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

v1.6.0

• Moved file conversion into its own job in BIOMERO, so now added this is an intermediate step in Run_Workflow.py. This fixes a possible deadlock if you have more 'parent' jobs than nodes on your cluster.

Full Changelog: v1.5.0...v1.6.0

v1.5.1

• Release BIOMERO v1.5.1

Perhaps just align biomero / biomero-scripts with minor versions in the future, not patch versions.
But for now, i'll just release both.

Full Changelog: v1.4.0...v1.5.1

v1.5.0

• (DEBUG) Unified logging from all scripts by default to biomero.log
• Update batch script to be up to date with workflow script

Full Changelog: v1.4.0...v1.5.0

v1.4.0

• Fix CellPose script to work with updated API
• Transfer ZARR with no options for channels (like OME-TIFF)
• Run export ZARR with the more generic omero host

Full Changelog: v1.3.0...v1.4.0

v1.3.0

• Extended support for CSV output from workflows. Now they can get uploaded automatically as OMERO.tables using the omero-metadata plugin (a new requirement). For example, it works with the spot counting workflow.

Note: this requires version 1.3.0 of biomero library too.

Full Changelog: v1.1.1...v1.3.0

v1.1.1

These are compatible with v1.1.1 of BIOMERO

Full Changelog: https://github.com/NL-BioImaging/biomero-scripts/commits/v1.1.1

Version 1

Publish the first version of the BIOMERO scripts to accompany the upcoming paper: BIOMERO.

Features:

• Initialize a Slurm environment
• Export data from OMERO to Slurm
• Import data from Slurm to OMERO
• Import job status / logs from Slurm to OMERO
• Run workflow on Slurm
• Run workflow batched on Slurm

Merry Christmas and a happy new year!

Full Changelog: https://github.com/NL-BioImaging/biomero-scripts/commits/v1.0.0