biomero - v2.0.0-alpha.6

BIOMERO Scripts

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

Full Changelog: https://github.com/NL-BioImaging/biomero/compare/v2.0.0-alpha.5...v2.0.0-alpha.6

- Python
Published by TorecLuik 11 months ago

biomero - 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: https://github.com/NL-BioImaging/biomero/compare/v2.0.0-alpha.4...v2.0.0-alpha.5

- Python
Published by TorecLuik 11 months ago

biomero - v2.0.0-alpha.4

What's Changed

• Improved zarr to multidimensional tiff converter by @maartenpaul in https://github.com/NL-BioImaging/biomero/pull/13
• Add data-bind and conversion-partition parameters by @maartenpaul in https://github.com/NL-BioImaging/biomero/pull/14

New Contributors

• @maartenpaul made their first contribution in https://github.com/NL-BioImaging/biomero/pull/13

Full Changelog: https://github.com/NL-BioImaging/biomero/compare/v2.0.0-alpha.3...v2.0.0-alpha.4

- Python
Published by TorecLuik 12 months ago

biomero - v2.0.0-alpha.3

• Also read config from /OMERO/slurm-config.ini (after /etc but before ~ ). This location is shared between OMERO containers generally.

Full Changelog: https://github.com/NL-BioImaging/biomero/compare/v2.0.0-alpha.2...v2.0.0-alpha.3

- Python
Published by TorecLuik about 1 year ago

biomero - v2.0.0-alpha.2

• Expand ~ to read config from user home dir.

Full Changelog: https://github.com/NL-BioImaging/biomero/compare/v2.0.0-alpha.1...v2.0.0-alpha.2

- Python
Published by TorecLuik about 1 year ago

biomero - v2.0.0-alpha.1

• Add the SlurmClient.from_config(config_only=True) option to load a lighter version of the SlurmClient that doesn't actually connect with Slurm or the database. This can be used for information / config calls, like finding out what workflows are configured.

Full Changelog: https://github.com/NL-BioImaging/biomero/compare/v2.0.0-alpha...v2.0.0-alpha.1

- Python
Published by TorecLuik about 1 year ago

biomero - v2.0.0-alpha

• Add full BIOMERO workflow execution tracking through eventsourcing and a postgres database

Full Changelog: https://github.com/NL-BioImaging/biomero/compare/v1.14.0...v2.0.0-alpha

- Python
Published by TorecLuik about 1 year ago

biomero - v1.14.0

• Bump to 1.14.0 for BIOMERO scripts update for duplicate parameter names
• Setup for multiple measurements workflows

Full Changelog: https://github.com/NL-BioImaging/biomero/compare/v1.13.0...v1.14.0

- Python
Published by TorecLuik over 1 year ago

biomero - v1.13.0

• Allow pulling a conversion container instead of building it on Slurm. This reduces the rights required on Slurm for BIOMERO.
  • We build and release our default converter with every BIOMERO version @ cellularimagingcf/convert_zarr_to_tiff, even if there are no changes. Just to be sure there is always a 'compatible' version to go with your BIOMERO version, which is true for the old way of doing it.
  • This image can be added in the slurm-config.ini under a new [CONVERTERS] subsection.
  • When you init the Slurm environment, it will check for this config and download this converter image. If there is no such config, it will default to previous behavior (which is building a Singularity image on the Slurm server itself).
  • Example setting: [CONVERTERS] # ------------------------------------- # Converters settings # ------------------------------------- # Settings for linking to external converters. # # By default, BIOMERO exports images as ZARR to the HPC. # But, the workflow you want to execute might require # a different filetype. E.g. most of our example workflows # require TIFF input files. # # By default we will build a converter on Slurm for you. # Theoretically you can add other converters here to pull # those instead. These should be available on dockerhub. # # ------------------------------------- # ZARR TO TIFF # ------------------------------------- # Uncomment this if you want to pull the image instead of # build it. E.g. if you don't have singularity build rights # on your Slurm. # # Please pin it to a specific version to reduce unforeseen errors. # # Key should be the types "X_to_Y" and value should be the docker image zarr_to_tiff=cellularimagingcf/convert_zarr_to_tiff:1.13.0

