0.2.0rc1

What's Changed

• Fix SSHContextFactory retrieval logic by @LanderOtto in #931
• Fix uv pip uninstall in cwl conformance tests script by @LanderOtto in #934
• Implement __hash__ method in the ExecutionLocation by @LanderOtto in #933
• Added restore method by @LanderOtto in #864
• Refactor DirectedGraph class by @LanderOtto in #919
• Added type checking with mypy by @GlassOfWhiskey in #938
• Fix trivial mypy errors by @GlassOfWhiskey in #943
• Fix trivial mypy [var-annotated] errors by @GlassOfWhiskey in #944
• Migrate from cachetools to cachebox by @GlassOfWhiskey in #945
• Substitute manual quoting with shlex and mslex by @GlassOfWhiskey in #946
• Fix StreamFlowPath comparison by @GlassOfWhiskey in #948
• Add UnrecoverableWorkflowException by @LanderOtto in #954
• Improved InterWorkflowPort by @LanderOtto in #951
• Use official Docker setup action by @GlassOfWhiskey in #956
• Fix optional empty list output in CWL by @LanderOtto in #959
• Implement persistent shells for improved performance by @GlassOfWhiskey in #960
• Close Shell if an error occurs by @GlassOfWhiskey in #962
• Improve LoopCombinator by @LanderOtto in #952
• Improve RemotePathMapper performance by @GlassOfWhiskey in #970
• Adjust the get_path_processor method by @GlassOfWhiskey in #973
• Optimize SQLite performance and concurrency by @GlassOfWhiskey in #974
• Improve LocalStreamFlowPath.checksum() performance by @GlassOfWhiskey in #975
• Fix database relative path by @LanderOtto in #969
• Support files deduplication in RunCrate by @GlassOfWhiskey in #978
• Fix provenance with multiple equal files by @GlassOfWhiskey in #988
• Fix empty glob by @LanderOtto in #989
• Added --validate flag to streamflow run by @GlassOfWhiskey in #995
• Add tag to JobToken by @LanderOtto in #999
• Add Status.RECOVERED by @LanderOtto in #958
• Change propagation condition of InterWorkflowPort by @LanderOtto in #1001
• Fixed recovery of loops by @LanderOtto in #826
• Fixed synchronization of multiple recovery workflows by @LanderOtto in #822
• Implemented template validation in the CommandTemplateMap class by @LanderOtto in #916
• Fix notify of stacked locations by @LanderOtto in #1006
• Add FaultTolerance documentation by @LanderOtto in #1004
• Validate CWL when condition dependencies by @LanderOtto in #825
• Propagate mounts to wrapped locations in QueueManagerConnector by @GlassOfWhiskey in #947
• Fixed retrieving disk information in SingularityConnector by @LanderOtto in #894

Dependencies

• Bump aiohttp from 3.13.3 to 3.13.4 by @dependabot[bot] in #1010
• Bump cachetools from 6.2.4 to 6.2.6 by @dependabot[bot] in #932
• Bump cachetools from 6.2.6 to 7.0.0 by @dependabot[bot] in #936
• Bump cryptography from 46.0.3 to 46.0.5 by @dependabot[bot] in #949
• Bump cryptography from 46.0.5 to 46.0.6 by @dependabot[bot] in #1009
• Bump cwltool from 3.1.20260108082145 to 3.1.20260315121657 by @dependabot[bot] in #992
• Bump importlib-metadata from 8.7.1 to 8.8.0 by @dependabot[bot] in #996
• Bump importlib-metadata from 8.8.0 to 9.0.0 by @dependabot[bot] in #997
• Bump kubernetes-asyncio from 34.3.3 to 35.0.0 by @dependabot[bot] in #953
• Bump kubernetes-asyncio from 35.0.0 to 35.0.1 by @dependabot[bot] in #967
• Bump orjson from 3.11.5 to 3.11.6 by @dependabot[bot] in #991
• Bump plotly from 6.5.2 to 6.6.0 by @dependabot[bot] in #980
• Bump psutil from 7.2.1 to 7.2.2 by @dependabot[bot] in #935
• Bump pygments from 2.19.2 to 2.20.0 by @dependabot[bot] in #1011
• Bump rdflib from 7.5.0 to 7.6.0 by @dependabot[bot] in #993
• Bump requests from 2.32.5 to 2.33.0 by @dependabot[bot] in #1007

