Merge pull request #8 from nipype/develop

Switched the latest package version to drop micro/patch component

.github/workflows/ci-cd.yaml

@@ -41,7 +41,7 @@ jobs:
     - name: Run automatic Nipype > Pydra conversion
       run: ./nipype-auto-conv/generate
 
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       with:
         name: converted-nipype
         path: pydra/tasks/afni/auto
@@ -65,7 +65,7 @@ jobs:
       run: git checkout $(git tag -l | grep 'v.*' | tail -n 1 | awk -F post '{print $1}')
 
     - name: Download tasks converted from Nipype 
-      uses: actions/download-artifact@v3
+      uses: actions/download-artifact@v4
       with:
         name: converted-nipype
         path: pydra/tasks/afni/auto
@@ -128,7 +128,7 @@ jobs:
         sudo bash OS_notes.linux_ubuntu_22_64_a_admin.txt 2>&1 | tee o.ubuntu_22_a.txt
     
     - name: Download tasks converted from Nipype 
-      uses: actions/download-artifact@v3
+      uses: actions/download-artifact@v4
       with:
         name: converted-nipype
         path: pydra/tasks/afni/auto
@@ -279,7 +279,7 @@ jobs:
       run: git checkout ${{ steps.latest_tag.outputs.TAG }}
 
     - name: Download tasks converted from Nipype 
-      uses: actions/download-artifact@v3
+      uses: actions/download-artifact@v4
       with:
         name: converted-nipype
         path: pydra/tasks/afni/auto
@@ -298,12 +298,10 @@ jobs:
     - name: Strip auto package from gitignore so it is included in package
       run: |
         sed -i '/\/pydra\/tasks\/afni\/auto/d' .gitignore
-        cat .gitignore
 
     - name: Install task package to calculate post-release tag
       run: |
         pip install "./related-packages/fileformats" "./related-packages/fileformats-extras" ".[test]"
-        tree /opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/pydra/
 
     - name: Generate post-release tag based on Nipype and Nipype2Pydra versions
       id: post_release_tag
@@ -334,7 +332,7 @@ jobs:
     - name: Check distributions
       run: twine check dist/*
 
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       with:
         name: distributions
         path: dist/

nipype-auto-conv/generate

@@ -5,6 +5,7 @@ from warnings import warn
 from pathlib import Path
 import shutil
 from importlib import import_module
+from tqdm import tqdm
 import yaml
 import nipype
 import nipype2pydra.utils
@@ -36,7 +37,9 @@ if auto_dir.exists():
     shutil.rmtree(auto_dir)
 
 all_interfaces = []
-for fspath in sorted(SPECS_DIR.glob("**/*.yaml")):
+for fspath in tqdm(
+    sorted(SPECS_DIR.glob("**/*.yaml")), "converting interfaces from Nipype to Pydra"
+):
     with open(fspath) as f:
         spec = yaml.load(f, Loader=yaml.SafeLoader)
 
@@ -70,7 +73,9 @@ post_release = (nipype_version + nipype2pydra_version).replace(".", "")
 """
     )
 
-auto_init += "\n\n__all__ = [\n" + "\n".join(f"    \"{i}\"," for i in all_interfaces) + "\n]\n"
+auto_init += (
+    "\n\n__all__ = [\n" + "\n".join(f'    "{i}",' for i in all_interfaces) + "\n]\n"
+)
 
 with open(PKG_ROOT / "pydra" / "tasks" / PKG_NAME / "auto" / "__init__.py", "w") as f:
     f.write(auto_init)

nipype-auto-conv/requirements.txt

@@ -1,6 +1,7 @@
 black
 attrs>=22.1.0
 nipype
+tqdm
 pydra
 PyYAML>=6.0
 fileformats >=0.8

nipype-auto-conv/specs/a_boverlap.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_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

nipype-auto-conv/specs/afn_ito_nifti.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: '"afni_output.3D"'
       # type=file|default=<undefined>: input file to 3dAFNItoNIFTI
       out_file: ' "afni_output.nii"'
       # type=file: output file

nipype-auto-conv/specs/align_epi_anat_py.yaml

@@ -205,9 +205,9 @@ 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#)

nipype-auto-conv/specs/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.

nipype-auto-conv/specs/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

nipype-auto-conv/specs/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.

nipype-auto-conv/specs/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

nipype-auto-conv/specs/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

nipype-auto-conv/specs/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

nipype-auto-conv/specs/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

nipype-auto-conv/specs/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

nipype-auto-conv/specs/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)

nipype-auto-conv/specs/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

nipype-auto-conv/specs/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

nipype-auto-conv/specs/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

nipype-auto-conv/specs/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

nipype-auto-conv/specs/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

nipype-auto-conv/specs/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

nipype-auto-conv/specs/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

nipype-auto-conv/specs/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

nipype-auto-conv/specs/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

nipype-auto-conv/specs/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

nipype-auto-conv/specs/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

nipype-auto-conv/specs/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).

nipype-auto-conv/specs/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

nipype-auto-conv/specs/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