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Appion/Leginon 3.3

closed

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320 issues   (274 closed — 46 open)

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10/13
Related issues
Leginon - Bug #1198: Gonimodeler measure button does not recover from "preset is unknown error" after a preset is sent Actions
Leginon - Bug #3016: need to account for different projection submode orientation for image shift Actions
Leginon - Bug #3033: jahc finder error when template is larger than image Actions
Bug #3752: Generating missing virtual substack from virtual substack gives header nz is None error Actions
Leginon - Bug #3757: FutureWarning: comparison to `None` will result in an elementwise object comparison in the future. Actions
Bug #4016: ctffind4 crashes when resmax is low Actions
Bug #4028: polishStack.py box too small if the particle stack is binned but not the ddstack that will be processed Actions
Bug #4055: eman whole image phase flipping does not take non-square image Actions
Leginon - Bug #4065: K2 shutter control on system with FEI cameras Actions
Bug #4085: Rubinstein Particle Polishing polishStich.py output have wrong mrc header Actions
Bug #4088: uploaded images failed frealign preparation due to lack of sensor pixel size Actions
Bug #4089: frealign refine form parameter import gave wrong lp hp Actions
Bug #4106: error msg from auto align tilt pair Actions
Leginon - Bug #4114: Insert/Retract automated aperture according to jeol.cfg settings Actions
Bug #4122: ctf plot for envelope normalization looks wrong on an unusually good image Actions
Bug #4137: Krios1 K2 references were not copied Actions
Bug #4140: Manual Masker does not Update Donedict when Combining with Automasker Run Actions
Bug #4148: continue AppionLoop if a image gives invalid result Actions
Bug #4152: Stand alone DogPicker only picks in square area ? Actions
Bug #4164: appionPBS submit parallel jobs too fast for some clusters Actions
Bug #4167: apParallelTasks.py apTaskMonitor.py do not run Actions
Leginon - Bug #4173: projects not sorted by name in Leginon setup wizard Actions
Leginon - Bug #4176: all mis-spelled leginon client hosts show up as history of clients Actions
Bug #4179: multiimgassessor.php updates mask status when switching maskruns with the status of the previous run Actions
Bug #4182: validation to prevent bad values set in makeDDStackForm Actions
Bug #4187: image contrast invert option for DoGPicker and Template Picker are confusing Actions
Bug #4188: makeDEAlignedSum.py requires display setting to produce summary image Actions
Bug #4190: DogPicker has two maxsize flags Actions
Leginon - Bug #4192: mrc file written by mrc.py does not include extyp and nversion Actions
Bug #4194: Falcon frame file waiting loop looks for 0.mrc Actions
Bug #4198: mathdomain error in printSummary of imageloader.py after a few uploads Actions
Bug #4204: catch error in validation and commit and move on Actions
Bug #4205: tanh Filter fails on rectangluar images Actions
Bug #4208: users in guest group should not be allowed to process data Actions
Bug #4212: Template Picking - Unknown commandline options Actions
Bug #4217: ctfreport.php and ctfdownload.php results are not separated by preset Actions
Leginon - Bug #4234: ddinfo.py Actions
Bug #4237: pillow uses frombytes not fromstring to read from buffer Actions
Bug #4241: different ctf validation fit between super resolution bin=1 and bin=2 Actions
Leginon - Bug #4244: RCT tracking fail on gold grid Actions
Leginon - Bug #4251: tomography node imageviewer image value scales badly by default Actions
Bug #4252: manualmasker.py got an recursion depth exceeded error from numpil.fromstring while saving mask to png format Actions
Bug #4254: OptiMod nproc allows only 1 Actions
Bug #4262: download CTF calculations fails Actions
Bug #4280: ctffind4 parameter displayed in the pop up of ctfreport run table are not complete Actions
Leginon - Bug #4294: Eucentric height measurement by stage tilt does not return to zero tilt if an exception occurs during the measurement Actions
Leginon - Bug #4296: Screen up and down buttons in Beam Size Calibrator is not linked to a function Actions
Bug #4297: redux cache is not identified by overlay Actions
Leginon - Bug #4312: removequeue.php does not work Actions
Bug #4318: Ctffind4 form need to validate bestdb against nominal Actions
Bug #4320: ctffind4 add check for --bestdb --nominal Actions
Bug #4328: can not unhide hidden 3d densities from myamiweb Actions
