Merge pull request #66 from nipype/updated-auto-conv-generate

updated auto-conv generate

Author: tclose

nipype-auto-conv/generate

@@ -1,3 +1,51 @@
 #!/usr/bin/env bash
+set -e
+
 conv_dir=$(dirname $0)
+
+CURRENT_BRANCH=$(git rev-parse --abbrev-ref HEAD)
+AUTO_CONV_SUFFIX="-auto-conv"
+REBASED_SUFFIX="-rebased-on-auto-conv"
+
+if ! git diff-index --quiet HEAD --; then
+    echo "Current branch '$CURRENT_BRANCH' has uncommitted changes. Please commit or stash them before proceeding."
+    exit 1
+fi
+
+echo "Automatically converting Nipype tasks to Pydra tasks..."
+
+echo "Create '$CURRENT_BRANCH$REBASED_SUFFIX' and '$CURRENT_BRANCH$AUTO_CONV_SUFFIX' branches if not present and switch to $CURRENT_BRANCH$AUTO_CONV_SUFFIX"
+echo "NB: $CURRENT_BRANCH$AUTO_CONV_SUFFIX will contain the conversion specs from '$CURRENT_BRANCH' and the auto-converted tasks,"
+echo "wherease '$CURRENT_BRANCH$REBASED_SUFFIX' will be the changes in the current branch rebased on that"
+if [ "$CURRENT_BRANCH" == "*$REBASED_SUFFIX"]; then
+    BASE_BRANCH=${CURRENT_BRANCH%"$REBASED_SUFFIX"}$AUTO_CONV_SUFFIX
+    REBASE_BRANCH=$CURRENT_BRANCH
+    git checkout $BASE_BRANCH
+    git reset --hard $CURRENT_BRANCH
+else
+    REBASE_BRANCH=${CURRENT_BRANCH}$REBASED_SUFFIX
+    BASE_BRANCH=${CURRENT_BRANCH}$AUTO_CONV_SUFFIX
+    git checkout -b $REBASE_BRANCH
+    git checkout -b $BASE_BRANCH
+fi
+
+echo "Apply nipype-auto-conv spec changes between current branch and the main auto-conv branch to the rebase branch..."
+git fetch origin auto-conv
+git reset origin/auto-conv
+git add $conv_dir/specs
+git commit -m "Update auto-conv specs with latest changes from '$CURRENT_BRANCH'" || echo true
+# Ignore any other changes outside the nipype-auto-conv/specs directory
+git reset --hard HEAD
+
+echo "Running nipype2pydra conversion..."
 nipype2pydra convert $conv_dir/specs $conv_dir/..
+
+echo "Committing converted tasks to ${CURRENT_BRANCH}$AUTO_CONV_SUFFIX..."
+git add pydra/tasks/fsl
+git commit -m "Auto-converted Nipype tasks to Pydra tasks" || echo true
+
+echo "Rebasing '$REBASE_BRANCH' to apply changes..."
+git checkout $REBASE_BRANCH
+git rebase $BASE_BRANCH
+
+echo "Successfully converted Nipype tasks to Pydra tasks and rebased manual edits over the top of them in '$REBASE_BRANCH'

pydra/tasks/fsl/v6/aroma/ica__aroma.py

@@ -106,7 +106,7 @@ class ICA_AROMA(shell.Task["ICA_AROMA.Outputs"]):
         help="volume to be denoised", argstr="-i {in_file}"
     )
     out_dir: ty.Any | None = shell.arg(
-        help="output directory", formatter="out_dir_formatter", default="out"
+        help="output directory", formatter=out_dir_formatter, default="out"
     )
     mask: NiftiGz | None = shell.arg(help="path/name volume mask", argstr="-m {mask}")
     dim: int = shell.arg(

pydra/tasks/fsl/v6/dti/distance_map.py

@@ -89,7 +89,7 @@ class DistanceMap(shell.Task["DistanceMap.Outputs"]):
     )
     invert_input: bool = shell.arg(help="invert input image", argstr="--invert")
     local_max_file: ty.Any = shell.arg(
-        help="write an image of the local maxima", formatter="local_max_file_formatter"
+        help="write an image of the local maxima", formatter=local_max_file_formatter
     )
 
     class Outputs(shell.Outputs):

pydra/tasks/fsl/v6/dti/prob_track_x.py

@@ -232,11 +232,11 @@ class ProbTrackX(shell.Task["ProbTrackX.Outputs"]):
     )
     seed: ty.Any = shell.arg(
         help="seed volume(s), or voxel(s) or freesurfer label file",
-        formatter="seed_formatter",
+        formatter=seed_formatter,
     )
     target_masks: list[Nifti1] = shell.arg(
         help="list of target masks - required for seeds_to_targets classification",
-        formatter="target_masks_formatter",
+        formatter=target_masks_formatter,
     )
     waypoints: File = shell.arg(
         help="waypoint mask or ascii list of waypoint masks - only keep paths going through ALL the masks",

