v2.0.0-alpha

• To work with BIOMERO v2.0.0-alpha
  • Main changes is to track all workflows via eventsourcing in a postgres database.
  • So every wf will have a unique UUID and we can extract all required metadata and track progress while it's running.
• Reorder folder names to promote the use of run_workflow and demote the use of the other scripts

Full Changelog: v1.14.0...v2.0.0-alpha

v1.14.0

• Allow duplicate parameter names by making them unique within (BI)OMERO scripts
  • This supports having multiple measurement workflows with similar parameters

Full Changelog: v1.13.0...v1.14.0

v1.13.0

• Bump to BIOMERO v1.13.0
• Add some improved handling of conversion versions, like show versions in check setup script

Full Changelog: v1.12.0...v1.13.0

v1.12.0

• Print BIOMERO version in Check Setup script
• BIOMERO v1.12.0: https://github.com/NL-BioImaging/biomero/releases/tag/v1.12.0

Full Changelog: v1.11.0...v1.12.0

v1.11.0

• Show descriptors for every wf (if you point at it)
• Change CSV file handling: upload as attachment if table fails

Full Changelog: v1.10.0...v1.11.0

v1.10.0

• Script for manual (remote) conversion
• Move unzipping of data to image transfer (to support conversion script above)
• Improve check setup script to also pull the sing.log for more info
• Align version with BIOMERO v1.10.0

Full Changelog: v1.9.0...v1.10.0

v1.9.0

• Bump to BIOMERO v1.9.0
• Move more script variable names to BIOMERO library so that we can import them correctly in other scripts

Full Changelog: v1.8.0...v1.9.0

v1.8.0

• Cleanup after conversion too
• Don't copy metadata from original images anymore (it copied datatype too)

Full Changelog: v1.7.1...v1.8.0

v1.7.1

Fix bugs:

• Slurm job now stops complaining about missing Singularity
• CANCELLED+ state of job array is now handled properly (if you cancel a job array...)
• Cleanup now also removes the large amount of converter logs made by the job array
• Reduced DEBUG logging of imported modules from OMERO and Paramiko
• Fixed a printing bug in the minimal slurm script
• Turned more BIOMERO-scripts print statements into logger statements

Full Changelog: v1.7.0...v1.7.1

v1.7.0

Finetuning!

• Added an Azure deployment for both BIOMERO and SLURM, go see the new tutorial!
• Made the init script async, because we cannot wait in OMERO for all the container images to download on SLURM. That does not scale.
  • Split up a few of the init methods into their own methods so you could run them seperately
  • Added a new script to check the 'progress' of available workflows on SLURM, called 'SLURM_check_setup'.
  • Will probably rename the 'init' category to 'admin' if we keep adding more scripts that are not for end-users but for OMERO admins.

Full Changelog: v1.6.0...v1.7.0