Dev Dependencies

• Bump actions/download-artifact from 7 to 8 by @dependabot[bot] in #971
• Bump actions/upload-artifact from 6 to 7 by @dependabot[bot] in #972
• Bump bandit from 1.9.3 to 1.9.4 by @dependabot[bot] in #966
• Bump black from 26.1.0 to 26.3.0 by @dependabot[bot] in #987
• Bump black from 26.3.0 to 26.3.1 by @dependabot[bot] in #990
• Bump codecov/codecov-action from 5 to 6 by @dependabot[bot] in #1008
• Bump codespell from 2.4.1 to 2.4.2 by @dependabot[bot] in #986
• Bump docker/build-push-action from 6 to 7 by @dependabot[bot] in #985
• Bump docker/login-action from 3 to 4 by @dependabot[bot] in #983
• Bump docker/setup-buildx-action from 3 to 4 by @dependabot[bot] in #984
• Bump docker/setup-compose-action from 1 to 2 by @dependabot[bot] in #976
• Bump docker/setup-docker-action from 4 to 5 by @dependabot[bot] in #979
• Bump docker/setup-qemu-action from 3 to 4 by @dependabot[bot] in #982
• Bump helm/kind-action from 1.13.0 to 1.14.0 by @dependabot[bot] in #957
• Bump isort from 7.0.0 to 8.0.0 by @dependabot[bot] in #961
• Bump isort from 8.0.0 to 8.0.1 by @dependabot[bot] in #977
• Bump mypy from 1.19.0 to 1.19.1 by @dependabot[bot] in #940
• Bump pandas-stubs from 2.3.3.251201 to 2.3.3.260113 by @dependabot[bot] in #942
• Bump pytest-cov from 7.0.0 to 7.1.0 by @dependabot[bot] in #1002
• Bump types-cachetools from 6.2.0.20251022 to 6.2.0.20260317 by @dependabot[bot] in #994
• Bump types-jsonschema from 4.25.1.20251009 to 4.26.0.20260202 by @dependabot[bot] in #941
• Bump types-jsonschema from 4.26.0.20260202 to 4.26.0.20260324 by @dependabot[bot] in #1003
• Bump types-jsonschema from 4.26.0.20260324 to 4.26.0.20260325 by @dependabot[bot] in #1005
• Bump types-psutil from 7.1.3.20251202 to 7.2.2.20260130 by @dependabot[bot] in #939

Full Changelog: 0.2.0.dev14...0.2.0rc1

0.2.0.dev14

Breaking Changes

• Drop support for Python 3.9 by @GlassOfWhiskey in #827

What's Changed

• Refactor processors' logic for async execution by @GlassOfWhiskey in #789
• Make CommandOutputProcessor handle Future objs by @GlassOfWhiskey in #790
• Refactor TokenProcessor and CommandOutputProcessor classes by @GlassOfWhiskey in #793
• Add support for CWL v1.3 by @GlassOfWhiskey in #802
• Update versions in CI/CD pipeline by @GlassOfWhiskey in #806
• Refactor exit code evaluation by @LanderOtto in #799
• Fixed issues related to default values in CWL by @LanderOtto in #808
• Added a check for the chosen deployment in the tests by @LanderOtto in #814
• Fixed recoverable attribute in the ListToken and ObjectToken classes by @LanderOtto in #752
• Add support for Python 3.14 by @GlassOfWhiskey in #820
• Refactor handling of File and Directory literals by @LanderOtto in #811
• Fixed issue on multiple exampleOfWork on RunCrate provenance by @LanderOtto in #841
• Fixed issue in DependencyResolver by @LanderOtto in #839
• Fix Lima version to v1.2.2 by @GlassOfWhiskey in #850
• Remove disable-content-trust in DockerConnector by @GlassOfWhiskey in #856
• Remove Lima version from MacOS CI by @GlassOfWhiskey in #859
• Remove TransferStep from CWL ExpressionTool by @GlassOfWhiskey in #860
• Fixed loadContents in the collector step by @LanderOtto in #846
• Fix race condition with output unique paths by @GlassOfWhiskey in #863
• Fix minor issues on recovery by @LanderOtto in #862
• Adjust Python cache in GitHub CI/CD by @GlassOfWhiskey in #865
• Fixed CWLObjectCommandOutputProcessor to handle arrays of records by @LanderOtto in #858
• Added checks for CWL feature requirement by @GlassOfWhiskey in #866
• Fixed eval method of the DependencyResolver by @LanderOtto in #867
• Handle location storage retrieval errors by @LanderOtto in #871
• Fix StreamFlowContext by @LanderOtto in #880
• Update MacOS X CI/CD to version 15 by @GlassOfWhiskey in #819
• Fixed directory registration by @LanderOtto in #881
• Reduced overhead of the transfer_data method by @LanderOtto in #883
• Revert sphinx to v8.1.3 by @GlassOfWhiskey in #888
• Migrate to uv package manager by @GlassOfWhiskey in #889
• Fixed type checking in CWLCommandTokenProcessor by @LanderOtto in #895
• Respect available CPUs in LocalConnector by @mr-c in #896
• Fix issues in the ValueFromTransformer and LoopValueFromTransformer classes by @LanderOtto in #882
• Fixed StreamFlowContext creation by @LanderOtto in #901
• Added MatchingBindingFilter by @LanderOtto in #872
• Fixed transfer of hardlink by @LanderOtto in #891
• Fixed ExpressionTool outputs processing by @LanderOtto in #902
• Fix cwl.output.json behaviour by @GlassOfWhiskey in #851
• Fix ext show command by @GlassOfWhiskey in #927

