Merge remote-tracking branch 'upstream/maint/1.4.x'

Author: effigies

.circleci/config.yml

@@ -276,7 +276,7 @@ jobs:
 
   test_package:
     docker:
-      - image: circleci/python:3.8.5
+      - image: cimg/python:3.9
     working_directory: /tmp/src/niworkflows
     steps:
       - checkout
@@ -300,7 +300,7 @@ jobs:
 
   deploy_pypi:
     docker:
-      - image: circleci/python:3.8.5
+      - image: cimg/python:3.9
     working_directory: /tmp/src/niworkflows
     steps:
       - checkout
@@ -375,7 +375,7 @@ jobs:
 
   build_docs:
     docker:
-      - image: circleci/python:3.8.5
+      - image: cimg/python:3.9
     environment:
       - FSLOUTPUTTYPE: NIFTI
       - SUBJECTS_DIR: /tmp/subjects
@@ -392,6 +392,11 @@ jobs:
           command: |
             python -m pip install --no-cache-dir -U "pip>=20.3"
             python -m pip install --no-cache-dir -r docs/requirements.txt
+            eval "$(pyenv init -)"
+      - run:
+          name: Install Niworkflows
+          command: |
+            python -m pip install .
       - run:
           name: Build only this commit
           command: |

CHANGES.rst

@@ -9,6 +9,13 @@ This release upgrades the Dockerfile to use FSL6, and includes some new interfac
   * FIX: Scipy docs path (#681)
   * TEST: Drop excessively long interface equivalence tests (#674)
 
+1.4.6 (March 09, 2022)
+======================
+Patch release in the 1.4.x series.
+
+* FIX: Unlink destination files before saving derivative (#683)
+* FIX: Set pixdim[4] to match RepetitionTime (#679)
+
 1.4.5 (December 13, 2021)
 =========================
 Patch release in the 1.4.x series.
@@ -160,15 +167,22 @@ A list of prominent changes can be found below. (With thanks to Lea Waller for t
     * ``NormalizeMotionParams`` now under ``confounds``.
     * ``FMRISummary``, ``CompCorVariancePlot``, ``ConfoundsCorrelationPlot`` from ``plotting``
 
+1.3.6 (March 09, 2022)
+======================
+Bug-fix release in the 1.3.x series
+
+* FIX: Set pixdim[4] to match RepetitionTime (#679)
+* DOC: Fix doc builds for 1.3.x series (#692)
+
 1.3.5 (October 01, 2021)
 ========================
 Bug-fix release in the 1.3.x series
 
-  * FIX: Set slope and intercept to 1/0 if not otherwise provided (#649)
-  * FIX: DerivativesDataSink warning when it has multiple source files [backport #573] (#647)
-  * FIX: `FSDetectInputs` mutually exclusive options for `ReconAll` (#646)
-  * MNT: Update some version pinning and correct for *pandas* warning about keyword arguments (#645)
-  * CI: Use datalad-managed test data [BACKPORT] (#653)
+* FIX: Set slope and intercept to 1/0 if not otherwise provided (#649)
+* FIX: DerivativesDataSink warning when it has multiple source files [backport #573] (#647)
+* FIX: `FSDetectInputs` mutually exclusive options for `ReconAll` (#646)
+* MNT: Update some version pinning and correct for *pandas* warning about keyword arguments (#645)
+* CI: Use datalad-managed test data [BACKPORT] (#653)
 
 1.3.4 (June 8, 2021)
 ====================

docs/requirements.txt

@@ -10,3 +10,4 @@ sphinx ~= 4.2
 sphinxcontrib-apidoc
 sphinxcontrib-napoleon
 templateflow
+nitransforms >= 20.0.0rc3

niworkflows/interfaces/bids.py

@@ -630,12 +630,17 @@ def _run_interface(self, runtime):
                             (4, 4) if self.inputs.space in STANDARD_SPACES else (2, 2)
                         )
 
