BEE Release 0.1.9

Major features:

• Updated the Graph Database to use one instance of Neo4j for all workflows for a user vs. using one for each workflow.
• Added Python API for generating cwl specification of a workflow.
• Added coverage metrics for unit tests.
• Added resiliency to Task Manager to update tasks status when coming back up
• Enhanced pre/post script capabilities (added flux capability) and added checks for shell compatibility.
• Added capability to export dag of a workflow before and during execution

What's Changed

• Ensure failed tasks cause dependent tasks to fail by @jtronge in #806
• Update Neo4j to 5.x by @jtronge in #819
• Archive failed checkpoint restart workflows by @jtronge in #824
• Add pre/post script support to flux worker by @kchilleri in #818
• Add integration test for pre/post scripts (beeflow:ScriptRequirement) by @jtronge in #838
• Update Task Manager for task update resiliency by @jtronge in #827
• Restart GDB by @rstyd in #759
• Allow removal of a workflow with any Archive status by @pagrubel in #828
• Add Pytest coverage by @aquan9 in #843
• Test slurm commands worker in CI by @jtronge in #839
• Check for missing workflow inputs by @jtronge in #842
• Validate shell environment in pre/post script files by @kchilleri in #844
• Add Script Option to Pre/Post Script & Change MPI Call by @rstyd in #856
• Add MPI integration test code by @jtronge in #858
• Fix edge case in badge generation. by @aquan9 in #851
• Security concrete by @aquan9 in #852
• Remove enhanced client from github by @rstyd in #865
• Bump gunicorn from 20.1.0 to 22.0.0 by @dependabot in #862
• Bump urllib3 from 1.26.18 to 1.26.19 by @dependabot in #863
• Enable beeflow submit from working directory by @jtronge in #854
• Update work_dir path by @Leahh02 in #869
• Issue735/clear workflow by @kabir-vats in #872
• Pause running workflows when stopping beeflow with 'beeflow core stop' by @pagrubel in #830
• Bump certifi from 2024.6.2 to 2024.7.4 by @dependabot in #878
• Enable shell option on flux worker by @kchilleri in #866
• Issue871/delete_use_archive_config by @Leahh02 in #879
• Update documentation for the integration tests by @jtronge in #887
• Validate shell option in cwl file; ensure it matches shell interpreter in pre/post scripts by @kchilleri in #880
• Stop checking job state when it's completed by @Leahh02 in #892
• Add WorkerError exception handling by @jtronge in #888
• Add check for /tmp or /var/tmp by @Leahh02 in #885
• Generate CWL by @rstyd in #841
• Only Run One Neo4j Instance for a BEE Instance by @kabir-vats in #882
• Remove shebang lines from pre/post scripts by @kchilleri in #895
• Add "beeflow core info" by @aquan9 in #908
• Fix Reexecute by @kabir-vats in #902
• Update Poetry developer's guide by @Leahh02 in #899
• Update Git workflow documentation by @Leahh02 in #897
• Bump cryptography from 42.0.8 to 43.0.1 by @dependabot in #916
• Add Beeflow connect - A REST API for BEEflow itself. by @aquan9 in #837
• Add No Start for workflows submitted but not started by @Leahh02 in #914
• Add task state when creating task for checkpoint by @pagrubel in #923
• Export dag by @Leahh02 in #909
• Release 0.1.9 by @pagrubel in #925

Full Changelog: 0.1.8...0.1.9