Dependencies

• Bump aiohttp from 3.12.15 to 3.13.0 by @dependabot[bot] in #821
• Bump aiohttp from 3.13.0 to 3.13.1 by @dependabot[bot] in #832
• Bump aiohttp from 3.13.1 to 3.13.2 by @dependabot[bot] in #840
• Bump aiosqlite from 0.21.0 to 0.22.0 by @dependabot[bot] in #898
• Bump aiosqlite from 0.22.0 to 0.22.1 by @dependabot[bot] in #906
• Bump asyncssh from 2.21.0 to 2.21.1 by @dependabot[bot] in #815
• Bump asyncssh from 2.21.1 to 2.22.0 by @dependabot[bot] in #918
• Bump bcrypt from 4.3.0 to 5.0.0 by @dependabot[bot] in #812
• Bump cachetools from 6.1.0 to 6.2.0 by @dependabot[bot] in #792
• Bump cachetools from 6.2.0 to 6.2.1 by @dependabot[bot] in #828
• Bump cachetools from 6.2.1 to 6.2.2 by @dependabot[bot] in #861
• Bump cachetools from 6.2.2 to 6.2.3 by @dependabot[bot] in #897
• Bump cwl-utils from 0.39 to 0.40 by @dependabot[bot] in #803
• Bump filelock from 3.20.0 to 3.20.3 by @dependabot[bot] in #917
• Bump importlib-metadata from 8.7.0 to 8.7.1 by @dependabot[bot] in #907
• Bump jsonschema from 4.25.0 to 4.25.1 by @dependabot[bot] in #786
• Bump jsonschema from 4.25.1 to 4.26.0 by @dependabot[bot] in #923
• Bump kaleido from 1.0.0 to 1.1.0 by @dependabot[bot] in #804
• Bump kaleido from 1.1.0 to 1.2.0 by @dependabot[bot] in #848
• Bump kubernetes-asyncio from 32.3.2 to 33.3.0 by @dependabot[bot] in #783
• Bump kubernetes-asyncio from 33.3.0 to 34.3.3 by @dependabot[bot] in #915
• Bump pandas from 2.3.1 to 2.3.2 by @dependabot[bot] in #788
• Bump pandas from 2.3.2 to 2.3.3 by @dependabot[bot] in #816
• Bump plotly from 6.2.0 to 6.3.0 by @dependabot[bot] in #784
• Bump plotly from 6.3.0 to 6.3.1 by @dependabot[bot] in #818
• Bump plotly from 6.3.1 to 6.4.0 by @dependabot[bot] in #847
• Bump plotly from 6.4.0 to 6.5.0 by @dependabot[bot] in #869
• Bump plotly from 6.5.0 to 6.5.1 by @dependabot[bot] in #905
• Bump plotly from 6.5.1 to 6.5.2 by @dependabot[bot] in #920
• Bump psutil from 7.0.0 to 7.1.0 by @dependabot[bot] in #807
• Bump psutil from 7.1.0 to 7.1.1 by @dependabot[bot] in #833
• Bump psutil from 7.1.1 to 7.1.2 by @dependabot[bot] in #837
• Bump psutil from 7.1.2 to 7.1.3 by @dependabot[bot] in #844
• Bump psutil from 7.1.3 to 7.2.1 by @dependabot[bot] in #914
• Bump rdflib from 7.1.4 to 7.2.1 by @dependabot[bot] in #809
• Bump rdflib from 7.2.1 to 7.4.0 by @dependabot[bot] in #842
• Bump rdflib from 7.4.0 to 7.5.0 by @dependabot[bot] in #877
• Bump referencing from 0.36.2 to 0.37.0 by @dependabot[bot] in #830
• Bump typing-extensions from 4.14.1 to 4.15.0 by @dependabot[bot] in #791
• Bump urllib3 from 2.6.1 to 2.6.3 by @dependabot[bot] in #921

Dev Dependencies

• Bump actions/checkout from 4 to 5 by @dependabot[bot] in #782
• Bump actions/checkout from 5 to 6 by @dependabot[bot] in #874
• Bump actions/download-artifact from 4 to 5 by @dependabot[bot] in #780
• Bump actions/download-artifact from 5 to 6 by @dependabot[bot] in #836
• Bump actions/download-artifact from 6 to 7 by @dependabot[bot] in #899
• Bump actions/setup-node from 4 to 5 by @dependabot[bot] in #796...

