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CHANGELOG.md

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Version 4.1.2 - October 28, 2024

Swapped two colours in the status plot, to make RUNNING status more distinct.

Version 4.1.1 - October 9, 2024

Added type hints.

Version 4.1.0 - September 21, 2024

Added support for TOML specification files.

Version 4.0.20 - September 18, 2024

Fixed failing test.

Version 4.0.19 - September 18, 2024

Removed kaleido from the requirements in setup.py. No idea how that got there.

Version 4.0.18 - Aug 13, 2024

Reversed order of status categories displayed in bin/slurm-pipeline-status-plot.py plots.

Version 4.0.17 - Aug 11, 2024

Added "pandas" to test requirements in setup.py.

Version 4.0.16 - Aug 11, 2024

Small tweaks to improve the appearance of bin/slurm-pipeline-status-plot.py plots.

Version 4.0.15 - Aug 11, 2024

Added bin/slurm-pipeline-status-plot.py.

Version 4.0.14 - Dec 11, 2023

Make loading the JSON specification file give a better error message, including the specification filename.

Version 4.0.13 - May 22, 2022

Added missing < in command line providing input from *.bz2 files to the command being executed by sbatch.py.

Version 4.0.12 - April 1, 2022

Added --verbose option to sbatch.py.

Version 4.0.11 - April 1, 2022

Added --compressLevel and --randomSleep options to sbatch.py.

Version 4.0.10 - March 31, 2022

Added compression of input files to sbatch.py and an --uncompress option to turn this off. Thanks to @holtgrewe for this suggestion.

Version 4.0.9 - November 2, 2021

Updated .travis.yml and build status image URL on README.md.

Version 4.0.8 - November 2, 2021

Added conda install instructions to README.md.

Version 4.0.7 - November 2, 2021

Improved README.md description of sbatch.py.

Version 4.0.6 - November 2, 2021

Added JSON output of all SLURM job numbers and added to README.md to describe how to easily use the output with jq to pass job ids to sacct, squeue, scancel or sbatch.py --afterOk. Fixed silly bug causing --then, --else, and --finally commands not to be wrapped in a script for submission to sbatch.

Version 4.0.5 - October 26, 2021

Improved README.md.

Version 4.0.4 - October 26, 2021

Moved test directory back to top level.

Version 4.0.3 - October 26, 2021

Moved test directory under slurm_pipeline.

Version 4.0.2 - October 26, 2021

Use getpass.getuser() instead of pwd.getpwuid(os.getuid()).pw_name to get the user's name (since the import pwd fails on windows).

Version 4.0.1 - October 26, 2021

Added LICENSE.txt for conda forge distribution.

Version 4.0.0 - October 23, 2021

Removed support for Python 2.7. Added conda building.

Version 3.2.2 - October 23, 2021

Added sbatch.py utility script (and remove-repeated-headers.py helper).

Version 3.2.1 - June 7, 2021

Added --printOutput option to tell slurm-pipeline.py to print the output of running each step.

Version 3.2.0 - June 5, 2021

The distinction between simulated and skipped steps has been removed as it was too subtle and complicated. Only step skipping remains now, and step scripts need to decide what to do based on the value of SP_SKIP. For backwards compatibility, the SP_SIMULATE variable is still set in the environment, but its value is always identical to SP_SKIP.

Removed use of now-outdated ugly mocking code for open. This might break Python 2 compatibility, but at this point I don't care.

Version 3.1.1 - August 29, 2019

The --nice argument put into the SP_NICE_ARG environment variable changed to be e.g., --nice=50 (used to be --nice 50 which causes sbatch to complain "sbatch: error: Unable to open file 50").

Version 3.1.0 - April 4, 2019

Removed unused specification argument to SAcct class.

Version 3.0.2 - October 16, 2018

Added missing --scriptArgs to README.md. Thanks @avatar-lavventura!

Version 3.0.1 - June 4, 2018

Added env PYTHONPATH=../.. to all example Makefiles.

Version 3.0.0

  • Added --scriptArgs to slurm-pipeline.py to formalize giving arguments on the command line that should be passed to initial step scripts (i.e., those that have no dependencies). This prevents the possibility of putting unrecognized arguments (like --startStep) on the command line which are then passed to the script steps.

Version 2.0.11 - April 16, 2018

Added Travis CI build messaging to IRC.

Version 2.0.10 - April 16, 2018

Updated funding acknowledgements in README.md.

Version 2.0.9 - April 16, 2018

Added "error step" setting to per-step information printed by slurm-pipeline-status.py.

Version 2.0.8 - April 15, 2018

Added JobName to list of default job status fields printed by slurm-pipeline-status.py.

Version 2.0.7 - April 15, 2018

Added printing of SP_* environment variables to per-step output of slurm-pipeline-status.py.

Version 2.0.6 - April 15, 2018

Added "Collect step:" to per-step output of slurm-pipeline-status.py.

Version 2.0.5 - April 15, 2018

sacct now used instead of squeue

This change is not backward-compatible with earlier versions, hence the major version number change.

  • SLURM job status reporting was changed to use sacct rather than squeue as a result of a pull request submitted by healther. This has the advantage of being able to show status information for jobs that have completed.
  • The squeueArgs command line option to slurm-pipeline.py was removed.
  • A fieldNames argument was added to slurm-pipeline-status.py. This can be used to specify what job fields you want to see in the summary output. The default is State, Elapsed, and Nodelist. You can set SP_STATUS_FIELD_NAMES to a comma-separated list of job fields to set your own default preference. See man sacct for the full list of field names.

Other changes

  • It is now possible to specify error step: true for a step that has no dependencies. This used to be flagged as an error, but it makes sense to allow it as the user might use --startAfter on the command line, and the jobs which the no-dependency step is suppose to start after may fail.
  • The Makefile now uses pycodestyle instead of pep8 to check Python style (this is just a new name for the pep8 tool).
  • An --output option was added to slurm-pipeline.py to allow the specification of an output file for the JSON status. The default is to print it to standard output.
  • SP_DEPENDENCY_ARG is now set for all steps that don't have dependencies if --startAfter is used when invoking slurm-pipeline.py.
  • The all-step summary section of the slurm-pipeline-status.py output is slightly improved, to list an overall count of jobs started and finished.