Streamflow

What's Changed
* Fix additional files in RunCrate provenance by GlassOfWhiskey in https://github.com/alpha-unito/streamflow/pull/136
* Fix `list` and `report` subcommands by GlassOfWhiskey in https://github.com/alpha-unito/streamflow/pull/144
* Added `streamflow ext` subcommand by GlassOfWhiskey in https://github.com/alpha-unito/streamflow/pull/145
* Added no regression tests for provenance by LanderOtto in https://github.com/alpha-unito/streamflow/pull/150
* Adding explicit options to queue connectors by GlassOfWhiskey in https://github.com/alpha-unito/streamflow/pull/151
* Added curl flags in Dockerfile to retry server connection when it fails by LanderOtto in https://github.com/alpha-unito/streamflow/pull/158
* Handling `allOf` directives in config schemas by GlassOfWhiskey in https://github.com/alpha-unito/streamflow/pull/164

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


**Full Changelog**: https://github.com/alpha-unito/streamflow/compare/0.2.0.dev5...0.2.0.dev6

What's Changed
* Fix InitialWorkDirRequirement with subdirs by GlassOfWhiskey in https://github.com/alpha-unito/streamflow/pull/118
* Improved StreamFlow provenance support by GlassOfWhiskey in https://github.com/alpha-unito/streamflow/pull/122
* Improved CLI for plugin inspection by GlassOfWhiskey in https://github.com/alpha-unito/streamflow/pull/130
* Added package and version to plugin description by GlassOfWhiskey in https://github.com/alpha-unito/streamflow/pull/134

Dependencies
* Bump aiosqlite from 0.18.0 to 0.19.0 by dependabot in https://github.com/alpha-unito/streamflow/pull/115
* Bump cwltool from 3.1.20230325110543 to 3.1.20230425144158 by dependabot in https://github.com/alpha-unito/streamflow/pull/129
* Bump cwl-utils from 0.23 to 0.24 by dependabot in https://github.com/alpha-unito/streamflow/pull/114
* Bump cwl-utils from 0.24 to 0.25 by dependabot in https://github.com/alpha-unito/streamflow/pull/133
* Bump importlib-metadata from 6.3.0 to 6.5.0 by dependabot in https://github.com/alpha-unito/streamflow/pull/119
* Bump importlib-metadata from 6.5.0 to 6.6.0 by dependabot in https://github.com/alpha-unito/streamflow/pull/124
* Bump kubernetes-asyncio from 24.2.2 to 24.2.3 by dependabot in https://github.com/alpha-unito/streamflow/pull/132
* Bump pandas from 2.0.0 to 2.0.1 by dependabot in https://github.com/alpha-unito/streamflow/pull/125
* Bump psutil from 5.9.4 to 5.9.5 by dependabot in https://github.com/alpha-unito/streamflow/pull/120
* Bump pytest from 7.3.0 to 7.3.1 by dependabot in https://github.com/alpha-unito/streamflow/pull/117
* Bump pyupgrade from 3.3.1 to 3.3.2 by dependabot in https://github.com/alpha-unito/streamflow/pull/128
* Bump sphinx from 6.1.3 to 6.2.0 by dependabot in https://github.com/alpha-unito/streamflow/pull/123
* Bump sphinx from 6.2.0 to 6.2.1 by dependabot in https://github.com/alpha-unito/streamflow/pull/126
* Bump sphinx from 6.2.1 to 7.0.0 by dependabot in https://github.com/alpha-unito/streamflow/pull/131

