_acquisition._sphericalAberration', 2.7), ('_acquisition._amplitudeContrast', None), ('_acquisition._doseInitial', 0.0), ('_acquisition._dosePerFrame', 1.0), ('_micName', None), [ RUN OK ] TestObject.test_getObjDict (0.000 secs)

[==========] run 11 tests (1.412 secs) [ PASSED ] 11 tests bwang@pagoda$ scipion3 tests pyworkflowtests.tests.test_mappers Scipion v3.0.10 - Eugenius Running tests.... Row(id=1, x=12, y=11.0, name='jose') Row(id=1, x=12, y=11.0, name='pepe') [ RUN OK ] TestDataSet.test_Table (0.013 secs)

test empty set: dbName = '/data1/bwang/cryoem/ScipionUserData/Tests/TestSqliteFlatMapper/empty.sqlite' [ RUN OK ] TestSqliteFlatMapper.test_emtpySet (0.001 secs) test_insertObjects: dbName = '/data1/bwang/cryoem/ScipionUserData/Tests/TestSqliteFlatMapper/images.sqlite' [ RUN OK ] TestSqliteFlatMapper.test_insertObjects (1.260 secs) Checking that Relations table is updated and version to 1 {'id': 1, 'parent_id': 1, 'name': 'testRelation', 'classname': None, 'value': None, 'label': None, 'comment': None, 'object_parent_id': 2, 'object_child_id': 3, 'creation': '2022-01-12 18:40:31', 'object_parent_extended': None, 'object_child_extended': None} {'id': 2, 'parent_id': 1, 'name': 'testRelation', 'classname': None, 'value': None, 'label': None, 'comment': None, 'object_parent_id': 2, 'object_child_id': 4, 'creation': '2022-01-12 18:40:31', 'object_parent_extended': None, 'object_child_extended': None} {'id': 3, 'parent_id': 1, 'name': 'testRelation', 'classname': None, 'value': None, 'label': None, 'comment': None, 'object_parent_id': 3, 'object_child_id': 5, 'creation': '2022-01-12 18:40:31', 'object_parent_extended': None, 'object_child_extended': None} {'id': 4, 'parent_id': 1, 'name': 'testRelation', 'classname': None, 'value': None, 'label': None, 'comment': None, 'object_parent_id': 4, 'object_child_id': 5, 'creation': '2022-01-12 18:40:31', 'object_parent_extended': None, 'object_child_extended': None} [ RUN OK ] TestSqliteMapper.test_SqliteMapper (0.189 secs) Using db: /data1/bwang/cryoem/ScipionUserData/Tests/TestSqliteMapper/pointers.sqlite [ RUN OK ] TestSqliteMapper.test_StorePointers (0.289 secs) Using db: /data1/bwang/cryoem/ScipionUserData/Tests/TestSqliteMapper/lists.sqlite [ RUN OK ] TestSqliteMapper.test_removeFromLists (0.292 secs) [ RUN OK ] TestXmlMapper.test_XMLMapper (0.000 secs)

[==========] run 7 tests (2.047 secs) [ PASSED ] 7 tests bwang@pagoda$ scipion3 tests pwem.tests.data.test_data Scipion v3.0.10 - Eugenius Running tests.... defU=None, defV=None, ast=0.00, psh=None, res=None, fit=None defU=2.45, defV=None, ast=2.45, psh=None, res=None, fit=None [ RUN OK ] TestCTFModel.test_stringContext (0.000 secs) Creating project at: /data1/bwang/cryoem/ScipionUserData/projects/dummy_protocol/project.sqlite ** Running command: 'python3 /data2/bwang/software/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/apps/pw_protocol_run.py "/data1/bwang/cryoem/ScipionUserData/projects/dummy_protocol" "Runs/000002_EMProtocol/logs/run.db" 2' getExtraLogInfo failed: list index out of range getExtraLogInfo failed: list index out of range getExtraLogInfo failed: list index out of range getExtraLogInfo failed: list index out of range [ RUN OK ] TestCoordinatesTiltPair.test_mapper (0.974 secs)

