v0.2.1

What's Changed

• fix ict->clt conversion for directory by @vjaganat90 in #290
• default network access for ICT to CLT conversion and handle single node wfb payload by @vjaganat90 in #291
• Separate dir creation from compilation by @sameeul in #293
• Fix Pypy miniconda version by @sameeul in #294
• Increase workflow timeout by @sameeul in #295
• one step wfb, cwl dict format and uuid by @vjaganat90 in #292
• remove jsonschema version constrain by @sameeul in #287
• fix re-serializing 'string' input and general array input by @vjaganat90 in #297
• docker_image and docker-compose for restapi by @vjaganat90 in #296
• Link order fix by @sameeul in #299
• Update ICT to CLT test by @sameeul in #300
• Update linking of the outputs and inputs by @sameeul in #301
• Publish docker image by @sameeul in #302
• V021 by @sameeul in #303

Full Changelog: v0.2.0...v0.2.1

v0.2.1-dev0

What's Changed

• fix ict->clt conversion for directory by @vjaganat90 in #290
• default network access for ICT to CLT conversion and handle single node wfb payload by @vjaganat90 in #291
• Separate dir creation from compilation by @sameeul in #293
• Fix Pypy miniconda version by @sameeul in #294
• Increase workflow timeout by @sameeul in #295
• one step wfb, cwl dict format and uuid by @vjaganat90 in #292
• remove jsonschema version constrain by @sameeul in #287
• fix re-serializing 'string' input and general array input by @vjaganat90 in #297
• docker_image and docker-compose for restapi by @vjaganat90 in #296
• Link order fix by @sameeul in #299
• Update ICT to CLT test by @sameeul in #300
• Update linking of the outputs and inputs by @sameeul in #301
• Publish docker image by @sameeul in #302
• V021 by @sameeul in #303

Full Changelog: v0.2.0...v0.2.1-dev0

v0.2.0

What's Changed

• REST API : Object transformation by @vjaganat90 in #270
• adjust for modified 'schema' of input objects with 'plugins(ICT)' by @vjaganat90 in #273
• (Modified) Add flag to only compile workflow to cwl without running by @vjaganat90 in #274
• (Modified) Add ict to clt conversion by @vjaganat90 in #275
• replace --user-space-docker-cmd with --singularity by @ndonyapour in #278
• Replace mambaforge with miniforge by @sameeul in #279
• Fix ci miniforge v3 by @sameeul in #280
• Fix for running workflows with singularity by @vjaganat90 in #281
• Add flag to only compile workflow to cwl without running by @JesseMckinzie in #272
• REST API : add the logic of converting wfb plugins (ICT) to CWL (CLT) by @vjaganat90 in #276
• ICT spec updates and WFB payload fix by @JesseMckinzie in #282
• add user args for workflows built with python api by @vjaganat90 in #283
• remove redundant io in main & remove irrelevant warning/exit in compiler by @vjaganat90 in #284
• Refactor some common transformations by @vjaganat90 in #285
• Release 015 by @vjaganat90 in #286

New Contributors

• @JesseMckinzie made their first contribution in #272

Full Changelog: v0.1.4...v0.2.0

v0.1.4

What's Changed

• remove metags from inline cwl in runtag by @vjaganat90 in #266
• fix config gen from arbitrary directory (dev) by @vjaganat90 in #267
• add --generate_config flag by @vjaganat90 in #268

