Merge branch 'master' into fix-draw-gantt-chart

Author: effigies

Diff for: .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,afile - 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,afile

Diff for: .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 for: .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 for: .github/workflows/contrib.yml

@@ -22,6 +22,9 @@ concurrency:
   group: contrib-${{ github.ref }}
   cancel-in-progress: true
 
+permissions:
+  contents: read # to fetch code (actions/checkout)
+
 jobs:
   stable:
     # Check each OS, all supported Python, minimum versions and latest releases

Diff for: .github/workflows/tests.yml

@@ -29,8 +29,12 @@ concurrency:
   group: tests-${{ github.ref }}
   cancel-in-progress: true
 
+permissions: {}
 jobs:
   build:
+    permissions:
+      contents: read # to fetch code (actions/checkout)
+
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
@@ -80,24 +84,34 @@ jobs:
 
   stable:
     # Check each OS, all supported Python, minimum versions and latest releases
+    permissions:
+      contents: read # to fetch code (actions/checkout)
+
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: ['ubuntu-latest']
-        python-version: [3.7, 3.8, 3.9, "3.10"]
+        os: ['ubuntu-22.04']
+        python-version: ['3.8', '3.9', '3.10', '3.11']
         check: ['test']
         pip-flags: ['']
         depends: ['REQUIREMENTS']
         deb-depends: [false]
         nipype-extras: ['doc,tests,profiler']
         include:
-          - os: ubuntu-latest
-            python-version: 3.8
+          - os: ubuntu-22.04
+            python-version: '3.8'
             check: test
             pip-flags: ''
             depends: REQUIREMENTS
             deb-depends: true
-            nipype-extras: doc,tests,nipy,profiler,duecredit,ssh
+            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
     env:
       DEPENDS: ${{ matrix.depends }}
       CHECK_TYPE: ${{ matrix.check }}

Diff for: .github/workflows/tutorials.yml

@@ -9,6 +9,7 @@ concurrency:
   group: tutorials-${{ github.ref }}
   cancel-in-progress: true
 
+permissions: {}
 jobs:
   tutorial:
     runs-on: ubuntu-latest

Diff for: .gitignore

@@ -30,4 +30,4 @@ __pycache__/
 .ruby-version
 .pytest_cache
 .vscode/
-venv/
+venv/

Diff for: .pre-commit-config.yaml

@@ -1,14 +1,18 @@
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
--   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v3.4.0
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    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
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-added-large-files
+  - repo: https://github.com/psf/black
+    rev: 23.3.0
     hooks:
-    -   id: black
+      - id: black
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.5
+    hooks:
+    - id: codespell

Diff for: .readthedocs.yml

@@ -4,6 +4,12 @@
 # Required
 version: 2
 
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   configuration: doc/conf.py
@@ -12,9 +18,10 @@ sphinx:
 formats:
   - htmlzip
 
-# Optionally set the version of Python and requirements required to build your docs
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
 python:
-  version: 3.7
   install:
     - requirements: doc/requirements.txt
     - method: pip

Diff for: .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"
@@ -374,6 +379,11 @@
     {
       "name": "Schwartz, Yannick"
     },
+    {
+      "affiliation": "Medical College of Wisconsin",
+      "name": "Espana, Lezlie",
+      "orcid": "0000-0002-6466-4653"
+    },
     {
       "affiliation": "The University of Iowa",
       "name": "Ghayoor, Ali",
@@ -414,11 +424,6 @@
     {
       "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",
@@ -844,6 +849,11 @@
       "name": "Pannetier, Nicolas",
       "orcid": "0000-0002-0744-5155"
     },
+    {
+      "affiliation": "Flywheel.io, Minneapolis, MN, USA.",
+      "name": "Velasco, Pablo",
+      "orcid": "0000-0002-5749-6049"
+    },
     {
       "affiliation": "Max Planck Institute for Human Cognitive and Brain Sciences",
       "name": "Numssen, Ole",
@@ -890,7 +900,17 @@
       "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"
+    },
+    {
+      "affiliation": "Research Centre Juelich",
+      "name": "Wu, Jianxiao",
+      "orcid": "0000-0002-4866-272X",
+    },
   ],
   "keywords": [
     "neuroimaging",

Diff for: 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