Commited auto-generated code with new syntax

.github/workflows/ci-cd.yaml

@@ -9,11 +9,13 @@ name: CI/CD
 on:
   push:
     branches: [ main, develop ]
-    tags: [ '*' ]
   pull_request:
     branches: [ main, develop ]
+  release:
+    types: [published]
   repository_dispatch:
-    types: [create-release]
+    types: [create-post-release]
+
 
 jobs:
   nipype-conv:
@@ -143,7 +145,7 @@ jobs:
       if: ${{ always() }}
       with:
         files: coverage.xml
-        name: pydra-mriqc
+        name: pydra-tasks-mriqc
 
   deploy:
     needs: [test]

.gitignore

@@ -137,4 +137,3 @@ dmypy.json
 # Mac garbarge
 .DS_store
 
-/pydra

docs/conf.py

@@ -17,7 +17,7 @@
 
 # -- Project information -----------------------------------------------------
 
-project = "pydra-mriqc"
+project = "pydra-tasks-mriqc"
 copyright = "2020, Xihe Xie"
 author = "Xihe Xie"
 

nipype-auto-conv/generate.py

@@ -0,0 +1,14 @@
+from pathlib import Path
+from click.testing import CliRunner
+from nipype2pydra.cli import convert
+
+
+spec_dir = Path(__file__).parent / "specs"
+conv_dir = Path(__file__).parent.parent
+
+runner = CliRunner()
+result = runner.invoke(
+    convert,
+    args=[str(spec_dir), str(conv_dir)],
+    catch_exceptions=False,
+)