0.2.0.dev13

What's Changed

• Fix requirement propagation in CWLTranslator by @GlassOfWhiskey in #688
• Refactor private functions by @LanderOtto in #684
• Always wait for DataLocation to be available by @GlassOfWhiskey in #690
• Refactor unit tests by @LanderOtto in #691
• Fix concurrent output retrieval by @LanderOtto in #689
• Improved WorkflowBuilder by @LanderOtto in #692
• Fixed cleanup in unit tests by @LanderOtto in #695
• Fixed invalidate_location method by @LanderOtto in #694
• Improved is_available method of the FileToken class by @LanderOtto in #696
• Added ROLLBACK status by @LanderOtto in #697
• Refactored TransferStep by @LanderOtto in #698
• Added recoverable attribute to the Token object in the FailureManager by @LanderOtto in #699
• Implemented fault tolerance based on Database module by @LanderOtto in #169
• Refactored the no-cycles check for stacked deployment definitions by @LanderOtto in #705
• Improved handling of File literals by @LanderOtto in #693
• Check if bindings exist in the workflow by @LanderOtto in #708
• Removed comparison operators from Hardware class by @LanderOtto in #711
• Fixed CloneTransformer persistence by @LanderOtto in #719
• Fix InitialWorkDirRequirement for nested dirs by @GlassOfWhiskey in #735
• Capture TimeoutError when retrieving disk usage by @GlassOfWhiskey in #737
• Fixed persistence of CWLCommandOutputProcessor classes by @LanderOtto in #740
• Improve JSONSchema specificaton by @GlassOfWhiskey in #745
• Add a check to verify object instantiation in persistence tests by @LanderOtto in #741
• Added llms.txt to StreamFlow documentation by @GlassOfWhiskey in #754
• Fixed preparation of workdir for list and object inputs by @LanderOtto in #732
• Refactor the invocation of FailureManager within the Step by @LanderOtto in #753
• Improved token processing logic in CWLObjectTokenProcessor by @LanderOtto in #758
• Make Scheduler helper methods raise exceptions by @GlassOfWhiskey in #759
• Remove the StreamWrapperContextManager class by @GlassOfWhiskey in #760
• Fixed tag sorting in the GatherStep by @LanderOtto in #761
• Improve StreamFlow type system by @GlassOfWhiskey in #762
• Fixed CWLMapCommandOutputProcessor persistence by @LanderOtto in #765
• Make StreamFlowContext constructor self-contained by @GlassOfWhiskey in #767
• Improved Combinator persistence tests by @LanderOtto in #764
• Fixed CWLCommand persistence by @LanderOtto in #771
• Improved provenance of the task executions by @LanderOtto in #772
• Fixed the transferBufferSize parameter in the FutureConnector by @LanderOtto in #775
• Fixed subworkflows case in the RunCrateProvenanceManager by @LanderOtto in #774
• Remove support for nested Token objects by @GlassOfWhiskey in #777
• Fixed DefaultRetagTransformer within scatter by @LanderOtto in #742

Dependencies

• Bump aiohttp from 3.11.13 to 3.11.14 by @dependabot[bot] in #700
• Bump aiohttp from 3.11.14 to 3.11.16 by @dependabot[bot] in #712
• Bump aiohttp from 3.11.16 to 3.11.18 by @dependabot[bot] in #715
• Bump aiohttp from 3.11.18 to 3.12.2 by @dependabot[bot] in #724
• Bump aiohttp from 3.12.2 to 3.12.6 by @dependabot[bot] in #729
• Bump aiohttp from 3.12.6 to 3.12.8 by @dependabot[bot] in #731
• Bump aiohttp from 3.12.8 to 3.12.9 by @dependabot[bot] in #733
• Bump aiohttp from 3.12.9 to 3.12.12 by @dependabot[bot] in #738
• Bump aiohttp from 3.12.12 to 3.12.13 by @dependabot[bot] in #744
• Bump aiohttp from 3.12.13 to 3.12.14 by @dependabot[bot] in #757
• Bump aiohttp from 3.12.14 to 3.12.15 by @dependabot[bot] in #773
• Bump asyncssh from 2.20.0 to 2.21.0 by @dependabot[bot] in #718
• Bump bcrypt from 4.2.1 to 4.3.0 by @dependabot[bot] in #683
• Bump cachetools from 5.5.2 to 6.0.0 by @dependabot[bot] in #722
• Bump cachetools from 6.0.0 to 6.1.0 by @dependabot[bot] in #746
• Bump cwltool from 3.1.20250110105449 to 3.1.20250715140722 by @dependabot[bot] in #769
• Bump cwl-utils from 0.37 to 0.38 by @dependabot[bot] in #726
• Bump cwl-utils from 0.38 to 0.39 by @dependabot[bot] in #770
• Bump importlib-metadata from 8.6.1 to 8.7.0 by @dependabot[bot] in #716
• Bump jinja2 from 3.1.5 to 3.1.6 by @dependabot[bot] in #687
• Bump jsonschema from 4.23.0 to 4.24.0 by @dependabot[bot] in #723
• Bump jsonschema from 4.24.0 to 4.24.1 by @dependabot[bot] in #766
• Bump jsonschema from 4.24.1 to 4.25.0 by @dependabot[bot] in #768
• Bump kaleido from 0.4.2 to 1.0.0 by @dependabot[bot] in #749
• Bump kubernetes-asyncio from 32.0.0 to 32.3.0 by @dependabot[bot] in #707
• Bump kubernetes-asyncio from 32.3.0 to 32.3.2 by @dependabot[bot] in #717
• Bump pandas from 2.2.3 to 2.3.0 by @dependabot[bot] in #734
• Bump pandas from 2.3.0 to 2.3.1 by @dependabot[bot] in #756
• Bump plotly from 6.0.0 to 6.0.1 by @dependabot[bot] in #702
• Bump plotly from 6.0.1 to 6.1.2 by @dependabot[bot] in #727
• Bump plotly from 6.1.2 to 6.2.0 by @dependabot[bot] in #750
• Bump rdflib from 7.1.3 to 7.1.4 by @dependabot[bot] in #706