Leginon - Bug #4331: only TargetFinder with focus target should reset last focused target list Actions
Leginon - Bug #4332: SingleFocuser needs its own settings Actions
Leginon - Bug #4335: checkBeamTilt randomly found values from wrong prejection mode Actions
Bug #4338: Template picking false positives on the sides of the micrographs Actions
Leginon - Bug #4391: phase correlator invalid value encountered in divid Actions
Leginon - Bug #4392: can not write jpg image if min is the same as max Actions
Bug #4396: Relion 2d alignment fails on upload with empty classes Actions
Bug #4403: aux directory prevents git checkout on Windows Actions
Leginon - Bug #4448: Show the actual acquired time of derived image Actions
Bug #4454: makestack does not recognize frame aligned preset other than "-a" in params as a result of dd stack Actions
Bug #4455: Exception in returning geDoseFromImage in apDatabase.py Actions
Bug #4460: ctfreport.php info pop up for ctffind4 does not include the highest resolution it fits to Actions
Bug #4472: setUseGPUFlat fails Actions
Leginon - Bug #4474: Analog direct detector needs dark image acquired immediately before bright image when calculating norm Actions
Leginon - Bug #4475: various j1230 problem with bad stage movement and defocus setting Actions
Bug #4481: ctffind 3 not working Actions
Leginon - Bug #4487: mrc header exttype keyword incorrect Actions
Leginon - Bug #4492: start simulate target on acquisition tool does not reset player Actions
Bug #4500: gautomatch fails Actions
Bug #4505: apCtf crashes on bad display rather than moving on Actions
Bug #4533: DE20 frame transfer -- wrong frames being transferred Actions
Leginon - Bug #4537: stage position does not return after going to reference target if have exception when Focus node is moved by image shift Actions
Leginon - Bug #4538: Phase plate aligner charge phase plate wihout first wait for drift to settle Actions
Bug #4544: frame alignment log filename from MotionCor includes binning Actions
Leginon - Bug #4547: validatemrc2014.py bugs Actions
Bug #4556: makestack2.py acecorrect error caused by extra phase shift field Actions
Bug #4560: ctf 2D from package graph show up only in the default 2D graph Actions
Bug #4566: Relion 2D tool in appion uploads wrong results Actions
Leginon - Bug #4573: make sure users update phase plate aligner current patch position when Leginon is restarted. Actions
Bug #4585: DE20 frame alignment no longer use apDDprocess and database insertion error Actions
Bug #4591: gctf - nominal defocus entered twice in command line Actions
Bug #4595: parallel unlock failure Actions
Bug #4597: no stack created from rerun of makestack Actions
Bug #4614: Log file font color in Appion default to black so that it become invisible with black background Actions
Bug #4622: AverageStack fails with Stack is too large error when the computer has too much memory Actions
Leginon - Bug #4634: Setup wizard creates two session database entry with two different passcode Actions
Bug #4651: Xmipp Actions
Leginon - Bug #4655: New instrument does not show up in client list Actions
Leginon - Bug #4669: Align ZLP preset change too fast Actions
Leginon - Bug #4672: Leginon client listening port may be used by other applications Actions
Bug #4674: uploadMaxlikeAlignment.py particle insertion is slow Actions
Leginon - Bug #4678: z height go to another Actions
Leginon - Bug #4689: Leginon tomography reset learning not reset with custom value but take on the mag model Actions
Bug #4691: no mechanism is in use with register option in myamiweb Actions
Bug #4694: MotionCor2 log file error when Throw is not 0 or Trunc is not 0 Actions
Leginon - Bug #4714: Some image acquisition should never save frames Actions
Bug #4720: Makestack not working Actions
Bug #4725: Makestack fails to create average stack when generating only Eman boxes Actions
Bug #4726: makestack checks ctf values of images rejected by --best-image option Actions
Bug #4728: Makestack (mean filtering) fails Actions
Bug #4730: makestack ctf correction validation for tilted images fails when the session contains tomography data collection Actions
Bug #4739: makeDEAlignedSum.py still try to commit trajectory when no-commit is requested Actions
Bug #4741: switching cluster for appion job submission causes appion loop commit flag to change to on regardless testimage status Actions
Bug #4746: motionCor2 error when dose weighting mode is on but no dose Actions