nipype-auto-conv/specs/interfaces/derivatives_data_sink.yaml

@@ -5,7 +5,7 @@
 #
 # Docs
 # ----
-# 
+#
 task_name: DerivativesDataSink
 nipype_name: DerivativesDataSink
 nipype_module: mriqc.interfaces
@@ -15,11 +15,11 @@ inputs:
   rename:
   # dict[str, str] - fields to rename in the Pydra interface
   types:
-  # dict[str, type] - override inferred types (use "mime-like" string for file-format types,
-  # e.g. 'medimage/nifti-gz'). For most fields the type will be correctly inferred
-  # from the nipype interface, but you may want to be more specific, particularly
-  # for file types, where specifying the format also specifies the file that will be
-  # passed to the field in the automatically generated unittests.
+    # dict[str, type] - override inferred types (use "mime-like" string for file-format types,
+    # e.g. 'medimage/nifti-gz'). For most fields the type will be correctly inferred
+    # from the nipype interface, but you may want to be more specific, particularly
+    # for file types, where specifying the format also specifies the file that will be
+    # passed to the field in the automatically generated unittests.
     base_directory: generic/directory
     # type=directory|default='': Path to the base directory for storing data.
     in_file: generic/file+list-of
@@ -37,15 +37,15 @@ outputs:
   rename:
   # dict[str, str] - fields to rename in the Pydra interface
   types:
-  # dict[str, type] - override inferred types (use "mime-like" string for file-format types,
-  # e.g. 'medimage/nifti-gz'). For most fields the type will be correctly inferred
-  # from the nipype interface, but you may want to be more specific, particularly
-  # for file types, where specifying the format also specifies the file that will be
-  # passed to the field in the automatically generated unittests.
+    # dict[str, type] - override inferred types (use "mime-like" string for file-format types,
+    # e.g. 'medimage/nifti-gz'). For most fields the type will be correctly inferred
+    # from the nipype interface, but you may want to be more specific, particularly
+    # for file types, where specifying the format also specifies the file that will be
+    # passed to the field in the automatically generated unittests.
     out_file: generic/file+list-of
-    # type=outputmultiobject: 
+    # type=outputmultiobject:
     out_meta: generic/file+list-of
-    # type=outputmultiobject: 
+    # type=outputmultiobject:
   callables:
   # dict[str, str] - names of methods/callable classes defined in the adjacent `*_callables.py`
   # to set to the `callable` attribute of output fields
@@ -54,38 +54,38 @@ outputs:
   requirements:
   # dict[str, list[str]] - input fields that are required to be provided for the output field to be present
 tests:
-- inputs:
-  # dict[str, str] - values to provide to inputs fields in the task initialisation
-  # (if not specified, will try to choose a sensible value)
-    base_directory:
-    # type=directory|default='': Path to the base directory for storing data.
-    check_hdr:
-    # type=bool|default=True: fix headers of NIfTI outputs
-    compress:
-    # type=inputmultiobject|default=[]: whether ``in_file`` should be compressed (True), uncompressed (False) or left unmodified (None, default).
-    data_dtype:
-    # type=str|default='': NumPy datatype to coerce NIfTI data to, or `source` tomatch the input file dtype
-    dismiss_entities:
-    # type=inputmultiobject|default=[]: a list entities that will not be propagated from the source file
-    in_file:
-    # type=inputmultiobject|default=[]: the object to be saved
-    meta_dict:
-    # type=dict|default={}: an input dictionary containing metadata
-    source_file:
-    # type=inputmultiobject|default=[]: the source file(s) to extract entities from
-  imports:
-  # list[nipype2pydra.task.base.explicitimport] - list import statements required by the test, with each list item
-  # consisting of 'module', 'name', and optionally 'alias' keys
-  expected_outputs:
-  # dict[str, str] - expected values for selected outputs, noting that tests will typically
-  # be terminated before they complete for time-saving reasons, and therefore
-  # these values will be ignored, when running in CI
-  timeout: 10
-  # int - the value to set for the timeout in the generated test, 
-  # after which the test will be considered to have been initialised 
-  # successfully. Set to 0 to disable the timeout (warning, this could
-  # lead to the unittests taking a very long time to complete)
-  xfail: true
-  # bool - whether the unittest is expected to fail or not. Set to false
-  # when you are satisfied with the edits you have made to this file
+  - inputs:
+      # dict[str, str] - values to provide to inputs fields in the task initialisation
+      # (if not specified, will try to choose a sensible value)
+      base_directory:
+      # type=directory|default='': Path to the base directory for storing data.
+      check_hdr:
+      # type=bool|default=True: fix headers of NIfTI outputs
+      compress:
+      # type=inputmultiobject|default=[]: whether ``in_file`` should be compressed (True), uncompressed (False) or left unmodified (None, default).
+      data_dtype:
+      # type=str|default='': NumPy datatype to coerce NIfTI data to, or `source` tomatch the input file dtype
+      dismiss_entities:
+      # type=inputmultiobject|default=[]: a list entities that will not be propagated from the source file
+      in_file:
+      # type=inputmultiobject|default=[]: the object to be saved
+      meta_dict:
+      # type=dict|default={}: an input dictionary containing metadata
+      source_file:
+      # type=inputmultiobject|default=[]: the source file(s) to extract entities from
+    imports:
+    # list[nipype2pydra.task.base.explicitimport] - list import statements required by the test, with each list item
+    # consisting of 'module', 'name', and optionally 'alias' keys
+    expected_outputs:
+    # dict[str, str] - expected values for selected outputs, noting that tests will typically
+    # be terminated before they complete for time-saving reasons, and therefore
+    # these values will be ignored, when running in CI
+    timeout: 10
+    # int - the value to set for the timeout in the generated test,
+    # after which the test will be considered to have been initialised
+    # successfully. Set to 0 to disable the timeout (warning, this could
+    # lead to the unittests taking a very long time to complete)
+    xfail: true
+    # bool - whether the unittest is expected to fail or not. Set to false
+    # when you are satisfied with the edits you have made to this file
 doctests: []

nipype-auto-conv/specs/interfaces/iqm_file_sink.yaml

@@ -99,3 +99,4 @@ tests:
 doctests: []
 find_replace:
   - [config\.loggers\.\w+\., logger.]
+  - ["value=Undefined", "value=attrs.NOTHING"]

