Release v1.8.7

.github/Dockerfiles/C-PAC.develop-ABCD-HCP-bionic.Dockerfile

@@ -1,4 +1,4 @@
-FROM ghcr.io/fcp-indi/c-pac/stage-base:abcd-hcp-v1.8.6.dev1
+FROM ghcr.io/fcp-indi/c-pac/stage-base:abcd-hcp-v1.8.7.dev1
 LABEL org.opencontainers.image.description "Full C-PAC image with software dependencies version-matched to [ABCD-HCP BIDS fMRI Pipeline](https://github.com/DCAN-Labs/abcd-hcp-pipeline/blob/e480a8f99534f1b05f37bf44c64827384b69b383/Dockerfile)"
 LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC
 USER root

.github/Dockerfiles/C-PAC.develop-fMRIPrep-LTS-xenial.Dockerfile

@@ -1,4 +1,4 @@
-FROM ghcr.io/fcp-indi/c-pac/stage-base:fmriprep-lts-v1.8.6.dev1
+FROM ghcr.io/fcp-indi/c-pac/stage-base:fmriprep-lts-v1.8.7.dev1
 LABEL org.opencontainers.image.description "Full C-PAC image with software dependencies version-matched to [fMRIPrep LTS](https://reproducibility.stanford.edu/fmriprep-lts#long-term-support-lts)"
 LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC
 USER root

.github/Dockerfiles/C-PAC.develop-jammy.Dockerfile

@@ -14,7 +14,7 @@
 
 # You should have received a copy of the GNU Lesser General Public
 # License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
-FROM ghcr.io/fcp-indi/c-pac/stage-base:standard-v1.8.6.dev1
+FROM ghcr.io/fcp-indi/c-pac/stage-base:standard-v1.8.7.dev1
 LABEL org.opencontainers.image.description "Full C-PAC image"
 LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC
 USER root

.github/Dockerfiles/C-PAC.develop-lite-jammy.Dockerfile

@@ -14,7 +14,7 @@
 
 # You should have received a copy of the GNU Lesser General Public
 # License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
-FROM ghcr.io/fcp-indi/c-pac/stage-base:lite-v1.8.6.dev1
+FROM ghcr.io/fcp-indi/c-pac/stage-base:lite-v1.8.7.dev1
 LABEL org.opencontainers.image.description "Full C-PAC image without FreeSurfer"
 LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC
 USER root

.github/Dockerfiles/base-ABCD-HCP.Dockerfile

@@ -2,7 +2,6 @@
 FROM ghcr.io/fcp-indi/c-pac/afni:21.1.00-bionic as AFNI
 FROM ghcr.io/fcp-indi/c-pac/ants:2.2.0.neurodocker-bionic as ANTs
 FROM ghcr.io/fcp-indi/c-pac/c3d:1.0.0-bionic as c3d
-FROM ghcr.io/fcp-indi/c-pac/connectome-workbench:1.3.2-1.neurodebian-bionic as connectome-workbench
 FROM ghcr.io/fcp-indi/c-pac/freesurfer:6.0.0-min.neurodocker-bionic as FreeSurfer
 FROM ghcr.io/fcp-indi/c-pac/fsl:5.0.10-bionic as FSL
 FROM ghcr.io/fcp-indi/c-pac/ica-aroma:0.4.3-beta-bionic as ICA-AROMA
@@ -43,7 +42,7 @@ COPY --from=ANTs /ants_template /ants_template
 # install FSL
 COPY --from=FSL /usr/bin/tclsh /usr/bin/tclsh
 COPY --from=FSL /usr/bin/wish /usr/bin/wish
-COPY --from=FSL /usr/share/fsl/ /usr/share/fsl/
+COPY --from=FSL /usr/share/fsl /usr/share/fsl
 COPY --from=FSL /lib/x86_64-linux-gnu/lib*so* /lib/x86_64-linux-gnu/
 COPY --from=FSL /usr/lib/lib*so* /usr/lib/
 # set up FSL environment
@@ -76,9 +75,14 @@ ENV MSMBINDIR=/opt/msm/Ubuntu \
     PATH=$PATH:/opt/msm/Ubuntu
 
