v2.0.0-alpha.6

BIOMERO Scripts

• Bugfixes
  • Fix full workflow metadata being added to the result image again

Full Changelog: v2.0.0-alpha.5...v2.0.0-alpha.6

v2.0.0-alpha.5

BIOMERO changes:

• Bugfixes:
  • Added support for hyphens "-" in workflow parameters (e.g. in file suffix for cellprofiler measurements)

BIOMERO Scripts changes:

• Bugfixes:
  • Now actually fail the whole workflow (via the event sourced database, for the dashboard) when subtasks encounter errors (e.g. slurm job failed)
  • Fix attaching resulting images as attachment to the original image; was dependent on wrong variable
• New Features:
  • Add workflow ID to the image export folder filename (instead of timestamp)
  • Add workflow ID to the resulting image name iff we attach it (so you can find it in OMERO); not if we add it to a dataset, then user still controls the name
  • Add workflow ID to the resulting CSV file name when we attach it (so you can find it in OMERO)
  • Add workflow ID to the resulting description of images/datasets/logfile that we create in OMERO (not just 'job id')

Full Changelog: v2.0.0-alpha.4...v2.0.0-alpha.5

v2.0.0-alpha.4

What's Changed

• more reliable import for 5D images to omero by @maartenpaul in #3

New Contributors

• @maartenpaul made their first contribution in #3

Full Changelog: v2.0.0-alpha...v2.0.0-alpha.4

v2.0.0-alpha.3

• Align with BIOMERO v2.0.0-alpha.3

Full Changelog: v1.14.0...v2.0.0-alpha.3

v2.0.0-alpha.2

• To align with BIOMERO v2.0.0-alpha.2

Full Changelog: v1.14.0...v2.0.0-alpha.2

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