🚧 [WIP] 🚑️ Hotfix 1.8.7: Restore longitudinal functionality

.circleci/main.yml

@@ -184,8 +184,8 @@ jobs:
           key: coverage-docker--{{ .Revision }}
       # - restore_cache:
       #     key: coverage-singularity--{{ .Revision }}
-      - restore_cache:
-          key: coverage-docker-ABCD-HCP-{{ .Revision }}
+      # - restore_cache:
+      #     key: coverage-docker-ABCD-HCP-{{ .Revision }}
       # - restore_cache:
       #     key: coverage-singularity-ABCD-HCP-{{ .Revision }}
       - restore_cache:
@@ -280,9 +280,9 @@ workflows:
             # - "Test in Singularity"
             - "Test lite variant in Docker"
             # - "Test lite variant in Singularity"
-            - "Test ABCD-HCP variant in Docker"
+            # - "Test ABCD-HCP variant in Docker"
             # - "Test ABCD-HCP variant in Singularity"
-            - "Test fMRIPrep-LTS variant in Docker"
+            # - "Test fMRIPrep-LTS variant in Docker"
       - push-branch-to-docker-hub:
           filters:
             branches:
@@ -293,18 +293,18 @@ workflows:
               variant:
                 - ""
                 - lite
-                - ABCD-HCP
-                - fMRIPrep-LTS
+                # - ABCD-HCP
+                # - fMRIPrep-LTS
           requires:
             - "Combine coverage"
       - pytest-docker:
           name: "Test in Docker"
-      - pytest-docker:
-          name: "Test ABCD-HCP variant in Docker"
-          variant: ABCD-HCP
-      - pytest-docker:
-          name: "Test fMRIPrep-LTS variant in Docker"
-          variant: fMRIPrep-LTS
+      # - pytest-docker:
+      #     name: "Test ABCD-HCP variant in Docker"
+      #     variant: ABCD-HCP
+      # - pytest-docker:
+      #     name: "Test fMRIPrep-LTS variant in Docker"
+      #     variant: fMRIPrep-LTS
       - pytest-docker:
           name: "Test lite variant in Docker"
           variant: lite

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

@@ -1,4 +1,4 @@
-FROM ghcr.io/fcp-indi/c-pac/stage-base:abcd-hcp-v1.8.7.dev1
+FROM ghcr.io/fcp-indi/c-pac/stage-base:abcd-hcp-v1.8.7.post1.dev3
 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-v1.8.7.dev1
+FROM ghcr.io/fcp-indi/c-pac/stage-base:fmriprep-lts-v1.8.7.post1.dev3
 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-v1.8.7.dev1
+FROM ghcr.io/fcp-indi/c-pac/stage-base:standard-v1.8.7.post1.dev3
 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-v1.8.7.dev1
+FROM ghcr.io/fcp-indi/c-pac/stage-base:lite-v1.8.7.post1.dev3
 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-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-v1.8.7.dev1
+FROM ghcr.io/fcp-indi/c-pac/stage-base:lite-v1.8.7.post1.dev3
 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

@@ -18,7 +18,14 @@
 # License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
 
 # Update version comment strings
-cd CPAC
+function wait_for_git_lock() {
+    while [ -f "./.git/index.lock" ]; do
+        echo "Waiting for the git lock file to be removed..."
+        sleep 1
+    done
+}
+
+cd CPAC || exit 1
 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
@@ -30,8 +37,8 @@ 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` )
+wait_for_git_lock && git add version
+VERSIONS=( `git show $(git log --pretty=format:'%h' -n 1 version | tail -n 1):version` `cat version` )
 export PATTERN="(declare|typeset) -a"
 if [[ "$(declare -p VERSIONS)" =~ $PATTERN ]]
 then
@@ -52,11 +59,12 @@ then
   done
   unset IFS
 fi
-git add CPAC/resources/configs .github/Dockerfiles
+wait_for_git_lock && 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
+wait_for_git_lock && cp .github/Dockerfiles/C-PAC.develop-jammy.Dockerfile Dockerfile
+wait_for_git_lock && cp .github/Dockerfiles/C-PAC.develop-lite-jammy.Dockerfile variant-lite.Dockerfile
+for DOCKERFILE in $(ls *Dockerfile)
+do
+  wait_for_git_lock && git add $DOCKERFILE
+done

.github/stage_requirements/phase_three.txt

@@ -1,3 +1 @@
-lite
-ABCD-HCP
-fMRIPrep-LTS
+lite

.github/workflows/build_and_test.yml

@@ -317,25 +317,25 @@ jobs:
     with:
       variant: lite
 
-  C-PAC-ABCD-HCP:
-    needs: build-base
-    uses: ./.github/workflows/build_C-PAC.yml
-    with:
-      variant: ABCD-HCP
+  # C-PAC-ABCD-HCP:
+  #   needs: build-base
+  #   uses: ./.github/workflows/build_C-PAC.yml
+  #   with:
+  #     variant: ABCD-HCP
 