Dev Dependencies

• Bump bandit from 1.8.3 to 1.8.5 by @dependabot[bot] in #747
• Bump bandit from 1.8.5 to 1.8.6 by @dependabot[bot] in #755
• Bump cwltest from 2.5.20241122133319 to 2.6.20250314152537 by @dependabot[bot] in #701
• Bump pytest from 8.3.4 to 8.3.5 by @dependabot[bot] in #685
• Bump pytest from 8.3.5 to 8.4.0 by @dependabot[bot] in #730
• Bump pytest from 8.4.0 to 8.4.1 by @dependabot[bot] in #748
• Bump pytest-asyncio from 0.25.3 to 0.26.0 by @dependabot[bot] in #704
• Bump pytest-asyncio from 0.26.0 to 1.0.0 by @dependabot[bot] in #743
• Bump pytest-asyncio from 1.0.0 to 1.1.0 by @dependabot[bot] in #763
• Bump pytest-cov from 6.0.0 to 6.1.0 by @dependabot[bot] in #709
• Bump pytest-cov from 6.1.0 to 6.1.1 by @dependabot[bot] in #713
• Bump pytest-cov from 6.1.1 to 6.2.1 by @dependabot[bot] in #739
• Bump pytest-xdist from 3.6.1 to 3.7.0 by @dependabot[bot] in #725
• Bump pytest-xdist from 3.7.0 to 3.8.0 by @dependabot[bot] in https://github.co...

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...

0.2.0.dev11

What's Changed

• Add support for Python 3.12 by @GlassOfWhiskey in #256
• Added possibility to load ports and steps in a different workflow by @LanderOtto in #274
• Fixed minor issue with port-targets documentation by @paoloviviani in #276
• Update Node.js version in CI pipeline by @GlassOfWhiskey in #286
• Update CWL v1.2 conformance tests by @GlassOfWhiskey in #288
• Refactor conftest.py by @LanderOtto in #287
• Fixed Config persistence by @LanderOtto in #289
• Fixed loop termination combinator persistence by @LanderOtto in #290
• Removed deprecated pkg_resources API by @GlassOfWhiskey in #291
• Replace cgi and logging.warn with new APIs by @GlassOfWhiskey in #292
• Improve test_download logic by @GlassOfWhiskey in #293
• Add warning messages for default connector params by @GlassOfWhiskey in #294
• Add optional param to composite processors by @GlassOfWhiskey in #295
• Fix copy remote-to-remote using ConnectorWrapper by @LanderOtto in #301
• Adjusted local-to-remote copy with folders by @GlassOfWhiskey in #308
• Fixed remote-to-local copy of nested directories by @LanderOtto in #309
• Fixed template environment variables by @LanderOtto in #310
• Fixed SSHClientConnection closing by @LanderOtto in #311
• Fixed incomplete stream reading by @LanderOtto in #314
• Fix valueFrom type checking behaviour by @GlassOfWhiskey in #323
• Fixed data location invalidation by @LanderOtto in #324
• Fixed job name by @LanderOtto in #325
• Fixed typo errors by @LanderOtto in #326
• Added missing task creation in some gathers by @LanderOtto in #327
• Fixed symbolic link remote input data error by @LanderOtto in #328
• Added StreamWrapper documentation by @GlassOfWhiskey in #329
• Fixed CWLConditionalStep persistence by @LanderOtto in #330
• Fixed provenance issues by @LanderOtto in #331
• Improved error message of batch systems when job fails by @LanderOtto in #332
• Added check after the creation data by @LanderOtto in #336
• Add no regression test for Sphinx documentation by @GlassOfWhiskey in #337
• Reduce size of database metadata by @LanderOtto in #338
• Fixed get method of RemotePathMapper by @LanderOtto in #343
• Move CWL 1.2 conformance to main branch by @GlassOfWhiskey in #346
• Improved scatter/gather performance by @LanderOtto in #348
• Added new queries to the Database by @LanderOtto in #356
• Added retries and retryDelay parameters in the SSHConnector configuration by @LanderOtto in #361
• Fixed some bugs by @LanderOtto in #333
• Fix Codecov GitHub action by @GlassOfWhiskey in #374
• Fix CWL Docker Requirement config example by @GlassOfWhiskey in #375
• Remove SSH deployment from MacOS CI by @GlassOfWhiskey in #376
• Fix Codecov GitHub Action by @GlassOfWhiskey in #379
• Fix Codecov GitHub Action by @GlassOfWhiskey in #380
• Add codecov.yml configuration file by @GlassOfWhiskey in #382
• Support for nested Location objects by @GlassOfWhiskey in #383
• Add __slots__ attribute to Token objects by @GlassOfWhiskey in #385
• Fixed provenance for the size tokens by @LanderOtto in #370
• Remove __eq__ and __hash__ from Location by @GlassOfWhiskey in #389
• Refactor the Location class hierarchy by @GlassOfWhiskey in #390
• Fixed asyncio.Event synchronizations when an exception occurs by @LanderOtto in #395
• Fixed input ports of DotProductSizeTransformer by @LanderOtto in #396
• Fixed wrapped connector calls for QueueManagerConnector classes by @LanderOtto in #403
• Fix ListMergeCombinator port names by @LanderOtto in #407
• Update MacOS X CI/CD pipeline by @GlassOfWhiskey in #408
• Fixed glob on symbolic link path by @LanderOtto in #417
• Removed scheduling_policy attribute in Target class by @LanderOtto in #421
• Removed scheduling_groups attribute by @LanderOtto in #422
• Changed retrieval of location hardware in the SSHConnector class by @LanderOtto in #424
• Refactor test_scheduler by @LanderOtto in #425
• Fixed ValueFromTransformer by @LanderOtto in #446
• Fixed scheduler timeout in Python<3.11 by @LanderOtto in #449