-                    if curr_codes != xcodes or curr_units != units:
+                    curr_zooms = zooms = hdr.get_zooms()
+                    if "RepetitionTime" in self.inputs.get():
+                        zooms = curr_zooms[:3] + (self.inputs.RepetitionTime,)
+
+                    if (curr_codes, curr_units, curr_zooms) != (xcodes, units, zooms):
                         self._results["fixed_hdr"][i] = True
                         new_header = hdr.copy()
                         new_header.set_qform(nii.affine, xcodes[0])
                         new_header.set_sform(nii.affine, xcodes[1])
                         new_header.set_xyzt_units(*units)
+                        new_header.set_zooms(zooms)
 
                 if data_dtype == "source":  # match source dtype
                     try:
@@ -664,6 +669,7 @@ def _run_interface(self, runtime):
                         new_header.set_data_dtype(data_dtype)
                 del nii
 
+            out_file.unlink(missing_ok=True)
             if new_data is new_header is None:
                 _copy_any(orig_file, str(out_file))
             else:
@@ -704,9 +710,11 @@ def _run_interface(self, runtime):
                             legacy_metadata[key] = self._metadata.pop(key)
                     if legacy_metadata:
                         sidecar = out_file.parent / f"{_splitext(str(out_file))[0]}.json"
+                        sidecar.unlink(missing_ok=True)
                         sidecar.write_text(dumps(legacy_metadata, sort_keys=True, indent=2))
                 # The future: the extension is the first . and everything after
                 sidecar = out_file.parent / f"{out_file.name.split('.', 1)[0]}.json"
+                sidecar.unlink(missing_ok=True)
                 sidecar.write_text(dumps(self._metadata, sort_keys=True, indent=2))
                 self._results["out_meta"] = str(sidecar)
         return runtime

niworkflows/interfaces/confounds.py

@@ -80,24 +80,26 @@ class _ExpandModelInputSpec(BaseInterfaceInputSpec):
 Formula for generating model expansions. By default, the
 32-parameter expansion will be generated. Note that any expressions
 to be expanded *must* be in parentheses, even if they include only
-a single variable (e.g., ``(x)^2``, not ``x^2``). Examples:
-
-* ``rps + wm + csf + gsr`` : 9-parameter model. ``rps`` denotes realignment
-  parameters, ``wm`` denotes mean white matter signal, ``csf`` denotes mean
-  cerebrospinal fluid signal, and ``gsr`` denotes mean global signal.
-* ``(dd1(rps + wm + csf + gsr))^^2`` : 36-parameter expansion.
-  ``rps + wm + csf + gsr`` denotes that realignment parameters and mean
-  WM, CSF, and global signals should be included. ``dd1`` denotes that
-  these signals should be augmented with their first temporal
-  derivatives. ``^^2`` denotes that the original signals and temporal
-  derivatives should be augmented with quadratic expansions.
-* ``(dd1(rps))^^2`` : 24-parameter expansion. ``rps`` denotes that
-  realignment parameters should be included. ``dd1`` and ``^^2`` denote
-  temporal derivative and quadratic expansions as above.
-* ``(dd1(rps + wm + csf + gsr))^^2 + others`` : generate all expansion
-  terms necessary for a 36-parameter model as above, and
-  concatenate those expansion terms to all other regressor columns
-  in the confounds file.
+a single variable (e.g., ``(x)^2``, not ``x^2``).
+
+Examples:
+
+  * ``rps + wm + csf + gsr`` : 9-parameter model. ``rps`` denotes realignment
+    parameters, ``wm`` denotes mean white matter signal, ``csf`` denotes mean
+    cerebrospinal fluid signal, and ``gsr`` denotes mean global signal.
+  * ``(dd1(rps + wm + csf + gsr))^^2`` : 36-parameter expansion.
+    ``rps + wm + csf + gsr`` denotes that realignment parameters and mean
+    WM, CSF, and global signals should be included. ``dd1`` denotes that
+    these signals should be augmented with their first temporal
+    derivatives. ``^^2`` denotes that the original signals and temporal
+    derivatives should be augmented with quadratic expansions.
+  * ``(dd1(rps))^^2`` : 24-parameter expansion. ``rps`` denotes that
+    realignment parameters should be included. ``dd1`` and ``^^2`` denote
+    temporal derivative and quadratic expansions as above.
+  * ``(dd1(rps + wm + csf + gsr))^^2 + others`` : generate all expansion
+    terms necessary for a 36-parameter model as above, and
+    concatenate those expansion terms to all other regressor columns
+    in the confounds file.
 
 """,
     )