Merge pull request #23 from bids-apps/test_latest

[MAINT] add GH workflow to test latest stable version

.circleci/config.yml

@@ -47,16 +47,15 @@ jobs:
         name: print version
         command: |
           docker run -ti --rm --read-only \
-            -v /tmp/workspace/data/ds114_test1_with_freesurfer:/bids_dataset \
-            -v ${HOME}/outputs1:/outputs \
+            -v /tmp/workspace/data/ds114_test1_with_freesurfer:/home/jovyan/work/data \
               bids/${CIRCLE_PROJECT_REPONAME,,} --version
     - run:
         name: run participant 1
         command: |
           docker run -ti --rm --read-only \
-            -v /tmp/workspace/data/ds114_test1_with_freesurfer:/bids_dataset \
+            -v /tmp/workspace/data/ds114_test1_with_freesurfer:/home/jovyan/work/data \
             -v ${HOME}/outputs1:/outputs \
-              bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs participant --participant_label 01
+              bids/${CIRCLE_PROJECT_REPONAME,,} /home/jovyan/work/data /home/jovyan/work/data/derivatives participant --participant_label 01
         no_output_timeout: 6h
 
   deploy:

.github/workflows/test_latest.yml

@@ -0,0 +1,65 @@
+---
+name: test latest image
+
+on:
+  pull_request:
+    branches: ['*']
+  schedule:
+  - cron: 0 0 1 * *
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+defaults:
+  run:
+    shell: bash -l {0}
+
+jobs:
+
+  test_latest_image:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Install dependencies
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y tree
+
+    - name: Clone repo
+      uses: actions/checkout@v3
+
+    - name: pull docker image
+      run: docker pull bids/mindboggle:latest
+
+    - name: print version
+      run: |
+        docker run -t --rm \
+              bids/mindboggle:latest -v
+        docker run -t --rm \
+              bids/mindboggle:latest -h
+
+    - name: get data
+      run: |
+        wget https://raw.githubusercontent.com/bids-apps/maintenance-tools/main/utils/get_data_from_osf.sh
+        bash get_data_from_osf.sh ds114_test1
+
+    - name: prepare output dir
+      run: mkdir -p ${HOME}/outputs
+
+    - name: participant level test
+      run: |
+        docker run -t --rm \
+          -v ${HOME}/data/ds114_test1:/home/jovyan/work/bids_dataset \
+          -v ${HOME}/outputs1:/home/jovyan/work/outputs \
+            bids/mindboggle \
+              /home/jovyan/work/bids_dataset \
+              /home/jovyan/work/outputs \
+              participant \
+              --participant_label 01
+
+
+    - name: check output
+      run: tree ${HOME}/data/ds114_test1_with_freesurfer/derivatives

README.md

@@ -16,21 +16,28 @@ docker pull bids/mindboggle
 
 To run the docker, do:
 
-```
-docker run -ti -v $PWD/ds114_test1:/home/jovyan/work/data bids/mindboggle /home/jovyan/work/data /home/jovyan/work/data/derivatives/ participant
+```bash
+docker run -ti \
+    -v $PWD/ds114_test1:/home/jovyan/work/data \
+    bids/mindboggle \
+        /home/jovyan/work/data \
+        /home/jovyan/work/data/derivatives/ participant
 ```
 
 Its important to mount to a directory in `/home/jovyan/` because you are not root in this Docker image.
 
 To use bash:
 
-```
- docker run -ti -v /Users/keshavan/Downloads/mindboggle_input_example/bids:/home/jovyan/work/data --entrypoint /bin/bash bids/mindboggle
+```bash
+ docker run -ti \
+    -v /Users/keshavan/Downloads/mindboggle_input_example/bids:/home/jovyan/work/data \
+    --entrypoint /bin/bash \
+        bids/mindboggle
 ```
 
 For developers, you can make changes to the Dockerfile, and build the docker image, by running
 
-```
+```bash
 docker build -t bids/mindboggle .
 ```