0.2.0.dev12

Breaking Changes

• Drop support for Python 3.8 by @LanderOtto in #561

What's Changed

• Fix PyPI release pipeline by @GlassOfWhiskey in #450
• Moved the _retrieve_output calls inside try-except clauses by @LanderOtto in #451
• Fix workdir handling in SlurmConnector by @GlassOfWhiskey in #456
• Re-introduced log level option in DockerComposeConnector by @LanderOtto in #457
• Fixed StreamFlow name by @LanderOtto in #458
• Fixed prefix of input union types by @LanderOtto in #455
• Fixed record field name in CWLObjectTokenProcessor by @LanderOtto in #460
• Fixed workdir of wrapped deployments by @LanderOtto in #461
• Added NoContainerCWLDockerTranslator by @LanderOtto in #453
• Check job status when it terminates by @LanderOtto in #452
• Refactor command tokens by @GlassOfWhiskey in #469
• Fix remote write by @LanderOtto in #471
• Fix SingularityConnector environment variables by @LanderOtto in #470
• Fixed output step when it is an empty list by @LanderOtto in #472
• Optimize scheduling logic by @GlassOfWhiskey in #474
• Fix input directory path by @LanderOtto in #475
• Improve performance of local copies by @GlassOfWhiskey in #476
• Added get_stream_writer method to Connector by @GlassOfWhiskey in #477
• Implementing stacked locations scheduling by @GlassOfWhiskey in #480
• Update Apptainer version in CI pipeline by @GlassOfWhiskey in #482
• Make ContainerConnector extend ConnectorWrapper by @GlassOfWhiskey in #481
• Removed duplicate package import by @LanderOtto in #492
• Created CWLWorkflow class by @LanderOtto in #504
• Fixed CONTENT_LIMIT checks by @LanderOtto in #491
• Added explicit return in _copy_remote_to_remote by @LanderOtto in #515
• Moved Graph reference from CWLTokenProcessor to CWLWorkflow by @LanderOtto in #516
• Changed propagation of failure termination by @LanderOtto in #373
• Improved description about location storage in the Hardware class by @LanderOtto in #423
• Temporarily disable MacOS X GitHub Actions by @GlassOfWhiskey in #459
• Fixed minor bugs by @LanderOtto in #535
• Enable StreamFlow JSON Schema dump by @GlassOfWhiskey in #543
• Fix MacOS X CI on GitHub Actions by @GlassOfWhiskey in #547
• Fixed job input for the CWL InitialWorkDirRequirement by @LanderOtto in #536
• Fix follow_symlink function return value by @LanderOtto in #542
• Fix ValueFromTransformer without input deps by @GlassOfWhiskey in #553
• Handle lists in CWL glob field by @GlassOfWhiskey in #555
• Fixed optional CWL parameter by @LanderOtto in #466
• Add support for Python 3.13 by @LanderOtto in #539
• Fix report feature in case of empty workflow by @GlassOfWhiskey in #568
• Improved SSHConnector error message by @LanderOtto in #574
• Support stacked storage in scheduling by @GlassOfWhiskey in #552
• Fix requirement eval in CWL WorkflowStep by @GlassOfWhiskey in #578