 # install Connectome Workbench
-COPY --from=connectome-workbench /lib64/* /lib64.
-COPY --from=connectome-workbench /lib/x86_64-linux-gnu/* /lib/x86_64-linux-gnu/
-COPY --from=connectome-workbench /usr/* /usr/
+RUN APT_KEY_DONT_WARN_ON_DANGEROUS_USAGE=1 apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 04EE7237B7D453EC && \
+    APT_KEY_DONT_WARN_ON_DANGEROUS_USAGE=1 apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 648ACFD622F3D138 && \
+    APT_KEY_DONT_WARN_ON_DANGEROUS_USAGE=1 apt-key adv --keyserver keyserver.ubuntu.com --recv-keys DCC9EFBF77E11517 && \
+    printf '\ndeb http://httpredir.debian.org/debian/ buster main non-free' >> /etc/apt/sources.list && \
+    apt-get update --allow-insecure-repositories && \
+    apt-get install connectome-workbench=1.3.2-1 -y && \
+    strip --remove-section=.note.ABI-tag /usr/lib/x86_64-linux-gnu/libQt5Core.so.5
+ENV PATH=/usr:$PATH
 
 # install ICA-AROMA
 COPY --from=ICA-AROMA /opt/ICA-AROMA /opt/ICA-AROMA

.github/Dockerfiles/base-standard.Dockerfile

@@ -16,7 +16,7 @@
 # License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
 FROM ghcr.io/fcp-indi/c-pac/freesurfer:6.0.0-min.neurodocker-jammy as FreeSurfer
 
-FROM ghcr.io/fcp-indi/c-pac/stage-base:lite-v1.8.6.dev1
+FROM ghcr.io/fcp-indi/c-pac/stage-base:lite-v1.8.7.dev1
 LABEL org.opencontainers.image.description "NOT INTENDED FOR USE OTHER THAN AS A STAGE IMAGE IN A MULTI-STAGE BUILD \
 Standard software dependencies for C-PAC standard images"
 LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC

.github/scripts/autoversioning.sh

@@ -0,0 +1,62 @@
+#!/bin/bash
+
+# Copyright (C) 2024  C-PAC Developers
+
+# This file is part of C-PAC.
+
+# C-PAC is free software: you can redistribute it and/or modify it under
+# the terms of the GNU Lesser General Public License as published by the
+# Free Software Foundation, either version 3 of the License, or (at your
+# option) any later version.
+
+# C-PAC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
+# License for more details.
+
+# You should have received a copy of the GNU Lesser General Public
+# License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
+
+# Update version comment strings
+cd CPAC
+VERSION=$(python -c "from info import __version__; print(('.'.join(('.'.join(__version__[::-1].split('-')[1].split('.')[1:])[::-1], __version__.split('-')[1])) if '-' in __version__ else __version__).split('+', 1)[0])")
+cd ..
+echo "v${VERSION}" > version
+export _SED_COMMAND="s/^(# [Vv]ersion ).*$/# Version ${VERSION}/g"
+if [[ "$OSTYPE" == "darwin"* ]]; then
+    # Mac OSX
+    find ./CPAC/resources/configs -name "*.yml" -exec sed -i '' -E "${_SED_COMMAND}" {} \;
+else
+    # Linux and others
+    find ./CPAC/resources/configs -name "*.yml" -exec sed -i'' -r "${_SED_COMMAND}" {} \;
+fi
+git add version
+VERSIONS=( `git show $(git log --pretty=format:'%h' -n 2 version | tail -n 1):version` `cat version` )
+export PATTERN="(declare|typeset) -a"
+if [[ "$(declare -p VERSIONS)" =~ $PATTERN ]]
+then
+  for DOCKERFILE in $(find ./.github/Dockerfiles -name "*.Dockerfile")
+  do
+    export IFS=""
+    for LINE in $(grep "FROM ghcr\.io/fcp\-indi/c\-pac/.*\-${VERSIONS[0]}" ${DOCKERFILE})
+    do
+      echo "Updating stage tags in ${DOCKERFILE}"
+      if [[ "$OSTYPE" == "darwin"* ]]; then
+          # Mac OSX
+          sed -i "" "s/\-${VERSIONS[0]}/\-${VERSIONS[1]}/g" ${DOCKERFILE}
+      else
+          # Linux and others
+          sed -i "s/\-${VERSIONS[0]}/\-${VERSIONS[1]}/g" ${DOCKERFILE}
+      fi
+    done
+  done
+  unset IFS
+fi
+git add CPAC/resources/configs .github/Dockerfiles
+
+# Overwrite top-level Dockerfiles with the CI Dockerfiles
+cp .github/Dockerfiles/C-PAC.develop-jammy.Dockerfile Dockerfile
+cp .github/Dockerfiles/C-PAC.develop-ABCD-HCP-bionic.Dockerfile variant-ABCD-HCP.Dockerfile
+cp .github/Dockerfiles/C-PAC.develop-fMRIPrep-LTS-xenial.Dockerfile variant-fMRIPrep-LTS.Dockerfile
+cp .github/Dockerfiles/C-PAC.develop-lite-jammy.Dockerfile variant-lite.Dockerfile
+git add *Dockerfile

