Merge pull request #67 from Shotgunosine/fs_7

WIP: Add Freesurfer 7
bids-apps · Aug 30, 2023 · 4663559 · 4663559
2 parents 6b76873 + 765a747
commit 4663559
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -5,29 +5,39 @@ jobs:
   build:
     machine:
       image: ubuntu-2204:2022.10.2
+    parameters:
+      version:
+        type: string
     steps:
     - checkout
     - restore_cache:
         keys:
-        - v_0-image_cache-{{ checksum "Dockerfile" }}
+        - v_0-image_cache_fs<< parameters.version >>-{{ checksum "Dockerfile_fs<< parameters.version >>" }}
     - run:
         name: load and build
         command: |
-          wget https://raw.githubusercontent.com/bids-apps/maintenance-tools/main/circleci/build_docker.sh
-          bash build_docker.sh
+          tar_name=image_fs<< parameters.version >>.tar
+          if [[ -e ~/docker/${tar_name} ]]; then
+            docker load -i ~/docker/${tar_name}
+          fi
+          git describe --tags > version
+          docker build -t bids/${CIRCLE_PROJECT_REPONAME}_fs<< parameters.version >> -f Dockerfile_fs<< parameters.version >> .
+          mkdir -p ~/docker; docker save "bids/${CIRCLE_PROJECT_REPONAME}_fs<< parameters.version >>" > ~/docker/${tar_name}
+          mkdir -p ~/license_fs<< parameters.version >>
           mkdir -p ~/license
           echo "cHJpbnRmICJEeWxhbi5OaWVsc29uQGdtYWlsLmNvbVxuMzcwNjNcbiAqQ1lrZWhQYUNvRDlNXG4gRlM2N1BTWmRFV2lqb1xuIiA+IH4vbGljZW5zZS9saWNlbnNlLnR4dA==" | base64 -d | sh
-        no_output_timeout: 6h
+          cp ~/license/license.txt ~/license_fs<< parameters.version >>/license.txt
+          rm -r ~/license
     - save_cache:
-        key: v_0-image_cache-{{ checksum "Dockerfile" }}-{{ .Revision }}-{{ epoch }}
+        key: v_0-image_cache_fs<< parameters.version >>-{{ checksum "Dockerfile_fs<< parameters.version >>" }}-{{ .Revision }}-{{ epoch }}
         paths:
         - ~/docker
-        - ~/license
+        - ~/license_fs<< parameters.version >>
     - persist_to_workspace:
         root: /home/circleci
         paths:
-        - docker/image.tar
-        - license/license.txt
+        - docker/image_fs<< parameters.version >>.tar
+        - license_fs<< parameters.version >>/license.txt
 
   get_data:
     machine:
@@ -60,51 +70,65 @@ jobs:
   test:
     machine:
       image: ubuntu-2204:2022.10.2
+    parameters:
+      version:
+        type: string
     steps:
     - checkout
-
     - attach_workspace:
         at: /tmp/workspace
+
     - run:
         command: |
-          docker load -i /tmp/workspace/docker/image.tar
+          docker load -i /tmp/workspace/docker/image_fs<< parameters.version >>.tar
 