python3 /data2/bwang/software/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/apps/pw_sync_data.py --download model Selected datasets: model Local copy of dataset model detected. Checking for updates... Verifying MD5s... ...done. Updated files: 0 [ RUN OK ] TestCopyItems.test_listAttribute (0.218 secs) [ RUN OK ] TestFSC.testIO (0.000 secs) [ RUN OK ] TestFSC.testMd (0.001 secs) python3 /data2/bwang/software/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/apps/pw_sync_data.py --download xmipp_tutorial Selected datasets: xmipp_tutorial Local copy of dataset xmipp_tutorial detected. Checking for updates... Verifying MD5s... ...done. Updated files: 0 [ RUN OK ] TestImage.testLocation (0.001 secs) [ RUN OK ] TestImage.testOrigin (0.001 secs) python3 /data2/bwang/software/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/apps/pw_sync_data.py --download xmipp_tutorial Selected datasets: xmipp_tutorial Local copy of dataset xmipp_tutorial detected. Checking for updates... Verifying MD5s... ...done. Updated files: 0 python3 /data2/bwang/software/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/apps/pw_sync_data.py --download movies Selected datasets: movies Local copy of dataset movies detected. Checking for updates... Regenerating local MANIFEST... Calculating md5 for local FoilHole_29355520_Data_29330528_29330530_20200329_234551_Fractions.mrc.eer ... DONE! Calculating md5 for local dark.mrc ... DONE! Calculating md5 for local c3-adp-se-xyz-0228_200.tif ... DONE! Calculating md5 for local Falcon_2012_06_12-14_33_35_0_movie.mrcs.bz2 ... DONE! Calculating md5 for local Falcon_2012_06_12-17_26_54_0_movie.mrcs ... DONE! Calculating md5 for local SuperRef_c3-adp-se-xyz-0228_001.dm4 ... DONE! Calculating md5 for local dark.spi ... DONE! Calculating md5 for local Falcon_2012_06_12-16_55_40_0_movie.mrcs ... DONE! Calculating md5 for local gain.spi ... DONE! Calculating md5 for local gain.mrc ... DONE! Calculating md5 for local Falcon_2012_06_12-17_26_54_0_movie.mrcs ... DONE! Calculating md5 for local Falcon_2012_06_12-14_33_35_0_movie.mrcs ... DONE! Calculating md5 for local Falcon_2012_06_12-16_55_40_0_movie.mrcs ... DONE! Calculating md5 for local cct_1_aligned_mic.pos ... DONE! Calculating md5 for local cct_1.em ... DONE! Calculating md5 for local qbeta_aligned_mic.pos ... DONE! Calculating md5 for local qbeta.mrc ... DONE! Verifying MD5s... ...done. Updated files: 0 python3 /data2/bwang/software/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/apps/pw_sync_data.py --download relion_tutorial Selected datasets: relion_tutorial Local copy of dataset relion_tutorial detected. Checking for updates... Regenerating local MANIFEST... Calculating md5 for local 112.mrc ... DONE! Calculating md5 for local 116.mrc ... DONE! Calculating md5 for local 060.mrc ... DONE! Calculating md5 for local 101.mrc ... DONE! Calculating md5 for local 006.mrc ... DONE! Calculating md5 for local 069.mrc ... DONE! Calculating md5 for local 071.mrc ... DONE! Calculating md5 for local 008.mrc ... DONE! Calculating md5 for local 129.mrc ... DONE! Calculating md5 for local 165.mrc ... DONE! Calculating md5 for local 019.mrc ... DONE! Calculating md5 for local 142.mrc ... DONE! Calculating md5 for local 151.mrc ... DONE! Calculating md5 for local 124.mrc ... DONE! Calculating md5 for local 066.mrc ... DONE! Calculating md5 for local 136.mrc ... DONE! Calculating md5 for local 016.mrc ... DONE! Calculating md5 for local 068.mrc ... DONE! Calculating md5 for local 128.mrc ... DONE! Calculating md5 for local 106.mrc ... DONE! Calculating md5 for local reference_masked.vol ... DONE! Calculating md5 for local reference_rotated_masked.vol ... DONE! Calculating md5 for local reference.mrc ... DONE! Calculating md5 for local reference_rotated.vol ... DONE! Calculating md5 for local .eman2log.txt ... DONE! Calculating md5 for local .eman2settings.dat ... DONE! Calculating md5 for local .eman2settings.dir ... DONE! Calculating md5 for local .eman2settings.bak ... DONE! Calculating md5 for local 129.json ... DONE! Calculating md5 for local 006.json ... DONE! Calculating md5 for local 060.json ... DONE! Calculating md5 for local 112.json ... DONE! Calculating md5 for local 124.json ... DONE! Calculating md5 for local 071.json ... DONE! Calculating md5 for local 136.json ... DONE! Calculating md5 for local 069.json ... DONE! Calculating md5 for local 116.json ... DONE! Calculating md5 for local 128.json ... DONE! Calculating md5 for local 008.json ... DONE! Calculating md5 for local 106.json ... DONE! Calculating md5 for local gauss_box_DB.json ... DONE! Calculating md5 for local swarm_panel.json ... DONE! Calculating md5 for local 165.json ... DONE! Calculating md5 for local 101.json ... DONE! Calculating md5 for local 019.json ... DONE! Calculating md5 for local 066.json ... DONE! Calculating md5 for local base.json ... DONE! Calculating md5 for local 142.json ... DONE! Calculating md5 for local 068.json ... DONE! Calculating md5 for local 151.json ... DONE! Calculating md5 for local 016.json ... DONE! Calculating md5 for local coarse_sigma_image.bdb ... DONE! Calculating md5 for local coarse_flat_image_487x487x1 ... DONE! Calculating md5 for local coarse_sigma_image_487x487x1 ... DONE! Calculating md5 for local flcf_image_487x487x1 ... DONE! Calculating md5 for local flcf_image.bdb ... DONE! Calculating md5 for local 00image_counts.bdb ... DONE! Calculating md5 for local coarse_flat_image.bdb ... DONE! Calculating md5 for local 068_info.json ... DONE! Calculating md5 for local 016_info.json ... DONE! Calculating md5 for local 060_info.json ... DONE! Calculating md5 for local 112_info.json ... DONE! Calculating md5 for local 019_info.json ... DONE! Calculating md5 for local 106_info.json ... DONE! Calculating md5 for local 101_info.json ... DONE! Calculating md5 for local 129_info.json ... DONE! Calculating md5 for local 142_info.json ... DONE! Calculating md5 for local 071_info.json ... DONE! Calculating md5 for local 116_info.json ... DONE! Calculating md5 for local 151_info.json ... DONE! Calculating md5 for local 066_info.json ... DONE! Calculating md5 for local 069_info.json ... DONE! Calculating md5 for local 006_info.json ... DONE! Calculating md5 for local 128_info.json ... DONE! Calculating md5 for local 136_info.json ... DONE! Calculating md5 for local 124_info.json ... DONE! Calculating md5 for local 165_info.json ... DONE! Calculating md5 for local 008_info.json ... DONE! Calculating md5 for local 129.pos ... DONE! Calculating md5 for local 071.pos ... DONE! Calculating md5 for local scipion_128.pos ... DONE! Calculating md5 for local model_training.txt ... DONE! Calculating md5 for local 165.pos ... DONE! Calculating md5 for local 151.pos ... DONE! Calculating md5 for local 101.pos ... DONE! Calculating md5 for local scipion_071.pos ... DONE! Calculating md5 for local scipion_101.pos ... DONE! Calculating md5 for local scipion_116.pos ... DONE! Calculating md5 for local scipion_006.pos ... DONE! Calculating md5 for local 124.pos ... DONE! Calculating md5 for local config.xmd ... DONE! Calculating md5 for local templates.stk ... DONE! Calculating md5 for local scipion_016.pos ... DONE! Calculating md5 for local scipion_129.pos ... DONE! Calculating md5 for local scipion_019.pos ... DONE! Calculating md5 for local scipion_066.pos ... DONE! Calculating md5 for local scipion_142.pos ... DONE! Calculating md5 for local scipion_124.pos ... DONE! Calculating md5 for local 019.pos ... DONE! Calculating md5 for local 112.pos ... DONE! Calculating md5 for local scipion_068.pos ... DONE! Calculating md5 for local 069.pos ... DONE! Calculating md5 for local 068.pos ... DONE! Calculating md5 for local 006.pos ... DONE! Calculating md5 for local 116.pos ... DONE! Calculating md5 for local 142.pos ... DONE! Calculating md5 for local model_rotpca_model.xmd ... DONE! Calculating md5 for local scipion_069.pos ... DONE! Calculating md5 for local scipion_008.pos ... DONE! Calculating md5 for local model_particle_avg.xmp ... DONE! Calculating md5 for local scipion_112.pos ... DONE! Calculating md5 for local 106.pos ... DONE! Calculating md5 for local scipion_136.pos ... DONE! Calculating md5 for local scipion_060.pos ... DONE! Calculating md5 for local coordinates.sqlite ... DONE! Calculating md5 for local model_rotpca_model.stk ... DONE! Calculating md5 for local 128.pos ... DONE! Calculating md5 for local 008.pos ... DONE! Calculating md5 for local model_pca_model.stk ... DONE! Calculating md5 for local 060.pos ... DONE! Calculating md5 for local 066.pos ... DONE! Calculating md5 for local scipion_106.pos ... DONE! Calculating md5 for local scipion_151.pos ... DONE! Calculating md5 for local scipion_165.pos ... DONE! Calculating md5 for local 016.pos ... DONE! Calculating md5 for local model_svm.txt ... DONE! Calculating md5 for local 136.pos ... DONE! Calculating md5 for local relion_it020_data.star ... DONE! Calculating md5 for local relion_it020_data_newlabels.star ... DONE! Calculating md5 for local particles.sqlite ... DONE! Calculating md5 for local input_particles.star ... DONE! Calculating md5 for local 006.stk ... DONE! Calculating md5 for local averages.mrcs ... DONE! Calculating md5 for local particles.sqlite ... DONE! Calculating md5 for local relion_volumes.mrc ... DONE! Calculating md5 for local relion_it015_sampling.star ... DONE! Calculating md5 for local particles.sqlite ... DONE! Calculating md5 for local relion_it015_class002_angdist.bild ... DONE! Calculating md5 for local relion_it015_class001.mrc ... DONE! Calculating md5 for local relion_it015_data.star ... DONE! Calculating md5 for local relion_it015_class003.mrc ... DONE! Calculating md5 for local relion_it015_classes_scipion.sqlite ... DONE! Calculating md5 for local relion_it015_optimiser.star ... DONE! Calculating md5 for local relion_it015_class003_angdist.bild ... DONE! Calculating md5 for local relion_volumes.stk ... DONE! Calculating md5 for local relion_it015_class002.mrc ... DONE! Calculating md5 for local relion_it015_class001_angdist.bild ... DONE! Calculating md5 for local volume.mrc ... DONE! Calculating md5 for local relion_it015_model.star ... DONE! Calculating md5 for local particles.mrcs ... DONE! Calculating md5 for local classes3D.sqlite ... DONE! Calculating md5 for local input_particles.mrcs ... DONE! Calculating md5 for local input_particles.star ... DONE! Calculating md5 for local relion_it010_class003.mrc ... DONE! Calculating md5 for local relion_it014_sampling.star ... DONE! Calculating md5 for local relion_it012_optimiser.star ... DONE! Calculating md5 for local relion_it012_sampling.star ... DONE! Calculating md5 for local relion_it000_sampling.star ... DONE! Calculating md5 for local relion_it005_class001.mrc ... DONE! Calculating md5 for local relion_it006_optimiser.star ... DONE! Calculating md5 for local relion_it007_class001.mrc ... DONE! Calculating md5 for local relion_it009_class003.mrc ... DONE! Calculating md5 for local relion_it013_class002.mrc ... DONE! Calculating md5 for local relion_it002_sampling.star ... DONE! Calculating md5 for local relion_it015_classes_scipion.sqlite ... DONE! Calculating md5 for local relion_it012_class002.mrc ... DONE! Calculating md5 for local relion_it006_model.star ... DONE! Calculating md5 for local relion_it013_optimiser.star ... DONE! Calculating md5 for local relion_it015_data_sorted_xmipp.star ... DONE! Calculating md5 for local relion_it004_class003.mrc ... DONE! Calculating md5 for local relion_it002_class001.mrc ... DONE! Calculating md5 for local relion_it011_data.star ... DONE! Calculating md5 for local relion_it006_class001.mrc ... DONE! Calculating md5 for local relion_it012_data.star ... DONE! Calculating md5 for local relion_it005_class003.mrc ... DONE! Calculating md5 for local relion_it008_class001.mrc ... DONE! Calculating md5 for local relion_it015_model.star ... DONE! Calculating md5 for local relion_it002_class002.mrc ... DONE! Calculating md5 for local relion_it004_optimiser.star ... DONE! Calculating md5 for local relion_it007_optimiser.star ... DONE! Calculating md5 for local relion_it000_data.star ... DONE! Calculating md5 for local relion_it007_class003.mrc ... DONE! Calculating md5 for local relion_it010_class002.mrc ... DONE! Calculating md5 for local relion_it010_model.star ... DONE! Calculating md5 for local relion_it015_angularDist_xmipp.xmd ... DONE! Calculating md5 for local relion_it008_class002.mrc ... DONE! Calculating md5 for local relion_it014_class003.mrc ... DONE! Calculating md5 for local relion_it004_data.star ... DONE! Calculating md5 for local relion_it006_class003.mrc ... DONE! Calculating md5 for local relion_it002_optimiser.star ... DONE! Calculating md5 for local relion_it013_class001.mrc ... DONE! Calculating md5 for local relion_it008_data.star ... DONE! Calculating md5 for local relion_it011_optimiser.star ... DONE! Calculating md5 for local relion_it009_data.star ... DONE! Calculating md5 for local relion_it004_model.star ... DONE! Calculating md5 for local relion_it003_class001.mrc ... DONE! Calculating md5 for local relion_it005_optimiser.star ... DONE! Calculating md5 for local relion_it001_class003.mrc ... DONE! Calculating md5 for local relion_it005_sampling.star ... DONE! Calculating md5 for local relion_it013_sampling.star ... DONE! Calculating md5 for local relion_it015_optimiser.star ... DONE! Calculating md5 for local relion_it013_class003.mrc ... DONE! Calculating md5 for local relion_it003_optimiser.star ... DONE! Calculating md5 for local relion_it007_data.star ... DONE! Calculating md5 for local relion_it014_model.star ... DONE! Calculating md5 for local relion_it015_class002.mrc ... DONE! Calculating md5 for local relion_it011_class002.mrc ... DONE! Calculating md5 for local relion_it001_data.star ... DONE! Calculating md5 for local relion_it006_sampling.star ... DONE! Calculating md5 for local relion_it002_data.star ... DONE! Calculating md5 for local relion_it003_class003.mrc ... DONE! Calculating md5 for local relion_it007_sampling.star ... DONE! Calculating md5 for local relion_it008_class003.mrc ... DONE! Calculating md5 for local relion_it004_sampling.star ... DONE! Calculating md5 for local relion_it011_sampling.star ... DONE! Calculating md5 for local relion_it008_model.star ... DONE! Calculating md5 for local relion_it005_class002.mrc ... DONE! Calculating md5 for local relion_it015_class001.mrc ... DONE! Calculating md5 for local relion_it015_data.star ... DONE! Calculating md5 for local relion_it010_data.star ... DONE! Calculating md5 for local relion_it004_class001.mrc ... DONE! Calculating md5 for local relion_it015_class003.mrc ... DONE! Calculating md5 for local relion_it001_class001.mrc ... DONE! Calculating md5 for local relion_it002_class003.mrc ... DONE! Calculating md5 for local relion_it006_data.star ... DONE! Calculating md5 for local relion_it004_class002.mrc ... DONE! Calculating md5 for local relion_it001_sampling.star ... DONE! Calculating md5 for local relion_it001_optimiser.star ... DONE! Calculating md5 for local relion_it002_model.star ... DONE! Calculating md5 for local relion_it008_optimiser.star ... DONE! Calculating md5 for local relion_it013_data.star ... DONE! Calculating md5 for local relion_it007_model.star ... DONE! Calculating md5 for local relion_it013_model.star ... DONE! Calculating md5 for local relion_it010_class001.mrc ... DONE! Calculating md5 for local relion_it010_sampling.star ... DONE! Calculating md5 for local relion_it000_class002.mrc ... DONE! Calculating md5 for local relion_it008_sampling.star ... DONE! Calculating md5 for local relion_it000_optimiser.star ... DONE! Calculating md5 for local relion_it010_optimiser.star ... DONE! Calculating md5 for local relion_it015_sampling.star ... DONE! Calculating md5 for local relion_it003_class002.mrc ... DONE! Calculating md5 for local relion_it009_optimiser.star ... DONE! Calculating md5 for local relion_it011_class001.mrc ... DONE! Calculating md5 for local relion_it012_model.star ... DONE! Calculating md5 for local relion_it009_model.star ... DONE! Calculating md5 for local relion_it009_class002.mrc ... DONE! Calculating md5 for local relion_it000_model.star ... DONE! Calculating md5 for local relion_it011_class003.mrc ... DONE! Calculating md5 for local relion_viewer_volumes.xmd ... DONE! Calculating md5 for local relion_it014_optimiser.star ... DONE! Calculating md5 for local relion_it014_class001.mrc ... DONE! Calculating md5 for local relion_it011_model.star ... DONE! Calculating md5 for local relion_it009_sampling.star ... DONE! Calculating md5 for local relion_it014_class002.mrc ... DONE! Calculating md5 for local relion_it005_data.star ... DONE! Calculating md5 for local relion_it014_data.star ... DONE! Calculating md5 for local relion_it003_model.star ... DONE! Calculating md5 for local relion_it007_class002.mrc ... DONE! Calculating md5 for local relion_it003_sampling.star ... DONE! Calculating md5 for local relion_it005_model.star ... DONE! Calculating md5 for local relion_it001_model.star ... DONE! Calculating md5 for local relion_it000_class003.mrc ... DONE! Calculating md5 for local relion_it000_class001.mrc ... DONE! Calculating md5 for local relion_it012_class003.mrc ... DONE! Calculating md5 for local relion_it012_class001.mrc ... DONE! Calculating md5 for local relion_it001_class002.mrc ... DONE! Calculating md5 for local relion_it006_class002.mrc ... DONE! Calculating md5 for local relion_it009_class001.mrc ... DONE! Calculating md5 for local relion_it003_data.star ... DONE! Calculating md5 for local run.stderr ... DONE! Calculating md5 for local run.db ... DONE! Calculating md5 for local run.stdout ... DONE! Calculating md5 for local run.log ... DONE! Calculating md5 for local steps.sqlite ... DONE! Calculating md5 for local iterations_changes_xmipp.xmd ... DONE! Calculating md5 for local classify3d_small_it038_sampling.star ... DONE! Calculating md5 for local classify3d_small_it038_optimiser.star ... DONE! Calculating md5 for local classify3d_small_it038_model.star ... DONE! Calculating md5 for local classify3d_small_it038_data.star ... DONE! Calculating md5 for local input_particles.mrcs ... DONE! Calculating md5 for local input_particles.star ... DONE! Calculating md5 for local relion_sampling.star ... DONE! Calculating md5 for local relion_it000_sampling.star ... DONE! Calculating md5 for local relion_it000_half2_model.star ... DONE! Calculating md5 for local relion_it000_half1_model.star ... DONE! Calculating md5 for local relion_it025_optimiser.star ... DONE! Calculating md5 for local relion_it025_data.star ... DONE! Calculating md5 for local relion_data.star ... DONE! Calculating md5 for local relion_it025_sampling.star ... DONE! Calculating md5 for local relion_it000_half1_classes.mrcs ... DONE! Calculating md5 for local relion_it000_optimiser.star ... DONE! Calculating md5 for local relion_it025_half2_class001.mrc ... DONE! Calculating md5 for local relion_model.star ... DONE! Calculating md5 for local relion_it001_half1_classes.mrcs ... DONE! Calculating md5 for local relion_it025_half2_model.star ... DONE! Calculating md5 for local relion_it025_half1_class001.mrc ... DONE! Calculating md5 for local relion_it000_half2_classes.mrcs ... DONE! Calculating md5 for local relion_it001_sampling.star ... DONE! Calculating md5 for local relion_it001_optimiser.star ... DONE! Calculating md5 for local relion_it001_half1_model.star ... DONE! Calculating md5 for local relion_it001_half2_classes.mrcs ... DONE! Calculating md5 for local relion_it025_half1_model.star ... DONE! Calculating md5 for local relion_it001_data.star ... DONE! Calculating md5 for local relion_it000_data.star ... DONE! Calculating md5 for local relion_class001.mrc ... DONE! Calculating md5 for local relion_it001_half2_model.star ... DONE! Calculating md5 for local run.stderr ... DONE! Calculating md5 for local run.db ... DONE! Calculating md5 for local run.stdout ... DONE! Calculating md5 for local run.log ... DONE! Calculating md5 for local steps.sqlite ... DONE! Calculating md5 for local Falcon_2012_06_12-16_55_40_0_movie_aligned_mic_DW.mrcs ... DONE! Calculating md5 for local Falcon_2012_06_12-14_33_35_0_movie_aligned_mic_DW.mrcs ... DONE! Calculating md5 for local Falcon_2012_06_12-17_26_54_0_movie_aligned_mic_DW.mrcs ... DONE! Calculating md5 for local relion_data.star ... DONE! Calculating md5 for local relion_model.star ... DONE! Calculating md5 for local input_particles.mrcs ... DONE! Calculating md5 for local classes2D.sqlite ... DONE! Calculating md5 for local input_particles.star ... DONE! Calculating md5 for local relion_it015_optimiser.star ... DONE! Calculating md5 for local relion_it015_sampling.star ... DONE! Calculating md5 for local relion_it015_classes_scipion_selection.sqlite ... DONE! Calculating md5 for local relion_it015_classes.mrcs ... DONE! Calculating md5 for local relion_it015_data.star ... DONE! Calculating md5 for local relion_it015_model.star ... DONE! Calculating md5 for local relion_it015_classes_scipion.sqlite ... DONE! Calculating md5 for local run.stderr ... DONE! Calculating md5 for local run.db ... DONE! Calculating md5 for local run.stdout ... DONE! Calculating md5 for local run.log ... DONE! Calculating md5 for local steps.sqlite ... DONE! Verifying MD5s... ...done. Updated files: 0 [ RUN OK ] TestImageHandler.testExistLocation (0.000 secs) [ RUN OK ] TestImageHandler.testGetDimensions (0.005 secs) Converting: /data2/bwang/software/scipion/data/tests/xmipp_tutorial/micrographs/BPV_1386.mrc -> /tmp/BPV_1386.img [ FAILED ] TestImageHandler.test_convertMicrographs