Full Changelog: https://github.com/NL-BioImaging/biomero/compare/v1.12.0...v1.13.0

- Python
Published by TorecLuik over 1 year ago

biomero - v1.13.0-alpha.6

Full Changelog: https://github.com/NL-BioImaging/biomero/compare/v1.13.0-alpha.5...v1.13.0-alpha.6

- Python
Published by TorecLuik over 1 year ago

biomero - v1.13.0-alpha.5

Full Changelog: https://github.com/NL-BioImaging/biomero/compare/v1.13.0-alpha.4...v1.13.0-alpha.5

- Python
Published by TorecLuik over 1 year ago

biomero - v1.13.0-alpha.4

Full Changelog: https://github.com/NL-BioImaging/biomero/compare/v1.13.0-alpha.3...v1.13.0-alpha.4

- Python
Published by TorecLuik over 1 year ago

biomero - v1.13.0-alpha.3

Full Changelog: https://github.com/NL-BioImaging/biomero/compare/v1.13.0-alpha.2...v1.13.0-alpha.3

- Python
Published by TorecLuik over 1 year ago

biomero - v1.13.0-alpha.2

Full Changelog: https://github.com/NL-BioImaging/biomero/compare/v1.13.0-alpha.1...v1.13.0-alpha.2

- Python
Published by TorecLuik over 1 year ago

biomero - v1.13.0-alpha.1

Full Changelog: https://github.com/NL-BioImaging/biomero/compare/v1.13.0-alpha...v1.13.0-alpha.1

- Python
Published by TorecLuik over 1 year ago

biomero - v1.13.0-alpha

• Builds the converter image so that we can pull it instead of build it

Full Changelog: https://github.com/NL-BioImaging/biomero/compare/v1.12.0...v1.13.0-alpha

- Python
Published by TorecLuik over 1 year ago

biomero - v1.12.0

• Conversion ZARR to TIFF: write TIFF with extra metadata for (handling of > 3 channels in) cellprofiler/imagej

Full Changelog: https://github.com/NL-BioImaging/biomero/compare/v1.11.0...v1.12.0

- Python
Published by TorecLuik almost 2 years ago

biomero - v1.11.0

• Bump for updated scripts v1.11.0
  • Improved CSV handling and description tooltips for all workflows.

Full Changelog: https://github.com/NL-BioImaging/biomero/compare/v1.10.0...v1.11.0

- Python
Published by TorecLuik almost 2 years ago

biomero - v1.10.0

• Bump for updated scripts v1.10.0

Full Changelog: https://github.com/NL-BioImaging/biomero/compare/v1.9.1...v1.10.0

- Python
Published by TorecLuik almost 2 years ago

biomero - v1.9.1

• Fix a breaking bug in the init method, introduced with escaping folder names. Should be able to setup new workflows again w/ v1.9.1.

Full Changelog: https://github.com/NL-BioImaging/biomero/compare/v1.9.0...v1.9.1

- Python
Published by TorecLuik almost 2 years ago

biomero - v1.9.0

What's Changed

• Fixed handling of OMERO datasets/folders with spaces in the name: #12
• Fixed handling of a GIT repo for (job) scripts #11
• changed target folder for slurm-config.ini in description by @jo-mueller in https://github.com/NL-BioImaging/biomero/pull/10

New Contributors

• @jo-mueller made their first contribution in https://github.com/NL-BioImaging/biomero/pull/10

Full Changelog: https://github.com/NL-BioImaging/biomero/compare/v1.8.0...v1.9.0

- Python
Published by TorecLuik almost 2 years ago

biomero - v1.8.0

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

Full Changelog: https://github.com/NL-BioImaging/biomero/compare/v1.7.1...v1.8.0

- Python
Published by TorecLuik almost 2 years ago

biomero - 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: https://github.com/NL-BioImaging/biomero/compare/v1.7.0...v1.7.1

- Python
Published by TorecLuik almost 2 years ago

biomero - 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 'SLURMchecksetup'.
  • 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: https://github.com/NL-BioImaging/biomero/compare/v1.6.0...v1.7.0

