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Release 0.2.0 - #13

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delarosatrevin wants to merge 170 commits into

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devel

Commits on Dec 3, 2024
- Exporting OTF data to CryoSparc
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Commits on Dec 19, 2024
- Some updates in ProcessingPipeline
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Commits on Jan 4, 2025
- Added context manager for tmpDir in Path class
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- Created Batch class as a utility subclass from dict
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Commits on Jan 5, 2025
- Added helper Args class
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  c483317
- Bumped devel version
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  f2d5413
- Allow to pass input to process as stdin
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Commits on Jan 7, 2025
- Added functions to Batch class
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- Some fixs in Args
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Commits on Jan 9, 2025
- Minor fixes and new Table.fromDict function
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  b4543fa
- Moved ProcessingPipeline from emtools to emwrap
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Commits on Jan 11, 2025
- Introduced FolderManager class
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Commits on Jan 14, 2025
- Check if folder exists
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  918d65f
- Added helper function StarFile.getTableFromFile
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Commits on Jan 15, 2025
- added emt-star utility program
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Commits on Jan 24, 2025
- Allow to dump json files in the folder
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Commits on Jan 27, 2025
- Add more methods to Batch
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Commits on Jan 31, 2025
- Used another threading.Condition to allow maxsize in TaskQueue
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Commits on Feb 3, 2025
- Added utility to read image dimensions
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  7277664
- Added 'group_by' option to emt-star
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Commits on Feb 5, 2025
- Added prototype to split star files
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Commits on Feb 6, 2025
- Allow to pass print function
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  c9e710b
- Added more logging to Batch
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  6d23991
- Allow missing coordinate files
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  0f88eea
- Added queueMaxSize for TaskProcessor
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  39f1f6f
Commits on Feb 7, 2025
- Moved create to FolderManager
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  8ec00bb
- Added methods to Mdoc
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  3193b16
- Moved create to FolderManager
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  69ea1ca
Commits on Feb 11, 2025
- Working on Workflow tools
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  a333ffc
Commits on Feb 12, 2025
- More on Workflow
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  122ddc4
- Moved log function and more on Workflow
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  1e113fb
Commits on Feb 13, 2025
- Minor fixes in Workflow jobIndex
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  b2b868a
Commits on Feb 14, 2025
- Moved Acqusition and RelionStar to metadata
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  c938f7d
- Added function Job.hasOutput
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  b244b8a
Commits on Feb 17, 2025
- Added Timer to Batch
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  cdfa949
Commits on Feb 18, 2025
- Added Mdoc.glob and fixed circular import
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  41ab96d
- Added more funcs to Batch and new class MdocBatchManager
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  11643ed
- Added table for tiltseries
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  064744c
- Added global table for tiltseries
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  eefb14f
Commits on Feb 20, 2025
- Added Path.rsync method
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  edad74c
Commits on Feb 21, 2025
- Fixed typo
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  525e6df
Commits on Feb 24, 2025
- Fixed typos
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  c7b30bf
Commits on Feb 26, 2025
- Minor updates
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  7f6a751
Commits on Feb 28, 2025
- Added flush to log function
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  d0078f4
Commits on Mar 1, 2025
- Added Vars helper class
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  92fc202
Commits on Mar 3, 2025
- emt-image utility and added fractions.mrc as movie suffix
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  49c2af2
Commits on Mar 4, 2025
- Added some utilities
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  8c121bb
Commits on Mar 9, 2025
- Allow to avoid creation of batch folder
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  99be009
Commits on Mar 10, 2025
- Fixed bug in getTable with non-existing table
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  ee190c3
Commits on Mar 12, 2025
- Allow imageId in micrograph_table
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  1c428bb
- Added Timer.parse_timedelta function
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  f97daaf
Commits on Mar 16, 2025
- Moved dump function to FolderManager
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  c4d59b5
Commits on Mar 18, 2025
- Check if input star file exists
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  d8b183c
Commits on Mar 25, 2025
- Updated some utils methods
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  3803714
- Move utils methods
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  986ca87
- Merge branch 'devel' of github.com:3dem/emtools into devel
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  6037d64
Commits on Apr 13, 2025
- Allow additional options to rsync
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  7ae3bff