nipype-auto-conv/specs/interfaces/synth_strip.yaml

@@ -5,7 +5,7 @@
 #
 # Docs
 # ----
-# 
+#
 task_name: SynthStrip
 nipype_name: SynthStrip
 nipype_module: mriqc.interfaces.synthstrip
@@ -15,11 +15,11 @@ inputs:
   rename:
   # dict[str, str] - fields to rename in the Pydra interface
   types:
-  # dict[str, type] - override inferred types (use "mime-like" string for file-format types,
-  # e.g. 'medimage/nifti-gz'). For most fields the type will be correctly inferred
-  # from the nipype interface, but you may want to be more specific, particularly
-  # for file types, where specifying the format also specifies the file that will be
-  # passed to the field in the automatically generated unittests.
+    # dict[str, type] - override inferred types (use "mime-like" string for file-format types,
+    # e.g. 'medimage/nifti-gz'). For most fields the type will be correctly inferred
+    # from the nipype interface, but you may want to be more specific, particularly
+    # for file types, where specifying the format also specifies the file that will be
+    # passed to the field in the automatically generated unittests.
     in_file: generic/file
     # type=file|default=<undefined>: Input image to be brain extracted
     model: generic/file
@@ -34,18 +34,20 @@ inputs:
   # dict[str, str] - names of methods/callable classes defined in the adjacent `*_callables.py`
   # to set as the `default` method of input fields
   metadata:
+    in_file:
+      copyfile: true
   # dict[str, dict[str, any]] - additional metadata to set on any of the input fields (e.g. out_file: position: 1)
 outputs:
   omit:
   # list[str] - fields to omit from the Pydra interface
   rename:
   # dict[str, str] - fields to rename in the Pydra interface
   types:
-  # dict[str, type] - override inferred types (use "mime-like" string for file-format types,
-  # e.g. 'medimage/nifti-gz'). For most fields the type will be correctly inferred
-  # from the nipype interface, but you may want to be more specific, particularly
-  # for file types, where specifying the format also specifies the file that will be
-  # passed to the field in the automatically generated unittests.
+    # dict[str, type] - override inferred types (use "mime-like" string for file-format types,
+    # e.g. 'medimage/nifti-gz'). For most fields the type will be correctly inferred
+    # from the nipype interface, but you may want to be more specific, particularly
+    # for file types, where specifying the format also specifies the file that will be
+    # passed to the field in the automatically generated unittests.
     out_file: generic/file
     # type=file: brain-extracted image
     # type=file|default=<undefined>: store brain-extracted input to file
@@ -60,42 +62,42 @@ outputs:
   requirements:
   # dict[str, list[str]] - input fields that are required to be provided for the output field to be present
 tests:
-- inputs:
-  # dict[str, str] - values to provide to inputs fields in the task initialisation
-  # (if not specified, will try to choose a sensible value)
-    in_file:
-    # type=file|default=<undefined>: Input image to be brain extracted
-    use_gpu:
-    # type=bool|default=False: Use GPU
-    model:
-    # type=file|default=<undefined>: file containing model's weights
-    border_mm:
-    # type=int|default=1: Mask border threshold in mm
-    out_file:
-    # type=file: brain-extracted image
-    # type=file|default=<undefined>: store brain-extracted input to file
-    out_mask:
-    # type=file: brain mask
-    # type=file|default=<undefined>: store brainmask to file
-    num_threads:
-    # type=int|default=0: Number of threads
-    args:
-    # type=str|default='': Additional parameters to the command
-    environ:
-    # type=dict|default={}: Environment variables
-  imports:
-  # list[nipype2pydra.task.base.explicitimport] - list import statements required by the test, with each list item
-  # consisting of 'module', 'name', and optionally 'alias' keys
-  expected_outputs:
-  # dict[str, str] - expected values for selected outputs, noting that tests will typically
-  # be terminated before they complete for time-saving reasons, and therefore
-  # these values will be ignored, when running in CI
-  timeout: 10
-  # int - the value to set for the timeout in the generated test, 
-  # after which the test will be considered to have been initialised 
-  # successfully. Set to 0 to disable the timeout (warning, this could
-  # lead to the unittests taking a very long time to complete)
-  xfail: true
-  # bool - whether the unittest is expected to fail or not. Set to false
-  # when you are satisfied with the edits you have made to this file
+  - inputs:
+      # dict[str, str] - values to provide to inputs fields in the task initialisation
+      # (if not specified, will try to choose a sensible value)
+      in_file:
+      # type=file|default=<undefined>: Input image to be brain extracted
+      use_gpu:
+      # type=bool|default=False: Use GPU
+      model:
+      # type=file|default=<undefined>: file containing model's weights
+      border_mm:
+      # type=int|default=1: Mask border threshold in mm
+      out_file:
+      # type=file: brain-extracted image
+      # type=file|default=<undefined>: store brain-extracted input to file
+      out_mask:
+      # type=file: brain mask
+      # type=file|default=<undefined>: store brainmask to file
+      num_threads:
+      # type=int|default=0: Number of threads
+      args:
+      # type=str|default='': Additional parameters to the command
+      environ:
+      # type=dict|default={}: Environment variables
+    imports:
+    # list[nipype2pydra.task.base.explicitimport] - list import statements required by the test, with each list item
+    # consisting of 'module', 'name', and optionally 'alias' keys
+    expected_outputs:
+    # dict[str, str] - expected values for selected outputs, noting that tests will typically
+    # be terminated before they complete for time-saving reasons, and therefore
+    # these values will be ignored, when running in CI
+    timeout: 10
+    # int - the value to set for the timeout in the generated test,
+    # after which the test will be considered to have been initialised
+    # successfully. Set to 0 to disable the timeout (warning, this could
+    # lead to the unittests taking a very long time to complete)
+    xfail: true
+    # bool - whether the unittest is expected to fail or not. Set to false
+    # when you are satisfied with the edits you have made to this file
 doctests: []

