Merge branch 'master' into issue-3553_add_mvecs_to_Dcm2niix

nipy · Jul 5, 2023 · f9ca616 · f9ca616
2 parents 4195b9e + 4a6a7d9
commit f9ca616
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diff --git a/.codespellrc b/.codespellrc
@@ -0,0 +1,12 @@
+[codespell]
+skip = .git,*.pdf,*.svg,external
+# nd,nam - import module short
+# fith - oddness coming from AFNI
+# whos - smth used in matlab things
+# SMAL - Stanford CNI MRS Library
+# Suh - name
+# noo,crasher - field/var name used
+# Reson - short journal name
+# ALS, FWE - neuroimaging specific abbrevs
+# Comision - foreign word used
+ignore-words-list = te,inport,objekt,jist,nd,hel,inout,fith,whos,fot,ue,shs,smal,nam,filetest,suh,noo,reson,als,fwe,crasher,comision
diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
@@ -1,19 +1,80 @@
-# Commits with messages like "STY: black" or "run black"
+# Wed Apr 5 14:01:05 2023 -0400 - [email protected] - STY: black [ignore-rev]
+a9ce9b78a402ebacf7726ad6454bb75b1447f52f
+# Wed Sep 14 14:12:07 2022 -0400 - [email protected] - STY: Black
+f4a779223c6b0dffa47138d24ec9ef378c7164a9
+# Tue Apr 19 14:09:31 2022 -0400 - [email protected] - STY: black [ignore-rev]
+b9716ebd46541f7fb1b96a94cc35b5e2ea6c3bba
+# Fri Apr 15 06:59:48 2022 -0700 - [email protected] - STY: black [ignore-rev]
+d223fbccda6dee0ef39e00084296a3292f2ccf87
+# Fri Apr 8 21:34:43 2022 -0400 - [email protected] - STY: black [ignore-rev]
+e3f56da124fd58041018c2e70d16a130ef189a66
+# Sun Apr 3 10:27:07 2022 -0400 - [email protected] - STY: black [ignore-rev]
+988c382ebfc7df964874b6287b9d9e27e274a4a4
+# Sat Apr 2 21:32:56 2022 -0400 - [email protected] - STY: black [ignore-rev]
+230fac6149d4dfbd5da669a983332a1fe318ef57
+# Sat Apr 2 12:49:15 2022 -0400 - [email protected] - STY/TEST: Make specs and run black [ignore-rev]
+2ba8dacb8cc1f6f9c5b15b1cfb7b0395d45dcfb3
+# Sun Mar 20 21:19:39 2022 -0400 - [email protected] - STY: black [ignore-rev]
+87cc1b54981113024ec3fd594881f72cf67513fb
+# Wed Dec 8 17:02:09 2021 -0500 - [email protected] - STY: black [ignore-rev]
+5ac2f18ac116832d81a13f0c83e0a6aeda1457cf
+# Thu Dec 2 09:30:42 2021 -0500 - [email protected] - STY: black
+ee50279ebf061a70ff502e7d2e51385b285cfda4
+# Tue Oct 26 11:18:02 2021 +0200 - [email protected] - sty: run black
+5d9adbbb77b7047b9b47cd2fa079dee0094cfc91
+# Wed Oct 20 12:07:15 2021 +0200 - [email protected] - run black on the preprocess.py file to improve formatting
+674e9b0eeca082efb5322b61fea57ee89a3e4a24
+# Wed Oct 13 16:08:23 2021 -0400 - [email protected] - ENH: Add expected steps for FreeSurfer 7 recon-all (#3389)
+8f7c0bf2ec9c819844a2736a9ae2f6eef19a8e7f
+# Wed Oct 13 14:26:48 2021 -0400 - [email protected] - STY: black
+d8dbc6f7b6a5385535e2fa53b7c6af7aa1370f46
+# Wed Sep 29 16:53:54 2021 +0200 - [email protected] - sty: run black on affected files
+5f280da629bb7b5dce908633d2deea85b55dd67b
+# Thu Jun 24 17:43:22 2021 +0200 - [email protected] - sty: run black
+135ce497a18adbe0811441c2b720910ec549aa6f
+# Thu Sep 23 08:56:28 2021 -0400 - [email protected] - STY: black
+f69b3fb09560616822737764bb07272cd587e4a0
+# Fri Apr 30 17:19:55 2021 -0400 - [email protected] - STY: black
+04718ac71436b6f283af7575dda0f6998b64f893
+# Fri Apr 30 16:50:00 2021 -0400 - [email protected] - STY: black
 12deb959cccc431fb8222cc5854f1c92a0080021
+# Thu Apr 1 12:26:08 2021 -0400 - [email protected] - STY: black
 f64bf338f630a9ee5cbe7a3ec98c68292897e720
+# Thu Dec 3 09:24:05 2020 +1100 - [email protected] - run black over touched files
+c81259bc3b28baa1f18f95f6b056c228c6bfd115
+# Fri Aug 14 17:15:15 2020 -0400 - [email protected] - STY: Black
 83358d7f17aac07cb90d0330f11ea2322e2974d8
+# Sat Mar 14 12:44:20 2020 -0400 - [email protected] - STY: black
 faef7d0f93013a700c882f709e98fb3cd36ebb03
+# Sun Mar 8 15:05:28 2020 +0100 - [email protected] - FIX: get length of generator + STY: Black
+02991da67458b879d7c6360aa6457eb3c1bd5a07
+# Wed Mar 4 16:30:39 2020 -0500 - [email protected] - STY: black
 d50c1858564c0b3073fb23c54886a0454cb66afa
+# Thu Feb 27 15:08:42 2020 -0800 - [email protected] - sty: black
 417b8897a116fcded5000e21e2b6ccbe29452a52
+# Thu Jan 2 11:29:05 2020 -0800 - [email protected] - sty: black
 aaf677a87f64c485f3e305799e4a5dc73b69e5fb
+# Sun Dec 29 17:47:51 2019 -0800 - [email protected] - sty: black
 f763008442d88d8ce00ec266698268389415f8d6
+# Thu Jan 2 11:29:05 2020 -0800 - [email protected] - sty: black
 b1eccafd4edc8503b02d715f5b5f6f783520fdf9
+# Sun Dec 29 17:47:51 2019 -0800 - [email protected] - sty: black
 70db90349598cc7f26a4a513779529fba7d0a797
+# Thu Dec 19 09:22:22 2019 -0500 - [email protected] - STY: Black
 6c1d91d71f6f0db0e985bd2adc34206442b0653d
+# Thu Dec 19 15:51:11 2019 -0500 - [email protected] - STY: Black
 97bdbd5f48ab242de5288ba4715192a27619a803
+# Fri Nov 15 14:38:10 2019 -0500 - [email protected] - run black
 78fa360f5b785224349b8b85b07e510d2233bb63
+# Fri Nov 15 14:34:03 2019 -0500 - [email protected] - run black
 7f85f43a34de8bff8e634232c939b17cee8e8fc5
+# Thu Nov 14 11:14:51 2019 -0500 - [email protected] - Merge pull request #3096 from effigies/sty/black
+1a869991adc024577536689d557fc748c764f15d
+# Thu Nov 14 09:15:20 2019 -0500 - [email protected] - STY: Black setup.py
 9c50b5daa797def5672dd057155b0e2c658853e2
+# Thu Nov 14 09:14:38 2019 -0500 - [email protected] - STY: Black for tools/
 47194993ae14aceeec436cfb3769def667196668
+# Wed Nov 13 23:41:15 2019 -0500 - [email protected] - STY: Black
 75653feadc6667d5313d83e9c62a5d5819771a9c
+# Tue Nov 12 09:43:34 2019 -0500 - [email protected] - STY: Black files pre-merge
 497b44d680eee0892fa59c6aaaae22a17d70a536
diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml
@@ -0,0 +1,19 @@
+---
+name: Codespell
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v1
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -105,13 +105,13 @@ jobs:
             depends: REQUIREMENTS
             deb-depends: true
             nipype-extras: doc,tests,profiler,duecredit,ssh
-          - os: ubuntu-20.04
-            python-version: 3.8
-            check: test
-            pip-flags: ''
-            depends: NUMPY123
-            deb-depends: true
-            nipype-extras: doc,tests,nipy,profiler,duecredit,ssh
+          # - os: ubuntu-20.04
+          #   python-version: 3.8
+          #   check: test
+          #   pip-flags: ''
+          #   depends: NUMPY123
+          #   deb-depends: true
+          #   nipype-extras: doc,tests,nipy,profiler,duecredit,ssh
     env:
       DEPENDS: ${{ matrix.depends }}
       CHECK_TYPE: ${{ matrix.check }}