.github/workflows/on_push.yml

@@ -35,77 +35,8 @@ jobs:
         uses: actions/checkout@v3
         with:
           fetch-depth: 2
-      - uses: actions/setup-python@v4 
-        with:
-          python-version: '3.9'
-          cache: 'pip'
-      - name: Check if version updated
-        id: version_updated
-        run: |
-          git config --global user.email "[email protected]"
-          git config --global user.name "Theodore (Machine User)"
-          GITHUB_BRANCH=$(echo ${GITHUB_REF} | cut -d '/' -f 3-)
-          export PYTHONPATH=$PWD
-          pip install -q wheel
-          pip install -q nipype numpy matplotlib pandas pathvalidate pytz pyyaml voluptuous
-          python ./CPAC/utils/configuration/yaml_template.py
-          if [[ ! -z $(git diff origin/${GITHUB_BRANCH}) ]]
-          then
-            git add CPAC/resources/configs
-            git commit -m ":bulb: Update comments based on default preconfig"
-          fi
-          COMMIT_MESSAGE=$(git log -1 --pretty=%B)
-          if [[ ! "$COMMIT_MESSAGE" == *"Update version to"* ]]
-          then
-            cd CPAC
-            VERSION=$(python -c "from info import __version__; print(('.'.join(('.'.join(__version__[::-1].split('-')[1].split('.')[1:])[::-1], __version__.split('-')[1])) if '-' in __version__ else __version__).split('+', 1)[0])")
-            cd ..
-            echo "v${VERSION}" > version
-            find ./CPAC/resources/configs -name "*.yml" -exec sed -i -r "s/^(# [Vv]ersion ).*$/# Version ${VERSION}/g" {} \;
-            git add version
-            VERSIONS=($(git diff origin/${GITHUB_BRANCH} -- version | tail -n 2))
-            export PATTERN="(declare|typeset) -a"
-            if [[ "$(declare -p VERSIONS)" =~ $PATTERN ]]
-            then
-              for DOCKERFILE in $(find ./.github/Dockerfiles -name "*.Dockerfile")
-              do
-                export IFS=""
-                for LINE in $(grep "FROM ghcr\.io/fcp\-indi/c\-pac/.*\-${VERSIONS[0]:1}" ${DOCKERFILE})
-                do
-                  echo "Updating stage tags in ${DOCKERFILE}"
-                  sed -i "s/\-${VERSIONS[0]:1}/\-${VERSIONS[1]:1}/g" ${DOCKERFILE}
-                done
-              done
-              unset IFS
-            fi
-            if [[ ! -z $(git diff origin/${GITHUB_BRANCH}) ]]
-            then
-              git add CPAC/resources/configs .github/Dockerfiles
-              git commit -m ":bookmark: Update version to ${VERSION} ($COMMIT_MESSAGE)" || true
-              git push origin HEAD:${GITHUB_BRANCH} || true
-            fi
-            cd ..
-          fi
-          if [[ "${GITHUB_REF_TYPE}" == "tag" ]]
-          then
-            cd $HOME/work/C-PAC/C-PAC
-            for DOCKERFILE in $(ls .github/Dockerfiles/C-PAC.develop-*.Dockerfile)
-            do
-              if [[ "$DOCKERFILE" =~ .*C-PAC.develop-(.*)-(bionic|xenial).Dockerfile ]]
-              then
-                cp $DOCKERFILE variant-${BASH_REMATCH[1]}.Dockerfile
-              else
-                cp $DOCKERFILE Dockerfile
-              fi
-            done
-            git add *ockerfile
-            git commit -m ":truck: Copy develop Dockerfiles to root directory \
-            \
-            [skip ci]"
-            git push origin HEAD:${GITHUB_BRANCH} || true
-          fi
       - name: Get changed files since last commit
-        uses: tj-actions/changed-files@v35.7.6
+        uses: tj-actions/changed-files@v41.0.0
         id: changed-files
         with:
           since_last_remote_commit: "true"