• Improved job propagation after scheduling by @GlassOfWhiskey in #580
• Simplify DataManager logic for local transfers by @GlassOfWhiskey in #582
• Fixed InputInjectorStep in remote location data case by @LanderOtto in #566
• Simplify data movement logic by @GlassOfWhiskey in #583
• Improve LocalConnector performance by @GlassOfWhiskey in #585
• Fix concurrency in DefaultScheduler by @GlassOfWhiskey in #584
• Enable multi-workflow reports by @GlassOfWhiskey in #581
• Refactor DataManager class and fix local copy by @GlassOfWhiskey in #587
• Fixed workdir inheritance in wrapped deployments by @LanderOtto in #588
• Stop loading contents on Directory objects by @GlassOfWhiskey in #594
• Improve logging of copy methods by @GlassOfWhiskey in #599
• Added check to mkdir return code by @LanderOtto in #595
• Modernize pytest suite by @GlassOfWhiskey in #600
• Improve mount handling on SingularityConnector by @GlassOfWhiskey in #601
• Fix PBSConnector behaviour by @GlassOfWhiskey in #606
• Add local field to ExecutionLocation by @GlassOfWhiskey in #593
• Refactored unit tests by @LanderOtto in #615
• Fixed Hardware operation methods by @LanderOtto in #616
• Improve MacOS CI performance by @GlassOfWhiskey in #609
• Propagate DataLocation relations to stacked envs by @GlassOfWhiskey in #608
• Migrate CWL parsing from cwltool to cwl-utils by @GlassOfWhiskey in #58
• Add isort to the lint pipeline by @GlassOfWhiskey in #621
• Refactored remotepath module by @GlassOfWhiskey in #618
• Update coverage command and add badge by @GlassOfWhiskey in #625
• Improved ssh retry mechanism by @LanderOtto in #501
• Fixed some CWL translator issues by @LanderOtto in #628
• Optimize remote commands through StreamFlowPath by @GlassOfWhiskey in #626
• Fixed remote ports by @LanderOtto in #643
• Modernize base Docker image and Helm version by @GlassOfWhiskey in #655
• Fix remote files handling by @LanderOtto in #648
• Migrate Docker container to Debian by @GlassOfWhiskey in #658
• Added timeout to SSHConnector by @LanderOtto in #644
• Refactor SSHConnector class by @LanderOtto in #661
• Improve CWL parsing performance by @GlassOfWhiskey in #660
• Fixed ChannelOpenError handling on the SSHConnector by @LanderOtto in #664
• Remove useless LocalConnector deps by @GlassOfWhiskey in #665
• Uniform StreamFlow output format to CWL ecosystem by @GlassOfWhiskey in #667
• Fixed tag hierarchy check by @LanderOtto in #670
• Fix ANTLR4 script generator by @LanderOtto in #674
• Remove unused code by @LanderOtto in #673
• Handle single-element output lists in CWL by @GlassOfWhiskey in #672
• Fix CWL pickValue with all_non_null option by @GlassOfWhiskey in #677
• Improved remote file creation by @LanderOtto in #679
• Update Linux GitHub runners to 24.04 by @GlassOfWhiskey in #680
• Update PostgreSQL plugin documentation by @GlassOfWhiskey in #681

