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[MAINT] add workflow to test latest #79

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27 changes: 27 additions & 0 deletions .circleci/config.yml
Original file line number Diff line number Diff line change
Expand Up @@ -74,10 +74,37 @@ jobs:
wget https://raw.githubusercontent.com/bids-apps/maintenance-tools/main/circleci/push_docker.sh
bash push_docker.sh

test_latest:
machine:
image: ubuntu-2204:2022.10.2
steps:
- run:
name: Get test data
command: |
wget https://raw.githubusercontent.com/bids-apps/maintenance-tools/main/utils/get_data_from_osf.sh
bash get_data_from_osf.sh hcp_example_bids_v3
- run:
name: Pull image
command: docker pull bids/${CIRCLE_PROJECT_REPONAME,,}
- run:
name: participant level tests for single session dataset
command: |
docker run -ti --rm --read-only \
-v ~/data/hcp_example_bids_v3:/bids_dataset \
bids/${CIRCLE_PROJECT_REPONAME,,} \
/bids_dataset \
/outputs \
participant --participant_label 100307 \
--stages PreFreeSurfer \
--processing_mode legacy \
--license_key="*CxjskRdd7" \
--n_cpus 2

workflows:
build-test-deploy:
jobs:
- build
- test_latest
- test:
requires:
- build
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67 changes: 67 additions & 0 deletions .github/workflows/test_latest.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,67 @@
---
name: test latest image

on:
push:
branches: ['*']
schedule:
- cron: 0 0 1 * *
workflow_dispatch:

concurrency:
group: ${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: true

jobs:

test_dataset_without_session:

runs-on: ubuntu-latest

steps:
- name: Install dependencies
run: |
sudo apt-get update
sudo apt-get install -y tree

- name: pull docker image
run: docker pull bids/hcppipelines

- name: print version
run: |
docker run -t --rm --read-only \
--tmpfs /tmp \
--tmpfs /var/tmp \
bids/hcppipelines --help
docker run -t --rm --read-only \
--tmpfs /tmp \
--tmpfs /var/tmp \
bids/hcppipelines --version

- 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 hcp_example_bids_v3

- name: prepare output dir
run: |
mkdir -p ${HOME}/outputs

- name: participant 01
run: |
docker run -t --rm --read-only \
-v ${HOME}/data/hcp_example_bids_v3:/bids_dataset \
-v ${HOME}/outputs:/outputs \
--tmpfs /tmp \
--tmpfs /var/tmp \
bids/hcppipelines \
/bids_dataset \
/outputs \
participant \
--participant_label 100307 \
--stages PreFreeSurfer \
--license_key="*CxjskRdd7" \
--n_cpus 2

- name: check output
run: tree ${HOME}/outputs
25 changes: 0 additions & 25 deletions .travis.yml

This file was deleted.

8 changes: 4 additions & 4 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -101,10 +101,10 @@ This App has the following command line arguments:
To run it in participant level mode (for one participant):

docker run -i --rm \
-v /Users/filo/data/ds005:/bids_dataset:ro \
-v /Users/filo/outputs:/outputs \
bids/hcppipelines \
/bids_dataset /outputs participant --participant_label 01 --license_key "XXXXXX"
-v /Users/filo/data/ds005:/bids_dataset:ro \
-v /Users/filo/outputs:/outputs \
bids/hcppipelines \
/bids_dataset /outputs participant --participant_label 01 --license_key "XXXXXX"

### Commercial use

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