Dependencies

• Bump actions/setup-node from 3 to 4 by @dependabot in #263
• Bump actions/setup-python from 4 to 5 by @dependabot in #306
• Bump actions/upload-artifact from 3 to 4 by @dependabot in #318
• Bump aiohttp from 3.8.6 to 3.9.0 by @dependabot in #283
• Bump aiohttp from 3.9.0 to 3.9.1 by @dependabot in #296
• Bump aiohttp from 3.9.1 to 3.9.2 by @dependabot in #364
• Bump aiohttp from 3.9.2 to 3.9.3 by @dependabot in #367
• Bump aiohttp from 3.9.3 to 3.9.4 by @dependabot in #429
• Bump aiohttp from 3.9.4 to 3.9.5 by @dependabot in #431
• Bump aiosqlite from 0.19.0 to 0.20.0 by @dependabot in #388
• Bump asyncssh from 2.14.0 to 2.14.1 by @dependabot in #277
• Bump asyncssh from 2.14.1 to 2.14.2 by @dependabot in #322
• Bump bandit from 1.7.5 to 1.7.6 by @dependabot in #313
• Bump bandit from 1.7.6 to 1.7.7 by @dependabot in #360
• Bump bandit from 1.7.7 to 1.7.8 by @dependabot in #405
• Bump bcrypt from 4.0.1 to 4.1.1 by @dependabot in #299
• Bump bcrypt from 4.1.1 to 4.1.2 by @dependabot in #320
• Bump bcrypt from 4.1.2 to 4.1.3 by @dependabot in #448
• Bump black from 23.9.1 to 23.10.0 by @dependabot in #260
• Bump black from 23.10.0 to 23.10.1 by @dependabot in #264
• Bump black from 23.10.1 to 23.11.0 by @dependabot in #275
• Bump black from 23.11.0 to 23.12.0 by @dependabot in #315
• Bump black from 23.12.0 to 23.12.1 by @dependabot in #335
• Bump black from 23.12.1 to 24.1.0 by @dependabot in #362
• Bump black from 24.1.0 to 24.1.1 by @dependabot in #366
• Bump black from 24.1.1 to 24.2.0 by @dependabot in #381
• Bump black from 24.2.0 to 24.3.0 by @dependabot in #413
• Bump black from 24.3.0 to 24.4.0 by @dependabot in #430
• Bump black from 24.4.0 to 24.4.1 by @dependabot in https://github.com/alpha-unito/strea...