**Full Changelog**: https://github.com/alpha-unito/streamflow/compare/0.2.0.dev4...0.2.0.dev5

What's Changed
* Fix StreamFlow MPI example by GlassOfWhiskey in https://github.com/alpha-unito/streamflow/pull/95
* Added explicit version check for DockerCompose by GlassOfWhiskey in https://github.com/alpha-unito/streamflow/pull/96
* Updated and fixed StreamFlow Dockerfile by GlassOfWhiskey in https://github.com/alpha-unito/streamflow/pull/97
* Fixed Docker and Helm features by GlassOfWhiskey in https://github.com/alpha-unito/streamflow/pull/109
* Added flux framework connector by vsoch in https://github.com/alpha-unito/streamflow/pull/107
* Added configurable DockerRequirement conversion by GlassOfWhiskey in https://github.com/alpha-unito/streamflow/pull/111

Dependencies
* Bump black from 23.1.0 to 23.3.0 by dependabot in https://github.com/alpha-unito/streamflow/pull/105
* Bump cwltool from 3.1.20230302145532 to 3.1.20230325110543 by dependabot in https://github.com/alpha-unito/streamflow/pull/103
* Bump flake8-bugbear from 23.2.13 to 23.3.12 by dependabot in https://github.com/alpha-unito/streamflow/pull/91
* Bump flake8-bugbear from 23.3.12 to 23.3.23 by dependabot in https://github.com/alpha-unito/streamflow/pull/102
* Bump importlib-metadata from 6.0.0 to 6.1.0 by dependabot in https://github.com/alpha-unito/streamflow/pull/100
* Bump importlib-metadata from 6.1.0 to 6.3.0 by dependabot in https://github.com/alpha-unito/streamflow/pull/112
* Bump pandas from 1.5.2 to 1.5.3 by dependabot in https://github.com/alpha-unito/streamflow/pull/92
* Bump pandas from 1.5.3 to 2.0.0 by dependabot in https://github.com/alpha-unito/streamflow/pull/108
* Bump plotly from 5.11.0 to 5.13.1 by dependabot in https://github.com/alpha-unito/streamflow/pull/93
* Bump plotly from 5.13.1 to 5.14.0 by dependabot in https://github.com/alpha-unito/streamflow/pull/106
* Bump plotly from 5.14.0 to 5.14.1 by dependabot in https://github.com/alpha-unito/streamflow/pull/110
* Bump pytest from 7.2.2 to 7.3.0 by dependabot in https://github.com/alpha-unito/streamflow/pull/113
* Bump pytest-asyncio from 0.20.3 to 0.21.0 by dependabot in https://github.com/alpha-unito/streamflow/pull/101
* Bump pytest-xdist from 3.2.0 to 3.2.1 by dependabot in https://github.com/alpha-unito/streamflow/pull/90
* Bump rdflib from 6.2.0 to 6.3.2 by dependabot in https://github.com/alpha-unito/streamflow/pull/104

New Contributors
* vsoch made their first contribution in https://github.com/alpha-unito/streamflow/pull/107