.markdownlint.yml

@@ -20,3 +20,7 @@ MD013: false
 # no duplicate headers
 MD024:
   siblings_only: true
+# allow specific inline HTML elements
+MD033:
+  allowed_elements:
+  - span

.pre-commit-config.yaml

@@ -0,0 +1,36 @@
+# Copyright (C) 2024  C-PAC Developers
+
+# This file is part of C-PAC.
+
+# C-PAC is free software: you can redistribute it and/or modify it under
+# the terms of the GNU Lesser General Public License as published by the
+# Free Software Foundation, either version 3 of the License, or (at your
+# option) any later version.
+
+# C-PAC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
+# License for more details.
+
+# You should have received a copy of the GNU Lesser General Public
+# License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
+
+repos:
+  - repo: local
+    hooks:
+      - id: autoversioning
+        name: Update Dockerfiles and version comments
+        entry: .github/scripts/autoversioning.sh
+        language: script
+        files: '.*Dockerfile$|.*\.yaml$|^CPAC/info\.py$'
+      - id: update-yaml-comments
+        name: Update YAML comments
+        entry: CPAC/utils/configuration/yaml_template.py
+        language: python
+        files: '^CPAC/resources/configs/pipeline_config_.*\.ya?ml'
+        additional_dependencies:
+          - "click"
+          - "nipype"
+          - "pathvalidate"
+          - "pyyaml"
+          - "voluptuous"

CHANGELOG.md

@@ -14,9 +14,31 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [1.8.6]
+## [1.8.7] - 2024-05-03
 
-## Added
+### Added
+
+- `Robustfov` feature in `FSL-BET` to crop images ensuring removal of neck regions that may appear in the skull-stripped images. 
+- Ability to throttle nodes, estimating all available memory when threading.
+- Ability to configure FreeSurfer ingress from the command line.
+
+### Changed
+
+- The ABCD-pipeline based surface post-processing workflows have been modularized to be more robust, resolving a running issue with this part of the pipeline stalling or crashing in some runs.
+- Moved autoversioning from CI to pre-commit
+- Updated `FSL-BET` config to default `-mask-boolean` flag as on, and removed all removed `mask-boolean` keys from configs.
+- Added `dvars` as optional output in `cpac_outputs`.
+
+### Fixed
+
+- Fixed a bug where ingressing fmriprep outputs into C-PAC with a blank nuisance confounds field in the C-PAC pipeline configuration file would cause a crash.
+- Fixed a bug where spatial smoothing and z-scoring of final outputs would sometimes fail to run when running a C-PAC pipeline that would ingress fmriprep outputs.
+- Fixed a bug where ingress of distortion correction-related field map metadata would sometimes fail to recognize both echo times, when there were two present, leading to an error message claiming an echo time is missing.
+- Changed an extraneous default pipeline configuration setting - `surface_connectivity` is now disabled in the default configuration as intended.
+
+## [1.8.6] - 2024-01-15
+
+### Added
 
 - Some automatic handling of user-provided BIDSy atlas names.
 - `sig_imports` static method decorator for `Function` nodes, to accommodate type hinting in signatures of `Function` node functions.
@@ -26,7 +48,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - `switch_is_off`, `switch_is_on` and `switch_is_on_off` methods to `Configuration` class
 - `__repr__` and `__str__` methods to `ResourcePool`s and `NodeBlockFunction`s
 
