Sync new_docs branch with main repo develop

.circleci/config.yml

@@ -1,7 +1,7 @@
 setup: true
 version: 2.1
 orbs:
-  continuation: circleci/continuation@0.3.1
+  continuation: circleci/continuation@1.1.0
 
 parameters:
   run_tests:

.circleci/main.yml

@@ -2,6 +2,9 @@
 version: 2.1
 # Singularity started failing to set up on Circle circa May 2023, so those tests are currently disabled
 
+orbs:
+  codecov: codecov/[email protected]
+
 parameters:
   branch:
     type: string
@@ -36,7 +39,8 @@ commands:
           name: "Combining and reporting coverage"
           command: |
               coverage combine
-              coverage html --ignore-errors
+              coverage xml -o coverage.xml  # Generate XML report
+      - codecov/upload
   configure-git-user:
     steps:
       - add_ssh_keys:
@@ -45,10 +49,6 @@ commands:
       - run:
           name: "Configuring git user"
           command: |
-            sudo apt-key adv --recv-keys --keyserver keyserver.ubuntu.com 78BD65473CB3BD13
-            curl -L https://packagecloud.io/circleci/trusty/gpgkey | sudo apt-key add -
-            sudo apt-get update
-            sudo apt-get install git -y
             git config --global user.email "[email protected]"
             git config --global user.name "Theodore (machine user) @ CircleCI"
   create-docker-test-container:
@@ -64,11 +64,6 @@ commands:
             mkdir -p ~/project/test-results
             docker pull ${DOCKER_TAG}
             docker run -v /etc/passwd:/etc/passwd --user=$(id -u):c-pac -dit -P -e COVERAGE_FILE=<< parameters.coverage-file >> -v /home/circleci/project/test-results:/code/test-results -v /home/circleci:/home/circleci -v /home/circleci/project/CPAC/resources/configs/test_configs:/test_configs -v $PWD:/code -v $PWD/dev/circleci_data:$PWD/dev/circleci_data --workdir=/home/circleci/project --entrypoint=/bin/bash --name docker_test ${DOCKER_TAG}
-  get-sample-bids-data:
-    steps:
-      - run:
-          name: Getting Sample BIDS Data
-          command: git clone https://github.com/bids-standard/bids-examples.git
   get-singularity:
     parameters:
       version:
@@ -124,7 +119,7 @@ commands:
           coverage-file: .coverage.docker${VARIANT}
       - run:
           name: Running pytest in Docker image
-          command: docker exec --user $(id -u) docker_test /bin/bash /code/dev/circleci_data/test_in_image.sh
+          command: docker exec -e OSF_DATA --user $(id -u) docker_test /bin/bash /code/dev/circleci_data/test_in_image.sh
   set-python-version:
     steps:
       - restore_cache:
@@ -177,7 +172,7 @@ commands:
 jobs:
   combine-coverage:
     machine:
-      image: ubuntu-2004:2023.04.2
+      image: ubuntu-2404:2024.11.1
     steps:
       - checkout
       - restore_cache:
@@ -194,8 +189,6 @@ jobs:
       #     key: coverage-singularity-lite-{{ .Revision }}
       - set-python-version
       - combine-coverage
-      - store_artifacts:
-          path: htmlcov
   push-branch-to-docker-hub:
     parameters:
       variant:
@@ -231,7 +224,6 @@ jobs:
       - set-up-variant:
           variant: "<< parameters.variant >>"
       - set-python-version
-      - get-sample-bids-data
       - run-pytest-docker
       - store_test_results:
           path: test-results

.codecov.yml

@@ -0,0 +1,21 @@
+codecov:
+  branch: main
+
+comment:
+  layout: "diff, files"
+  behavior: default
+  require_changes: false
+  require_base: false
+  require_head: true
+  hide_project_coverage: false
+
+coverage:
+  precision: 1
+  range: "50..90"
+  round: nearest
+  status:
+    project:
+      default:   # default is the status check's name, not default settings
+        only_pulls: false
+        target: auto
+        threshold: "5"

.dockerignore

@@ -4,5 +4,6 @@ cpac_runs
 .env*
 .git
 .github
+!.github/CODEOWNERS
 !.github/scripts
 *.tar.gz

.github/CODEOWNERS

@@ -0,0 +1,30 @@
+# Copyright (C) 2025  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/>.
+
+# Global maintenance
+*                 @FCP-INDI/Maintenance
+
+# DevOps
+/pyproject.toml   @FCP-INDI/DevOps
+/requirements.txt @FCP-INDI/DevOps
+/setup.py         @FCP-INDI/DevOps
+/dev              @FCP-INDI/DevOps
+/scripts          @FCP-INDI/DevOps
+/.*               @FCP-INDI/DevOps
+/.circleci        @FCP-INDI/DevOps
+/.github          @FCP-INDI/DevOps
+**/*Dockerfile    @FCP-INDI/DevOps