- Python
Published by TorecLuik almost 2 years ago

biomero - v1.6.0

• Separated file conversion and slurm workflow into 2 jobs to avoid a deadlock
• Added a method to specifically run file conversion to biomero
• Added a slim / simple result class SlurmJob, to allow easier waiting on job completion on slurm. Note it is not asynchronous / concurrent. You just wait the current thread at this moment (which works fine with 1 workflow per omero job).
• Fixed the job status methods to handle job arrays too

Full Changelog: https://github.com/NL-BioImaging/biomero/compare/v1.5.1...v1.6.0

- Python
Published by TorecLuik almost 2 years ago

biomero - v1.5.1

• [BUG] Fix bug where conversion script cannot handle filenames with spaces in them. Now it lists them properly.

Full Changelog: https://github.com/NL-BioImaging/biomero/compare/v1.5.0...v1.5.1

- Python
Published by TorecLuik about 2 years ago

biomero - v1.5.0

• Match versions with updated (batch) biomero-scripts (v1.5.0)
• Small updates to README/comments

Full Changelog: https://github.com/NL-BioImaging/biomero/compare/v1.4.0...v1.5.0

- Python
Published by TorecLuik about 2 years ago

biomero - v1.4.0

Match version with new biomero-scripts release

Full Changelog: https://github.com/NL-BioImaging/biomero/compare/v1.3.0...v1.4.0

- Python
Published by TorecLuik about 2 years ago

biomero - v1.3.0

• Changes required for enabling BIOMERO scripts v1.3.0
  • BIOMERO scripts v1.3.0 added support for uploading CSV output files (from workflows) back into OMERO as OMERO.tables

Full Changelog: https://github.com/NL-BioImaging/biomero/compare/v1.2.0...v1.3.0

- Python
Published by CellularImagingCF about 2 years ago

biomero - v1.2.0

Renamed the whole package from omeroslurmclient / omero-slurm-client to biomero.

Install the new biomero package via GitHub or PyPI.

from biomero import SlurmClient

What's Changed

• Bump paramiko from 3.2.0 to 3.4.0 by @dependabot in https://github.com/NL-BioImaging/biomero/pull/7

Full Changelog: https://github.com/NL-BioImaging/biomero/compare/v1.1.1...v1.2.0

- Python
Published by CellularImagingCF about 2 years ago

biomero - v1.1.1

• Drop support for Python 3.6
• Use request cache 1.1.1 which supports conditional requests to GitHub, circumventing a lot of the rate limit.

Full Changelog: https://github.com/NL-BioImaging/omero-slurm-client/compare/v1.0.0...v1.1.1

- Python
Published by TorecLuik about 2 years ago

biomero - Version 1

Publish the first version of the OMERO Slurm Client to accompany the upcoming paper: BIOMERO.

Features: - Connect OMERO with generic remote HPC (over SSH). - Run generic containerized (FAIR) image analysis workflows from OMERO web on remote HPC. - Manage export and import of data to / from OMERO. - Publish all source code, scripts, tutorials, and a few containers for OMERO, Slurm and workflows.

Merry Christmas and a happy new year!

Full Changelog: https://github.com/NL-BioImaging/omero-slurm-client/compare/v0.2.0-alpha...v1.0.0

- Python
Published by TorecLuik about 2 years ago

biomero - v0.2.0-alpha

Let's release and publish a version.

Library should work for 2D image-to-image workflows, like CellPose.

Recent upgrades: - Add support for ZARR export (to bypass the 'rendering engine' interpreting the image) - Add support for (an array of) conversion containers; add a ZARR to TIFF converter by default - Finalize some tutorials

Full Changelog: https://github.com/NL-BioImaging/omero-slurm-client/compare/v0.1.0-alpha...v0.2.0-alpha

- Python
Published by TorecLuik over 2 years ago

biomero - Version 0.1.1 (pre-release)

A release for Zenodo DOI

- Python
Published by TorecLuik over 2 years ago

biomero - Version 0.1.0 (alpha)

Initial pre-release version.

Full Changelog: https://github.com/NL-BioImaging/omero-slurm-client/commits/v0.1.0-alpha

- Python
Published by TorecLuik over 2 years ago