Dependencies

• Bump aiohttp from 3.9.5 to 3.10.1 by @dependabot in #514
• Bump aiohttp from 3.10.1 to 3.10.2 by @dependabot in #521
• Bump aiohttp from 3.10.2 to 3.10.4 by @dependabot in #524
• Bump aiohttp from 3.10.4 to 3.10.5 by @dependabot in #526
• Bump aiohttp from 3.10.5 to 3.10.6 by @dependabot in #551
• Bump aiohttp from 3.10.6 to 3.10.8 by @dependabot in #554
• Bump aiohttp from 3.10.8 to 3.10.9 by @dependabot in #557
• Bump aiohttp from 3.10.9 to 3.10.10 by @dependabot in #563
• Bump aiohttp from 3.10.10 to 3.11.0 by @dependabot in #592
• Bump aiohttp from 3.11.0 to 3.11.2 by @dependabot in #597
• Bump aiohttp from 3.11.2 to 3.11.4 by @dependabot in #602
• Bump aiohttp from 3.11.4 to 3.11.6 by @dependabot in #605
• Bump aiohttp from 3.11.6 to 3.11.7 by @dependabot in #607
• Bump aiohttp from 3.11.7 to 3.11.8 by @dependabot in #612
• Bump aiohttp from 3.11.8 to 3.11.9 by @dependabot in #613
• Bump aiohttp from 3.11.9 to 3.11.10 by @dependabot in #617
• Bump aiohttp from 3.11.10 to 3.11.11 by @dependabot in #632
• Bump aiohttp from 3.11.11 to 3.11.12 by @dependabot in #657
• Bump aiohttp from 3.11.12 to 3.11.13 by @dependabot in #678
• Bump aiosqlite from 0.20.0 to 0.21.0 by @dependabot in #656
• Bump antlr4-python3-runtime from 4.13.1 to 4.13.2 by @dependabot in #519
• Bump asyncssh from 2.14.2 to 2.17.0 by @dependabot in #534
• Bump asyncssh from 2.17.0 to 2.18.0 by @dependabot in #575
• Bump asyncssh from 2.18.0 to 2.19.0 by @dependabot in #622
• Bump asyncssh from 2.19.0 to 2.20.0 by @dependabot in #668
• Bump bcrypt from 4.1.3 to 4.2.0 by @dependabot in #508
• Bump bcrypt from 4.2.0 to 4.2.1 by @dependabot in #604
• Bump cachetools from 5.3.3 to 5.4.0 by @dependabot in #499
• Bump cachetools from 5.4.0 to 5.5.0 by @dependabot in #527
• Bump cachetools from 5.5.0 to 5.5.1 by @dependabot in #647
• Bump cachetools from 5.5.1 to 5.5.2 by @dependabot in #671
• Bump cwl-utils from 0.33 to 0.34 by @dependabot in #538
• Bump cwl-utils from 0.34 to 0.35 by @dependabot in #564
• Bump cwl-utils from 0.36 to 0.37 by @dependabot in #663
• Bump importlib-metadata from 7.1.0 to 7.2.1 by @dependabot in #487
• Bump importlib-metadata from 7.2.1 to 8.0.0 by @dependabot in #488
• Bump importlib-metadata from 8.0.0 to 8.2.0 by @dependabot in #510
• Bump importlib-metadata from 8.2.0 to 8.4.0 by @dependabot in #529
• Bump importlib-metadata from 8.4.0 to 8.5.0 by @dependabot in #544
• Bump importlib-metadata from 8.5.0 to 8.6.1 by @dependabot in #645
• Bump jinja2 from 3.1.4 to 3.1.5 by @dependabot in #635
• Bump jsonschema from 4.22.0 to 4.23.0 by @dependabot in #495
• Bump kaleido from 0.2.1 to 0.4.1 by @dependabot in #598
• Bump kaleido from 0.4.1 to 0.4.2 by @dependabot in #603
• Bump kubernetes-asyncio from 29.0.0 to 30.1.0 by @dependabot in #479
• Bump kubernetes-asyncio from 30.1.0 to 30.1.1 by @dependabot in #489
• Bump kubernetes-asyncio from 30.1.1 to 30.3.0 by @dependabot in #517
• Bump kubernetes-asyncio from 30.3.0 to 30.3.1 by @dependabot in #522
• Bump kubernetes-asyncio from 30.3.1 to 31.1.0 by @dependabot in #545
• Bump kubernetes-asyncio from 31.1.0 to 31.1.1 by @dependabot in #619
• Bump kubernetes-asyncio from 31.1.1 to 32.0.0 by @dependabot in #631
• Bump pandas from 2.2.2 to 2.2.3 by @dependabot in #548
• Bump plotly from 5.22.0 to 5.23.0 by @dependabot in #507
• Bump plotly from 5.23.0 to 5.24.0 by @dependabot in #533
• Bump plotly from 5.24.0 to 5.24.1 by @dependabot in #546
• Bump plotly from 5.24.1 to 6.0.0 by @dependabot in #651
• Bump psutil from 5.9.8 to 6.0.0 by @dependabot in #485
• Bump psutil from 6.0.0 to 6.1.0 by @dependabot in #570
• Bump psutil from 6.1.0 to 6.1.1 by @dependabot in #633
• Bump psutil from 6.1.1 to 7.0.0 by @dependabot in #662
• Bump rdflib from 7.0.0 to 7.1.1 by @dependabot in #576
• Bump rdflib from 7.1.1 to 7.1.2 by @dependabot in #640
• Bump rdflib from 7.1.2 to 7.1.3 by @dependabot in #642
• Bump referencing from 0.35.1 to 0.36.1 by @dependabot in #641
• Bump referencing from 0.36.1 to 0.36.2 by @dependabot in #649
• Bump yattag from 1.15.2 to 1.16.0 by @dependabot in #520
• Bump yattag from 1.16.0 to 1.16.1 by @dependabot in #586