Traceback (most recent call last): File "/data2/bwang/software/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/plugin.py", line 296, in _tryImportFromPlugin output = getattr(importlib.import_module(module), submodule) File "/data2/bwang/software/anaconda3/envs/scipion3/lib/python3.8/importlib/init.py", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "", line 1014, in _gcd_import File "", line 991, in _find_and_load File "", line 961, in _find_and_load_unlocked File "", line 219, in _call_with_frames_removed File "", line 1014, in _gcd_import File "", line 991, in _find_and_load File "", line 973, in _find_and_load_unlocked ModuleNotFoundError: No module named 'eman2'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/data2/bwang/software/anaconda3/envs/scipion3/lib/python3.8/unittest/case.py", line 60, in testPartExecutor yield File "/data2/bwang/software/anaconda3/envs/scipion3/lib/python3.8/unittest/case.py", line 676, in run self._callTestMethod(testMethod) File "/data2/bwang/software/anaconda3/envs/scipion3/lib/python3.8/unittest/case.py", line 633, in _callTestMethod method() File "/data2/bwang/software/anaconda3/envs/scipion3/lib/python3.8/site-packages/pwem/tests/data/test_data.py", line 255, in test_convertMicrographs ih.convert(micFn, outFn) File "/data2/bwang/software/anaconda3/envs/scipion3/lib/python3.8/site-packages/pwem/emlib/image/image_handler.py", line 158, in convert convertImage = Domain.importFromPlugin('eman2.convert', File "/data2/bwang/software/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/plugin.py", line 305, in importFromPlugin output = _tryImportFromPlugin(objects) File "/data2/bwang/software/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/plugin.py", line 302, in _tryImportFromPlugin Domain.pluginNotFound(plugName, errMsg, doRaise) File "/data2/bwang/software/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/plugin.py", line 448, in pluginNotFound raise Exception("\n\n" + raiseMsg) Exception:

error when importing from eman2: No module named 'eman2' File "", line 991, in _find_and_load Check the plugin manager (Configuration->Plugins in Scipion manager window) or use 'scipion installp --help --checkUpdates' in the command line to check for upgrades, it could be a versions compatibility issue.