Full Changelog: v0.1.3...v0.1.4

v0.1.3

What's Changed

• 'search_paths_cwl' when compile fail by @vjaganat90 in #264

Full Changelog: v0.1.2...v0.1.3

v0.1.2

What's Changed

• Minor documentation update by @sameeul in #239
• Minor doc update by @sameeul in #240
• 'when' tag support in Python API by @vjaganat90 in #233
• Minor refactor by @sameeul in #242
• minor correction to docstring by @vjaganat90 in #243
• copy & paste cwl-docker-extract code from main.py by @jfennick in #244
• update user guide with python API docs by @vjaganat90 in #245
• fix step_key evaluation in get_workflow_outputs by @vjaganat90 in #246
• add user docs by @misterbrandonwalker in #232
• add required files for rest api (core) by @vjaganat90 in #247
• partial codes range for partial failures by @vjaganat90 in #250
• Fix PyPy Docker build process by @sameeul in #251
• Update biobb fork by @sameeul in #252
• Update biobb fork by @sameeul in #253
• Update Jake's forks by @sameeul in #254
• remove duplicate io by @vjaganat90 in #255
• cwl inline runtag functionality by @vjaganat90 in #256
• Sophios yaml initialization and running from any directory by @vjaganat90 in #257
• Sophios yaml pip by @vjaganat90 in #258
• add --container-engine option to cwl-docker-extract by @vjaganat90 in #260
• simplify incoming wfb and correct outgoing object syntax by @vjaganat90 in #261
• Update pyproject.toml for release by @sameeul in #263

Full Changelog: v0.1.1...v0.1.2

v0.1.2-dev0

What's Changed

• Minor documentation update by @sameeul in #239
• Minor doc update by @sameeul in #240
• 'when' tag support in Python API by @vjaganat90 in #233
• Minor refactor by @sameeul in #242
• minor correction to docstring by @vjaganat90 in #243
• copy & paste cwl-docker-extract code from main.py by @jfennick in #244
• update user guide with python API docs by @vjaganat90 in #245
• fix step_key evaluation in get_workflow_outputs by @vjaganat90 in #246
• add user docs by @misterbrandonwalker in #232
• add required files for rest api (core) by @vjaganat90 in #247
• partial codes range for partial failures by @vjaganat90 in #250
• Fix PyPy Docker build process by @sameeul in #251
• Update biobb fork by @sameeul in #252
• Update biobb fork by @sameeul in #253
• Update Jake's forks by @sameeul in #254
• remove duplicate io by @vjaganat90 in #255
• cwl inline runtag functionality by @vjaganat90 in #256
• Sophios yaml initialization and running from any directory by @vjaganat90 in #257
• Sophios yaml pip by @vjaganat90 in #258
• add --container-engine option to cwl-docker-extract by @vjaganat90 in #260
• simplify incoming wfb and correct outgoing object syntax by @vjaganat90 in #261
• Update pyproject.toml for release by @sameeul in #263

Full Changelog: v0.1.1...v0.1.2-dev0

v0.1.1

What's Changed

• Release v011 by @sameeul in #249

Full Changelog: v0.1.0...v0.1.1

v0.1.1-dev0

Release v011 (#249)

* Minor documentation update

* Minor documentation update

* Minor documentation update

* 'when' tag support in Python API

* Minor refactor (#242)

* minor correction to docstring

* copy & paste cwl-docker-extract code from main.py

* update userguide with python API docs

* fix step_key evaluation in get_workflow_outputs

* add user docs (#232)

Co-authored-by: Brandon Duane Walker <walkerbd@UPDATEME.HOSTNAME.COM>

* add required files for rest api (core) (#247)

* add required files for rest api (core)

* add a single node/step workflow test rest api

* add orjson as dep and pytest fix gha

---------

Co-authored-by: Vasu Jaganath <vasu.jaganath@axleinfo.com>

* Update pyproject.toml for release

---------

Co-authored-by: Vasu Jaganath <vasu.jaganath@axleinfo.com>
Co-authored-by: Jake Fennick <jake.fennick@axleinfo.com>
Co-authored-by: Brandon Walker <43654521+misterbrandonwalker@users.noreply.github.com>
Co-authored-by: Brandon Duane Walker <walkerbd@UPDATEME.HOSTNAME.COM>
Co-authored-by: VasuJ <145879890+vjaganat90@users.noreply.github.com>

v0.1.0

Initial release of sophios package.