Merge branch 'master' into patch-1

.circleci/test_py3_pytest.sh → .circleci/test_pytest.sh

@@ -1,3 +1,3 @@
 #!/bin/bash
 
-docker run --rm=false -t -v $WORKDIR:/work -v $HOME/examples:/data/examples:ro -w /work -e CI_SKIP_TEST=1 -e NIPYPE_RESOURCE_MONITOR=1 "${DOCKER_IMAGE}:py36" /usr/bin/run_pytests.sh
+docker run --rm=false -t -v $WORKDIR:/work -v $HOME/examples:/data/examples:ro -w /work -e CI_SKIP_TEST=1 -e NIPYPE_RESOURCE_MONITOR=1 "${DOCKER_IMAGE}:py38" /usr/bin/run_pytests.sh

.codespellrc

@@ -0,0 +1,13 @@
+[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
+# expad - AFNI flag
+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,expad,burnin

.dockerignore

@@ -22,13 +22,12 @@ src/
 .git
 
 # other
-docs/**/*
-docs/
+doc/**/*
+doc/
 .cache/
 .circle/**/*
 .circle/
 circle.yml
-rtd_requirements.txt
 Vagrantfile
 .travis.yml
 .mailmap

.et

@@ -0,0 +1,4 @@
+{ "bad_versions" : [ "1.2.1",
+                     "1.2.3",
+                     "1.3.0"]
+}