pydra/tasks/fsl/v6/dti/prob_track_x2.py

@@ -338,11 +338,11 @@ class ProbTrackX2(shell.Task["ProbTrackX2.Outputs"]):
     )
     seed: ty.Any = shell.arg(
         help="seed volume(s), or voxel(s) or freesurfer label file",
-        formatter="seed_formatter",
+        formatter=seed_formatter,
     )
     target_masks: list[File] = shell.arg(
         help="list of target masks - required for seeds_to_targets classification",
-        formatter="target_masks_formatter",
+        formatter=target_masks_formatter,
     )
     waypoints: File = shell.arg(
         help="waypoint mask or ascii list of waypoint masks - only keep paths going through ALL the masks",

pydra/tasks/fsl/v6/dti/tract_skeleton.py

@@ -116,7 +116,7 @@ class TractSkeleton(shell.Task["TractSkeleton.Outputs"]):
     project_data: bool = shell.arg(
         help="project data onto skeleton",
         requires=["threshold", "distance_map", "data_file"],
-        formatter="project_data_formatter",
+        formatter=project_data_formatter,
     )
     threshold: float = shell.arg(help="skeleton threshold value")
     distance_map: File = shell.arg(help="distance map image")
@@ -135,7 +135,7 @@ class TractSkeleton(shell.Task["TractSkeleton.Outputs"]):
     )
     projected_data: Path = shell.arg(help="input data projected onto skeleton")
     skeleton_file: ty.Any = shell.arg(
-        help="write out skeleton image", formatter="skeleton_file_formatter"
+        help="write out skeleton image", formatter=skeleton_file_formatter
     )
 
     class Outputs(shell.Outputs):

pydra/tasks/fsl/v6/epi/apply_topup.py

@@ -82,7 +82,7 @@ class ApplyTOPUP(shell.Task["ApplyTOPUP.Outputs"]):
     in_topup_fieldcoef: NiftiGz | None = shell.arg(
         help="topup file containing the field coefficients",
         requires=["in_topup_movpar"],
-        formatter="in_topup_fieldcoef_formatter",
+        formatter=in_topup_fieldcoef_formatter,
     )
     in_topup_movpar: File | None = shell.arg(
         help="topup movpar.txt file", requires=["in_topup_fieldcoef"]

pydra/tasks/fsl/v6/epi/eddy.py

@@ -312,7 +312,7 @@ class Eddy(shell.Task["Eddy.Outputs"]):
     )
     out_base: str = shell.arg(
         help="Basename for output image",
-        formatter="out_base_formatter",
+        formatter=out_base_formatter,
         default="eddy_corrected",
     )
     session: File = shell.arg(
@@ -322,14 +322,14 @@ class Eddy(shell.Task["Eddy.Outputs"]):
     in_topup_fieldcoef: File | None = shell.arg(
         help="Topup results file containing the field coefficients",
         requires=["in_topup_movpar"],
-        formatter="in_topup_fieldcoef_formatter",
+        formatter=in_topup_fieldcoef_formatter,
     )
     in_topup_movpar: File | None = shell.arg(
         help="Topup results file containing the movement parameters (movpar.txt)",
         requires=["in_topup_fieldcoef"],
     )
     field: File = shell.arg(
-        help="Non-topup derived fieldmap scaled in Hz", formatter="field_formatter"
+        help="Non-topup derived fieldmap scaled in Hz", formatter=field_formatter
     )
     field_mat: File = shell.arg(
         help="Matrix specifying the relative positions of the fieldmap, --field, and the first volume of the input file, --imain",

pydra/tasks/fsl/v6/epi/topup.py

@@ -189,15 +189,15 @@ class TOPUP(shell.Task["TOPUP.Outputs"]):
     encoding_direction: list[ty.Any] = shell.arg(
         help="encoding direction for automatic generation of encoding_file",
         requires=["readout_times"],
-        formatter="encoding_direction_formatter",
+        formatter=encoding_direction_formatter,
     )
     readout_times: MultiInputObj = shell.arg(
         help="readout times (dwell times by # phase-encode steps minus 1)",
         requires=["encoding_direction"],
     )
     out_base: Path = shell.arg(
         help="base-name of output files (spline coefficients (Hz) and movement parameters)",
-        formatter="out_base_formatter",
+        formatter=out_base_formatter,
     )
     out_warp_prefix: str = shell.arg(
         help="prefix for the warpfield images (in mm)",

pydra/tasks/fsl/v6/maths/dilate_image.py

@@ -56,7 +56,7 @@ class DilateImage(shell.Task["DilateImage.Outputs"]):
     operation: ty.Any = shell.arg(
         help="filtering operation to perform in dilation",
         position=6,
-        formatter="operation_formatter",
+        formatter=operation_formatter,
     )
     kernel_shape: ty.Any = shell.arg(
         help="kernel shape to use", argstr="-kernel {kernel_shape}", position=4