**Full Changelog**: https://github.com/alpha-unito/streamflow/compare/0.2.0.dev3...0.2.0.dev4

What's Changed
* Colored output for Streamflow Run by paoloviviani in https://github.com/alpha-unito/streamflow/pull/17
* Changed test pipeline by GlassOfWhiskey in https://github.com/alpha-unito/streamflow/pull/33
* Prepend `isEnabledFor` to logger calls by GlassOfWhiskey in https://github.com/alpha-unito/streamflow/pull/37
* Added regression test scheduler by LanderOtto in https://github.com/alpha-unito/streamflow/pull/39
* Code reformat with pyupgrade by GlassOfWhiskey in https://github.com/alpha-unito/streamflow/pull/40
* Workflow Run RO-Crate support by GlassOfWhiskey in https://github.com/alpha-unito/streamflow/pull/45
* Added extension points to StreamFlowPlugin by GlassOfWhiskey in https://github.com/alpha-unito/streamflow/pull/46
* Revised setup.py classifiers by GlassOfWhiskey in https://github.com/alpha-unito/streamflow/pull/49
* Fix scheduler validation path by GlassOfWhiskey in https://github.com/alpha-unito/streamflow/pull/50
* Better job naming strategy for CWL by GlassOfWhiskey in https://github.com/alpha-unito/streamflow/pull/51
* Fixed cwl-runner entrypoint with no workflows entry by GlassOfWhiskey in https://github.com/alpha-unito/streamflow/pull/52
* Added nested files to main entity by GlassOfWhiskey in https://github.com/alpha-unito/streamflow/pull/53
* Avoid Sqlite race conditions during tests by GlassOfWhiskey in https://github.com/alpha-unito/streamflow/pull/57
* Added no regression tests for persistence by LanderOtto in https://github.com/alpha-unito/streamflow/pull/56
* Use JSON format for PBS output by GlassOfWhiskey in https://github.com/alpha-unito/streamflow/pull/63
* Moving aiotarstream to the deployment module by GlassOfWhiskey in https://github.com/alpha-unito/streamflow/pull/64
* Register job directories after creating them by GlassOfWhiskey in https://github.com/alpha-unito/streamflow/pull/65
* Moving some logic from Translator to utils by GlassOfWhiskey in https://github.com/alpha-unito/streamflow/pull/66
* Added persistence of Command class structure by LanderOtto in https://github.com/alpha-unito/streamflow/pull/74
* Fixed MacOS compatibility by GlassOfWhiskey in https://github.com/alpha-unito/streamflow/pull/77
* Stricter type checking for CWL outputs by GlassOfWhiskey in https://github.com/alpha-unito/streamflow/pull/70
* Fix CWL map processors behaviour by GlassOfWhiskey in https://github.com/alpha-unito/streamflow/pull/81
* Added support for nested connectors by GlassOfWhiskey in https://github.com/alpha-unito/streamflow/pull/86
* Migrate from `setup.py` to `pyproject.toml` by GlassOfWhiskey in https://github.com/alpha-unito/streamflow/pull/89