[ RUN OK ] TestImageHandler.test_convertMovie (0.129 secs) [ RUN OK ] TestImageHandler.test_createEmptyImage (0.006 secs) Converting: (1, '/data2/bwang/software/scipion/data/tests/movies/c3-adp-se-xyz-0228_200.tif') -> /tmp/c3-adp-se-xyz-0228_200.mrc [ RUN OK ] TestImageHandler.test_readCompressedTIF (0.558 secs) Converting: /data2/bwang/software/scipion/data/tests/movies/SuperRef_c3-adp-se-xyz-0228_001.dm4 -> /tmp/SuperRef_c3-adp-se-xyz-0228_001.mrc [ RUN OK ] TestImageHandler.test_readDM4 (0.252 secs) [ RUN OK ] TestImageHandler.test_scaleStack (0.315 secs) Running command: xmipp_image_resize -i /data2/bwang/software/scipion/data/tests/xmipp_tutorial/masks/mask.vol -o /tmp/mask.vol --dim 128 === XMIPP_WARNING === Do not apply large scale factor using B-splines choose fourier option. Input File: /data2/bwang/software/scipion/data/tests/xmipp_tutorial/masks/mask.vol Output File: /tmp/mask.vol Running command: xmipp_transform_threshold -i /tmp/mask.vol --select below 0 --substitute value 0 Input File: /tmp/mask.vol Selection method: below Threshold: 0 Substitution method: value New value: 0 ** Running command: xmipp_transform_threshold -i /tmp/mask.vol --select above 1 --substitute value 1 Input File: /tmp/mask.vol Selection method: above Threshold: 1 Substitution method: value New value: 1 [ RUN OK ] TestImageHandler.test_truncateMask (0.719 secs)

python3 /data2/bwang/software/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/apps/pw_sync_data.py --download model Selected datasets: model Local copy of dataset model detected. Checking for updates... Verifying MD5s... ...done. Updated files: 0 [ RUN OK ] TestSetOfClasses2D.test_basics (0.015 secs) getExtraLogInfo failed: list index out of range getExtraLogInfo failed: list index out of range getExtraLogInfo failed: list index out of range getExtraLogInfo failed: list index out of range [ RUN OK ] TestSetOfClasses2D.test_subsetsFromSelection (0.014 secs) Creating project at: /data1/bwang/cryoem/ScipionUserData/projects/dummy_protocol/project.sqlite Running command: 'python3 /data2/bwang/software/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/apps/pw_protocol_run.py "/data1/bwang/cryoem/ScipionUserData/projects/dummy_protocol" "Runs/000002_EMProtocol/logs/run.db" 2' getExtraLogInfo failed: list index out of range /data1/bwang/cryoem/ScipionUserData/projects/dummy_protocol/Runs/000002_EMProtocol/coordinates.sqlite Loop with INDEX took: 0:00:00.335310 Loop with INDEX and proper code, took: 0:00:00.164990 Loop with NO INDEX took: 0:00:01.388179 Loop with NO INDEX but proper code, took: 0:00:00.147043 getExtraLogInfo failed: list index out of range [ RUN OK ] TestSetOfCoordinates.test_mapper (2.970 secs) python3 /data2/bwang/software/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/apps/pw_sync_data.py --download xmipp_tutorial Selected datasets: xmipp_tutorial Local copy of dataset xmipp_tutorial detected. Checking for updates... Verifying MD5s... ...done. Updated files: 0 getExtraLogInfo failed: list index out of range getExtraLogInfo failed: list index out of range [ RUN OK ] TestSetOfMicrographs.testCreate (0.148 secs) Reading gold micrographs from: /data2/bwang/software/scipion/data/tests/xmipp_tutorial/gold/micrographs2_gold.sqlite [ RUN OK ] TestSetOfMicrographs.testRead (0.001 secs) Creating project at: /data1/bwang/cryoem/ScipionUserData/projects/dummy_protocol/project.sqlite Running command: 'python3 /data2/bwang/software/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/apps/pw_protocol_run.py "/data1/bwang/cryoem/ScipionUserData/projects/dummy_protocol" "Runs/000002_EMProtocol/logs/run.db" 2' [ RUN OK ] TestSetOfMicrographs.test_mapper (1.631 secs) python3 /data2/bwang/software/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/apps/pw_sync_data.py --download xmipp_tutorial Selected datasets: xmipp_tutorial Local copy of dataset xmipp_tutorial detected. Checking for updates... Verifying MD5s... ...done. Updated files: 0 [ RUN OK ] TestSetOfParticles.test_getFiles (0.118 secs) Creating a set of 10000 particles. (set SCIPION_TEST_HUGE environment var to other value) [ RUN OK ] TestSetOfParticles.test_hugeSet (0.449 secs) Creating a set of 10000 particles. (set SCIPION_TEST_HUGE environment var to other value) Writing metadata to: /data1/bwang/cryoem/ScipionUserData/Tests/TestSetOfParticles/huge_set.xmd [ RUN OK ] TestSetOfParticles.test_hugeSetToMd (0.051 secs) Creating a set of 10000 particles. (set SCIPION_TEST_HUGE environment var to other value) Writing to text file: /data1/bwang/cryoem/ScipionUserData/Tests/TestSetOfParticles/huge_set.txt [ RUN OK ] TestSetOfParticles.test_hugeSetToText (0.002 secs) Creating project at: /data1/bwang/cryoem/ScipionUserData/projects/dummy_protocol/project.sqlite ** Running command: 'python3 /data2/bwang/software/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/apps/pw_protocol_run.py "/data1/bwang/cryoem/ScipionUserData/projects/dummy_protocol" "Runs/000002_EMProtocol/logs/run.db" 2' [ RUN OK ] TestSetOfParticles.test_mapper (0.925 secs) getExtraLogInfo failed: list index out of range getExtraLogInfo failed: list index out of range getExtraLogInfo failed: list index out of range [ RUN OK ] TestSetOfParticles.test_orderBy (0.006 secs) writing particles to: /data1/bwang/cryoem/ScipionUserData/Tests/TestSetOfParticles/particles.sqlite getExtraLogInfo failed: list index out of range getExtraLogInfo failed: list index out of range [ RUN OK ] TestSetOfParticles.test_readStack (0.339 secs) [ RUN OK ] TestTransform.test_clone (0.001 secs) [ RUN OK ] TestTransform.test_scale (0.000 secs) [ RUN OK ] TestTransform.test_scaleShifts (0.000 secs)

[==========] run 32 tests (26.013 secs) [ FAILED ] 1 tests [ PASSED ] 31 tests

For that failing test you need to have Eman plugin installed.

El mié., 12 ene. 2022 19:54, bingwang14 @.***> escribió:

Hi there, I met the same issue with empty import tab. And I run some basic tests. All other is good except with the command "scipion3 tests pwem.tests.data.test_data" in which 1 tests failed and 31 tests passed. Here is the running log below. Does anyone know how to fix that?

@.***$ scipion3 tests pyworkflowtests.tests.test_object.TestObject Scipion v3.0.10 - Eugenius Running tests.... [ RUN OK ] TestObject.testWithPointer (0.000 secs) [ RUN OK ] TestObject.test_Dict (0.000 secs) [ RUN OK ] TestObject.test_Object (0.000 secs) [ RUN OK ] TestObject.test_ObjectsDict (0.000 secs) ERROR: Name collision (SetOfCoordinates) detected while discovering pwem.objects. It conflicts with pyworkflowtests [ RUN OK ] TestObject.test_Pointer (0.172 secs) Writing to sqlite: /data1/bwang/cryoem/ScipionUserData/Tests/TestObject/test_images2.sqlite Checking set iteration with limit:2 and skipRows: None Checking set iteration with limit:3 and skipRows: 2 Connection open for /data1/bwang/cryoem/ScipionUserData/Tests/TestObject/test_images2.sqlite Connection closed for /data1/bwang/cryoem/ScipionUserData/Tests/TestObject/test_images2.sqlite Connection closed for /data1/bwang/cryoem/ScipionUserData/Tests/TestObject/test_images2.sqlite [ RUN OK ] TestObject.test_Sets (1.236 secs) [ RUN OK ] TestObject.test_String (0.003 secs) [ RUN OK ] TestObject.test_copyAttributes (0.000 secs) [ RUN OK ] TestObject.test_equalAttributes (0.000 secs) [ RUN OK ] TestObject.test_formatString (0.000 secs) ('object.id', 1), ('object.label', 'test micrograph'), ('object.comment', 'Testing store and retrieve from dict.'), ('_index', 0), ('_filename', 'my_movie.mrc'), ('_samplingRate', 1.6), ('_acquisition', None), ('_acquisition._magnification', 50000.0), ('_acquisition._voltage', 200.0), ('_acquisition._sphericalAberration', 2.7), ('_acquisition._amplitudeContrast', None), ('_acquisition._doseInitial', 0.0), ('_acquisition._dosePerFrame', 1.0), ('_micName', None), [ RUN OK ] TestObject.test_getObjDict (0.000 secs)