.git-blame-ignore-revs

@@ -0,0 +1,90 @@
+# Tue Feb 27 14:28:18 2024 -0500 - effigies@gmail.com - STY: black 2024.2 [ignore-rev]
+f1cbc1c941f8d02659f8ef245aac0862efb80ccf
+# Mon Sep 11 13:36:40 2023 +0200 - 37933899+servoz@users.noreply.github.com - run black for nipype/interfaces/spm/preprocess.py
+b9cac5e993143febb01ade42e56b41009427a4b6
+# Wed Jul 5 16:31:45 2023 -0400 - effigies@gmail.com - STY: Run black and fix typo
+34a4ac6eeff8d4924b40875c45df5d84a97da90b
+# Wed Jul 5 11:30:42 2023 -0400 - effigies@gmail.com - STY: black
+3b89ca85faf2428ecf7844de9c0db4aa7c329c93
+# Wed Jul 5 09:49:31 2023 -0400 - effigies@gmail.com - STY: black
+4a6a7d9d25d5d1e1f0eb55828dede58f8b9c9f80
+# Wed Apr 5 14:01:05 2023 -0400 - effigies@gmail.com - STY: black [ignore-rev]
+a9ce9b78a402ebacf7726ad6454bb75b1447f52f
+# Wed Sep 14 14:12:07 2022 -0400 - mathiasg@stanford.edu - STY: Black
+f4a779223c6b0dffa47138d24ec9ef378c7164a9
+# Tue Apr 19 14:09:31 2022 -0400 - markiewicz@stanford.edu - STY: black [ignore-rev]
+b9716ebd46541f7fb1b96a94cc35b5e2ea6c3bba
+# Fri Apr 15 06:59:48 2022 -0700 - markiewicz@stanford.edu - STY: black [ignore-rev]
+d223fbccda6dee0ef39e00084296a3292f2ccf87
+# Fri Apr 8 21:34:43 2022 -0400 - markiewicz@stanford.edu - STY: black [ignore-rev]
+e3f56da124fd58041018c2e70d16a130ef189a66
+# Sun Apr 3 10:27:07 2022 -0400 - markiewicz@stanford.edu - STY: black [ignore-rev]
+988c382ebfc7df964874b6287b9d9e27e274a4a4
+# Sat Apr 2 21:32:56 2022 -0400 - markiewicz@stanford.edu - STY: black [ignore-rev]
+230fac6149d4dfbd5da669a983332a1fe318ef57
+# Sat Apr 2 12:49:15 2022 -0400 - markiewicz@stanford.edu - STY/TEST: Make specs and run black [ignore-rev]
+2ba8dacb8cc1f6f9c5b15b1cfb7b0395d45dcfb3
+# Sun Mar 20 21:19:39 2022 -0400 - markiewicz@stanford.edu - STY: black [ignore-rev]
+87cc1b54981113024ec3fd594881f72cf67513fb
+# Wed Dec 8 17:02:09 2021 -0500 - markiewicz@stanford.edu - STY: black [ignore-rev]
+5ac2f18ac116832d81a13f0c83e0a6aeda1457cf
+# Thu Dec 2 09:30:42 2021 -0500 - markiewicz@stanford.edu - STY: black
+ee50279ebf061a70ff502e7d2e51385b285cfda4
+# Tue Oct 26 11:18:02 2021 +0200 - code@oscaresteban.es - sty: run black
+5d9adbbb77b7047b9b47cd2fa079dee0094cfc91
+# Wed Oct 20 12:07:15 2021 +0200 - fabio.bernardoni@uniklinikum-dresden.de - run black on the preprocess.py file to improve formatting
+674e9b0eeca082efb5322b61fea57ee89a3e4a24
+# Wed Oct 13 16:08:23 2021 -0400 - markiewicz@stanford.edu - ENH: Add expected steps for FreeSurfer 7 recon-all (#3389)
+8f7c0bf2ec9c819844a2736a9ae2f6eef19a8e7f
+# Wed Oct 13 14:26:48 2021 -0400 - markiewicz@stanford.edu - STY: black
+d8dbc6f7b6a5385535e2fa53b7c6af7aa1370f46
+# Wed Sep 29 16:53:54 2021 +0200 - code@oscaresteban.es - sty: run black on affected files
+5f280da629bb7b5dce908633d2deea85b55dd67b
+# Thu Jun 24 17:43:22 2021 +0200 - code@oscaresteban.es - sty: run black
+135ce497a18adbe0811441c2b720910ec549aa6f
+# Thu Sep 23 08:56:28 2021 -0400 - markiewicz@stanford.edu - STY: black
+f69b3fb09560616822737764bb07272cd587e4a0
+# Fri Apr 30 17:19:55 2021 -0400 - markiewicz@stanford.edu - STY: black
+04718ac71436b6f283af7575dda0f6998b64f893
+# Fri Apr 30 16:50:00 2021 -0400 - markiewicz@stanford.edu - STY: black
+12deb959cccc431fb8222cc5854f1c92a0080021
+# Thu Apr 1 12:26:08 2021 -0400 - markiewicz@stanford.edu - STY: black
+f64bf338f630a9ee5cbe7a3ec98c68292897e720
+# Thu Dec 3 09:24:05 2020 +1100 - tom.g.close@gmail.com - run black over touched files
+c81259bc3b28baa1f18f95f6b056c228c6bfd115
+# Fri Aug 14 17:15:15 2020 -0400 - markiewicz@stanford.edu - STY: Black
+83358d7f17aac07cb90d0330f11ea2322e2974d8
+# Sat Mar 14 12:44:20 2020 -0400 - markiewicz@stanford.edu - STY: black
+faef7d0f93013a700c882f709e98fb3cd36ebb03
+# Sun Mar 8 15:05:28 2020 +0100 - 3453485+daniel-ge@users.noreply.github.com - FIX: get length of generator + STY: Black
+02991da67458b879d7c6360aa6457eb3c1bd5a07
+# Wed Mar 4 16:30:39 2020 -0500 - markiewicz@stanford.edu - STY: black
+d50c1858564c0b3073fb23c54886a0454cb66afa
+# Thu Feb 27 15:08:42 2020 -0800 - code@oscaresteban.es - sty: black
+417b8897a116fcded5000e21e2b6ccbe29452a52
+# Thu Jan 2 11:29:05 2020 -0800 - code@oscaresteban.es - sty: black
+aaf677a87f64c485f3e305799e4a5dc73b69e5fb
+# Sun Dec 29 17:47:51 2019 -0800 - code@oscaresteban.es - sty: black
+f763008442d88d8ce00ec266698268389415f8d6
+# Thu Jan 2 11:29:05 2020 -0800 - code@oscaresteban.es - sty: black
+b1eccafd4edc8503b02d715f5b5f6f783520fdf9
+# Sun Dec 29 17:47:51 2019 -0800 - code@oscaresteban.es - sty: black
+70db90349598cc7f26a4a513779529fba7d0a797
+# Thu Dec 19 09:22:22 2019 -0500 - markiewicz@stanford.edu - STY: Black
+6c1d91d71f6f0db0e985bd2adc34206442b0653d
+# Thu Dec 19 15:51:11 2019 -0500 - markiewicz@stanford.edu - STY: Black
+97bdbd5f48ab242de5288ba4715192a27619a803
+# Fri Nov 15 14:38:10 2019 -0500 - steve@steventilley.com - run black
+78fa360f5b785224349b8b85b07e510d2233bb63
+# Fri Nov 15 14:34:03 2019 -0500 - steve@steventilley.com - run black
+7f85f43a34de8bff8e634232c939b17cee8e8fc5
+# Thu Nov 14 11:14:51 2019 -0500 - markiewicz@stanford.edu - Merge pull request #3096 from effigies/sty/black
+1a869991adc024577536689d557fc748c764f15d
+# Thu Nov 14 09:15:20 2019 -0500 - markiewicz@stanford.edu - STY: Black setup.py
+9c50b5daa797def5672dd057155b0e2c658853e2
+# Thu Nov 14 09:14:38 2019 -0500 - markiewicz@stanford.edu - STY: Black for tools/
+47194993ae14aceeec436cfb3769def667196668
+# Wed Nov 13 23:41:15 2019 -0500 - markiewicz@stanford.edu - STY: Black
+75653feadc6667d5313d83e9c62a5d5819771a9c
+# Tue Nov 12 09:43:34 2019 -0500 - markiewicz@stanford.edu - STY: Black files pre-merge
+497b44d680eee0892fa59c6aaaae22a17d70a536