0.2.0.dev10

What's Changed

• Added parameter to choose the deployments to use in pytests by @LanderOtto in #232
• Fix _get_existing_parent behaviour by @GlassOfWhiskey in #253

Dependencies

• Bump aiohttp from 3.8.5 to 3.8.6 by @dependabot in #255
• Bump asyncssh from 2.13.2 to 2.14.0 by @dependabot in #250
• Bump black from 23.7.0 to 23.9.1 by @dependabot in #233
• Bump codespell from 2.2.5 to 2.2.6 by @dependabot in #252
• Bump docker/build-push-action from 4 to 5 by @dependabot in #237
• Bump docker/login-action from 2 to 3 by @dependabot in #235
• Bump docker/setup-buildx-action from 2 to 3 by @dependabot in #236
• Bump docker/setup-qemu-action from 2 to 3 by @dependabot in #234
• Bump flake8-bugbear from 23.7.10 to 23.9.16 by @dependabot in #239
• Bump jsonschema from 4.19.0 to 4.19.1 by @dependabot in #244
• Bump kubernetes-asyncio from 25.11.0 to 26.9.0 by @dependabot in #247
• Bump kubernetes-asyncio from 26.9.0 to 27.6.0 by @dependabot in #249
• Bump kubernetes-asyncio from 27.6.0 to 28.2.0 by @dependabot in #254
• Bump mukunku/tag-exists-action from 1.3.0 to 1.4.0 by @dependabot in #242
• Bump pandas from 2.1.0 to 2.1.1 by @dependabot in #245
• Bump plotly from 5.16.1 to 5.17.0 by @dependabot in #240
• Bump pyupgrade from 3.10.1 to 3.12.0 by @dependabot in #246
• Bump pyupgrade from 3.12.0 to 3.13.0 by @dependabot in #248
• Bump pyupgrade from 3.13.0 to 3.14.0 by @dependabot in #251
• Bump sphinx from 7.2.5 to 7.2.6 by @dependabot in #238

Full Changelog: 0.2.0.dev9...0.2.0.dev10

0.2.0.dev9

What's Changed

• Fix Python dependencies conflict in Mac OS CI by @GlassOfWhiskey in #214
• Connector and CWL Runner fixes by @GlassOfWhiskey in #216
• Fix template_map error when service has no file by @GlassOfWhiskey in #223
• Fix scheduler behaviour when retry_delay is set by @GlassOfWhiskey in #224
• Fix potential race condition on sqlite row_factory by @GlassOfWhiskey in #225
• Add configurable time option in HPC connectors by @GlassOfWhiskey in #227
• Avoid opening too many SSH sessions by @GlassOfWhiskey in #229
• Fix Flux Docker version to 0.28.0 by @GlassOfWhiskey in #230
• Update CWL v1.2 conformance tests by @GlassOfWhiskey in #231

Dependencies

• Bump actions/checkout from 3 to 4 by @dependabot in #221
• Bump antlr4-python3-runtime from 4.13.0 to 4.13.1 by @dependabot in #222
• Bump cwltool from 3.1.20230719185429 to 3.1.20230906142556 by @dependabot in #226
• Bump cwl-utils from 0.28 to 0.29 by @dependabot in #220
• Bump pandas from 2.0.3 to 2.1.0 by @dependabot in #217
• Bump pytest from 7.4.0 to 7.4.1 by @dependabot in #219
• Bump pytest from 7.4.1 to 7.4.2 by @dependabot in #228
• Bump sphinx from 7.2.3 to 7.2.4 by @dependabot in #215
• Bump sphinx from 7.2.4 to 7.2.5 by @dependabot in #218

Full Changelog: 0.2.0.dev8...0.2.0.dev9

0.2.0.dev8

What's Changed

• Updated MacOS CI in GitHub Actions by @GlassOfWhiskey in #204
• Change jsonschema loader by @GlassOfWhiskey in #205
• Enable distributed inheritance for plugins by @GlassOfWhiskey in #208
• Fix Flux and Mac OS CI steps by @GlassOfWhiskey in #209
• Adjust JSONSchema ids by @GlassOfWhiskey in #211
• Update docs to v0.2.0 by @GlassOfWhiskey in #213

##Dependencies

• Bump cwltest from 2.3.20230527113600 to 2.3.20230825125225 by @dependabot in #212
• Bump jsonschema from 4.18.6 to 4.19.0 by @dependabot in #197
• Bump kubernetes-asyncio from 24.2.3 to 25.11.0 by @dependabot in #206
• Bump mukunku/tag-exists-action from 1.2.0 to 1.3.0 by @dependabot in #198
• Bump plotly from 5.15.0 to 5.16.0 by @dependabot in #199
• Bump plotly from 5.16.0 to 5.16.1 by @dependabot in #201
• Bump sphinx from 7.1.2 to 7.2.2 by @dependabot in #203
• Bump sphinx from 7.2.2 to 7.2.3 by @dependabot in #210
• Bump sphinx-rtd-theme from 1.2.2 to 1.3.0 by @dependabot in #207

Full Changelog: 0.2.0.dev7...0.2.0.dev8

0.2.0.dev7

What's Changed

• Updated CWL v1.2 conformance tests by @GlassOfWhiskey in #168
• Added type definitions to ext CLI by @GlassOfWhiskey in #180
• Migrated JSONSchema to Draft 2019-09 by @GlassOfWhiskey in #185
• Fixed type checking in conftest by @GlassOfWhiskey in #195
• Moved black configuration to pyproject.toml by @GlassOfWhiskey in #196