[==========] run 11 tests (1.412 secs) [ PASSED ] 11 tests @.***$ scipion3 tests pyworkflowtests.tests.test_mappers Scipion v3.0.10 - Eugenius Running tests.... Row(id=1, x=12, y=11.0, name='jose') Row(id=1, x=12, y=11.0, name='pepe') [ RUN OK ] TestDataSet.test_Table (0.013 secs)

test empty set: dbName = '/data1/bwang/cryoem/ScipionUserData/Tests/TestSqliteFlatMapper/empty.sqlite' [ RUN OK ] TestSqliteFlatMapper.test_emtpySet (0.001 secs) test_insertObjects: dbName = '/data1/bwang/cryoem/ScipionUserData/Tests/TestSqliteFlatMapper/images.sqlite' [ RUN OK ] TestSqliteFlatMapper.test_insertObjects (1.260 secs) Checking that Relations table is updated and version to 1 {'id': 1, 'parent_id': 1, 'name': 'testRelation', 'classname': None, 'value': None, 'label': None, 'comment': None, 'object_parent_id': 2, 'object_child_id': 3, 'creation': '2022-01-12 18:40:31', 'object_parent_extended': None, 'object_child_extended': None} {'id': 2, 'parent_id': 1, 'name': 'testRelation', 'classname': None, 'value': None, 'label': None, 'comment': None, 'object_parent_id': 2, 'object_child_id': 4, 'creation': '2022-01-12 18:40:31', 'object_parent_extended': None, 'object_child_extended': None} {'id': 3, 'parent_id': 1, 'name': 'testRelation', 'classname': None, 'value': None, 'label': None, 'comment': None, 'object_parent_id': 3, 'object_child_id': 5, 'creation': '2022-01-12 18:40:31', 'object_parent_extended': None, 'object_child_extended': None} {'id': 4, 'parent_id': 1, 'name': 'testRelation', 'classname': None, 'value': None, 'label': None, 'comment': None, 'object_parent_id': 4, 'object_child_id': 5, 'creation': '2022-01-12 18:40:31', 'object_parent_extended': None, 'object_child_extended': None} [ RUN OK ] TestSqliteMapper.test_SqliteMapper (0.189 secs) Using db: /data1/bwang/cryoem/ScipionUserData/Tests/TestSqliteMapper/pointers.sqlite [ RUN OK ] TestSqliteMapper.test_StorePointers (0.289 secs) Using db: /data1/bwang/cryoem/ScipionUserData/Tests/TestSqliteMapper/lists.sqlite [ RUN OK ] TestSqliteMapper.test_removeFromLists (0.292 secs) [ RUN OK ] TestXmlMapper.test_XMLMapper (0.000 secs)

[==========] run 7 tests (2.047 secs) [ PASSED ] 7 tests @.*$ scipion3 tests pwem.tests.data.test_data Scipion v3.0.10 - Eugenius Running tests.... defU=None, defV=None, ast=0.00, psh=None, res=None, fit=None defU=2.45, defV=None, ast=2.45, psh=None, res=None, fit=None [ RUN OK ] TestCTFModel.test_stringContext (0.000 secs) Creating project at: /data1/bwang/cryoem/ScipionUserData/projects/dummy_protocol/project.sqlite Running command: 'python3 /data2/bwang/software/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/apps/pw_protocol_run.py "/data1/bwang/cryoem/ScipionUserData/projects/dummy_protocol" "Runs/000002_EMProtocol/logs/run.db" 2' getExtraLogInfo failed: list index out of range getExtraLogInfo failed: list index out of range getExtraLogInfo failed: list index out of range getExtraLogInfo failed: list index out of range [ RUN OK ] TestCoordinatesTiltPair.test_mapper (0.974 secs)