- Fixed error counting dirs
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  64d9633
- Fixed import
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  ec7774e
- Added option to count movies
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  de02625
Commits on Apr 18, 2025
- Added method EPU.count_movies
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Commits on May 5, 2025
- Make Process fail for Rsync and allow to check transfer size
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  2f872da
Commits on May 15, 2025
- Added duplicates check to emt-star and rename function to FolderManager
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  34ebd7b
- Print all duplicates
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  e6b2e89
Commits on May 20, 2025
- Added helper methods to determine filetype based on extension
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  5274a16
Commits on Jun 20, 2025
- Allow dict as input
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  b11656d
- Implemented TS batch manager from star input
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  33309cb
Commits on Jun 30, 2025
- Added utility functions to Batch and FolderManager
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  3e5f37a
Commits on Jul 12, 2025
- working on a gpu monitor tool
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  fd46e50
Commits on Jul 16, 2025
- Added WarpXml helper class
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  6e08731
Commits on Jul 22, 2025
- Added Batch.copy method
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  b55f6f0
Commits on Jul 24, 2025
- added dose properties to Acquisition class
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  b5f3db2
Commits on Aug 7, 2025
- allow string arguments
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  17dfd18
Commits on Aug 22, 2025
- emt-ps to catch program name in args
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  1e56134
Commits on Aug 23, 2025
- Improved Mdocs batch manager
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  285e839
Commits on Aug 25, 2025
- Added debug shortcut
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  b4a940c
Commits on Sep 2, 2025
- Allow to pass basename to link
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  bcda193
Commits on Sep 4, 2025
- Fix when there is no last file
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  8a956ce
Commits on Sep 30, 2025
- Some utils
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  ba7cee0
Commits on Nov 5, 2025
- Add rsync extra args at the end
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  957449e
Commits on Nov 10, 2025
- Fixed bug about new option computeFormat when writing StarFile tables
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  e5038df
Commits on Nov 11, 2025
- Method to clear a folder
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  bb00d65
- Added methods to read/write job.star and fixed bug in pipeline.star
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  40e240d
- Allow default to Workflow.getJob and added deleteJob
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  ee42714
Commits on Nov 12, 2025
- Allow left alignment in format and fixed boolean values
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  3084574
- Removed some debug print
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  f44430d
Commits on Nov 13, 2025
- Added method to worklflow Job.getOutput
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  25a8a26
- Added argument to write timeStamp
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  2d67b09
Commits on Nov 16, 2025
- Added missing requirement
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  87fc681
Commits on Dec 11, 2025
- Do not check stat if file does not exist
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  905d47d
Commits on Dec 16, 2025
- Added .eer as tiff image
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  c2c5553
Commits on Dec 22, 2025
- Added Table.cloneColumns method to create empty table using columns from another table
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  c102a8f
Commits on Jan 24, 2026
- Fixed double extension in .mdoc files
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  ae84c64
- Fixed handling of Relion's bool values
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  fe1c243
Commits on Jan 27, 2026
- Added method to validate missing data
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  02aaadc
Commits on Feb 1, 2026
- Updated Workflow class to use dict instead of lists
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  7941ba2
Commits on Feb 2, 2026
- Added method to clear inputs and more text extensions
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  2ed7f22
Commits on Feb 3, 2026
- Added subset method to Args
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  44b6966
Commits on Feb 6, 2026
- Added method to parse timedelta
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  533a906
Commits on Feb 11, 2026
- Add folder scanning and JSON snapshot functionality
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  b2a93cc
- added new textfiles extensions
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  699f173
- Added utility methods
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  0bf8762
Commits on Feb 23, 2026
- Added Thumbnail.Preview class and more file extensions
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  61e36b1
Commits on Mar 3, 2026
- Added helper class WarpPopulation
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  cf3f1b1
Commits on Mar 31, 2026
- Added a method to get starfile tables as dict
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  a515cd3
Commits on Apr 23, 2026
- Added extra validation for setting path in FolderManager
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  a1b00a3
Commits on Apr 27, 2026
- Added --relink option and fixed old options
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  eaf9928
Commits on May 4, 2026
- Added support for inverted_booleans and possible filters
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  0e6275c
Commits on May 5, 2026
- Fixed bug for possible checking
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  ddf4874
Commits on May 22, 2026
- Added compute hash and fixed rsync parsing for Mac
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  595f468
- Getting Species info from Warp output