Leginon - Bug #4768: Leginon module names conflict the python module names and causes crash on special case-insensitive file systems. Actions
Bug #4791: fatal error printing related to git repository checking when starting Leginon git sandbox Actions
Leginon - Bug #4801: new krios needs stage backlash correction in xy Actions
Leginon - Bug #4805: Falcon protector delays beam blank Actions
Leginon - Bug #4828: Parking reset alpha tilt even though the acquisition is at a tilt during the acquisition Actions
Leginon - Bug #4839: cdf scaling in myamiweb viewer gives error on some installation. Actions
Leginon - Bug #4870: leginon database session or project archive does not include all camera calibrations Actions
Leginon - Bug #4882: Leginon setup.py version error Actions
Leginon - Bug #4885: Redux image quality is poor / produces artifacts in imageviewer.php Actions
Leginon - Bug #4894: Defocus matrix query does not separate nano probe from micro probe values Actions
Leginon - Bug #4898: Alternate tilt scheme produces larger error than sequential and tracking failed between 30-40 degree on Krios but not Arctica Actions
Bug #4935: frame path can not be found on buffer server after alignment and moved to permanent frame path Actions
Leginon - Bug #4940: Multiple targeting of same holes Actions
Bug #4941: k-factor for DogPicker need to be between 1 and 5 Actions
Leginon - Bug #4951: Access Denied ComError in stage movement on Krios Actions
Bug #4960: uploadCtfEstimate.py does not work with new format with extra phase shift field Actions
Leginon - Bug #4988: raster finder not centerred on rectangular image Actions
Leginon - Bug #5047: ConfigParser reports NoSectionError when no config file is found Actions
Bug #5048: Generating missing stack file error Actions
Leginon - Bug #5050: default user set during myamiweb setup does not contain noleginon and advanced field entry Actions
Leginon - Bug #5059: stage alpha position slip over time Actions
Leginon - Bug #5060: tilt like parent does not work if the tilt is modified by focusing, alignment, or conditioning Actions
Bug #5072: uploadAppionParticles breaks when the particle coordinates is in float Actions
Bug #5079: Mean/std dev filtration failing Actions
Leginon - Bug #5114: Targeting drift away after multiple target adjustment Actions
Leginon - Bug #5145: make pyami surface.py appion independent Actions
Bug #5160: local plot field is not in all appion apCtfData Actions
Leginon - Bug #5161: pyami.filutil not found when running syscheck.py according to installation documentation Actions
Leginon - Bug #5164: pysetup.sh fails to install leginon Actions
Bug #5168: Using best db ctf estimate for new ctf estimation fails if it comes from gctf fast mode Actions
Bug #5169: Fails to find siblings of uploaded aligned image with -a label Actions
Leginon - Bug #5181: Bug in MSI-Tomography in Leginon trunk (or 3.3) version regarding changing exposure time with higher tilts and total dose Actions
Bug #5186: missed commit of ddinfo.py Actions
Leginon - Bug #5205: preset selection in myamiweb could not get the presets in leginon Actions
Leginon - Bug #5217: newer version of fs does not support recursive makedir Actions
Leginon - Bug #5255: testing of reference class moves to the reference target but does not move back. Actions
Leginon - Bug #5259: targetlist_reset_tilt not defined when simulate target in Focuser node Actions
Leginon - Bug #5263: redux cachefs may attempt to remove root diskcache_path Actions
Leginon - Bug #5281: tomography tilt correlator shift correction assume tilt axis is y Actions
Leginon - Bug #5291: tomography node displays image badly Actions
Bug #5295: apDDFrameAligner throws a parsing error with new MotionCor2_1.0.2 Actions
Leginon - Bug #5304: imagejpeg error on php 5.4 Actions
Leginon - Bug #5305: DE camera frame time selection needed in Corrector node Actions
Bug #5317: gctf phase shift graph not displayed in myamiweb Actions
Leginon - Bug #5347: clean up no longer used db table schema creation Actions
Bug #5354: need pixelsize and ctf phase shift in quickstack output star file to run relion processing Actions
Leginon - Bug #5370: imagestats graph does not display in myamiweb Actions
Leginon - Bug #5376: process target type settings default for Acquisition class node is meter instead of acquisition Actions
Leginon - Bug #5377: last cartridge is not loaded in Auto grid loader Actions
Leginon - Bug #5387: Ceta error - unable to get corrected image Actions
Leginon - Bug #5388: copy_mag_cal.py failed if no magnification exclusion needed Actions
