🔀 Merge branch 'feature/check_orientations' into 'many_pipes'

Author: shnizzedy

.circleci/main.yml

@@ -1,4 +1,4 @@
---- 
+---
 version: 2.1
 # Singularity started failing to set up on Circle circa May 2023, so those tests are currently disabled
 
@@ -139,7 +139,7 @@ commands:
             pip install -r dev/circleci_data/requirements.txt
       - save_cache:
           key: pip-ci-requirements-{{ checksum "dev/circleci_data/requirements.txt" }}-3.10.10
-          paths: 
+          paths:
             - /opt/circleci/.pyenv/versions/3.10.10
   set-up-variant:
     parameters:
@@ -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:
@@ -237,7 +237,7 @@ jobs:
           path: test-results
       - save_cache:
           key: coverage-docker-<< parameters.variant >>-{{ .Revision }}
-          paths: 
+          paths:
             - .coverage.docker
             - .coverage.docker-<< parameters.variant >>
   pytest-singularity:
@@ -266,7 +266,7 @@ jobs:
           path: test-results
       - save_cache:
           key: coverage-singularity-<< parameters.variant >>-{{ .Revision }}
-          paths: 
+          paths:
             - .coverage.singularity
             - .coverage.singularity-<<parameters.variant >>
 workflows:
@@ -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/AFNI.16.2.07.neurodocker-xenial.Dockerfile

@@ -1,4 +1,4 @@
-# Copyright (C) 2022-2023  C-PAC Developers
+# Copyright (C) 2022-2024  C-PAC Developers
 
 # This file is part of C-PAC.
 
@@ -14,23 +14,23 @@
 
 # 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-v1.8.8.dev1
 LABEL org.opencontainers.image.description "Full C-PAC image"
 LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC
 USER root
 
 # install C-PAC
 COPY dev/circleci_data/pipe-test_ci.yml /cpac_resources/pipe-test_ci.yml
 COPY . /code
-RUN pip cache purge && pip install -e /code
+RUN pip cache purge && pip install -e "/code[graphviz]"
 # set up runscript
 COPY dev/docker_data /code/docker_data
 RUN rm -Rf /code/docker_data/checksum && \
     mv /code/docker_data/* /code && \
     rm -Rf /code/docker_data && \
-    chmod +x /code/run.py && \
-    chmod +x /code/run-with-freesurfer.sh
-ENTRYPOINT ["/code/run-with-freesurfer.sh"]
+    chmod +x /code/CPAC/_entrypoints/run.py && \
+    chmod +x /code/CPAC/_entrypoints/run-with-freesurfer.sh
+ENTRYPOINT ["/code/CPAC/_entrypoints/run-with-freesurfer.sh"]
 
 # link libraries & clean up
 # link libraries & clean up
@@ -45,7 +45,8 @@ RUN rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* /root/.cache/* \
     && chmod 777 $(ls / | grep -v sys | grep -v proc)
 ENV PYTHONUSERBASE=/home/c-pac_user/.local
 ENV PATH=$PATH:/home/c-pac_user/.local/bin \
-    PYTHONPATH=$PYTHONPATH:$PYTHONUSERBASE/lib/python3.10/site-packages
+    PYTHONPATH=$PYTHONPATH:$PYTHONUSERBASE/lib/python3.10/site-packages \
+    _SHELL=/bin/bash
 
 # set user
 WORKDIR /home/c-pac_user