-## Fixed
+### Fixed
 
 - Fixed a bug where some connectivity matrices wouldn't generate if anatomical and functional outputs were in different resolutions.
 - Handling of `3dECM` outputs for AFNI ≥ 21.1.1.
@@ -272,6 +294,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 See [Version 1.8.1 Beta](https://fcp-indi.github.io/docs/user/release_notes/v1.8.1) for release notes for v1.8.1 and [Release Notes](https://fcp-indi.github.io/docs/user/release_notes) for all release notes back to v0.1.1.
 
+[unreleased]: https://github.com/FCP-INDI/C-PAC/compare/v1.8.6...develop
 [1.8.6]: https://github.com/FCP-INDI/C-PAC/releases/tag/v1.8.6
 [1.8.5]: https://github.com/FCP-INDI/C-PAC/releases/tag/v1.8.5
 [1.8.4]: https://github.com/FCP-INDI/C-PAC/releases/tag/v1.8.4

CONTRIBUTING.md

@@ -1,4 +1,4 @@
-<!-- Copyright (C) 2022  C-PAC Developers
+<!-- Copyright (C) 2022-2024  C-PAC Developers
 
 This file is part of C-PAC.
 
@@ -7,19 +7,47 @@ C-PAC is free software: you can redistribute it and/or modify it under the terms
 C-PAC is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
 
 You should have received a copy of the GNU Lesser General Public License along with C-PAC. If not, see <https://www.gnu.org/licenses/>. -->
+
+# CONTRIBUTING
+
+## pre-commit
+
+This project uses [pre-commit](https://pre-commit.com/), a framework for managing and maintaining git hooks. Pre-commit can be used to manage the hooks that run on every commit to automatically point out issues in code such as missing semicolons, trailing whitespace, and debug statements. By using these hooks, you can ensure code quality and prevent bad code from being uploaded.
+
+To install `pre-commit`, you can use `pip`:
+
+```bash
+pip install pre-commit
+```
+
+After installation, you can set up your git hooks with this command at the root of this repository:
+
+```bash
+pre-commit install
+```
+
+This will add a pre-commit script to your `.git/hooks/` directory. This script will run whenever you run `git commit`.
+
+For more details on how to configure and use pre-commit, please refer to the official documentation.
+
 ## Git branches, tags and continuous integration
+
 GitHub Actions builds C-PAC images for each branch and tag pushed to GitHub; these images are pushed to <span title="GitHub Container Registry">[GHCR](https://github.com/FCP-INDI/C-PAC/pkgs/container/c-pac/versions)</span> and deleted upon branch deletion on GitHub.
 
 If a commit is pushed or merged into [`develop` on GitHub](https://github.com/FCP-INDI/C-PAC/tree/develop), GitHub Actions will push [`nightly` and its variants to Docker Hub](https://hub.docker.com/repository/registry-1.docker.io/fcpindi/c-pac/tags?page=1&ordering=last_updated&name=nightly).
 
 If a tag is pushed to GitHub that matches the regular expression
+
 ```Regular Expression
 ^v[0-9]+\.[0-9]+\.[0-9]+$
 ```
+
 GitHub Actions will push [`release-${TAG}` and its variants](https://hub.docker.com/repository/registry-1.docker.io/fcpindi/c-pac/tags?page=1&ordering=last_updated&name=release-) and [`latest` and its variants to Docker Hub](https://hub.docker.com/repository/registry-1.docker.io/fcpindi/c-pac/tags?page=1&ordering=last_updated&name=latest).
 
 ## Software dependencies and variant images
+
 We currently have one main and 3 variant images:
+
 * `ABCD-HCP`: dependency versions matched to [ABCD-HCP BIDS fMRI Pipeline](https://github.com/DCAN-Labs/abcd-hcp-pipeline/releases/tag/v0.1.1) versions
 * `fMRIPrep-LTS`: dependency versions matched to [fMRIPrep Long-term support](https://reproducibility.stanford.edu/fmriprep-lts/) versions
 * `lite`: same dependency versions as main image without FreeSurfer (smaller image)