python3 /data2/bwang/software/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/apps/pw_sync_data.py --download model Selected datasets: model Local copy of dataset model detected. Checking for updates... Verifying MD5s... ...done. Updated files: 0 [ RUN OK ] TestCopyItems.test_listAttribute (0.218 secs) [ RUN OK ] TestFSC.testIO (0.000 secs) [ RUN OK ] TestFSC.testMd (0.001 secs) python3 /data2/bwang/software/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/apps/pw_sync_data.py --download xmipp_tutorial Selected datasets: xmipp_tutorial Local copy of dataset xmipp_tutorial detected. Checking for updates... Verifying MD5s... ...done. Updated files: 0 [ RUN OK ] TestImage.testLocation (0.001 secs) [ RUN OK ] TestImage.testOrigin (0.001 secs) python3 /data2/bwang/software/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/apps/pw_sync_data.py --download xmipp_tutorial Selected datasets: xmipp_tutorial Local copy of dataset xmipp_tutorial detected. Checking for updates... Verifying MD5s... ...done. Updated files: 0 python3 /data2/bwang/software/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/apps/pw_sync_data.py --download movies Selected datasets: movies Local copy of dataset movies detected. Checking for updates... Regenerating local MANIFEST... Calculating md5 for local FoilHole_29355520_Data_29330528_29330530_20200329_234551_Fractions.mrc.eer ... DONE! Calculating md5 for local dark.mrc ... DONE! Calculating md5 for local c3-adp-se-xyz-0228_200.tif ... DONE! Calculating md5 for local Falcon_2012_06_12-14_33_35_0_movie.mrcs.bz2 ... DONE! Calculating md5 for local Falcon_2012_06_12-17_26_54_0_movie.mrcs ... DONE! Calculating md5 for local SuperRef_c3-adp-se-xyz-0228_001.dm4 ... DONE! Calculating md5 for local dark.spi ... DONE! Calculating md5 for local Falcon_2012_06_12-16_55_40_0_movie.mrcs ... DONE! Calculating md5 for local gain.spi ... DONE! Calculating md5 for local gain.mrc ... DONE! Calculating md5 for local Falcon_2012_06_12-17_26_54_0_movie.mrcs ... DONE! Calculating md5 for local Falcon_2012_06_12-14_33_35_0_movie.mrcs ... DONE! Calculating md5 for local Falcon_2012_06_12-16_55_40_0_movie.mrcs ... DONE! Calculating md5 for local cct_1_aligned_mic.pos ... DONE! Calculating md5 for local cct_1.em ... DONE! Calculating md5 for local qbeta_aligned_mic.pos ... DONE! Calculating md5 for local qbeta.mrc ... DONE! Verifying MD5s... ...done. Updated files: 0 python3 /data2/bwang/software/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/apps/pw_sync_data.py --download relion_tutorial Selected datasets: relion_tutorial Local copy of dataset relion_tutorial detected. Checking for updates... Regenerating local MANIFEST... Calculating md5 for local 112.mrc ... DONE! Calculating md5 for local 116.mrc ... DONE! Calculating md5 for local 060.mrc ... DONE! Calculating md5 for local 101.mrc ... DONE! Calculating md5 for local 006.mrc ... DONE! Calculating md5 for local 069.mrc ... DONE! Calculating md5 for local 071.mrc ... DONE! Calculating md5 for local 008.mrc ... DONE! Calculating md5 for local 129.mrc ... DONE! Calculating md5 for local 165.mrc ... DONE! Calculating md5 for local 019.mrc ... DONE! Calculating md5 for local 142.mrc ... DONE! Calculating md5 for local 151.mrc ... DONE! Calculating md5 for local 124.mrc ... DONE! Calculating md5 for local 066.mrc ... DONE! Calculating md5 for local 136.mrc ... DONE! Calculating md5 for local 016.mrc ... DONE! Calculating md5 for local 068.mrc ... DONE! Calculating md5 for local 128.mrc ... DONE! Calculating md5 for local 106.mrc ... DONE! Calculating md5 for local reference_masked.vol ... DONE! Calculating md5 for local reference_rotated_masked.vol ... DONE! Calculating md5 for local reference.mrc ... DONE! Calculating md5 for local reference_rotated.vol ... DONE! Calculating md5 for local .eman2log.txt ... DONE! Calculating md5 for local .eman2settings.dat ... DONE! Calculating md5 for local .eman2settings.dir ... DONE! Calculating md5 for local .eman2settings.bak ... DONE! Calculating md5 for local 129.json ... DONE! Calculating md5 for local 006.json ... DONE! Calculating md5 for local 060.json ... DONE! Calculating md5 for local 112.json ... DONE! Calculating md5 for local 124.json ... DONE! Calculating md5 for local 071.json ... DONE! Calculating md5 for local 136.json ... DONE! Calculating md5 for local 069.json ... DONE! Calculating md5 for local 116.json ... DONE! Calculating md5 for local 128.json ... DONE! Calculating md5 for local 008.json ... DONE! Calculating md5 for local 106.json ... DONE! Calculating md5 for local gauss_box_DB.json ... DONE! Calculating md5 for local swarm_panel.json ... DONE! Calculating md5 for local 165.json ... DONE! Calculating md5 for local 101.json ... DONE! Calculating md5 for local 019.json ... DONE! Calculating md5 for local 066.json ... DONE! Calculating md5 for local base.json ... DONE! Calculating md5 for local 142.json ... DONE! Calculating md5 for local 068.json ... DONE! Calculating md5 for local 151.json ... DONE! Calculating md5 for local 016.json ... DONE! Calculating md5 for local coarse_sigma_image.bdb ... DONE! Calculating md5 for local coarse_flat_image_487x487x1 ... DONE! Calculating md5 for local coarse_sigma_image_487x487x1 ... DONE! Calculating md5 for local flcf_image_487x487x1 ... DONE! Calculating md5 for local flcf_image.bdb ... DONE! Calculating md5 for local 00image_counts.bdb ... DONE! Calculating md5 for local coarse_flat_image.bdb ... DONE! Calculating md5 for local 068_info.json ... DONE! Calculating md5 for local 016_info.json ... DONE! Calculating md5 for local 060_info.json ... DONE! Calculating md5 for local 112_info.json ... DONE! Calculating md5 for local 019_info.json ... DONE! Calculating md5 for local 106_info.json ... DONE! Calculating md5 for local 101_info.json ... DONE! Calculating md5 for local 129_info.json ... DONE! Calculating md5 for local 142_info.json ... DONE! Calculating md5 for local 071_info.json ... DONE! Calculating md5 for local 116_info.json ... DONE! Calculating md5 for local 151_info.json ... DONE! Calculating md5 for local 066_info.json ... DONE! Calculating md5 for local 069_info.json ... DONE! Calculating md5 for local 006_info.json ... DONE! Calculating md5 for local 128_info.json ... DONE! Calculating md5 for local 136_info.json ... DONE! Calculating md5 for local 124_info.json ... DONE! Calculating md5 for local 165_info.json ... DONE! Calculating md5 for local 008_info.json ... DONE! Calculating md5 for local 129.pos ... DONE! Calculating md5 for local 071.pos ... DONE! Calculating md5 for local scipion_128.pos ... DONE! Calculating md5 for local model_training.txt ... DONE! Calculating md5 for local 165.pos ... DONE! Calculating md5 for local 151.pos ... DONE! Calculating md5 for local 101.pos ... DONE! Calculating md5 for local scipion_071.pos ... DONE! Calculating md5 for local scipion_101.pos ... DONE! Calculating md5 for local scipion_116.pos ... DONE! Calculating md5 for local scipion_006.pos ... DONE! Calculating md5 for local 124.pos ... DONE! Calculating md5 for local config.xmd ... DONE! Calculating md5 for local templates.stk ... DONE! Calculating md5 for local scipion_016.pos ... DONE! Calculating md5 for local scipion_129.pos ... DONE! Calculating md5 for local scipion_019.pos ... DONE! Calculating md5 for local scipion_066.pos ... DONE! Calculating md5 for local scipion_142.pos ... DONE! Calculating md5 for local scipion_124.pos ... DONE! Calculating md5 for local 019.pos ... DONE! Calculating md5 for local 112.pos ... DONE! Calculating md5 for local scipion_068.pos ... DONE! Calculating md5 for local 069.pos ... DONE! Calculating md5 for local 068.pos ... DONE! Calculating md5 for local 006.pos ... DONE! Calculating md5 for local 116.pos ... DONE! Calculating md5 for local 142.pos ... DONE! Calculating md5 for local model_rotpca_model.xmd ... DONE! Calculating md5 for local scipion_069.pos ... DONE! Calculating md5 for local scipion_008.pos ... DONE! Calculating md5 for local model_particle_avg.xmp ... DONE! Calculating md5 for local scipion_112.pos ... DONE! Calculating md5 for local 106.pos ... DONE! Calculating md5 for local scipion_136.pos ... DONE! Calculating md5 for local scipion_060.pos ... DONE! Calculating md5 for local coordinates.sqlite ... DONE! Calculating md5 for local model_rotpca_model.stk ... DONE! Calculating md5 for local 128.pos ... DONE! Calculating md5 for local 008.pos ... DONE! Calculating md5 for local model_pca_model.stk ... DONE! Calculating md5 for local 060.pos ... DONE! Calculating md5 for local 066.pos ... DONE! Calculating md5 for local scipion_106.pos ... DONE! Calculating md5 for local scipion_151.pos ... DONE! Calculating md5 for local scipion_165.pos ... DONE! Calculating md5 for local 016.pos ... DONE! Calculating md5 for local model_svm.txt ... DONE! Calculating md5 for local 136.pos ... DONE! Calculating md5 for local relion_it020_data.star ... DONE! Calculating md5 for local relion_it020_data_newlabels.star ... DONE! Calculating md5 for local particles.sqlite ... DONE! Calculating md5 for local input_particles.star ... DONE! Calculating md5 for local 006.stk ... DONE! Calculating md5 for local averages.mrcs ... DONE! Calculating md5 for local particles.sqlite ... DONE! Calculating md5 for local relion_volumes.mrc ... DONE! Calculating md5 for local relion_it015_sampling.star ... DONE! Calculating md5 for local particles.sqlite ... DONE! Calculating md5 for local relion_it015_class002_angdist.bild ... DONE! Calculating md5 for local relion_it015_class001.mrc ... DONE! Calculating md5 for local relion_it015_data.star ... DONE! Calculating md5 for local relion_it015_class003.mrc ... DONE! Calculating md5 for local relion_it015_classes_scipion.sqlite ... DONE! Calculating md5 for local relion_it015_optimiser.star ... DONE! Calculating md5 for local relion_it015_class003_angdist.bild ... DONE! Calculating md5 for local relion_volumes.stk ... DONE! Calculating md5 for local relion_it015_class002.mrc ... DONE! Calculating md5 for local relion_it015_class001_angdist.bild ... DONE! Calculating md5 for local volume.mrc ... DONE! Calculating md5 for local relion_it015_model.star ... DONE! Calculating md5 for local particles.mrcs ... DONE! Calculating md5 for local classes3D.sqlite ... DONE! Calculating md5 for local input_particles.mrcs ... DONE! Calculating md5 for local input_particles.star ... DONE! Calculating md5 for local relion_it010_class003.mrc ... DONE! Calculating md5 for local relion_it014_sampling.star ... DONE! Calculating md5 for local relion_it012_optimiser.star ... DONE! Calculating md5 for local relion_it012_sampling.star ... DONE! Calculating md5 for local relion_it000_sampling.star ... DONE! Calculating md5 for local relion_it005_class001.mrc ... DONE! Calculating md5 for local relion_it006_optimiser.star ... DONE! Calculating md5 for local relion_it007_class001.mrc ... DONE! Calculating md5 for local relion_it009_class003.mrc ... DONE! Calculating md5 for local relion_it013_class002.mrc ... DONE! Calculating md5 for local relion_it002_sampling.star ... DONE! Calculating md5 for local relion_it015_classes_scipion.sqlite ... DONE! Calculating md5 for local relion_it012_class002.mrc ... DONE! Calculating md5 for local relion_it006_model.star ... DONE! Calculating md5 for local relion_it013_optimiser.star ... DONE! Calculating md5 for local relion_it015_data_sorted_xmipp.star ... DONE! Calculating md5 for local relion_it004_class003.mrc ... DONE! Calculating md5 for local relion_it002_class001.mrc ... DONE! Calculating md5 for local relion_it011_data.star ... DONE! Calculating md5 for local relion_it006_class001.mrc ... DONE! Calculating md5 for local relion_it012_data.star ... DONE! Calculating md5 for local relion_it005_class003.mrc ... DONE! Calculating md5 for local relion_it008_class001.mrc ... DONE! Calculating md5 for local relion_it015_model.star ... DONE! Calculating md5 for local relion_it002_class002.mrc ... DONE! Calculating md5 for local relion_it004_optimiser.star ... DONE! Calculating md5 for local relion_it007_optimiser.star ... DONE! Calculating md5 for local relion_it000_data.star ... DONE! Calculating md5 for local relion_it007_class003.mrc ... DONE! Calculating md5 for local relion_it010_class002.mrc ... DONE! Calculating md5 for local relion_it010_model.star ... DONE! Calculating md5 for local relion_it015_angularDist_xmipp.xmd ... DONE! Calculating md5 for local relion_it008_class002.mrc ... DONE! Calculating md5 for local relion_it014_class003.mrc ... DONE! Calculating md5 for local relion_it004_data.star ... DONE! Calculating md5 for local relion_it006_class003.mrc ... DONE! Calculating md5 for local relion_it002_optimiser.star ... DONE! Calculating md5 for local relion_it013_class001.mrc ... DONE! Calculating md5 for local relion_it008_data.star ... DONE! Calculating md5 for local relion_it011_optimiser.star ... DONE! Calculating md5 for local relion_it009_data.star ... DONE! Calculating md5 for local relion_it004_model.star ... DONE! Calculating md5 for local relion_it003_class001.mrc ... DONE! Calculating md5 for local relion_it005_optimiser.star ... DONE! Calculating md5 for local relion_it001_class003.mrc ... DONE! Calculating md5 for local relion_it005_sampling.star ... DONE! Calculating md5 for local relion_it013_sampling.star ... DONE! Calculating md5 for local relion_it015_optimiser.star ... DONE! Calculating md5 for local relion_it013_class003.mrc ... DONE! Calculating md5 for local relion_it003_optimiser.star ... DONE! Calculating md5 for local relion_it007_data.star ... DONE! Calculating md5 for local relion_it014_model.star ... DONE! Calculating md5 for local relion_it015_class002.mrc ... DONE! Calculating md5 for local relion_it011_class002.mrc ... DONE! Calculating md5 for local relion_it001_data.star ... DONE! Calculating md5 for local relion_it006_sampling.star ... DONE! Calculating md5 for local relion_it002_data.star ... DONE! Calculating md5 for local relion_it003_class003.mrc ... DONE! Calculating md5 for local relion_it007_sampling.star ... DONE! Calculating md5 for local relion_it008_class003.mrc ... DONE! Calculating md5 for local relion_it004_sampling.star ... DONE! Calculating md5 for local relion_it011_sampling.star ... DONE! Calculating md5 for local relion_it008_model.star ... DONE! Calculating md5 for local relion_it005_class002.mrc ... DONE! Calculating md5 for local relion_it015_class001.mrc ... DONE! Calculating md5 for local relion_it015_data.star ... DONE! Calculating md5 for local relion_it010_data.star ... DONE! Calculating md5 for local relion_it004_class001.mrc ... DONE! Calculating md5 for local relion_it015_class003.mrc ... DONE! Calculating md5 for local relion_it001_class001.mrc ... DONE! Calculating md5 for local relion_it002_class003.mrc ... DONE! Calculating md5 for local relion_it006_data.star ... DONE! Calculating md5 for local relion_it004_class002.mrc ... DONE! Calculating md5 for local relion_it001_sampling.star ... DONE! Calculating md5 for local relion_it001_optimiser.star ... DONE! Calculating md5 for local relion_it002_model.star ... DONE! Calculating md5 for local relion_it008_optimiser.star ... DONE! Calculating md5 for local relion_it013_data.star ... DONE! Calculating md5 for local relion_it007_model.star ... DONE! Calculating md5 for local relion_it013_model.star ... DONE! Calculating md5 for local relion_it010_class001.mrc ... DONE! Calculating md5 for local relion_it010_sampling.star ... DONE! Calculating md5 for local relion_it000_class002.mrc ... DONE! Calculating md5 for local relion_it008_sampling.star ... DONE! Calculating md5 for local relion_it000_optimiser.star ... DONE! Calculating md5 for local relion_it010_optimiser.star ... DONE! Calculating md5 for local relion_it015_sampling.star ... DONE! Calculating md5 for local relion_it003_class002.mrc ... DONE! Calculating md5 for local relion_it009_optimiser.star ... DONE! Calculating md5 for local relion_it011_class001.mrc ... DONE! Calculating md5 for local relion_it012_model.star ... DONE! Calculating md5 for local relion_it009_model.star ... DONE! Calculating md5 for local relion_it009_class002.mrc ... DONE! Calculating md5 for local relion_it000_model.star ... DONE! Calculating md5 for local relion_it011_class003.mrc ... DONE! Calculating md5 for local relion_viewer_volumes.xmd ... DONE! Calculating md5 for local relion_it014_optimiser.star ... DONE! Calculating md5 for local relion_it014_class001.mrc ... DONE! Calculating md5 for local relion_it011_model.star ... DONE! Calculating md5 for local relion_it009_sampling.star ... DONE! Calculating md5 for local relion_it014_class002.mrc ... DONE! Calculating md5 for local relion_it005_data.star ... DONE! Calculating md5 for local relion_it014_data.star ... DONE! Calculating md5 for local relion_it003_model.star ... DONE! Calculating md5 for local relion_it007_class002.mrc ... DONE! Calculating md5 for local relion_it003_sampling.star ... DONE! Calculating md5 for local relion_it005_model.star ... DONE! Calculating md5 for local relion_it001_model.star ... DONE! Calculating md5 for local relion_it000_class003.mrc ... DONE! Calculating md5 for local relion_it000_class001.mrc ... DONE! Calculating md5 for local relion_it012_class003.mrc ... DONE! Calculating md5 for local relion_it012_class001.mrc ... DONE! Calculating md5 for local relion_it001_class002.mrc ... DONE! Calculating md5 for local relion_it006_class002.mrc ... DONE! Calculating md5 for local relion_it009_class001.mrc ... DONE! Calculating md5 for local relion_it003_data.star ... DONE! Calculating md5 for local run.stderr ... DONE! Calculating md5 for local run.db ... DONE! Calculating md5 for local run.stdout ... DONE! Calculating md5 for local run.log ... DONE! Calculating md5 for local steps.sqlite ... DONE! Calculating md5 for local iterations_changes_xmipp.xmd ... DONE! Calculating md5 for local classify3d_small_it038_sampling.star ... DONE! Calculating md5 for local classify3d_small_it038_optimiser.star ... DONE! Calculating md5 for local classify3d_small_it038_model.star ... DONE! Calculating md5 for local classify3d_small_it038_data.star ... DONE! Calculating md5 for local input_particles.mrcs ... DONE! Calculating md5 for local input_particles.star ... DONE! Calculating md5 for local relion_sampling.star ... DONE! Calculating md5 for local relion_it000_sampling.star ... DONE! Calculating md5 for local relion_it000_half2_model.star ... DONE! Calculating md5 for local relion_it000_half1_model.star ... DONE! Calculating md5 for local relion_it025_optimiser.star ... DONE! Calculating md5 for local relion_it025_data.star ... DONE! Calculating md5 for local relion_data.star ... DONE! Calculating md5 for local relion_it025_sampling.star ... DONE! Calculating md5 for local relion_it000_half1_classes.mrcs ... DONE! Calculating md5 for local relion_it000_optimiser.star ... DONE! Calculating md5 for local relion_it025_half2_class001.mrc ... DONE! Calculating md5 for local relion_model.star ... DONE! Calculating md5 for local relion_it001_half1_classes.mrcs ... DONE! Calculating md5 for local relion_it025_half2_model.star ... DONE! Calculating md5 for local relion_it025_half1_class001.mrc ... DONE! Calculating md5 for local relion_it000_half2_classes.mrcs ... DONE! Calculating md5 for local relion_it001_sampling.star ... DONE! Calculating md5 for local relion_it001_optimiser.star ... DONE! Calculating md5 for local relion_it001_half1_model.star ... DONE! Calculating md5 for local relion_it001_half2_classes.mrcs ... DONE! Calculating md5 for local relion_it025_half1_model.star ... DONE! Calculating md5 for local relion_it001_data.star ... DONE! Calculating md5 for local relion_it000_data.star ... DONE! Calculating md5 for local relion_class001.mrc ... DONE! Calculating md5 for local relion_it001_half2_model.star ... DONE! Calculating md5 for local run.stderr ... DONE! Calculating md5 for local run.db ... DONE! Calculating md5 for local run.stdout ... DONE! Calculating md5 for local run.log ... DONE! Calculating md5 for local steps.sqlite ... DONE! Calculating md5 for local Falcon_2012_06_12-16_55_40_0_movie_aligned_mic_DW.mrcs ... DONE! Calculating md5 for local Falcon_2012_06_12-14_33_35_0_movie_aligned_mic_DW.mrcs ... DONE! Calculating md5 for local Falcon_2012_06_12-17_26_54_0_movie_aligned_mic_DW.mrcs ... DONE! Calculating md5 for local relion_data.star ... DONE! Calculating md5 for local relion_model.star ... DONE! Calculating md5 for local input_particles.mrcs ... DONE! Calculating md5 for local classes2D.sqlite ... DONE! Calculating md5 for local input_particles.star ... DONE! Calculating md5 for local relion_it015_optimiser.star ... DONE! Calculating md5 for local relion_it015_sampling.star ... DONE! Calculating md5 for local relion_it015_classes_scipion_selection.sqlite ... DONE! Calculating md5 for local relion_it015_classes.mrcs ... DONE! Calculating md5 for local relion_it015_data.star ... DONE! Calculating md5 for local relion_it015_model.star ... DONE! Calculating md5 for local relion_it015_classes_scipion.sqlite ... DONE! Calculating md5 for local run.stderr ... DONE! Calculating md5 for local run.db ... DONE! Calculating md5 for local run.stdout ... DONE! Calculating md5 for local run.log ... DONE! Calculating md5 for local steps.sqlite ... DONE! Verifying MD5s... ...done. Updated files: 0 [ RUN OK ] TestImageHandler.testExistLocation (0.000 secs) [ RUN OK ] TestImageHandler.testGetDimensions (0.005 secs) Converting: /data2/bwang/software/scipion/data/tests/xmipp_tutorial/micrographs/BPV_1386.mrc -> /tmp/BPV_1386.img [ FAILED ] TestImageHandler.test_convertMicrographs

