7.0.0

What's Changed

• Respect job local-ness when chaining by @adamnovak in #4809
• Fix Python 3.8 support by @adamnovak in #4823
• Fix missing description on PyPI by @mr-c in #4820
• Install build module for CI by @stxue1 in #4826
• Use a sentinel location instead of an unmodified location to mark missing files by @adamnovak in #4818
• Bump mypy from 1.8.0 to 1.9.0 by @dependabot in #4830
• Make sure output directory exists before using it by @adamnovak in #4832
• Pass through debugged job status code to prevent infinite loop by @stxue1 in #4829
• Add tests for environment pickling by @adamnovak in #4837
• Add colored logging by @stxue1 in #4828
• Remove unused CI test by @stxue1 in #4843
• Measure CPU and memory usage in WDL Docker containers by @adamnovak in #4819
• Allow debugging jobs by name (and status improvements) by @adamnovak in #4840
• Improve exception handling to not output tracebacks by @stxue1 in #4839
• Update pytest-cov requirement from <5,>=2.12.1 to >=2.12.1,<6 by @dependabot in #4851
• Update docutils requirement from <0.21,>=0.16 to >=0.16,<0.22 by @dependabot in #4866
• Update galaxy-util requirement from <23 to <25 by @dependabot in #4862
• Update galaxy-tool-util requirement from <23 to <25 by @dependabot in #4861
• Bump cwltool from 3.1.20240112164112 to 3.1.20240404144621 by @dependabot in #4870
• Bump gunicorn from 21.2.0 to 22.0.0 by @dependabot in #4871
• Retry Slurm interactions more by @adamnovak in #4869
• Replace use of boto with boto3 for awsProvisioner.py by @stxue1 in #4859
• Allow fetching job inputs for debugging by @adamnovak in #4848
• Make leader wait for expected updates to be visible in the job store, or fail the job by @adamnovak in #4811
• Enable FUSE for privileged Toil clusters by @stxue1 in #4824
• Detect if the GridEngine worker thread has crashed to prevent hanging the workflow by @stxue1 in #4873
• Bump mypy from 1.9.0 to 1.10.0 by @dependabot in #4878
• Support caching on SLURM by @stxue1 in #4884
• Add debug logging for single machine batchsystem to signal worker issue and startup by @stxue1 in #4881
• Update WDL conformance tests on CI by @stxue1 in #4876
• Replace all usage of boto2 with boto3 by @stxue1 in #4868
• Revert ensurepip to get-pip to fix Python 3.10 ARM CI appliance builds by @stxue1 in #4900
• docs cleanup by @mr-c in #4889
• Bump to a new major version by @adamnovak in #4885
• Warn user about wait times for stats gathering with a large quantity of jobs. by @DailyDreaming in #4893
• Allow symlinks to inputs as WDL outputs by @adamnovak in #4883
• bye pytz by @mr-c in #4890
• Stop suggesting infinity when validating half-open intervals by @adamnovak in #4887
• Fix WDL option spelling and tolerate Cromwell-isms by @adamnovak in #4906
• Remove wrapped CWL doc example. by @DailyDreaming in #4892
• Add retries to DockerCheckTest.testBadGoogleRepo by @stxue1 in #4909
• Fix 3.8 backport.timezone import by @stxue1 in #4908
• Update to Python 3.12 by @stxue1 in #4901
• Bump flask-cors from 4.0.0 to 4.0.1 by @dependabot in #4916
• Try /tmp before the workdir for the Toil coordination directory by @stxue1 in #4914
• CWL biocontainer tests: use version corresponding to v2 Docker Image Format by @mr-c in #4912
• Revert "Update to Python 3.12" by @DailyDreaming in #4917
• Bump miniwdl from 1.11.1 to 1.12.0 by @dependabot in #4920
• Support Python 3.12 by @stxue1 in #4919
• Add documentation for installing batch system plugins by @stxue1 in #4926
• Update Werkzeug to appease the Github security police by @adamnovak in #4925
• Revert "Update Werkzeug to appease the Github security police" by @DailyDreaming in #4928
• Bump cwltool from 3.1.20240404144621 to 3.1.20240508115724 by @dependabot in #4936
• Add batchsystem plugin test by @stxue1 in #4933
• Fix bad test paths. by @DailyDreaming in #4938
• Add better logic in finding a temp directory for the Toil coordination directory by @stxue1 in #4918
• Add supported workflow language versions to README by @adamnovak in #4923