update workflows to use new Sophios API and names

.github/workflows/ci_send_pull_request.yml

@@ -65,5 +65,5 @@ jobs:
           sender_repo_owner: ${{ github.event.pull_request.head.repo.owner.login }}
           sender_repo_ref: ${{ github.event.pull_request.head.ref }}
           commit_message: ${{ env.commit_message }}
-          target_repository: workflow-inference-compiler
-          access_token: ${{ steps.generate_token.outputs.token }}
+          target_repository: sophios
+          access_token: ${{ steps.generate_token.outputs.token }}

.github/workflows/ci_send_push.yml

@@ -29,5 +29,5 @@ jobs:
           sender_repo_owner: ${{ github.repository_owner }}
           sender_repo_ref: ${{ github.ref_name }}
           commit_message: ${{ github.event.head_commit.message }}
-          target_repository: workflow-inference-compiler
-          access_token: ${{ steps.generate_token.outputs.token }}
+          target_repository: sophios
+          access_token: ${{ steps.generate_token.outputs.token }}

.gitignore

@@ -0,0 +1,9 @@
+__pycache__/
+*.py[cod]
+
+.mypy_cache/
+.pytest_cache/
+
+autogenerated/
+provenance/
+output_*.json

workflows/bbbc.py

@@ -1,9 +1,10 @@
 from pathlib import Path
 
-from sophios.apis.python.api import Step, Workflow
+from sophios.api.python.workflow import Step, Workflow
+
 
 def workflow() -> Workflow:
-    bbbcdownload = Step(clt_path='../image-workflows/cwl_adapters/bbbcdownload.cwl')
+    bbbcdownload = Step(clt_path='cwl_adapters/bbbcdownload.cwl')
     # NOTE: object fields monkey patched at runtime from *.cwl file
     bbbcdownload.name = 'BBBC001'
     bbbcdownload.outDir = Path('bbbcdownload.outDir')
@@ -12,30 +13,30 @@ def workflow() -> Workflow:
     subdirectory.directory = bbbcdownload.outDir
     subdirectory.glob_pattern = 'bbbcdownload.outDir/BBBC/BBBC001/raw/Images/human_ht29_colon_cancer_1_images/'
 
-    filerenaming = Step(clt_path='../image-workflows/cwl_adapters/file-renaming.cwl')
+    filerenaming = Step(clt_path='cwl_adapters/file-renaming.cwl')
     # NOTE: FilePattern {} syntax shadows python f-string {} syntax
     filerenaming.filePattern = '.*_{row:c}{col:dd}f{f:dd}d{channel:d}.tif'
     filerenaming.inpDir = subdirectory.subdirectory
     filerenaming.outDir = Path('file-renaming.outDir')
     filerenaming.outFilePattern = 'x{row:dd}_y{col:dd}_p{f:dd}_c{channel:d}.tif'
 
-    omeconverter = Step(clt_path='../image-workflows/cwl_adapters/ome-converter.cwl')
+    omeconverter = Step(clt_path='cwl_adapters/ome-converter.cwl')
     omeconverter.inpDir = filerenaming.outDir
     omeconverter.filePattern = '.*.tif'
     omeconverter.outDir = Path('omeconverter.outDir')
 
-    montage = Step(clt_path='../image-workflows/cwl_adapters/montage.cwl')
+    montage = Step(clt_path='cwl_adapters/montage.cwl')
     montage.inpDir = omeconverter.outDir
     montage.filePattern = 'x00_y03_p{p:dd}_c0.ome.tif'
     montage.layout = 'p'
     montage.outDir = Path('montage.outDir')
 
-    image_assembler = Step(clt_path='../image-workflows/cwl_adapters/image_assembler.cwl')
+    image_assembler = Step(clt_path='cwl_adapters/image_assembler.cwl')
     image_assembler.stitchPath = montage.outDir
     image_assembler.imgPath = omeconverter.outDir
     image_assembler.outDir = Path('image_assembler.outDir')
 
-    precompute_slide = Step(clt_path='../image-workflows/cwl_adapters/precompute_slide.cwl')
+    precompute_slide = Step(clt_path='cwl_adapters/precompute_slide.cwl')
     precompute_slide.inpDir = image_assembler.outDir
     precompute_slide.pyramidType = 'Zarr'
     precompute_slide.imageType = 'image'

workflows/bbbc_sub.py

@@ -1,16 +1,15 @@
 from pathlib import Path
 
-from sophios import plugins
-from sophios.apis.python import api
-from sophios.apis.python.api import Step, Workflow
+from sophios.api.python.workflow import Step, Workflow
+
 
 def workflow() -> Workflow:
     bbbcdownload = Step(clt_path='cwl_adapters/bbbcdownload.cwl')
     # NOTE: object fields monkey patched at runtime from *.cwl file
     bbbcdownload.name = 'BBBC001'
     bbbcdownload.outDir = Path('bbbcdownload.outDir')
 
