v0.4.0 release

What's Changed

• fix basepath issue in run_cwl_serialized_async and fix erroneous _inline extension by @vjaganat90 in #331
• fix install doc snippet by @vjaganat90 in #332
• hot fix for path issue by @vjaganat90 in #333
• Fix whitespace in basepath and workflow_name and outdir location issue when using run_cwl_workflow by @vjaganat90 in #334
• correct the deletion of autogenerated by @vjaganat90 in #335
• Ci fixes by @vjaganat90 in #337
• remove reference to pypy in CI GHA and remove deadcode needed for pypy by @vjaganat90 in #338
• add run_local_async with desired async behavior by @vjaganat90 in #336
• minor clarity and perf improvements by @vjaganat90 in #340
• Refactoring docs and internals to improve readability by @vjaganat90 in #339
• Fix inline runtag with no io and duplicate outs in compiled cwl by @vjaganat90 in #341
• Minor readability refactor by @vjaganat90 in #342
• run_local_refactor and fix blocking calls in async by @vjaganat90 in #343
• fix the hardcoded dir flags and streamline explicit copying for cwltool by @vjaganat90 in #344
• Remove toil git src by @vjaganat90 in #345
• Fix behavior of and flags of cwl runners by @vjaganat90 in #346
• remove superflous and dead code in Python API by @vjaganat90 in #347
• add missing dependency and merging of namespaces in inlined runtag workflows by @vjaganat90 in #348
• remove py ver restriction and allow passthrough flags for both runners by @vjaganat90 in #349
• A necessary name change and reorg of Sophios APIs by @vjaganat90 in #350
• simplify core run_local function and the call path by @vjaganat90 in #351
• Add run_compute by @vjaganat90 in #352
• remove args from core sophios 1\3 by @vjaganat90 in #353
• remove args from core sophios 2/3 by @vjaganat90 in #354
• remove args from core sophios 3/3 by @vjaganat90 in #355
• Fix inputs yaml to account correctly for input types by @vjaganat90 in #356
• Pypi release 03112026 by @vjaganat90 in #357

Full Changelog: v0.3.0.1...v0.4.0

v0.4.0

What's Changed

• fix basepath issue in run_cwl_serialized_async and fix erroneous _inline extension by @vjaganat90 in #331
• fix install doc snippet by @vjaganat90 in #332
• hot fix for path issue by @vjaganat90 in #333
• Fix whitespace in basepath and workflow_name and outdir location issue when using run_cwl_workflow by @vjaganat90 in #334
• correct the deletion of autogenerated by @vjaganat90 in #335
• Ci fixes by @vjaganat90 in #337
• remove reference to pypy in CI GHA and remove deadcode needed for pypy by @vjaganat90 in #338
• add run_local_async with desired async behavior by @vjaganat90 in #336
• minor clarity and perf improvements by @vjaganat90 in #340
• Refactoring docs and internals to improve readability by @vjaganat90 in #339
• Fix inline runtag with no io and duplicate outs in compiled cwl by @vjaganat90 in #341
• Minor readability refactor by @vjaganat90 in #342
• run_local_refactor and fix blocking calls in async by @vjaganat90 in #343
• fix the hardcoded dir flags and streamline explicit copying for cwltool by @vjaganat90 in #344
• Remove toil git src by @vjaganat90 in #345
• Fix behavior of and flags of cwl runners by @vjaganat90 in #346
• remove superflous and dead code in Python API by @vjaganat90 in #347
• add missing dependency and merging of namespaces in inlined runtag workflows by @vjaganat90 in #348
• remove py ver restriction and allow passthrough flags for both runners by @vjaganat90 in #349
• A necessary name change and reorg of Sophios APIs by @vjaganat90 in #350
• simplify core run_local function and the call path by @vjaganat90 in #351
• Add run_compute by @vjaganat90 in #352
• remove args from core sophios 1\3 by @vjaganat90 in #353
• remove args from core sophios 2/3 by @vjaganat90 in #354
• remove args from core sophios 3/3 by @vjaganat90 in #355
• Fix inputs yaml to account correctly for input types by @vjaganat90 in #356
• Pypi release 03112026 by @vjaganat90 in #357

Full Changelog: v0.3.0.1...0.4.0

v0.3.1

What's Changed

• fix upload artefact in test-publish gha by @vjaganat90 in #329
• Pypi release 03122025 by @vjaganat90 in #330

Full Changelog: v0.3.0...v0.3.1

v0.3.0

What's Changed

• feature: add get_cwl_workflow() method to Python API by @vjaganat90 in #316
• chore: roll back temporary CI workaround and streamline global config generation by @sameeul in #314
• simplify args dependencies by @vjaganat90 in #318
• chore: move testing infra code out of core by @sameeul in #317
• fix upload-artifcat to v4 by @vjaganat90 in #321
• Don't copy output to outdir if not using cwltool by @vjaganat90 in #319
• append name of workflow to default outdir_toil by @vjaganat90 in #320
• remove cwltool git dependency by @vjaganat90 in #322
• tech debt cleanup by @vjaganat90 in #325
• add (minimum) pass through flags for Toil by @vjaganat90 in #323
• Fixing syntax for passing arguments in Python API by @vjaganat90 in #326
• add run_cwl* functions for running serailized workflows in run_local by @vjaganat90 in #327
• Pypi release 03122025 by @vjaganat90 in #328

Full Changelog: v0.2.2...v0.3.0

v0.2.2

What's Changed

• (chore): Add wheel build workflow by @sameeul in #304
• Fix input type inference when input type's type itself is an array by @vjaganat90 in #305
• fix CI failure due to name change to sophios by @vjaganat90 in #306
• fix gen_schema due to arr handling by @vjaganat90 in #307
• fix weekly/fuzzy CI failure due to name change by @vjaganat90 in #309
• Remove explicit pypy3 docker files and builds by @vjaganat90 in #308
• remove pypy3 miniforge & bump version to 24.7.1-2 by @vjaganat90 in #310
• bugfix: Add missing inputs and outputs in REST API JSON payload by @sameeul in #312
• fix fuzzy_compile to get current branch and setup test_fuzzzy by @vjaganat90 in #311
• chore: Release prep v022 by @sameeul in #313

Full Changelog: v0.2.1...v0.2.2

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