     - run:
         name: print version
         command: |
           docker run -ti --rm --read-only \
-            -v /tmp/workspace/license/license.txt:/license.txt \
+            -v /tmp/workspace/license_fs<< parameters.version >>/license.txt:/license.txt \
+            -v /tmp/workspace/ds114_test1:/bids_dataset \
             --tmpfs /tmp --tmpfs /var/tmp \
-            -v $PWD/ds114_test1:/bids_dataset \
-              bids/${CIRCLE_PROJECT_REPONAME} --version
+              bids/${CIRCLE_PROJECT_REPONAME}_fs<< parameters.version >> --version
+
+    - run:
+        name: print help
+        command: |
           docker run -ti --rm --read-only \
-            -v /tmp/workspace/license/license.txt:/license.txt \
-            --tmpfs /tmp --tmpfs /var/tmp \
+            -v /tmp/workspace/license_fs<< parameters.version >>/license.txt:/license.txt \
             -v /tmp/workspace/data/ds114_test1:/bids_dataset \
-              bids/${CIRCLE_PROJECT_REPONAME} -h
+            --tmpfs /tmp --tmpfs /var/tmp \
+              bids/${CIRCLE_PROJECT_REPONAME}_fs<< parameters.version >> -h
+
+    - run: mkdir -p ${HOME}/outputs1 ${HOME}/outputs2
+
     - run:
         name: test 1
         command: |
           docker run -ti --rm --read-only \
-            -v /tmp/workspace/license/license.txt:/license.txt \
-            --tmpfs /tmp --tmpfs /var/tmp \
+            -v /tmp/workspace/license_fs<< parameters.version >>/license.txt:/license.txt \
             -v /tmp/workspace/data/ds114_test1:/bids_dataset \
-            -v ${HOME}/outputs1:/outputs bids/${CIRCLE_PROJECT_REPONAME} \
-            /bids_dataset /outputs participant \
-              --participant_label 01 \
-              --license_file=/license.txt --stages autorecon1
+            -v ${HOME}/outputs1:/outputs \
+            --tmpfs /tmp --tmpfs /var/tmp \
+              bids/${CIRCLE_PROJECT_REPONAME}_fs<< parameters.version >> \
+                /bids_dataset \
+                /outputs \
+                participant \
+                --participant_label 01 \
+                --license_file=/license.txt \
+                --stages autorecon1
 
           cat ${HOME}/outputs1/sub-01/scripts/recon-all.done
-        no_output_timeout: 6h
+
     - run:
         name: test 2
         command: |
           docker run -ti --rm --read-only \
-            -v /tmp/workspace/license/license.txt:/license.txt \
-            --tmpfs /tmp --tmpfs /var/tmp \
+            -v /tmp/workspace/license_fs<< parameters.version >>/license.txt:/license.txt \
             -v /tmp/workspace/data/ds114_test2:/bids_dataset \
             -v ${HOME}/outputs2:/outputs \
-              bids/${CIRCLE_PROJECT_REPONAME} \
+            --tmpfs /tmp --tmpfs /var/tmp \
+              bids/${CIRCLE_PROJECT_REPONAME}_fs<< parameters.version >> \
                 /bids_dataset \
                 /outputs \
                 participant \
@@ -115,41 +139,41 @@ jobs:
                 --stages autorecon1
 
           cat ${HOME}/outputs2/sub-01_ses-test/scripts/recon-all.done
-        no_output_timeout: 6h
+
     - run:
         name: group2 test 1
         command: |
           docker run -ti --rm --read-only \
-            -v /tmp/workspace/license/license.txt:/license.txt \
-            --tmpfs /tmp --tmpfs /var/tmp \
+            -v /tmp/workspace/license_fs<< parameters.version >>/license.txt:/license.txt \
             -v /tmp/workspace/data/ds114_test1:/bids_dataset \
             -v /tmp/workspace/data/ds114_test1_freesurfer_precomp_v6.0.0:/outputs \
-              bids/${CIRCLE_PROJECT_REPONAME} \
+            --tmpfs /tmp --tmpfs /var/tmp \
+              bids/${CIRCLE_PROJECT_REPONAME}_fs<< parameters.version >> \
                 /bids_dataset \
                 /outputs \
                 group2 \
-                  --license_file=/license.txt
-            mkdir -p ${HOME}/outputs1/
-            sudo mv ${HOME}/data/ds114_test1_freesurfer_precomp_v6.0.0/00_group* ${HOME}/outputs1/
-            cat ${HOME}/outputs1/00_group2_stats_tables/lh.aparc.thickness.tsv
-            cat ${HOME}/outputs1/00_group2_stats_tables/euler.tsv
-        no_output_timeout: 6h
+                --license_file=/license.txt
+
+          sudo mv /tmp/workspace/data/ds114_test1_freesurfer_precomp_v6.0.0/00_group* ${HOME}/outputs1/
+          cat ${HOME}/outputs1/00_group2_stats_tables/lh.aparc.thickness.tsv
+          cat ${HOME}/outputs1/00_group2_stats_tables/euler.tsv
+
     - run:
         name: group2 test 2
         command: |
           docker run -ti --rm --read-only \
-            -v ~/license/license.txt:/license.txt --tmpfs /tmp --tmpfs /var/tmp \
+            -v /tmp/workspace/license_fs<< parameters.version >>/license.txt:/license.txt \
             -v /tmp/workspace/data/ds114_test2:/bids_dataset \
             -v /tmp/workspace/data/ds114_test2_freesurfer_precomp_v6.0.0:/outputs \
-              bids/${CIRCLE_PROJECT_REPONAME} \
+            --tmpfs /tmp --tmpfs /var/tmp \
+              bids/${CIRCLE_PROJECT_REPONAME}_fs<< parameters.version >> \
                 /bids_dataset /outputs group2 \
                 --license_file=/license.txt
 