Traceback (most recent call last): File "/data2/bwang/software/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/plugin.py", line 296, in _tryImportFromPlugin output = getattr(importlib.import_module(module), submodule) File "/data2/bwang/software/anaconda3/envs/scipion3/lib/python3.8/importlib/ init.py", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "", line 1014, in _gcd_import File "", line 991, in _find_and_load File "", line 961, in _find_and_load_unlocked File "", line 219, in _call_with_frames_removed File "", line 1014, in _gcd_import File "", line 991, in _find_and_load File "", line 973, in _find_and_load_unlocked ModuleNotFoundError: No module named 'eman2'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/data2/bwang/software/anaconda3/envs/scipion3/lib/python3.8/unittest/case.py", line 60, in testPartExecutor yield File "/data2/bwang/software/anaconda3/envs/scipion3/lib/python3.8/unittest/case.py", line 676, in run self._callTestMethod(testMethod) File "/data2/bwang/software/anaconda3/envs/scipion3/lib/python3.8/unittest/case.py", line 633, in _callTestMethod method() File "/data2/bwang/software/anaconda3/envs/scipion3/lib/python3.8/site-packages/pwem/tests/data/test_data.py", line 255, in test_convertMicrographs ih.convert(micFn, outFn) File "/data2/bwang/software/anaconda3/envs/scipion3/lib/python3.8/site-packages/pwem/emlib/image/image_handler.py", line 158, in convert convertImage = Domain.importFromPlugin('eman2.convert', File "/data2/bwang/software/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/plugin.py", line 305, in importFromPlugin output = _tryImportFromPlugin(objects) File "/data2/bwang/software/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/plugin.py", line 302, in _tryImportFromPlugin Domain.pluginNotFound(plugName, errMsg, doRaise) File "/data2/bwang/software/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/plugin.py", line 448, in pluginNotFound raise Exception("\n\n" + raiseMsg) Exception:

error when importing from eman2: No module named 'eman2' File "", line 991, in _find_and_load Check the plugin manager (Configuration->Plugins in Scipion manager window) or use 'scipion installp --help --checkUpdates' in the command line to check for upgrades, it could be a versions compatibility issue.