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  f1163a8
Commits on Jun 13, 2026
- Handling ending slash in jobids for relion pipeline
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  f246b88
Commits on Jun 23, 2026
- Added relion tomo alignment constants
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  376e969
Commits on Jun 26, 2026
- Added more text file extensions
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  53721db
- Added option to print some STAR file columns
  delarosatrevin
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  e9d7452
- Merge pull request #12 from 3dem/relion5-compat
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  authored
  a087545
Commits on Jul 6, 2026
- TsStarBatchManager now also reads tsMdoc and is passed to the batch
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  committed
  a02e260
- Merge branch 'devel' of https://github.com/3dem/emtools into devel
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  committed
  54e36d4
- Added binary_boolean filter to get 0/1 for boolean params
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  d3a9215
- Condensed in elif
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  9c494b3
Commits on Jul 7, 2026
- Args subset function modified with multiple values
  Marchán
  committed
  94a3569
- Added Job.getInput method and renamed label to rlnTomoMdocFile
  delarosatrevin
  committed
  aadfed9
- Merge branch 'devel' of github.com:3dem/emtools into devel
  delarosatrevin
  committed
  3aa3a31
- Using regex to detect args with - or --
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  a471a37
- Added mdoc as text file
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  3fd53ff
Commits on Jul 8, 2026
- Some Relion tomo colums refactoring
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  e10db1d
Commits on Jul 15, 2026
- Pass the whole row as a dict
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  2ffde73
Commits on Jul 17, 2026
- Added some more text extension
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  9678161
Commits on Jul 23, 2026
Commits on Jul 24, 2026
- Allow to sort zsections by the DateTime value
  delarosatrevin
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  7025d8a
- Added methods to clearOutputs
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  4340bed
Commits on Jul 27, 2026
- Added alignment conversion from Imod to Relion and fixed comment space in STAR column headers
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  28caa8b
Commits on Jul 28, 2026
- Added some tomo functions to RelionStar
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  a481153
Commits on Jul 29, 2026
- Added helper methods
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  6888403
Commits on Aug 5, 2026
- Added method to getAcquisition from STAR file
  delarosatrevin
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  ff12028
- Bumped version to 0.2.0-rc260805
  delarosatrevin
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  4f390d5
- add alignment to xf conversion function
  Marchán
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  caebbee
Commits on Aug 10, 2026
- allow to checkChild given job pid
  delarosatrevin
  committed
  f8558e0
- Added methods to validate optimisation_sets.tar and particles.star
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  97ffc63
Commits on Aug 12, 2026
- fixed optimisation set validation
  delarosatrevin
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  0db72e3
- Added image helper methods
  delarosatrevin
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  e33269d
Commits on Aug 14, 2026
- Minor fix to detect volumes
  delarosatrevin
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  838d142
- Added Table.filter and Table.update, also accessible via emt-star
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  92987d5
Commits on Aug 17, 2026
- Merge remote-tracking branch 'origin/devel' into dmt_missalignment
  Marchán
  committed
  6d7c7a7
Commits on Aug 18, 2026
- Merge pull request #14 from 3dem/dmt_missalignment
  delarosatrevin
  authored
  ac70861
Commits on Aug 21, 2026
- Added more image info and constant labels
  delarosatrevin
  committed
  f3f5927
- Merge branch 'devel' of github.com:3dem/emtools into devel
  delarosatrevin
  committed
  740565e
Commits on Aug 24, 2026
- Make default output datatype more robust
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  committed
  fabe01f
Commits on Aug 28, 2026
- Added some methods to WarpPopulation helper class
  delarosatrevin
  committed
  6f0776f
- Allow batch.call to pass cwd
  delarosatrevin
  committed
  68deb8b
- Added method to convert Relion centered coordinates
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  committed
  a70e500
Commits on Sep 11, 2026
- Some fixes when clearing inputs
  delarosatrevin
  committed
  adecd67
- Added NumericList helper class
  delarosatrevin
  committed
  3d0a26f
- Working on fourier_crop and image display
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  committed
  8335ca7
Commits on Sep 15, 2026
- Added function to merge star files
  delarosatrevin
  committed
  934ccd9
- iterTable define types for NominalStageTiltAngle and TiltAxisAngle
  Marchán
  committed
  d0075c3
- Merge pull request #16 from 3dem/dmt_relion_tutorial
  delarosatrevin
  authored
  d52253c
Commits on Sep 18, 2026
- Improved system info functions
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  committed
  0006987
Commits on Sep 22, 2026
- Missed sysinfo script
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  7224630
- Return subprocess exit status and created Population digest
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  committed
  5366bf0
Commits on Sep 25, 2026
- Fixed unused tableNames cache
  delarosatrevin
  committed
  0a57665
Commits on Oct 1, 2026
- Parse single letter args
  delarosatrevin
  committed
  081d483
- Some fixes when monitoring STAR files
  delarosatrevin
  committed
  9c4ca35
- Fixed partial writes on star file monitoring
  delarosatrevin
  committed
  55969ac
Commits on Oct 6, 2026
- Add imagecodecs requirement
  
  Marchán
  and
  claude
  committed
  8e0e8a4
Commits on Oct 7, 2026
- Merge pull request #17 from 3dem/dmt_upsampling_eer
  delarosatrevin
  authored
  b6e1294
Commits on Oct 8, 2026
- Added more logs
  delarosatrevin
  committed
  57ac316
- Added more functions to WarpXml helper class
  delarosatrevin
  committed
  4e6a32e

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