-    subdirectory = Step(clt_path='../workflow-inference-compiler/cwl_adapters/subdirectory.cwl')
+    subdirectory = Step(clt_path='../sophios/cwl_adapters/subdirectory.cwl')
     subdirectory.directory = bbbcdownload.outDir
     subdirectory.glob_pattern = 'bbbcdownload.outDir/BBBC/BBBC001/raw/Images/human_ht29_colon_cancer_1_images/'
 
@@ -21,14 +20,8 @@ def workflow() -> Workflow:
     filerenaming.outDir = Path('file-renaming.outDir')
     filerenaming.outFilePattern = 'x{row:dd}_y{col:dd}_p{f:dd}_c{channel:d}.tif'
 
-    # Trivially wrap the subdirectory step in a subworkflow.
-    # But notice that we are still linking the individual Steps above,
-    # which defeats the whole purpose of having reusable black boxes.
-    steps = [bbbcdownload,
-             Workflow([subdirectory], 'bbbc_sub_sub_py'),
-             filerenaming]
-    filename = 'bbbc_sub_py'  # .yml
-    return Workflow(steps, filename)
+    steps = [bbbcdownload, subdirectory, filerenaming]
+    return Workflow(steps, 'bbbc_sub_py')
 
 
 def workflow2() -> Workflow:
@@ -37,40 +30,24 @@ def workflow2() -> Workflow:
     bbbcdownload.name = 'BBBC001'
     bbbcdownload.outDir = Path('bbbcdownload.outDir')
 
-    subdirectory = Step(clt_path='../workflow-inference-compiler/cwl_adapters/subdirectory.cwl')
-    subworkflow = Workflow([subdirectory], 'bbbc_sub_sub_py')  # fails validation, due to
-    # https://workflow-inference-compiler.readthedocs.io/en/latest/dev/algorithms.html#deferred-satisfaction
-
-    # First link all inputs within the subworkflow to the explicit inputs: tag.
-    # i.e. This is the API for the subworkflow.
-    subworkflow.steps[0].directory = subworkflow.directory
-    subworkflow.steps[0].glob_pattern = subworkflow.glob_pattern
-
-    # Then apply arguments at the call site.
-    # Notice how the caller does not need to know about the internal details of the subworkflow
-    # (For example, that the subdirectory step is index 0)
-    subworkflow.directory = bbbcdownload.outDir
-    subworkflow.glob_pattern = 'bbbcdownload.outDir/BBBC/BBBC001/raw/Images/human_ht29_colon_cancer_1_images/'
+    subdirectory = Step(clt_path='../sophios/cwl_adapters/subdirectory.cwl')
+    subworkflow = Workflow([subdirectory], 'bbbc_sub_sub_py')
+    subdirectory.inputs.directory = subworkflow.inputs.directory
+    subdirectory.inputs.glob_pattern = subworkflow.inputs.glob_pattern
+    # Intentionally leave directory unbound; Sophios infers it from bbbcdownload.outDir.
+    subworkflow.inputs.glob_pattern = 'bbbcdownload.outDir/BBBC/BBBC001/raw/Images/human_ht29_colon_cancer_1_images/'
 
     filerenaming = Step(clt_path='cwl_adapters/file-renaming.cwl')
     # NOTE: FilePattern {} syntax shadows python f-string {} syntax
     filerenaming.filePattern = '.*_{row:c}{col:dd}f{f:dd}d{channel:d}.tif'
-    filerenaming.inpDir = subworkflow.steps[0].subdirectory  # TODO: workflow outputs: tag
+    # Intentionally leave inpDir unbound; Sophios infers it from the preceding subworkflow output.
     filerenaming.outDir = Path('file-renaming.outDir')
     filerenaming.outFilePattern = 'x{row:dd}_y{col:dd}_p{f:dd}_c{channel:d}.tif'
 
-    steps = [bbbcdownload,
-             subworkflow,
-             filerenaming]
-    filename = 'bbbc_sub_py'  # .yml
-    return Workflow(steps, filename)
+    steps = [bbbcdownload, subworkflow, filerenaming]
+    return Workflow(steps, 'bbbc_sub_py')
 
 
-# viz = workflow()
-# viz.compile() # Do NOT .run() here
-
 if __name__ == '__main__':
-    api.global_config = plugins.get_tools_cwl(str(Path().home()))  # Use path fallback
-
     viz = workflow2()
     viz.run()  # .run() here, inside main