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

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

@@ -169,7 +169,7 @@ 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 3dBandpass
     highpass: '0.005'
     # type=float|default=0.0: highpass

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

@@ -148,9 +148,9 @@ 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 3dSkullStrip
-    mask:
+    mask: '"mask.nii"'
     # type=file|default=<undefined>: Mask dataset, if desired.  Blurring will occur only within the mask. Voxels NOT in the mask will be set to zero in the output.
     fwhm: '5.0'
     # type=float|default=0.0: fwhm kernel size

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

@@ -142,7 +142,7 @@ 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: '"epi.nii"'
     # type=file|default=<undefined>: The dataset that will be smoothed
     fwhm: '2.5'
     # type=float|default=0.0: Blur until the 3D FWHM reaches this value (in mm)

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

@@ -138,9 +138,9 @@ 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 3dmaskave
-    mask:
+    mask: '"skeleton_mask.nii.gz"'
     # type=file|default=<undefined>: -mask dset = use dset as mask to include/exclude voxels
     min: 'True'
     # type=bool|default=False: print the minimum value in dataset

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

@@ -196,9 +196,9 @@ 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 to 3dcalc
-    in_file_b:
+    in_file_b: '"functional2.nii"'
     # type=file|default=<undefined>: operand file to 3dcalc
     expr: '"a*b"'
     # type=str|default='': expr
@@ -218,7 +218,7 @@ 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_a:
+    in_file_a: '"functional.nii"'
     # type=file|default=<undefined>: input file to 3dcalc
     expr: '"1"'
     # type=str|default='': expr

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

@@ -155,7 +155,7 @@ doctests:
   # '.mock()' method of the corresponding class is used instead.
     sel: '"''[0,2]''"'
     # type=str|default='': Apply the same column/row selection string to all filenames on the command line.
-    in_files:
+    in_files: '["f1.1D", "f2.1D"]'
     # type=list|default=[]: 
     out_file: '"catout.1d"'
     # type=file: output file

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

@@ -149,7 +149,7 @@ 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 to 3dCM
     cm_file: '"cm.txt"'
     # type=file: file with the center of mass coordinates

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

@@ -122,7 +122,7 @@ 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: '"anatomical.nii"'
     # type=file|default=<undefined>: input file to 3dClipLevel
   imports:
   # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item

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

@@ -133,7 +133,7 @@ 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: '"lh.pial_converted.gii"'
     # type=file|default=<undefined>: input file to ConvertDset
     out_type: '"niml_asc"'
     # type=enum|default='niml'|allowed['1D','1Dp','1Dpt','gii','gii_asc','gii_b64','gii_b64gz','niml','niml_asc','niml_bi']: output type

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

@@ -210,7 +210,7 @@ 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 3dcopy
   imports:
   # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item

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

@@ -248,7 +248,7 @@ 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_files:
+    in_files: '["functional.nii", "functional2.nii"]'
     # type=inputmultiobject|default=[]: filenames of 3D+time input datasets. More than one filename can be given and the datasets will be auto-catenated in time. You can input a 1D time series file here, but the time axis should run along the ROW direction, not the COLUMN direction as in the 'input1D' option.
     out_file: '"output.nii"'
     # type=file: output statistics file

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

@@ -155,9 +155,9 @@ 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 3dDegreeCentrality
-    mask:
+    mask: '"mask.nii"'
     # type=file|default=<undefined>: mask file to mask input data
     sparsity: '1 # keep the top one percent of connections'
     # type=float|default=0.0: only take the top percent of connections

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

@@ -124,7 +124,7 @@ 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 3dDespike
   imports:
   # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item

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

@@ -131,7 +131,7 @@ 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 3dDetrend
     args: '"-polort 2"'
     # type=str|default='': Additional parameters to the command

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

@@ -161,7 +161,7 @@ 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_files:
+    in_files: '["functional.nii[0]", "structural.nii"]'
     # type=list|default=[]: list of input files, possibly with subbrick selectors
     dodice: 'True'
     # type=bool|default=False: Return the Dice coefficient (the Sorensen-Dice index).

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

@@ -163,9 +163,9 @@ 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 3dECM
-    mask:
+    mask: '"mask.nii"'
     # type=file|default=<undefined>: mask file to mask input data
     sparsity: '0.1 # keep top 0.1% of connections'
     # type=float|default=0.0: only take the top percent of connections

example-specs/task/nipype/afni/edge_3.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: '"functional.nii"'
     # type=file|default=<undefined>: input file to 3dedge3
     out_file: '"edges.nii"'
     # type=file: output file

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

@@ -160,9 +160,9 @@ 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: '"seed.1D"'
     # type=file|default=<undefined>: input file to 1deval
-    in_file_b:
+    in_file_b: '"resp.1D"'
     # type=file|default=<undefined>: operand file to 1deval
     expr: '"a*b"'
     # type=str|default='': expr

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

@@ -146,9 +146,9 @@ 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 3dfim+
-    ideal_file:
+    ideal_file: '"seed.1D"'
     # type=file|default=<undefined>: ideal time series file name
     out_file: '"functional_corr.nii"'
     # type=file: output file

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

@@ -140,7 +140,7 @@ 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 3dFourier
     retrend: 'True'
     # type=bool|default=False: Any mean and linear trend are removed before filtering. This will restore the trend after filtering.

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

@@ -245,7 +245,7 @@ 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 dataset
   imports:
   # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item

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

@@ -127,7 +127,7 @@ 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 dataset to compute the GCOR over
     nfirst: '4'
     # type=int|default=0: specify number of initial TRs to ignore