Merge pull request #17 from nipype/develop

Bug fix of doctest generation

Author: tclose

.github/workflows/ci-cd.yml

@@ -122,31 +122,17 @@ jobs:
       matrix:
           repo:
           - afni
-          - ants
-          - fsl
-          - freesurfer
-    env:
-      SECRET: ""
+          # - ants
+          # - fsl
+          # - freesurfer
+          # - mriqc
     steps:
-    - name: Get secret for corresponding repo
-      id: get_secret
-      run: |
-        if [ "${{ matrix.repo }}" == "afni" ]; then
-          SECRET="${{ secrets.AFNI_PAT }}"
-        elif [ "${{ matrix.repo }}" == "ants" ]; then
-          SECRET="${{ secrets.ANTS_PAT }}"
-        elif [ "${{ matrix.repo }}" == "fsl" ]; then
-          SECRET="${{ secrets.FSL_PAT }}"
-        elif [ "${{ matrix.repo }}" == "freesurfer" ]; then
-          SECRET="${{ secrets.FREESURFER_PAT }}"
-        fi
-        echo "SECRET=$SECRET" >> $GITHUB_ENV
 
     - name: Trigger post-release on downstream repos
-      if: github.event_name == 'release' && env.SECRET
+      if: github.event_name == 'release'
       run: |
-        curl -XPOST -u "${{ env.SECRET }}" -H "Accept: application/vnd.github.everest-preview+json" \
+        curl -XPOST -u "${{ env.POST_RELEASE_PAT }}" -H "Accept: application/vnd.github.everest-preview+json" \
         "https://api.github.com/repos/nipype/pydra-${{ matrix.repo }}/dispatches" \
         -d '{"event_type": "create-post-release"}'
       env:
-        PAT: ${{ env.SECRET }}
+        PAT: ${{ env.POST_RELEASE_PAT }}

example-specs/task/nipype/afni/a_boverlap.yaml

@@ -142,9 +142,9 @@ doctests:
   # dict[str, str] - name-value pairs for inputs to be provided to the doctest.
   # If the field is of file-format type and the value is None, then the
   # '.mock()' method of the corresponding class is used instead.
-    in_file_a:
+    in_file_a: '"functional.nii"'
     # type=file|default=<undefined>: input file A
-    in_file_b:
+    in_file_b: '"structural.nii"'
     # type=file|default=<undefined>: input file B
     out_file: ' "out.mask_ae_overlap.txt"'
     # type=file: output file

example-specs/task/nipype/afni/afn_ito_nifti.yaml

@@ -137,7 +137,7 @@ doctests:
   # dict[str, str] - name-value pairs for inputs to be provided to the doctest.
   # If the field is of file-format type and the value is None, then the
   # '.mock()' method of the corresponding class is used instead.
-    in_file:
+    in_file: '"afni_output.3D"'
     # type=file|default=<undefined>: input file to 3dAFNItoNIFTI
     out_file: ' "afni_output.nii"'
     # type=file: output file

example-specs/task/nipype/afni/align_epi_anat_py.yaml

@@ -203,9 +203,9 @@ doctests:
   # dict[str, str] - name-value pairs for inputs to be provided to the doctest.
   # If the field is of file-format type and the value is None, then the
   # '.mock()' method of the corresponding class is used instead.
-    anat:
+    anat: '"structural.nii"'
     # type=file|default=<undefined>: name of structural dataset
-    in_file:
+    in_file: '"functional.nii"'
     # type=file|default=<undefined>: EPI dataset to align
     epi_base: '0'
     # type=traitcompound|default=None: the epi base used in alignmentshould be one of (0/mean/median/max/subbrick#)