Dev Dependencies

• Bump bandit from 1.7.8 to 1.7.9 by @dependabot in #483
• Bump bandit from 1.7.9 to 1.7.10 by @dependabot in #550
• Bump bandit from 1.7.10 to 1.8.0 by @dependabot in #611
• Bump bandit from 1.8.0 to 1.8.2 by @dependabot in #639
• Bump bandit from 1.8.2 to 1.8.3 by @dependabot in #666
• Bump black from 24.4.2 to 24.8.0 by @dependabot in #513
• Bump black from 24.8.0 to 24.10.0 by @dependabot in #559
• Bump black from 24.10.0 to 25.1.0 by @dependabot in #653
• Bump codecov/codecov-action from 4 to 5 by @dependabot in #596
• Bump codespell from 2.2.6 to 2.3.0 by @dependabot in #465
• Bump codespell from 2.3.0 to 2.4.0 by @dependabot in #646
• Bump codespell from 2.4.0 to 2.4.1 by @dependabot in #654
• Bump cwltest from 2.5.20240425111257 to 2.5.20240714110256 by @dependabot in #497
• Bump cwltest from 2.5.20240714110256 to 2.5.20240906231108 by @dependabot in #537
• Bump cwltest from 2.5.20240906231108 to 2.5.20241122133319 by @dependabot in #610
• Bump cwltool from 3.1.20240404144621 to 3.1.20240508115724 by @dependabot in #454
• Bump cwltool from 3.1.20240508115724 to 3.1.20240708091337 by @dependabot in #493
• Bump cwltool from 3.1.20240708091337 to 3.1.20241112140730 by @dependabot in #591
• Bump cwltool from 3.1.20241112140730 to 3.1.20241217163858 by @dependabot in #630
• Bump cwltool from 3.1.20241217163858 to 3.1.20250110105449 by @dependabot in #638
• Bump docker/build-push-action from 5 to 6 by @dependabot in #484
• Bump flake8-bugbear from 24.4.26 to 24.8.19 by @dependabot in #532
• Bump flake8-bugbear from 24.8.19 to 24.10.31 by @dependabot in #579
• Bump flake8-bugbear from 24.10.31 to 24.12.12 by @dependabot in #623
• Bump helm/kind-action from 1.10.0 to 1.11.0 by @dependabot in #627
• Bump helm/kind-action from 1.11.0 to 1.12.0 by @dependabot in #634
• Bump isort from 5.13.2 to 6.0.0 by @dependabot in #650
• Bump isort from 6.0.0 to 6.0.1 by @dependabot in #682
• Bump pytest from 8.1.1 to 8.2.1 by @dependabot in #462
• Bump pytest from 8.2.1 to 8.2.2 by @dependabot in #473
• Bump pytest from 8.2.2 to 8.3.1 by @dependabot in #505
• Bump pytest from 8.3.1 to 8.3.2 by @dependabot in #512
• Bump pytest from 8.3.2 to 8.3.3 by @dependabot in #549
• Bump pytest from 8.3.3 to 8.3.4 by @dependabot in #614
• Bump pytest-asyncio from 0.24.0 to 0.25.0 by @dependabot in #624
• Bump pytest-asyncio from 0.25.0 to 0.25.1 by @dependabot in #636
• Bump pytest-asyncio from 0.25.1 to 0.25.3 by @dependabot in #652
• Bump pytest-cov from 5.0.0 to 6.0.0 by @dependabot in #577
• Bump pyupgrade from 3.15.2 to 3.16.0 by @dependabot in #478
• Bump pyupgrade from 3.16.0 to 3.17.0 by @dependabot in #511
• Bump pyupgrade from 3.17.0 to 3.18.0 by @dependabot in #567
• Bump pyupgrade from 3.18.0 to 3.19.0 by @dependabot in #572
• Bump pyupgrade from 3.19.0 to 3.19.1 by @dependabot in #629
• Bump sphinx from 7.3.7 to 7.4.5 by @dependabot in #500
• Bump sphinx from 7.4.5 to 7.4.6 by @dependabot in #502
• Bump sphinx from 7.4.6 to 7.4.7 by @dependabot in #506
• Bump sphinx from 7.4.7 to 8.0.2 by @dependabot in #518
• Bump sphinx from 8.0.2 to 8.1.3 by @dependabot in #565
• Bump sphinx from 8.1.3 to 8.2.0 by @dependabot in #669
• Bump sphinx from 8.2.0 to 8.2.1 by @dependabot in #676
• Bump sphinx-rtd-theme from 2.0.0 to 3.0.0 by @dependabot in #556
• Bump sphinx-rtd-theme from 3.0.0 to 3.0.1 by @dependabot in #560
• Bump sphinx-rtd-theme from 3.0.1 to 3.0.2 by @dependabot in #590

Full Changelog: 0.2.0.dev11...0.2.0.dev12