CHANGELOG.rst

2.1.4 - 02/05/24

• Get python versions from python_versions.json

2.1.3 - 02/03/25

• Revert change caused by isort version

2.1.2 - 01/31/25

• Linting

2.1.1 - 12/16/24

• Defer defining randomness additional seed to RandomnessManager

2.1.0 - 11/06/24

• Drop support for Python 3.9
• Modernize type hinting

2.0.4 - 10/07/24

• Update how vivarium work horse gets number of simulation steps

2.0.3 - 09/10/24

• Bugfix for job_parameters with simulation backups

2.0.2 - 08/30/24

• Strengthen the API documentation
• Update existing documentation to include new psimulate options

2.0.1 - 08/21/24

• Use script to install dependencies in CI

2.0.0 - 08/13/24

Breaking changes:

• Implement Vivarium's new results processing

Major changes:

• Add ability to back up simulations periodically during runs, and to restart from these backups

Other changes:

• Use external layered-config-tree package instead of Vivarium ConfigTree class
• Raise instead of log when there are more jobs than expected from a previous run
• Stop installing vivarium inside the package directory during github actions
• Automatically run Jenkins builds on push or pull request

1.6.1 - 06/17/24

• Hotfix pin numpy below 2.0

1.6.0 - 03/12/24

• Limit max number of draws to 500.

1.5.6 - 02/27/24

• Give user option to continue psimulate restart if environment has changed

1.5.5 - 02/12/24

• Add central performance logging and testing

1.5.4 - 01/29/24

• Fix broken readthedocs build

1.5.3 - 01/04/24

• Hard-code psimulate test cluster requirements
• Implement hardware constraint option for psimulate commands
• Make -P/--project a psimulate required option

1.5.2 - 12/29/23

• Automatically remove duplicative perf logs after log_summary.csv is created

1.5.1 - 12/15/23

• Add logging documentation for psimulate

1.5.0 - 10/27/23

• Remove default results directory for 'psimulate run'
• Modify default output directory for 'psimulate test'
• Add --max-workers default of 8000

1.4.3 - 10/25/23

• Bugfix implement --max-workers option for psimulate restart, expand, and test
• Bugfix update default output directory
• Update runtime error message if env is different on restart or expand

1.4.2 - 10/13/23

• Bugfix checking for max_workers arg

1.4.1 - 10/13/23

• Bugfix checking for max_workers arg

1.4.0 - 10/09/23

• Drop support for Python 3.8
• Add priorities for draw/seed/branch job groups

1.3.13 - 10/02/23

• Bugfixes for psimulate introduced by previous bugfix

1.3.12 - 09/22/23

• Bugfixes for psimulate

1.3.11 - 09/07/23

• Made job failures more prominent in end of jobs logging

1.3.10 - 07/12/23

• Allow for specifying random seeds and draws in branches file
• Bugfixes for make_artifacts -l all
• Changes version metadata to use setuptools_scm
• Increments version of Vivarium required

1.3.9 - 06/01/23

• Increments version of Vivarium required
• Prevent sorting of model specification keys

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.