example-specs/task/nipype/afni/allineate.yaml

@@ -331,12 +331,12 @@ doctests:
   # dict[str, str] - name-value pairs for inputs to be provided to the doctest.
   # If the field is of file-format type and the value is None, then the
   # '.mock()' method of the corresponding class is used instead.
-    in_file:
+    in_file: '"functional.nii"'
     # type=file|default=<undefined>: input file to 3dAllineate
     out_file: '"functional_allineate.nii"'
     # type=file: output image file name
     # type=file|default=<undefined>: output file from 3dAllineate
-    in_matrix:
+    in_matrix: '"cmatrix.mat"'
     # type=file|default=<undefined>: matrix to align input file
   imports:
   # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item
@@ -349,9 +349,9 @@ doctests:
   # dict[str, str] - name-value pairs for inputs to be provided to the doctest.
   # If the field is of file-format type and the value is None, then the
   # '.mock()' method of the corresponding class is used instead.
-    in_file:
+    in_file: '"functional.nii"'
     # type=file|default=<undefined>: input file to 3dAllineate
-    reference:
+    reference: '"structural.nii"'
     # type=file|default=<undefined>: file to be used as reference, the first volume will be used if not given the reference will be the first volume of in_file.
     allcostx: '"out.allcostX.txt"'
     # type=file: Compute and print ALL available cost functionals for the un-warped inputs
@@ -367,9 +367,9 @@ doctests:
   # dict[str, str] - name-value pairs for inputs to be provided to the doctest.
   # If the field is of file-format type and the value is None, then the
   # '.mock()' method of the corresponding class is used instead.
-    in_file:
+    in_file: '"functional.nii"'
     # type=file|default=<undefined>: input file to 3dAllineate
-    reference:
+    reference: '"structural.nii"'
     # type=file|default=<undefined>: file to be used as reference, the first volume will be used if not given the reference will be the first volume of in_file.
     nwarp_fixmot: '["X", "Y"]'
     # type=list|default=[]: To fix motion along directions.

example-specs/task/nipype/afni/auto_tcorrelate.yaml

@@ -151,13 +151,13 @@ doctests:
   # dict[str, str] - name-value pairs for inputs to be provided to the doctest.
   # If the field is of file-format type and the value is None, then the
   # '.mock()' method of the corresponding class is used instead.
-    in_file:
+    in_file: '"functional.nii"'
     # type=file|default=<undefined>: timeseries x space (volume or surface) file
     polort: '-1'
     # type=int|default=0: Remove polynomical trend of order m or -1 for no detrending
     eta2: 'True'
     # type=bool|default=False: eta^2 similarity
-    mask:
+    mask: '"mask.nii"'
     # type=file|default=<undefined>: mask of voxels
     mask_only_targets: 'True'
     # type=bool|default=False: use mask only on targets voxels

example-specs/task/nipype/afni/auto_tlrc.yaml

@@ -125,7 +125,7 @@ doctests:
   # dict[str, str] - name-value pairs for inputs to be provided to the doctest.
   # If the field is of file-format type and the value is None, then the
   # '.mock()' method of the corresponding class is used instead.
-    in_file:
+    in_file: '"structural.nii"'
     # type=file|default=<undefined>: Original anatomical volume (+orig).The skull is removed by this scriptunless instructed otherwise (-no_ss).
     no_ss: 'True'
     # type=bool|default=False: Do not strip skull of input data set (because skull has already been removed or because template still has the skull) NOTE: The ``-no_ss`` option is not all that optional. Here is a table of when you should and should not use ``-no_ss``    +------------------+------------+---------------+   | Dataset          | Template                   |   +==================+============+===============+   |                  | w/ skull   | wo/ skull     |   +------------------+------------+---------------+   | WITH skull       | ``-no_ss`` | xxx           |   +------------------+------------+---------------+   | WITHOUT skull    | No Cigar   | ``-no_ss``    |   +------------------+------------+---------------+  Template means: Your template of choice Dset. means: Your anatomical dataset ``-no_ss`` means: Skull stripping should not be attempted on Dset xxx means: Don't put anything, the script will strip Dset No Cigar means: Don't try that combination, it makes no sense.

example-specs/task/nipype/afni/autobox.yaml

@@ -144,7 +144,7 @@ doctests:
   # dict[str, str] - name-value pairs for inputs to be provided to the doctest.
   # If the field is of file-format type and the value is None, then the
   # '.mock()' method of the corresponding class is used instead.
-    in_file:
+    in_file: '"structural.nii"'
     # type=file|default=<undefined>: input file
     padding: '5'
     # type=int|default=0: Number of extra voxels to pad on each side of box

example-specs/task/nipype/afni/automask.yaml

@@ -145,7 +145,7 @@ doctests:
   # dict[str, str] - name-value pairs for inputs to be provided to the doctest.
   # If the field is of file-format type and the value is None, then the
   # '.mock()' method of the corresponding class is used instead.
-    in_file:
+    in_file: '"functional.nii"'
     # type=file|default=<undefined>: input file to 3dAutomask
     dilate: '1'
     # type=int|default=0: dilate the mask outwards

example-specs/task/nipype/afni/axialize.yaml

@@ -139,7 +139,7 @@ doctests:
   # dict[str, str] - name-value pairs for inputs to be provided to the doctest.
   # If the field is of file-format type and the value is None, then the
   # '.mock()' method of the corresponding class is used instead.
-    in_file:
+    in_file: '"functional.nii"'
     # type=file|default=<undefined>: input file to 3daxialize
     out_file: '"axialized.nii"'
     # type=file: output file