diff --git a/.gitignore b/.gitignore
@@ -30,4 +30,4 @@ __pycache__/
 .ruby-version
 .pytest_cache
 .vscode/
-venv/
+venv/
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -2,13 +2,13 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v3.4.0
+    rev: v4.4.0
     hooks:
     -   id: trailing-whitespace
     -   id: end-of-file-fixer
     -   id: check-yaml
     -   id: check-added-large-files
 -   repo: https://github.com/psf/black
-    rev: 20.8b1
+    rev: 23.3.0
     hooks:
     -   id: black
diff --git a/.zenodo.json b/.zenodo.json
@@ -116,15 +116,15 @@
     {
       "name": "Yvernault, Benjamin"
     },
-    {
-      "name": "Hamalainen, Carlo",
-      "orcid": "0000-0001-7655-3830"
-    },
     {
       "affiliation": "Institute for Biomedical Engineering, ETH and University of Zurich",
       "name": "Christian, Horea",
       "orcid": "0000-0001-7037-2449"
     },
+    {
+      "name": "Hamalainen, Carlo",
+      "orcid": "0000-0001-7655-3830"
+    },
     {
       "affiliation": "Stanford University",
       "name": "Ćirić , Rastko",
@@ -193,6 +193,9 @@
       "name": "Dias, Maria de Fatima",
       "orcid": "0000-0001-8878-1750"
     },
+    {
+      "name": "Moloney, Brendan"
+    },
     {
       "affiliation": "Otto-von-Guericke-University Magdeburg, Germany",
       "name": "Hanke, Michael",
@@ -202,9 +205,6 @@
       "affiliation": "Child Mind Institute",
       "name": "Giavasis, Steven"
     },
-    {
-      "name": "Moloney, Brendan"
-    },
     {
       "affiliation": "SRI International",
       "name": "Nichols, B. Nolan",
@@ -363,6 +363,11 @@
       "name": "Schaefer, Alexander",
       "orcid": "0000-0001-6488-4739"
     },
+    {
+      "affiliation": "CEA",
+      "name": "Papadopoulos Orfanos, Dimitri",
+      "orcid": "0000-0002-1242-8990"
+    },
     {
       "affiliation": "UniversityHospital Heidelberg, Germany",
       "name": "Kleesiek, Jens"
@@ -414,11 +419,6 @@
     {
       "name": "Haselgrove, Christian"
     },
-    {
-      "affiliation": "CEA",
-      "name": "Papadopoulos Orfanos, Dimitri",
-      "orcid": "0000-0002-1242-8990"
-    },
     {
       "affiliation": "Department of Psychology, Stanford University; Parietal, INRIA",
       "name": "Durnez, Joke",
@@ -895,6 +895,11 @@
       "affiliation": "MIT, HMS",
       "name": "Ghosh, Satrajit",
       "orcid": "0000-0002-5312-6729"
+    },
+    {
+      "affiliation": "University of Tübingen and MPI for Biological Cybernertics",
+      "name": "Bannert, Michael M.",
+      "orcid": "0000-0003-1010-7517"
     }
   ],
   "keywords": [