nipype-auto-conv/specs/package.yaml

@@ -22,6 +22,10 @@ config_params:
     varname: config.environment
     type: struct
     module: mriqc
+  inputs_entities:
+    varname: config.workflow.inputs_entities
+    type: struct
+    module: mriqc
 omit_functions:
   - nipype.external.due.BibTeX
 omit_classes:
@@ -35,6 +39,12 @@ omit_constants:
 import_translations:
   - [nireports, pydra.tasks.nireports]
   - [niworkflows, pydra.tasks.niworkflows]
+import_find_replace:
+  - ["from \\.\\. import config, logging", ""]
+  - ["_ReadDWIMetadataOutputSpec,", ""]
+  - ["from pydra.tasks.mriqc.nipype_ports.interfaces import utility as niu", ""]
+  - ["\\s+config,(\\s+)fname_presuffix,", "\\1fname_presuffix,"]
+  - ["from pydra.tasks.io.auto import add_traits\n", ""]
 find_replace:
   - [config\.loggers\.\w+\., logger.]
   - [config.to_filename\(\), ""]
@@ -55,9 +65,6 @@ find_replace:
   # - ["\\bdict\\[", "ty.Dict["]
 omit_modules:
   - "mriqc.config"
-import_find_replace:
-  - ["from \\.\\. import config, logging", ""]
-  - ["_ReadDWIMetadataOutputSpec,", ""]
-  - ["from pydra.tasks.mriqc.nipype_ports.interfaces import utility as niu", ""]
 copy_packages:
   - mriqc.data
+  - mriqc.synthstrip

nipype-auto-conv/specs/workflows/mriqc.workflows.anatomical.base.anat_qc_workflow.yaml

@@ -6,6 +6,13 @@ nipype_name: anat_qc_workflow
 nipype_module: mriqc.workflows.anatomical.base
 # Name of the node that is to be considered the input of the workflow, i.e. its outputs will be the inputs of the workflow
 input_node: inputnode
+inputs:
+  in_file:
+    type: medimage/t1w+nifti-gz-x
+  modality:
+    type: field/text
+    connections:
+      - [norm, modality]
 # name of the workflow variable that is returned
 workflow_variable: workflow
 # the names of the nested workflows that are defined in other modules and need to be imported
@@ -21,3 +28,8 @@ find_replace:
       "# fmt: off\\n\\s*workflow.set_output\\(\\[\\('iqmswf_measures', workflow.iqmswf.lzout.measures\\)\\]\\)",
       "",
     ]
+  - [
+      "modality=workflow.lzin.modality,(\\s+)name=\"norm\"",
+      "modality=workflow.lzin.modality,\\1name=\"spatial_norm\"",
+    ]
+  - ["workflow\\.norm\\b", "workflow.spatial_norm"]

nipype-auto-conv/specs/workflows/mriqc.workflows.shared.synthstrip_wf.yaml

@@ -13,6 +13,7 @@ find_replace:
   - ["config = NipypeConfig\\(\\)", ""]
   - ["iflogger = logging.getLogger\\(\"nipype.interface\"\\)", ""]
   - ["logging = Logging\\(config\\)", ""]
+  - ["save_bias=True", "bias_image=True"]
 # name of the workflow variable that is returned
 workflow_variable: workflow
 # the names of the nested workflows that are defined in other modules and need to be imported