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CHANGELOG.rst

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1.3.14 - 06/01/23

  • Blah

1.3.13 - 06/01/23

  • Blah

1.3.9 - 06/01/23

  • Increments version of Vivarium required

1.3.8 - 12/27/22

  • Updates CI and setup to build python 3.7-3.10
  • Updates codeowners

1.3.7 - 10/28/22

  • Adds a test psimulate test large_results for scale testing
  • Sets the default project to proj_simscience_prod

1.3.6 - 10/04/22

  • Increments version of Vivarium required

1.3.5 - 09/20/22

  • Standardize results directories
  • Adds ability to run without artifact
  • Specify correct permissions when creating directories and files

1.3.4 - 07/01/22

  • Mend key mismatch for random_seed and input_draw columns
  • Make draw and seed generation deterministic in parallel simulations
  • Add CODEOWNERS to repo

1.3.3 - 05/16/22

  • Add results directory to model specification in psimulate runs.

1.3.2 - 05/05/22

  • Fix pandas json deprecation.
  • Fix new slurm atexit error.
  • Update black version used in CI.

1.3.1 - 03/30/22

  • Fix output directory naming based on location.

1.3.0 - 02/28/22

  • Refactor and reorganize codebase.
  • Add load testing capabilities.
  • Switch from UGE to SLURM.
  • Fix failure accounting in the registry.
  • Fail earlier from bad arguments.

1.2.13 - 02/15/22

  • Autoformat code with black and isort.
  • Add black and isort checks to CI.

1.2.12 - 02/11/22

  • Update pip freeze behavior to be more robust
  • Add logging and error handling when the node with the main process can't view the filesystem.

1.2.11 - 02/11/22

  • CI configuration updates.

1.2.10 - 10/28/21

  • Add Zenodo metadata and update license to BSD 3-clause

1.2.9 - 10/14/21

  • Set log-level to debug for both redis server and workers
  • Create separate redis logs for each redis server
  • Fix bug inherited from rq hiding worker processes from scheduler
  • Fix incorrect help text for psimulate max-runtime flag

1.2.8 - 08/16/21

  • Don't write sim results in worker logs.

1.2.6 - 08/10/21

  • Standardize CI scripts
  • Upgrade readthedocs
  • Add API documentation
  • Allow psimulate to create result root directories

1.2.5 - 06/08/21

  • Unpin redis and rq dependencies

1.2.4 - 05/12/21

  • Add artifact path as an argument to psimulate
  • Fix redis connection bug
  • Add no_cleanup option to prevent auto-deletion on a failure
  • Add additional timing messages in the worker logs
  • Add JSON telemetry logging for each job run
  • Add vipin tool which logs job stats and outputs them to a csv or hdf file
  • Remove vparse functionality which is superseded by vipin
  • Remove references to deprecated DataFrame's msgpack functionality

1.2.3 - 01/05/21

  • Fix deploy script

1.2.2 - 01/05/21

  • Github actions replaces Travis for CI
  • Unpin pandas and numpy

1.2.1 - 10/02/20

  • Pin rq to 1.2.2

1.2.0 - 08/31/20

  • Update output.hdf to remove duplicate draw and random seed from the index.
  • Adds option for choosing scheduling queue.
  • Adds typing to internal functions.
  • Removed references to old IHME cluster.
  • Separated run configuration from cluster configuration.
  • Added utility function to make directories with consistent permissions.
  • Added functionality to serialize unwritten in-memory results on exit.
  • Added functionality to clean up directories if psimulate fails to produce results.

1.1.2 - 01/03/20

  • Set cluster queue dynamically based on max runtime argument.

1.1.1 - 12/08/19

  • Fix bug in random seed generation so that seeds are unique.

1.1.0 - 11/18/19

  • Move artifact from vivarium_public_health to vivarium proper. Remove the package dependency.
  • Clean up context interface and simulation creation.
  • Switch all logging to loguru.

1.0.15 - 09/11/2019

  • Add max runtime option
  • Set output directory permissions to 775
  • Prohibit launching from submit host

1.0.14 - 06/20/19

  • Bugfix in job enqueuing.

1.0.12 - 06/20/19

  • Bugfix in worker invocation

1.0.11 - 06/19/19

  • Namespace bugfix.

1.0.10 - 06/18/19

  • Added option to not batch results.
  • Updated yaml api usage.
  • Bugfix in dtypes when writing results.
  • Allow the usage of branch files without parameter variations.
  • Don't use ResultsWriter directly.
  • Switch to consistent pathlib usage.
  • Enable restart when no parameter variations present.
  • Setup log rotations.
  • Forward vivarium logs to worker logs.
  • New vparse command for parsing worker logs.

1.0.9 - 04/22/19

  • Bugfix in restart with string columns in outputs.
  • Extract common cli options.
  • Add verbosity levels to logging.
  • Add command to add draws/seeds to previous runs.

1.0.8 - 04/16/19

  • Switch to loguru for logging and cleanup usage.
  • Log cluster and node information from the workers.
  • Add serialized logs.
  • Client side sharding of redis instances.
  • More robustness in failure handling.
  • Tutorial documentation for yaml syntax.
  • Tutorial documentation for branches files.
  • Tutorial documentation for psimulate.
  • Readthedocs integration.
  • Extraction of shared CLI options

1.0.7 - 04/02/19

  • Be defensive about retrieving jobs.

1.0.6 - 03/29/19

  • Bugfix in tests.

1.0.5 - 03/29/19

  • Migrate to github.

1.0.4 - 03/28/19

  • Add debugger to cli.

1.0.3 - 03/20/19

  • Reduce requirements for simulation jobs.

1.0.2 - 03/19/19

  • Hack around hard to reproduce drmaa error.

1.0.1 - 03/15/19

  • Add additional project options.

1.0.0 - 02/22/19

  • Initial release.