Dependencies

* Bump actions/checkout from 2 to 3 by dependabot in https://github.com/alpha-unito/streamflow/pull/29
* Bump actions/setup-node from 2 to 3 by dependabot in https://github.com/alpha-unito/streamflow/pull/22
* Bump actions/setup-python from 2 to 4 by dependabot in https://github.com/alpha-unito/streamflow/pull/20
* Bump actions/upload-artifact from 2 to 3 by dependabot in https://github.com/alpha-unito/streamflow/pull/36
* Bump aiohttp from 3.8.3 to 3.8.4 by dependabot in https://github.com/alpha-unito/streamflow/pull/72
* Bump antlr4-python3-runtime from 4.10 to 4.11.1 by dependabot in https://github.com/alpha-unito/streamflow/pull/23
* Bump antlr4-python3-runtime from 4.11.1 to 4.12.0 by dependabot in https://github.com/alpha-unito/streamflow/pull/76
* Bump asyncssh from 2.13.0 to 2.13.1 by dependabot in https://github.com/alpha-unito/streamflow/pull/75
* Bump bandit from 1.7.4 to 1.7.5 by dependabot in https://github.com/alpha-unito/streamflow/pull/85
* Bump black from 22.12.0 to 23.1.0 by dependabot in https://github.com/alpha-unito/streamflow/pull/60
* Bump cachetools from 5.2.0 to 5.2.1 by dependabot in https://github.com/alpha-unito/streamflow/pull/35
* Bump cachetools from 5.2.1 to 5.3.0 by dependabot in https://github.com/alpha-unito/streamflow/pull/47
* Bump codespell from 2.2.2 to 2.2.4 by dependabot in https://github.com/alpha-unito/streamflow/pull/84
* Bump cwltool from 3.1.20221008225030 to 3.1.20221201130942 by dependabot in https://github.com/alpha-unito/streamflow/pull/25
* Bump cwltool from 3.1.20221201130942 to 3.1.20230127121939 by dependabot in https://github.com/alpha-unito/streamflow/pull/55
* Bump cwltool from 3.1.20230127121939 to 3.1.20230201224320 by dependabot in https://github.com/alpha-unito/streamflow/pull/61
* Bump cwltool from 3.1.20230201224320 to 3.1.20230209161050 by dependabot in https://github.com/alpha-unito/streamflow/pull/69
* Bump cwltool from 3.1.20230209161050 to 3.1.20230213100550 by dependabot in https://github.com/alpha-unito/streamflow/pull/71
* Bump cwltool from 3.1.20230213100550 to 3.1.20230302145532 by dependabot in https://github.com/alpha-unito/streamflow/pull/79
* Bump cwl-utils from 0.20 to 0.21 by dependabot in https://github.com/alpha-unito/streamflow/pull/26
* Bump cwl-utils from 0.21 to 0.22 by dependabot in https://github.com/alpha-unito/streamflow/pull/54
* Bump cwl-utils from 0.22 to 0.23 by dependabot in https://github.com/alpha-unito/streamflow/pull/62
* Bump docker/build-push-action from 2 to 3 by dependabot in https://github.com/alpha-unito/streamflow/pull/21
* Bump docker/build-push-action from 3 to 4 by dependabot in https://github.com/alpha-unito/streamflow/pull/59
* Bump docker/login-action from 1 to 2 by dependabot in https://github.com/alpha-unito/streamflow/pull/19
* Bump docker/setup-buildx-action from 1 to 2 by dependabot in https://github.com/alpha-unito/streamflow/pull/24
* Bump docker/setup-qemu-action from 1 to 2 by dependabot in https://github.com/alpha-unito/streamflow/pull/28
* Bump flake8-bugbear from 22.12.6 to 23.1.17 by dependabot in https://github.com/alpha-unito/streamflow/pull/44
* Bump flake8-bugbear from 23.1.17 to 23.1.20 by dependabot in https://github.com/alpha-unito/streamflow/pull/48
* Bump flake8-bugbear from 23.1.20 to 23.2.13 by dependabot in https://github.com/alpha-unito/streamflow/pull/73
* Bump importlib-metadata from 5.2.0 to 6.0.0 by dependabot in https://github.com/alpha-unito/streamflow/pull/30
* Bump jsonref from 1.0.1 to 1.1.0 by dependabot in https://github.com/alpha-unito/streamflow/pull/43
* Bump mukunku/tag-exists-action from 1.0.0 to 1.2.0 by dependabot in https://github.com/alpha-unito/streamflow/pull/27
* Bump pytest from 7.2.0 to 7.2.1 by dependabot in https://github.com/alpha-unito/streamflow/pull/41
* Bump pytest from 7.2.1 to 7.2.2 by dependabot in https://github.com/alpha-unito/streamflow/pull/80
* Bump pytest-xdist from 3.1.0 to 3.2.0 by dependabot in https://github.com/alpha-unito/streamflow/pull/67
* Bump sphinx from 6.0.0 to 6.1.0 by dependabot in https://github.com/alpha-unito/streamflow/pull/31
* Bump sphinx from 6.1.0 to 6.1.2 by dependabot in https://github.com/alpha-unito/streamflow/pull/34
* Bump sphinx from 6.1.2 to 6.1.3 by dependabot in https://github.com/alpha-unito/streamflow/pull/38
* Bump sphinx-rtd-theme from 1.1.1 to 1.2.0 by dependabot in https://github.com/alpha-unito/streamflow/pull/68
* Bump yattag from 1.15.0 to 1.15.1 by dependabot in https://github.com/alpha-unito/streamflow/pull/78

New Contributors
* paoloviviani made their first contribution in https://github.com/alpha-unito/streamflow/pull/17
* LanderOtto made their first contribution in https://github.com/alpha-unito/streamflow/pull/39

**Full Changelog**: https://github.com/alpha-unito/streamflow/compare/0.2.0.dev2...0.2.0.dev3