Dependencies

• Bump aiohttp from 3.8.4 to 3.8.5 by @dependabot in #187
• Bump asyncssh from 2.13.1 to 2.13.2 by @dependabot in #170
• Bump black from 23.3.0 to 23.7.0 by @dependabot in #178
• Bump codespell from 2.2.4 to 2.2.5 by @dependabot in #165
• Bump cwltool from 3.1.20230601100705 to 3.1.20230624081518 by @dependabot in #172
• Bump cwltool from 3.1.20230624081518 to 3.1.20230719185429 by @dependabot in #189
• Bump flake8-bugbear from 23.6.5 to 23.7.10 by @dependabot in #179
• Bump importlib-metadata from 6.6.0 to 6.7.0 by @dependabot in #167
• Bump importlib-metadata from 6.7.0 to 6.8.0 by @dependabot in #177
• Bump jsonschema from 4.17.3 to 4.18.0 by @dependabot in #175
• Bump jsonschema from 4.18.0 to 4.18.3 by @dependabot in #184
• Bump jsonschema from 4.18.3 to 4.18.4 by @dependabot in #186
• Bump jsonschema from 4.18.4 to 4.18.6 by @dependabot in #194
• Bump pandas from 2.0.2 to 2.0.3 by @dependabot in #173
• Bump pytest from 7.3.2 to 7.4.0 by @dependabot in #171
• Bump pytest-asyncio from 0.21.0 to 0.21.1 by @dependabot in #182
• Bump pyupgrade from 3.6.0 to 3.7.0 by @dependabot in #166
• Bump pyupgrade from 3.7.0 to 3.8.0 by @dependabot in #174
• Bump pyupgrade from 3.8.0 to 3.9.0 by @dependabot in #176
• Bump pyupgrade from 3.9.0 to 3.10.1 by @dependabot in #191
• Bump sphinx from 7.0.1 to 7.1.0 by @dependabot in #188
• Bump sphinx from 7.1.0 to 7.1.1 by @dependabot in #190
• Bump sphinx from 7.1.1 to 7.1.2 by @dependabot in #192

Full Changelog: 0.2.0.dev6...0.2.0.dev7

0.2.0.dev6

What's Changed

• Fix additional files in RunCrate provenance by @GlassOfWhiskey in #136
• Fix list and report subcommands by @GlassOfWhiskey in #144
• Added streamflow ext subcommand by @GlassOfWhiskey in #145
• Added no regression tests for provenance by @LanderOtto in #150
• Adding explicit options to queue connectors by @GlassOfWhiskey in #151
• Added curl flags in Dockerfile to retry server connection when it fails by @LanderOtto in #158
• Handling allOf directives in config schemas by @GlassOfWhiskey in #164

Dependencies

• Bump antlr4-python3-runtime from 4.12.0 to 4.13.0 by @dependabot in #147
• Bump cachetools from 5.3.0 to 5.3.1 by @dependabot in #152
• Bump cwltest from 2.3.20230108193615 to 2.3.20230527113600 by @dependabot in #155
• Bump cwltool from 3.1.20230425144158 to 3.1.20230513155734 by @dependabot in #140
• Bump cwltool from 3.1.20230513155734 to 3.1.20230527103121 by @dependabot in #154
• Bump cwltool from 3.1.20230527103121 to 3.1.20230601100705 by @dependabot in #156
• Bump cwl-utils from 0.25 to 0.26 by @dependabot in #138
• Bump cwl-utils from 0.26 to 0.27 by @dependabot in #142
• Bump cwl-utils from 0.27 to 0.28 by @dependabot in #157
• Bump flake8-bugbear from 23.3.23 to 23.5.9 by @dependabot in #137
• Bump flake8-bugbear from 23.5.9 to 23.6.5 by @dependabot in #159
• Bump pandas from 2.0.1 to 2.0.2 by @dependabot in #153
• Bump plotly from 5.14.1 to 5.15.0 by @dependabot in #161
• Bump pytest from 7.3.1 to 7.3.2 by @dependabot in #162
• Bump pytest-cov from 4.0.0 to 4.1.0 by @dependabot in #149
• Bump pytest-xdist from 3.2.1 to 3.3.0 by @dependabot in #141
• Bump pytest-xdist from 3.3.0 to 3.3.1 by @dependabot in #143
• Bump pyupgrade from 3.3.2 to 3.4.0 by @dependabot in #135
• Bump pyupgrade from 3.4.0 to 3.6.0 by @dependabot in #163
• Bump sphinx from 7.0.0 to 7.0.1 by @dependabot in #139
• Bump sphinx-rtd-theme from 1.2.0 to 1.2.1 by @dependabot in #148
• Bump sphinx-rtd-theme from 1.2.1 to 1.2.2 by @dependabot in #160

Full Changelog: 0.2.0.dev5...0.2.0.dev6