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Unreleased

🚀 Features

  • Updated the underlying CWL libraries to our commonwl library #236
  • Removed annotate command due to lack of usage
  • Removed init Option -a which could be used to create ARCs - from a long term perspective the ARC spec may change - if we are not able to provide updates everytime this feature obsoletes anyway

🐛 Bugfixes

  • ramping up runner conformance from 223/378 to 376/378

v1.2.0

🚀 Features

  • create has option --run-container to execute the command for CommandLineTool creation with provided container
  • execute local --apptainer or execute local --singularity to use apptainer/singularity for local execution

🐛 Bugfixes

Fixed bugs with s4n init and the error reporting

v1.1.0

  • create now has --env option to load in an .env file
  • made inputs and outputs prefix optional in connect

🐛 Bugfixes

  • default values are used on input connections
  • Fixed some bugs in command parsing (s4n create, fixes for python modules)
  • Better alignment with CWL spec in some points (e.g. glob)

🚜 Refactor

  • Major restructuring for better maintainability

v1.0.0

🚀 Features

  • Restructured CLI Commands #158 #151

Important

The commands have changed in v1.0.0 (Breaking Change). The mapping is as follows:

Old Command New Command
s4n tool create s4n create
s4n tool list s4n list
s4n tool remove s4n remove
s4n workflow create s4n create --name (optional!)
s4n workflow list s4n list
s4n workflow remove s4n remove
s4n workflow status s4n list [WORKFLOW_NAME]
s4n workflow connect s4n connect
s4n workflow disconnect s4n disconnect
s4n workflow visualize s4n visualize
s4n workflow save s4n save

v0.8.0

🚀 Features

  • Support Workflows in git submodules #137
  • Added s4n install and s4n uninstall commands #138
  • Runner supports scatter and linkMerge now
  • Support packed CWL Documents in Runner #144
  • Use ttl.sh to build Docker images for REANA on the fly (fixes #119)

🐛 Bugfixes

  • ramping up runner conformance from 204/378 to 223/378
  • fixed staging of arrays of files and dirs
  • fixed staging of iwdr arrays

🚜 Refactor

  • Code restructuring
  • Consolidation in REANA specific (De)Serialization code #145

v0.7.0

🚀 Features

  • Remote Execution using Reana #108
    • FAIRagro Reana Instance will be provided later, see #42
    • Credentials stored in keyring #118
    • Provenance RO-Crate can be created from remote execution 46808afdd219b68c69562fedce00e164b4fb0081
  • Possibility to connect all CWL Documents in s4n workflow connect #95
  • added --mount to s4n tool create to mount directories into working dir #103
  • added type hints in s4n tool create. Inputs prefixed like s:/mnt/ are then enforced to be of type string.

🐛 Bugfixes

  • Inputs and Outputs can not have same IDs #113

v0.6.1

🚀 Features

  • Added command s4n workflow visualize which accepts a path and either mermaid or dot as renderer outputting diagrams

v0.6.0

🚀 Features

  • Remote Execution s4n execute remote using REANA (testing) #101 + #108
  • Added workflow.toml as config format #102
  • added NetworkAccess Requirement via --net/--enable-network in s4n tool create #104
  • Support InlineTools in Workflow step #111
  • Support Expressions, Files and Directories as InitialWorkDirRequirement (in additon to Dirents)
  • Support Conditional Execution

🐛 Bugfixes

  • fixed a bug with Dockerfile path resolution
  • handle NetworkAccess Requirment in runner
  • inherit parents requirements correclty
  • ramping up runner conformance from 160/378 to 204/378

v0.5.2

🐛 Bugfixes

  • fixed bugs with the tool create -i argument

v0.5.1

🐛 Bugfixes

  • fixed serialisation error

v0.5.0

🚀 Features

  • Support automatic downloading if files are given with http:// or https:// protocol
  • Detect URLs as files if given with http:// or https:// protocol
  • Support Detection of Arrays as inputs in tool create #100
  • Support ExpressionLibs

🐛 Bugfixes

  • correctly support DockerRequirement.DockerOutputDirectory#96
  • made CommandOutputBinding.glob Optional #99
  • ramping up runner conformance from 131/378 to 160/378

v0.4.0

🚀 Features

  • Added --no-defaults flag to tool create which can be handy when using passwords as inputs

🐛 Bugfixes

  • fixed critical error in tool create where outputEval was set, even when null
  • 🏃CWL Runner
    • Fixed some bugs in CWL Runner ramping up its conformance from 126/378 to 131/378
    • Improved Array support in Runner
    • Support cwl.output.json handling in Runner
    • Support globs in Runner
  • Rewrite input ids if "bad words" are found (e.g. sql connection strings)

v0.3.0

🚀 Features

  • Added Containerization Support (Docker & Podman) for s4n execute local
  • Support CWL ExpressionTools

🐛 Bugfixes

  • Fixed some bugs in CWL Runner ramping up its conformance from 90/378 to 126/378

👀 Miscellaneous Tasks

  • Removed Nightly Builds CI Workflow

v0.2.0

🚀 Features

  • Allowed handling of nullable and array CWLTypes using File? or File[] notation
  • Added s4n execute make-template ./path/to.cwl to create job templates #75
  • Added support for the direct execution of files #79
  • Allow Directories as output

🐛 Bugfixes

  • Fixed setting correct InitialWorkDirRequirement when -i is used in s4n tool create #69
  • Fixed handling of json-Data #60
  • Fixed unreported Bug, where CWL CommandLineTool Output was ignored if not of type File, Directory, stdout, stderr or string. 781d20e
  • Fixed Command fail because of invalid git user config - prompts user if missing #78
  • Fixed cleanup if init fails #77
  • Fixed Files in subfolders can not be created in s4n tool create #88
  • Fixed Do not check for uncommited changes if --no-run #89

🚜 Refactor

  • Moved Runner into separate crate (Refactor)

👀 Miscellaneous Tasks

  • Added Tests for all Documentation examples #76
  • Added CWL Conformance Tests to CI Workflow
  • Added more integration tests

v0.1.0

Initial Release