Bug #5389: failed helical pick upload Actions
Leginon - Bug #5390: project summary link loose its login credential when webserver domain name is mapped to an ip instead Actions
Bug #5397: gctf.py: error: no such option: --refine_tilt Actions
Leginon - Bug #5404: removequeue.php does not insert dequeued targets to database from new installation Actions
Bug #5413: lm-bfgs Particle Polisher bugs Actions
Leginon - Bug #5417: xml initialization of database table field default 0 does not get applied Actions
Bug #5428: can not find siblings if the parent image was an reacquired image from target adjustment Actions
Bug #5435: divide by zero error in normalizeFromDarkAndBright Actions
Bug #5436: Norm image should not be calculated on every frame Actions
Leginon - Bug #5439: summary.php loads too slowly when the session becomes large Actions
Leginon - Bug #5445: rawtransfer.py not in path environment directives for standard installation Actions
Leginon - Bug #5446: multihole template index error for 9 hole template Actions
Leginon - Bug #5449: clean up in-development gui for release 3.3 Actions
Bug #5454: Strict Standards error in dogPicker form Actions
Bug #5455: quickstack get wrong pixelsize if the most recent image is not at the same pixel size as images in the particle pick images Actions
Bug #5456: apStack particle insertion failure if not all columns have value Actions
Bug #5457: learningStackCleaner.py need to be moved to appionlib Actions
Bug #5462: getFrameList function left over Actions
Bug #5469: No need to have user enter binning during image upload Actions
Bug #5475: uploadimage.php description not passed to command line Actions
Bug #5480: schema_update.py can not find new tags in branches not merged with git Actions
Leginon - Bug #5482: If more than one tem instrument is on the client, the tem description may not show up in slack notification Actions
Leginon - Bug #5485: open column valve first before execute in Reference node testing Actions
Bug #5502: frame correction sometimes flips the frames in the wrong way relative to the gain references Actions
Bug #5587: shift-only tilt series alignment broken Actions
Leginon - Bug #5617: Hardware dark reference acquisition during auto nitrogen fill corrupts the reference if K2 is not ready after early return movie collection Actions
Leginon - Bug #5625: tomography imageviewer error during initialization Actions
Leginon - Bug #5687: default for TiltListAlternator for MSI-T Tilt application can not be set in the gui Actions
Leginon - Bug #5871: application xml export does not contain application name Actions
Leginon - Bug #5898: autoinstaller checks sinedon import before configuration Actions
Bug #5925: ctf data file download is empty Actions
Leginon - Feature #3284: Tomography low-tilt first tilt scheme by alternating tilts in two tilt direction groups Actions
Feature #3358: john rubinstein's particle polisher Actions
Leginon - Feature #3668: A way to export and import settings between databases Actions
Leginon - Feature #3750: Gatan K2 Summit early return Actions
Leginon - Feature #3786: advance phase plate at fixed time interval Actions
Leginon - Feature #3814: program for copying leginon calibration Actions
Leginon - Feature #3850: Allow tilt +/- in beam-tilt based defocus measurement Actions
Feature #3859: template correlator runAppionLoop.php form conversion Actions
Feature #3889: Rubinstein Particle Polishing GUI Actions
Leginon - Feature #3909: account for image rotation in pixel to pixel transformation between mags Actions
Feature #3922: Frealign 9 with Appion Actions
Feature #3970: Simplify the particle picking interface Actions
Feature #3974: Add Gctf program to CTF menu Actions
Leginon - Feature #4009: tilt during movie acquisition Actions
Leginon - Feature #4034: download aligned tilt series from myamiweb page Actions
Leginon - Feature #4041: Put the screen down and measure screen current periodically Actions
Feature #4044: Make image-parallel appion loop submitable to cluster through scheduler Actions
Leginon - Feature #4051: beam shift calibration without condensed beam Actions
Leginon - Feature #4072: handle beam blanking between camera exchange of multiple retractable cameras Actions
Feature #4083: transfer stack into picks of unalign image if the ddstack specified for making picks is unaligned Actions
Leginon - Feature #4133: Display preview targets in web viewers Actions
Leginon - Feature #4142: Disable stage movement option when using image shift as the mover in presets manager Actions