[ RUN OK ] TestImageHandler.test_convertMovie (0.129 secs) [ RUN OK ] TestImageHandler.test_createEmptyImage (0.006 secs) Converting: (1, '/data2/bwang/software/scipion/data/tests/movies/c3-adp-se-xyz-0228_200.tif') -> /tmp/c3-adp-se-xyz-0228_200.mrc [ RUN OK ] TestImageHandler.test_readCompressedTIF (0.558 secs) Converting: /data2/bwang/software/scipion/data/tests/movies/SuperRef_c3-adp-se-xyz-0228_001.dm4 -> /tmp/SuperRef_c3-adp-se-xyz-0228_001.mrc [ RUN OK ] TestImageHandler.test_readDM4 (0.252 secs) [ RUN OK ] TestImageHandler.test_scaleStack (0.315 secs) Running command: xmipp_image_resize -i /data2/bwang/software/scipion/data/tests/xmipp_tutorial/masks/mask.vol -o /tmp/mask.vol --dim 128 === XMIPP_WARNING === Do not apply large scale factor using B-splines choose fourier option. Input File: /data2/bwang/software/scipion/data/tests/xmipp_tutorial/masks/mask.vol Output File: /tmp/mask.vol Running command: xmipp_transform_threshold -i /tmp/mask.vol --select below 0 --substitute value 0 Input File: /tmp/mask.vol Selection method: below Threshold: 0 Substitution method: value New value: 0 ** Running command: xmipp_transform_threshold -i /tmp/mask.vol --select above 1 --substitute value 1 Input File: /tmp/mask.vol Selection method: above Threshold: 1 Substitution method: value New value: 1 [ RUN OK ] TestImageHandler.test_truncateMask (0.719 secs)

python3 /data2/bwang/software/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/apps/pw_sync_data.py --download model Selected datasets: model Local copy of dataset model detected. Checking for updates... Verifying MD5s... ...done. Updated files: 0 [ RUN OK ] TestSetOfClasses2D.test_basics (0.015 secs) getExtraLogInfo failed: list index out of range getExtraLogInfo failed: list index out of range getExtraLogInfo failed: list index out of range getExtraLogInfo failed: list index out of range [ RUN OK ] TestSetOfClasses2D.test_subsetsFromSelection (0.014 secs) Creating project at: /data1/bwang/cryoem/ScipionUserData/projects/dummy_protocol/project.sqlite ** Running command: 'python3 /data2/bwang/software/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/apps/pw_protocol_run.py "/data1/bwang/cryoem/ScipionUserData/projects/dummy_protocol" "Runs/000002_EMProtocol/logs/run.db" 2' getExtraLogInfo failed: list index out of range

/data1/bwang/cryoem/ScipionUserData/projects/dummy_protocol/Runs/000002_EMProtocol/coordinates.sqlite Loop with INDEX took: 0:00:00.335310 Loop with INDEX and proper code, took: 0:00:00.164990 Loop with NO INDEX took: 0:00:01.388179 Loop with NO INDEX but proper code, took: 0:00:00.147043 getExtraLogInfo failed: list index out of range [ RUN OK ] TestSetOfCoordinates.test_mapper (2.970 secs) python3 /data2/bwang/software/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/apps/pw_sync_data.py --download xmipp_tutorial Selected datasets: xmipp_tutorial Local copy of dataset xmipp_tutorial detected. Checking for updates... Verifying MD5s... ...done. Updated files: 0 getExtraLogInfo failed: list index out of range getExtraLogInfo failed: list index out of range [ RUN OK ] TestSetOfMicrographs.testCreate (0.148 secs) Reading gold micrographs from: /data2/bwang/software/scipion/data/tests/xmipp_tutorial/gold/micrographs2_gold.sqlite [ RUN OK ] TestSetOfMicrographs.testRead (0.001 secs) Creating project at: /data1/bwang/cryoem/ScipionUserData/projects/dummy_protocol/project.sqlite Running command: 'python3 /data2/bwang/software/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/apps/pw_protocol_run.py "/data1/bwang/cryoem/ScipionUserData/projects/dummy_protocol" "Runs/000002_EMProtocol/logs/run.db" 2' [ RUN OK ] TestSetOfMicrographs.test_mapper (1.631 secs) python3 /data2/bwang/software/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/apps/pw_sync_data.py --download xmipp_tutorial Selected datasets: xmipp_tutorial Local copy of dataset xmipp_tutorial detected. Checking for updates... Verifying MD5s... ...done. Updated files: 0 [ RUN OK ] TestSetOfParticles.test_getFiles (0.118 secs) Creating a set of 10000 particles. (set SCIPION_TEST_HUGE environment var to other value) [ RUN OK ] TestSetOfParticles.test_hugeSet (0.449 secs) Creating a set of 10000 particles. (set SCIPION_TEST_HUGE environment var to other value) Writing metadata to: /data1/bwang/cryoem/ScipionUserData/Tests/TestSetOfParticles/huge_set.xmd [ RUN OK ] TestSetOfParticles.test_hugeSetToMd (0.051 secs) Creating a set of 10000 particles. (set SCIPION_TEST_HUGE environment var to other value) Writing to text file: /data1/bwang/cryoem/ScipionUserData/Tests/TestSetOfParticles/huge_set.txt [ RUN OK ] TestSetOfParticles.test_hugeSetToText (0.002 secs) Creating project at: /data1/bwang/cryoem/ScipionUserData/projects/dummy_protocol/project.sqlite Running command: 'python3 /data2/bwang/software/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/apps/pw_protocol_run.py "/data1/bwang/cryoem/ScipionUserData/projects/dummy_protocol" "Runs/000002_EMProtocol/logs/run.db" 2' [ RUN OK ] TestSetOfParticles.test_mapper (0.925 secs) getExtraLogInfo failed: list index out of range getExtraLogInfo failed: list index out of range getExtraLogInfo failed: list index out of range [ RUN OK ] TestSetOfParticles.test_orderBy (0.006 secs) writing particles to: /data1/bwang/cryoem/ScipionUserData/Tests/TestSetOfParticles/particles.sqlite getExtraLogInfo failed: list index out of range getExtraLogInfo failed: list index out of range [ RUN OK ] TestSetOfParticles.test_readStack (0.339 secs) [ RUN OK ] TestTransform.test_clone (0.001 secs) [ RUN OK ] TestTransform.test_scale (0.000 secs) [ RUN OK ] TestTransform.test_scaleShifts (0.000 secs)

[==========] run 32 tests (26.013 secs) [ FAILED ] 1 tests [ PASSED ] 31 tests

— Reply to this email directly, view it on GitHub https://github.com/scipion-em/scipion-pyworkflow/issues/319#issuecomment-1011353978, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAF7ZYPWZWEXLWZ7IEDEED3UVXE7XANCNFSM5KFVMSSQ . You are receiving this because you commented.Message ID: @.***>

@thibaut1998e , you still in the same situation?

I have just seen a similar issue when on the left panel I could see imod protocols but not aretomo, despite both plugins being installed. Ctrl+F also would not show aretomo protocol. To make it even more puzzling the problem showed up only when using ssh but not when starting scipion locally.

The problem was traced back to eman2 python being sourced in user's .cshrc file, which somehow conflicted with scipion's python

Do you know which variable was causing the issue ... PYTHON PATH.. other?

El jue., 8 feb. 2024 15:51, Grigory Sharov @.***> escribió:

I have just seen a similar issue when on the left panel I could see imod protocols in the list but not aretomo, despite both plugins being installed. Ctrl+F also would not show aretomo protocol. The problem was traced back to eman2 python being sourced in user's .cshrc file, which somehow conflicted with scipion's python

— Reply to this email directly, view it on GitHub https://github.com/scipion-em/scipion-pyworkflow/issues/319#issuecomment-1934283543, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAF7ZYL4MSICADMGMIA452TYSTRALAVCNFSM5KFVMSS2U5DIOJSWCZC7NNSXTN2JONZXKZKDN5WW2ZLOOQ5TCOJTGQZDQMZVGQZQ . You are receiving this because you commented.Message ID: @.***>

has to be PYTHONPATH

scipion-em / scipion-pyworkflow

Import tab empty in the interface #319