diff --git a/Makefile b/Makefile
@@ -9,6 +9,10 @@ PYTHON ?= python
 zipdoc: html
 	zip documentation.zip doc/_build/html
 
+.git-blame-ignore-revs: .git/HEAD
+	git log --grep "\[ignore-rev\]\|STY: black\|run black" -i --pretty=format:"# %ad - %ae - %s%n%H" > .git-blame-ignore-revs
+	echo >> .git-blame-ignore-revs
+
 sdist: zipdoc
 	@echo "Building source distribution..."
 	$(PYTHON) setup.py sdist

diff --git a/doc/changelog/0.X.X-changelog.rst b/doc/changelog/0.X.X-changelog.rst
@@ -15,7 +15,7 @@
 * ENH: Generate Dockerfiles with neurodocker (https://github.com/nipy/nipype/pull/2202)
 * ENH: FLAIR options for recon-all (https://github.com/nipy/nipype/pull/2279)
 * ENH: Config option for setting maxtasksperchild when multiprocessing (https://github.com/nipy/nipype/pull/2284)
-* FIX: Testing maintainance and improvements (https://github.com/nipy/nipype/pull/2252)
+* FIX: Testing maintenance and improvements (https://github.com/nipy/nipype/pull/2252)
 * ENH: Add elapsed_time and final metric_value to ants.Registration (https://github.com/nipy/nipype/pull/1985)
 * ENH: Improve terminal_output feature (https://github.com/nipy/nipype/pull/2209)
 * ENH: Simple interface to FSL std2imgcoords (https://github.com/nipy/nipype/pull/2209, prev #1398)
@@ -39,7 +39,7 @@
 * ENH: Add cosine-basis high-pass-filter to CompCor, allow skip of initial volumes (https://github.com/nipy/nipype/pull/2107, https://github.com/nipy/nipype/pull/#2122)
 * FIX: Catch more dcm2niix DTI conversions (https://github.com/nipy/nipype/pull/2110)
 * FIX: Retrieve aseg + wmparc stats properly (https://github.com/nipy/nipype/pull/2117)
-* ENH: ANTs MeasureImageSimilarity Inteface (https://github.com/nipy/nipype/pull/2128)
+* ENH: ANTs MeasureImageSimilarity Interface (https://github.com/nipy/nipype/pull/2128)
 * FIX: CompCor filter_basis of correct size, pre-filter column headers (https://github.com/nipy/nipype/pull/2136, https://github.com/nipy/nipype/pull/2138)
 * ENH: FreeSurfer lta_convert and mri_coreg interfaces (https://github.com/nipy/nipype/pull/2140, https://github.com/nipy/nipype/pull/2172)
 * ENH: Speed up S3DataGrabber (https://github.com/nipy/nipype/pull/2143)
@@ -311,16 +311,16 @@ Release 0.11.0 (September 15, 2015)
 Release 0.10.0 (October 10, 2014)
 =================================
 