Feature #4143: A way to update viewer image status from a file list Actions
Feature #4144: use Camera setup frame rotation to transform defects, references, and output in makeDEAlignedSum.py Actions
Leginon - Feature #4151: Copy grid atlas from an old session to new Actions
Leginon - Feature #4157: Offset focus target for gold grid to edge of the hole Actions
Leginon - Feature #4172: streamline automated holefinder set up Actions
Leginon - Feature #4175: help user recovering session beam tilt if crashed during tilting Actions
Leginon - Feature #4209: allow users to change session description Actions
Feature #4233: graph drift summary Actions
Leginon - Feature #4247: Scope selection for imaging sessions in web viewers Actions
Feature #4263: Port DBSCAN Automasker to Appion Actions
Feature #4267: deleteHidden.py Actions
Feature #4279: Show image and appion run stats by month when database is fairly new Actions
Leginon - Feature #4302: Stitch subsquare images into a quilt for target selection Actions
Feature #4308: display mrc files that has extension mrcs Actions
Leginon - Feature #4324: restore delete project owner function Actions
Leginon - Feature #4351: account for scale change of image shift coil due to defocus Actions
Feature #4378: Basic template picking Gautomatch function in Appion Actions
Leginon - Feature #4390: Make one instrument idle timeout button for all workflow Actions
Leginon - Feature #4418: Show exposure time range when it is outside the range Actions
Feature #4430: make radial averaged images of particle stack Actions
Feature #4438: fit phase shift from phase plate and display the results Actions
Feature #4444: Order Filenames by the time the original images are taken, not the file generation time Actions
Feature #4471: make ace2correct to correct for phase shift Actions
Feature #4489: Add phase plate options to GCTF Actions
Leginon - Feature #4493: Log phase plate condition for long term record Actions
Feature #4510: update ctffind4.py to run on 4.1.5 Actions
Feature #4511: Use MotionCorr2 program to flip and rotate gain reference Actions
Feature #4512: Add MotionCor2 from UCSF to appion Actions
Feature #4514: transfer ctf results from non dose-weighted images to dose-weighted ones Actions
Feature #4524: prepRefineRelion support for relion 2.0 Actions
Leginon - Feature #4527: Avoid using bad phase plate patches and save which phase plate patch position is used in the image acquired in database Actions
Leginon - Feature #4528: Advance to next phase plate manually and reset timer for the next advance Actions
Leginon - Feature #4539: Charge phase plate and check drift also at beam tilt focusing position Actions
Feature #4545: run ctf estimation on ddstack movie Actions
Feature #4557: bestdb ctf estimation that uses package resolution as matrix Actions
Feature #4558: clean up getacepreset.php output Actions
Feature #4561: Tools for analyzing and display phase plate test results Actions
Feature #4563: gpuid input for MotionCor2 and motioncorr Actions
Feature #4564: Default changes on running average options for MotionCo2 vs motioncorr Actions
Leginon - Feature #4609: advance phase plate at fixed number of exposures Actions
Feature #4641: display parameters from an particle alignment stack Actions
Leginon - Feature #4668: classes for artica and halo-titan Actions
Leginon - Feature #4673: Align ZLP of energy filter when phase plate advances to the next position. Actions
Leginon - Feature #4688: Force user to add focus target in target finders Actions
Leginon - Feature #4710: MSI phase plate application Actions
Feature #4747: Option to transfer raw frames to a buffer host other than the permanent session frame path Actions
Leginon - Feature #4750: beam tilt focuser at an angle Actions
Leginon - Feature #4756: Display which phase plate and patch is used in webviewer Actions
Feature #4775: allow force insert of template Actions
Leginon - Feature #4795: Go to reference target to perform Reference class testing if available Actions
Leginon - Feature #4796: control settle time after returning from reference target Actions
Leginon - Feature #4803: fix the exposure time in tomography tilt series with preset exposure time Actions
Leginon - Feature #4852: Park microscope at high mag during auto nitrogen filling Actions
Leginon - Feature #4901: stack mrc frame images to a stack in MRCO style Actions
Leginon - Feature #4970: script to export and import leginon calibrations from one database to another through json file Actions