-  C-PAC-fMRIPrep-LTS:
-    needs: build-base
-    uses: ./.github/workflows/build_C-PAC.yml
-    with:
-      variant: fMRIPrep-LTS
+  # C-PAC-fMRIPrep-LTS:
+  #   needs: build-base
+  #   uses: ./.github/workflows/build_C-PAC.yml
+  #   with:
+  #     variant: fMRIPrep-LTS
 
   smoke-tests-participant:
     name: Run participant-level smoke tests
     needs:
       - C-PAC
       - C-PAC-lite
-      - C-PAC-ABCD-HCP
-      - C-PAC-fMRIPrep-LTS
+      # - C-PAC-ABCD-HCP
+      # - C-PAC-fMRIPrep-LTS
     if: github.ref_name == 'develop' || github.ref_name == 'main'
     uses: ./.github/workflows/smoke_test_participant.yml
 
@@ -358,8 +358,8 @@ jobs:
     needs:
       - C-PAC
       - C-PAC-lite
-      - C-PAC-ABCD-HCP
-      - C-PAC-fMRIPrep-LTS
+      # - C-PAC-ABCD-HCP
+      # - C-PAC-fMRIPrep-LTS
     if: github.ref_type == 'branch'
     runs-on: ubuntu-latest
     steps:
@@ -425,22 +425,22 @@ jobs:
       variant: 'lite'
     secrets: inherit
 
-  Deploy_to_Docker_Hub-ABCD-HCP:
-    name: Deploy 'ABCD-HCP' to Docker Hub
-    needs:
-      - C-PAC-ABCD-HCP
-    if: github.ref_type == 'tag'
-    uses: ./.github/workflows/deploy_to_Docker_Hub.yml
-    with:
-      variant: 'ABCD-HCP'
-    secrets: inherit
+  # Deploy_to_Docker_Hub-ABCD-HCP:
+  #   name: Deploy 'ABCD-HCP' to Docker Hub
+  #   needs:
+  #     - C-PAC-ABCD-HCP
+  #   if: github.ref_type == 'tag'
+  #   uses: ./.github/workflows/deploy_to_Docker_Hub.yml
+  #   with:
+  #     variant: 'ABCD-HCP'
+  #   secrets: inherit
 
-  Deploy_to_Docker_Hub-fMRIPrep-LTS:
-    name: Deploy 'fMRIPrep-LTS' to Docker Hub
-    needs:
-      - C-PAC-fMRIPrep-LTS
-    if: github.ref_type == 'tag'
-    uses: ./.github/workflows/deploy_to_Docker_Hub.yml
-    with:
-      variant: 'fMRIPrep-LTS'
-    secrets: inherit
+  # Deploy_to_Docker_Hub-fMRIPrep-LTS:
+  #   name: Deploy 'fMRIPrep-LTS' to Docker Hub
+  #   needs:
+  #     - C-PAC-fMRIPrep-LTS
+  #   if: github.ref_type == 'tag'
+  #   uses: ./.github/workflows/deploy_to_Docker_Hub.yml
+  #   with:
+  #     variant: 'fMRIPrep-LTS'
+  #   secrets: inherit

.pre-commit-config.yaml

@@ -14,7 +14,9 @@
 
 # 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/>.
-
+ci:
+    skip:
+      - update-yaml-comments
 repos:
   - repo: local
     hooks:

CHANGELOG.md

@@ -14,6 +14,17 @@ 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).
 
+## [1.8.7.post1] - unreleased
+
+### Changed
+
+- Disabled variant image builds.
+
+### Fixed
+
+- A bug in which bandpass filters always assumed 1D regressor files have exactly 5 header rows.
+- Graph-building bugs that prevented longitudinal workflows from running.
+
 ## [1.8.7] - 2024-05-03
 
 ### Added
@@ -294,7 +305,8 @@ 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
+[1.8.7.post1]: https://github.com/FCP-INDI/C-PAC/compare/v1.8.7...v1.8.7.post1.dev3
+[1.8.7]: https://github.com/FCP-INDI/C-PAC/releases/tag/v1.8.7
 [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

CPAC/info.py

@@ -43,7 +43,7 @@
 _version_major = 1
 _version_minor = 8
 _version_micro = 7
-_version_extra = 'dev1'
+_version_extra = 'post1.dev3'
 
 
 def get_cpac_gitversion():

CPAC/longitudinal_pipeline/longitudinal_preproc.py

@@ -270,7 +270,8 @@ def flirt_node(in_img, output_img, output_mat):
     return node_list
 
 
-def template_creation_flirt(input_brain_list, input_skull_list, init_reg=None, avg_method='median', dof=12,
+def template_creation_flirt(input_brain_list, input_skull_list, init_reg=None,
+                            avg_method='median', dof=12,
                             interp='trilinear', cost='corratio', mat_type='matrix',
                             convergence_threshold=-1, thread_pool=2, unique_id_list=None):
     """