-* ENH: New miscelaneous interfaces: SplitROIs (mapper), MergeROIs (reducer)
+* ENH: New miscellaneous interfaces: SplitROIs (mapper), MergeROIs (reducer)
        to enable parallel processing of very large images.
 * ENH: Updated FSL interfaces: BEDPOSTX and XFibres, former interfaces are still
        available with the version suffix: BEDPOSTX4 and XFibres4. Added gpu
        versions of BEDPOSTX: BEDPOSTXGPU, BEDPOSTX5GPU, and BEDPOSTX4GPU
-* ENH: Added experimental support for MIPAV algorithms thorugh JIST plugins
+* ENH: Added experimental support for MIPAV algorithms through JIST plugins
 * ENH: New dipy interfaces: Denoise, Resample
 * ENH: New Freesurfer interfaces: Tkregister2 (for conversion of fsl style matrices to freesurfer format), MRIPretess
 * ENH: New FSL interfaces: WarpPoints, WarpPointsToStd, EpiReg, ProbTrackX2, WarpUtils, ConvertWarp
-* ENH: New miscelaneous interfaces: AddCSVRow, NormalizeProbabilityMapSet, AddNoise
+* ENH: New miscellaneous interfaces: AddCSVRow, NormalizeProbabilityMapSet, AddNoise
 * ENH: New AFNI interfaces:  Eval, Means, SVMTest, SVMTrain
 * ENH: FUGUE interface has been refactored to use the name_template system, 3 examples
        added to doctests, some bugs solved.
@@ -510,7 +510,7 @@ Release 0.5 (Mar 10, 2012)
 * API: By default inputs are removed from Node working directory
 * API: InterfaceResult class is now versioned and stores class type not instance
 * API: Added FIRST interface
-* API: Added max_jobs paramter to plugin_args. limits the number of jobs
+* API: Added max_jobs parameter to plugin_args. limits the number of jobs
        executing at any given point in time
 * API: crashdump_dir is now a config execution option
 * API: new config execution options for controlling hash checking, execution and

diff --git a/doc/changelog/1.X.X-changelog.rst b/doc/changelog/1.X.X-changelog.rst
@@ -1,3 +1,20 @@
+1.8.6 (April 05, 2023)
+======================
+
+Bug-fix release in the 1.8.x series.
+
+  * FIX: Update dcmstack interface for Py3 / newer pydicom (https://github.com/nipy/nipype/pull/3541)
+  * FIX: NiBabel 5, and NetworkX 3 and DIPY 1.6 compatibility (https://github.com/nipy/nipype/pull/3538)
+  * FIX: Check for non-mandatory output in DWIBiasCorrect (https://github.com/nipy/nipype/pull/3523)
+  * FIX: Removed leftover debug print statement in FEAT class (https://github.com/nipy/nipype/pull/3521)
+  * DOC: Fix a few more typos (https://github.com/nipy/nipype/pull/3516)
+  * DOC: Fix typos found by codespell (https://github.com/nipy/nipype/pull/3512)
+  * CI: Drop nipy tests until a fixed nipy is released (https://github.com/nipy/nipype/pull/3559)
+  * CI: Disable nipy tests generally, re-add with max numpy  (https://github.com/nipy/nipype/pull/3532)
+  * CI: GitHub Workflows security hardening  (https://github.com/nipy/nipype/pull/3519)
+  * CI: Allow tutorial test cancellation (https://github.com/nipy/nipype/pull/3514)
+
+
 1.8.5 (September 21, 2022)
 ==========================
 
@@ -426,7 +443,7 @@ Python 1.2.3 will be the last version to support Python 3.4.
 