Feature #5037: overwrite frame path in DD frame processing Actions
Leginon - Feature #5067: set stage alpha tilt to given value when acquiring grid atlas Actions
Leginon - Feature #5070: Use navigator to move to reference target iteratively Actions
Leginon - Feature #5078: basic TEM control through Leginon Actions
Leginon - Feature #5083: Abort one tilt series in a target list Actions
Leginon - Feature #5089: Keep navigator node at the end of node selector Actions
Leginon - Feature #5090: control toolbar and node icon size better Actions
Feature #5130: simple appion loop tester Actions
Leginon - Feature #5132: Pause collection on K2 pc's at midnight Actions
Leginon - Feature #5142: allow autoloader grid exchange through tem control node Actions
Leginon - Feature #5156: Filter holes in MSI-T by minimal standard deviation of ice thickness stats Actions
Feature #5159: Check all sibling images for CTF info Actions
Leginon - Feature #5170: adjust the number of tilt that are not fitted in tomography Actions
Leginon - Feature #5182: Ability to check focus after every 5 or 10 deg tilts in MSI-Tomography and view tilt axis in leginon for MSI-Tomography Actions
Feature #5188: hide images according to criteria Actions
Leginon - Feature #5209: Set tilt angle for all targets from the sam parent image Actions
Leginon - Feature #5220: Status icon for "Allow user verification"? Actions
Leginon - Feature #5241: Send messages from leginon/appion to a slack channel Actions
Leginon - Feature #5244: scale matrix calibration to other magnifications Actions
Leginon - Feature #5260: hide description when importing presets from session of other users Actions
Leginon - Feature #5267: queuable tilted image data collection application Actions
Leginon - Feature #5280: add blob statistics display to MosaicClickTargetFinder used to make grid atlas or square atlas Actions
Leginon - Feature #5297: acquire grid atlas in a spiral pattern Actions
Leginon - Feature #5319: convolute hole lattice with hole template to make template to find the center of multiple holes Actions
Feature #5351: process a range of images in appionloop Actions
Leginon - Feature #5360: dbschema installation setup script Actions
Leginon - Feature #5361: More space between submit target and process queue tools Actions
Leginon - Feature #5362: Display mosaic name when submit targets Actions
Leginon - Feature #5367: Option to force normalize all lens after magnification change Actions
Leginon - Feature #5369: Last image acquired display in myamiweb Actions
Leginon - Feature #5374: A general camera calibration copying script Actions
Leginon - Feature #5394: fei.cfg to set instrument specific configuration for FEI scopes Actions
Leginon - Feature #5416: Force users to check corrector settings before acquire image Actions
Leginon - Feature #5420: Send slack message when there is error Actions
Leginon - Feature #5437: display tilt axis in target finder Actions
Feature #5438: option to force keep ddstack Actions
Feature #5460: make a separate web gui for making unaligned ddstack Actions
Leginon - Feature #5461: delay simulate loop testing start Actions
Leginon - Feature #5471: Restrict reference session research and creation to a specified path Actions
Leginon - Feature #5476: gui for hiding applications Actions
Leginon - Feature #5477: hide some holders from leginon setup wizard Actions
Leginon - Feature #5501: Separate smooth fit data point number by tilt direction Actions
Task #4201: consolidate calls to things needs to be done when an image is looped Actions
Task #4346: support git for myami installation and upgrade Actions
Task #4366: rewrite makeDDRawFrameStack.py and its library for better extension Actions
Task #4370: make DEAlign parameter webform a table that can be inherited outside BasicLoopForm Actions
Task #4379: break up apDDprocess.py to separate camera selection and alignment program selection Actions
Task #4572: rename mis-spelled MotionCorr2 to MotionCor2 Actions
Leginon - Task #4769: commit protomo2 appion features from Alex Noble Actions
Leginon - Task #5269: deprecate TiltAcquisition class Actions
Task #5318: avoid calling MySQLdb directly to connect when sinedon.cfg is read as input kwargs Actions
Leginon - Task #5415: 3.3 applications and initializations Actions
Task #5440: remove selection of features no longer supported in menu Actions
Task #5465: appion-protomo github for 3.3 release Actions
Task #5466: allow Leginon correctorclient.py to load without numextension installation Actions