-            mkdir -p ${HOME}/outputs2/
-            sudo mv ${HOME}/data/ds114_test2_freesurfer_precomp_v6.0.0/00_group* ${HOME}/outputs2/
-            cat ${HOME}/outputs2/00_group2_stats_tables/lh.aparc.thickness.tsv
-            cat ${HOME}/outputs2/00_group2_stats_tables/euler.tsv
-        no_output_timeout: 6h
+          sudo mv /tmp/workspace/data/ds114_test2_freesurfer_precomp_v6.0.0/00_group* ${HOME}/outputs2/
+          cat ${HOME}/outputs2/00_group2_stats_tables/lh.aparc.thickness.tsv
+          cat ${HOME}/outputs2/00_group2_stats_tables/euler.tsv
+
     - store_artifacts:
         path: ~/outputs1
     - store_artifacts:
@@ -158,44 +182,84 @@ jobs:
   deploy:
     machine:
       image: ubuntu-2204:2022.10.2
+    parameters:
+      version:
+        type: string
     steps:
     - checkout
     - attach_workspace:
         at: /tmp/workspace
     - run:
         command: |
-          docker load -i /tmp/workspace/docker/image.tar
+          docker load -i /tmp/workspace/docker/image_fs<< parameters.version >>.tar
     - run:
         command: |
-          wget https://raw.githubusercontent.com/bids-apps/maintenance-tools/main/circleci/push_docker.sh
-          bash push_docker.sh
-        no_output_timeout: 6h
+          if [[ -n "${DOCKER_TOKEN}" ]]; then
+
+              # make sure we have a lowercase repo
+              user_name="bids"
+              repo_name=$(echo "${CIRCLE_PROJECT_REPONAME}_fs<< parameters.version >>" | tr '[:upper:]' '[:lower:]')
+
+              if [[ -n "${DOCKER_TOKEN}" ]]; then
+                  echo "${DOCKER_TOKEN}" | docker login -u "${DOCKER_USER}" --password-stdin
+
+                  : "Pushing to DockerHub ${user_name}/${repo_name}:unstable"
+                  docker tag "${user_name}/${repo_name}" "${user_name}/${repo_name}:unstable"
+                  docker push "${user_name}/${repo_name}:unstable"
+
+                  if [[ -n "${CIRCLE_TAG}" ]]; then
+                      : "Pushing to DockerHub ${user_name}/${repo_name}:${CIRCLE_TAG}"
+                      docker push "${user_name}/${repo_name}:latest"
+                      docker tag "${user_name}/${repo_name}" "${user_name}/${repo_name}:${CIRCLE_TAG}"
+                      docker push "${user_name}/${repo_name}:${CIRCLE_TAG}"
+                  fi
+
+              fi
+
+          else
+              : "No DOCKER_TOKEN, skipping push to DockerHub"
+              exit 1
+          fi
 
 workflows:
   build_test_deploy:
     jobs:
+
     - get_data:
         filters:
           tags:
             only: /.*/
           branches:
             only: /.*/
+
     - build:
+        name: build_<< matrix.version >>
+        matrix:
+          parameters:
+            version: ['6', '7']
         filters:
           tags:
             only: /.*/
           branches:
             only: /.*/
+
     - test:
+        matrix:
+          parameters:
+            version: ['6', '7']
         requires:
-        - build
+        - build_<< matrix.version >>
         - get_data
         filters:
           tags:
             only: /.*/
           branches:
             only: /.*/
+
     - deploy:
+        matrix:
+          parameters:
+            version: ['6', '7']
         context:
         - dockerhub
         requires: