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ChangeLog

2022-05-18

Added

  • Human-friendly time formatting
  • Common snakemake options to cookiecutter JSON [#80]
    • --use-singularity
    • --use-conda
    • --printshellcmds
    • --latency-wait
    • --max-jobs-per-second
    • --max-status-checks-per-second
    • --restart-times
  • Support for passing extra options to sbatch via the slurm parameter in a rule's resources [#86]
  • More control over job names and log paths with patterns
  • Print the job log path along with the job ID

2022-05-12

Changes

  • deprecate advanced argument conversion (#91, PR #93)
  • add support for sidecar (PR #85)

2021-03-10

Issues

  • serialize cookiecutter settings in json file and add CookieCutter class to access config (fixes #63)
  • demote pandas import to function (addresses #64)
  • add preliminary support for suffixes when specifying memory (fixes #62)

2020-10-23

This is a major rewrite of the testing framework, in an attempt to make it more accessible to users. In particular, it is now possible to run tests on an HPC.

Changes

  • the new ShellContainer class emulates container output and allows the tests to be executed on a HPC running SLURM
  • slurm-submit.py now submits sbatch jobs with the --parsable option
  • add profile option 'cluster_name' - some HPCs define multiple SLURM clusters. Simply adding --cluster=cluster_name to SBATCH_DEFAULTS will not suffice as slurm-status.py also needs to check status in the queue corresponding to the chosen cluster.
  • the advanced argument conversion has been much simplified and improved

Issues

  • options without arguments can now be set in SBATCH_DEFAULTS (fixes #52)

2020-09-11

Move CI infrastructure from circleCI to github actions.

2020-04-15

  • process string patterns in snakemake style (replace keywords in braces)

2020-03-31

  • map threads to --cpus-per-task (#35)
  • rewrite some tests to address changes

2020-02-29

  • major rewrite and merge of the slurm-submit.py script to support any sbatch argument
  • parse any argument via the sbatch_defaults option and
  • enable per-profile cluster (YAML/JSON) config file
  • make experimental sbatch argument adjustments optional via the advanced_argument_conversion option

2019-09-03

  • add qos option

2019-08-21

  • replace pytest_namespace with pytest_configure
  • make days optional (#18)

2018-10-18

  • add cookiecutter options to set sbatch output and error defaults

2018-10-09

  • add support for mem_mb in resources
  • add support for cluster configuration file
  • add advanced slurm-submit file
  • adjust resource requirements if they exceed partition configuration settings (#11)