.github/PULL_REQUEST_TEMPLATE.md

@@ -17,7 +17,3 @@ Fixes # .
 
 ## List of changes proposed in this PR (pull-request)
 <!-- We suggest using bullets (indicated by * or -) and filled checkboxes [x] here -->
-
-## Acknowledgment
-
-- [ ] \(Mandatory\) I acknowledge that this contribution will be available under the Apache 2 license.

.github/dependabot.yml

@@ -0,0 +1,11 @@
+# Dependabot configuration file <https://docs.github.com/en/code-security/dependabot>
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    groups:
+      actions-infrastructure:
+        patterns:
+          - "actions/*"

.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@v4
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2

.github/workflows/contrib.yml

@@ -0,0 +1,84 @@
+name: Contribution checks
+
+# This checks validate contributions meet baseline checks
+#
+# * specs - Ensure make
+
+on:
+  push:
+    branches:
+      - master
+      - maint/*
+  pull_request:
+    branches:
+      - master
+      - maint/*
+
+defaults:
+  run:
+    shell: bash
+
+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
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: ["ubuntu-latest"]
+        python-version: ["3.12"]
+        nipype-extras: ["dev"]
+        check: ["specs", "style"]
+    env:
+      DEPENDS: ""
+      CHECK_TYPE: ${{ matrix.check }}
+      NIPYPE_EXTRAS: ${{ matrix.nipype-extras }}
+      EXTRA_PIP_FLAGS: ""
+      INSTALL_DEB_DEPENDENCIES: false
+      INSTALL_TYPE: pip
+      CI_SKIP_TEST: 1
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: recursive
+          fetch-depth: 0
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Display Python version
+        run: python -c "import sys; print(sys.version)"
+      - name: Create virtual environment
+        run: tools/ci/create_venv.sh
+      - name: Build archive
+        run: |
+          source tools/ci/build_archive.sh
+          echo "ARCHIVE=$ARCHIVE" >> $GITHUB_ENV
+      - name: Install Debian dependencies
+        run: tools/ci/install_deb_dependencies.sh
+        if: ${{ matrix.os == 'ubuntu-18.04' }}
+      - name: Install dependencies
+        run: tools/ci/install_dependencies.sh
+      - name: Install Nipype
+        run: tools/ci/install.sh
+      - name: Run tests
+        run: tools/ci/check.sh
+        if: ${{ matrix.check != 'skiptests' }}
+      - uses: codecov/codecov-action@v4
+        with:
+          file: coverage.xml
+          token: ${{ secrets.CODECOV_TOKEN }}
+        if: ${{ always() }}
+      - name: Upload pytest test results
+        uses: actions/upload-artifact@v4
+        with:
+          name: pytest-results-${{ matrix.os }}-${{ matrix.python-version }}
+          path: test-results.xml
+        if: ${{ always() && matrix.check == 'test' }}