   * FIX: ANTS LaplacianThickness cmdline opts fixed up (https://github.com/nipy/nipype/pull/2846)
   * FIX: Resolve LinAlgError during SVD (https://github.com/nipy/nipype/pull/2838)
-  * ENH: Add interfaces wrapping DIPY worflows (https://github.com/nipy/nipype/pull/2830)
+  * ENH: Add interfaces wrapping DIPY workflows (https://github.com/nipy/nipype/pull/2830)
   * ENH: Update BIDSDataGrabber for pybids 0.7 (https://github.com/nipy/nipype/pull/2737)
   * ENH: Add FSL `eddy_quad` interface (https://github.com/nipy/nipype/pull/2825)
   * ENH: Support tckgen -select in MRtrix3 v3+ (https://github.com/nipy/nipype/pull/2823)

diff --git a/doc/interfaces.rst b/doc/interfaces.rst
@@ -8,7 +8,7 @@ Interfaces and Workflows
 :Release: |version|
 :Date: |today|
 
-Previous versions: `1.8.5 <http://nipype.readthedocs.io/en/1.8.5/>`_ `1.8.4 <http://nipype.readthedocs.io/en/1.8.4/>`_
+Previous versions: `1.8.6 <http://nipype.readthedocs.io/en/1.8.6/>`_ `1.8.5 <http://nipype.readthedocs.io/en/1.8.5/>`_
 
 Workflows
 ---------

diff --git a/nipype/__init__.py b/nipype/__init__.py
@@ -13,7 +13,7 @@
 """
 import os
 
-# XXX Deprecate this import
+# No longer used internally but could be used externally.
 from looseversion import LooseVersion
 
 from .info import URL as __url__, STATUS as __status__, __version__

diff --git a/nipype/algorithms/icc.py b/nipype/algorithms/icc.py
@@ -150,8 +150,8 @@ def ICC_rep_anova(Y, projection_matrix=None):
     SSR = SST - SSC - SSE
     MSR = SSR / dfr
 
-    # ICC(3,1) = (mean square subjeT - mean square error) /
-    #            (mean square subjeT + (k-1)*-mean square error)
+    # ICC(3,1) = (mean square subject - mean square error) /
+    #            (mean square subject + (k-1)*-mean square error)
     ICC = (MSR - MSE) / (MSR + dfc * MSE)
 
     e_var = MSE  # variance of error

diff --git a/nipype/info.py b/nipype/info.py
@@ -5,7 +5,7 @@
 
 # nipype version information
 # Remove .dev0 for release
-__version__ = "1.8.6.dev0"
+__version__ = "1.8.7.dev0"
 
 
 def get_nipype_gitversion():

diff --git a/nipype/interfaces/afni/base.py b/nipype/interfaces/afni/base.py
@@ -6,7 +6,9 @@
 from sys import platform
 import shutil
 
-from ... import logging, LooseVersion
+from looseversion import LooseVersion
+
+from ... import logging
 from ...utils.filemanip import split_filename, fname_presuffix
 from ..base import (
     CommandLine,

diff --git a/nipype/interfaces/ants/registration.py b/nipype/interfaces/ants/registration.py
@@ -865,7 +865,7 @@ class Registration(ANTSCommand):
 --write-composite-transform 0'
 
     One can use multiple similarity metrics in a single registration stage.The Node below first
-    performs a linear registation using only the Mutual Information ('Mattes')-metric.
+    performs a linear registration using only the Mutual Information ('Mattes')-metric.
     In a second stage, it performs a non-linear registration ('Syn') using both a
     Mutual Information and a local cross-correlation ('CC')-metric. Both metrics are weighted
     equally ('metric_weight' is .5 for both). The Mutual Information- metric uses 32 bins.

diff --git a/nipype/interfaces/ants/segmentation.py b/nipype/interfaces/ants/segmentation.py
@@ -1009,10 +1009,10 @@ def _run_interface(self, runtime, correct_return_codes=(0,)):
         runtime = super(BrainExtraction, self)._run_interface(runtime)
 
         # Still, double-check if it didn't found N4
-        if "we cant find" in runtime.stdout:
+        if "we can't find" in runtime.stdout:
             for line in runtime.stdout.split("\n"):
-                if line.strip().startswith("we cant find"):
-                    tool = line.strip().replace("we cant find the", "").split(" ")[0]
+                if line.strip().startswith("we can't find"):
+                    tool = line.strip().replace("we can't find the", "").split(" ")[0]
                     break
 
             errmsg = (