Merge pull request #325 from Australian-Imaging-Service/develop

syntax updates to match pydra2app instead of arcana

Author: tclose

.github/workflows/release.yml

@@ -59,6 +59,6 @@ jobs:
       env:
         PUSH: "${{ steps.deployable.outputs.PUSH }}"
       run: >
-        arcana deploy make-app ./australian-imaging-service xnat:XnatApp 
+        pydra2app make xnat ./australian-imaging-service
         --registry ghcr.io --check-registry --clean-up --tag-latest --loglevel info 
         --release pipelines-metapackage $RELEASE $PUSH

australian-imaging-service/mri/human/neuro/bidsapps/fmriprep.yaml

@@ -1,5 +1,5 @@
-title: 'Functional MRI data preprocessing pipeline'
-arcana_spec_version: 1.0
+title: "Functional MRI data preprocessing pipeline"
+schema_version: 1.0
 version:
   package: &package_version "23.1.4"
 base_image:
@@ -110,7 +110,7 @@ command:
       configuration:
         path: fmap/magnitude
       column_defaults:
-        datatype: medimage/dicom-series 
+        datatype: medimage/dicom-series
     fmap_phasediff:
       datatype: medimage/nifti-gz-x
       help: "Field map - BIDS Case 1: phasediff image corresponding to the phase-diff map between echo times"
@@ -171,5 +171,5 @@ command:
     app_output_dir: /work/bids-app-output
     app_work_dir: /work/nipype-work
     json_edits:
-      path: 'fmap/.*'
+      path: "fmap/.*"
       jq_expr: '.IntendedFor = "{bold}"'

australian-imaging-service/mri/human/neuro/bidsapps/mriqc.yaml

@@ -1,5 +1,5 @@
-arcana_spec_version: 1.0
-title: 'Extract quality control metrics from T1w, T2W and fMRI data'
+schema_version: 1.0
+title: "Extract quality control metrics from T1w, T2W and fMRI data"
 version:
   package: &package_version "22.0.6"
   build: "3"
@@ -11,7 +11,7 @@ base_image:
   tag: *package_version
   package_manager: apt
 docs:
-  info_url: https://mriqc.readthedocs.io  
+  info_url: https://mriqc.readthedocs.io
   description: |
     MRIQC extracts no-reference IQMs (image quality metrics) from
     structural (T1w and T2w) and functional MRI (magnetic resonance

australian-imaging-service/mri/human/neuro/bidsapps/smriprep.yaml

@@ -1,5 +1,5 @@
 title: "Structural MRI data preprocessing pipeline"
-arcana_spec_version: 1.0
+schema_version: 1.0
 version:
   package: &package_version "0.9.2"
   build: "3"
@@ -69,4 +69,4 @@ command:
     executable: /opt/conda/bin/smriprep
     dataset: /work/bids-dataset
     app_output_dir: /work/bids-app-output
-    app_work_dir: /work/nipype-work  # We need to give a work directory outside of the pydra node as otherwise the file paths exceed Freesurfer's file-path char buffers
+    app_work_dir: /work/nipype-work # We need to give a work directory outside of the pydra node as otherwise the file paths exceed Freesurfer's file-path char buffers

requirements.txt

@@ -1,5 +1,5 @@
-arcana >=0.10.11
-arcana-xnat >= 0.3.6
+pipeline2app >=0.12
+pipeline2app-xnat >= 0.6.2
 fileformats >= 0.8.6
 fileformats-extras >= 0.2.1
 fileformats-datascience >= 0.1.0

scripts/debug_specific_case.py

@@ -53,7 +53,7 @@
 #         image_tag=image_tag,
 #         build_dir=build_dir,
 #         use_local_packages=True,
-#         use_test_config=True,
+#         for_localhost=True,
 #         license_src=license_src,
 #         arcana_install_extras=["test"],
 #         generate_only=True,

scripts/test_build.py

@@ -1,18 +1,18 @@
 from pathlib import Path
 from click.testing import CliRunner
-from arcana.core.cli.deploy import make_app
-from arcana.core.utils.misc import show_cli_trace
+from pipeline2app.core.cli import make
+from frametree.core.utils import show_cli_trace
 
 PKG_PATH = Path(__file__).parent.parent.absolute()
 
 runner = CliRunner()
 
 results = runner.invoke(
-    make_app,
+    make,
     [
         f"{PKG_PATH}/australian-imaging-service/mri/human/neuro/bidsapps/fmriprep.yaml",
         "xnat:XnatApp",
-        "--raise-errors"
+        "--raise-errors",
     ],
     catch_exceptions=False,
 )

tests/test_bids_apps.py

@@ -1,5 +1,5 @@
 import json
-from arcana.core.cli.deploy import make_app
+from arcana.core.cli.deploy import make
 from arcana.core.utils.misc import show_cli_trace
 from arcana.xnat.deploy import XnatApp
 from arcana.xnat.utils.testing import install_and_launch_xnat_cs_command
@@ -24,14 +24,14 @@ def test_bids_app(
         build_arg = "--build"
 
     result = cli_runner(
-        make_app,
+        make,
         [
             str(bp.spec_path),
             "pipelines-core-test",
             "--build-dir",
             str(build_dir),
             build_arg,
-            "--use-test-config",
+            "--for-localhost",
             "--use-local-packages",
             "--raise-errors",
             "--license-src",
@@ -46,17 +46,12 @@ def test_bids_app(
     with xnat_connect() as xlogin:
 
         with open(
-            build_dir
-            / image_spec.name
-            / "xnat_commands"
-            / (image_spec.name + ".json")
+            build_dir / image_spec.name / "xnat_commands" / (image_spec.name + ".json")
         ) as f:
             xnat_command = json.load(f)
         xnat_command.name = xnat_command.label = image_spec.name + run_prefix
 
-        test_xsession = next(
-            iter(xlogin.projects[bp.project_id].experiments.values())
-        )
+        test_xsession = next(iter(xlogin.projects[bp.project_id].experiments.values()))
 
         inputs_json = {}
 
@@ -78,7 +73,7 @@ def test_bids_app(
         for pname, pval in bp.parameters.items():
             inputs_json[pname] = pval
 
-        inputs_json['Arcana_flags'] = (
+        inputs_json["Arcana_flags"] = (
             "--plugin serial "
             "--work /work "  # NB: work dir moved inside container due to file-locking issue on some mounted volumes (see https://github.com/tox-dev/py-filelock/issues/147)
             "--dataset-name default "