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[FIX] fix push to docker hub on circle CI #1282

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Merged
merged 5 commits into from
Jul 10, 2024
Merged

[FIX] fix push to docker hub on circle CI #1282

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f07a31b
fix push to docker hub
Remi-Gau Jul 10, 2024
64f99ef
update circle ci workflow
Remi-Gau Jul 10, 2024
f13d2ee
typo
Remi-Gau Jul 10, 2024
ff7f08f
try to fix artefacts
Remi-Gau Jul 10, 2024
620b981
fix paths
Remi-Gau Jul 10, 2024
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152 changes: 101 additions & 51 deletions .circleci/config.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,26 +6,32 @@ jobs:

machine:
image: ubuntu-2204:2022.10.2
parameters:
dh_orga:
type: string
default: cpplab
dh_repo:
type: string
default: bidspm
steps:
- checkout
- run: make fix_submodule
- run:
name: update submodules
command: make fix_submodule
- restore_cache:
keys:
- my_cache
- run:
name: Build Docker image
name: build Docker image
command: |
set -eux -o pipefail
# make sure we have a lowercase repo
user_name=cpplab
repo_name=$(echo "${CIRCLE_PROJECT_REPONAME}" | tr '[:upper:]' '[:lower:]')
if [[ -e "${HOME}/docker/image.tar" ]]; then
docker load -i "${HOME}/docker/image.tar"
fi
git describe --tags --always > version
docker build -t "${user_name}/${repo_name}" .
docker build -t << parameters.dh_orga >>/<< parameters.dh_repo >> .
mkdir -p "${HOME}/docker"
docker save "${user_name}/${repo_name}" > "${HOME}/docker/image.tar"
docker save << parameters.dh_orga >>/<< parameters.dh_repo >> > "${HOME}/docker/image.tar"
docker images
- persist_to_workspace:
root: /home/circleci
Expand All @@ -38,7 +44,7 @@ jobs:
steps:
- checkout
- run:
name: Install dependencies
name: install dependencies
command: |
sudo apt-get update
sudo apt-get install -y python3 git-annex
Expand All @@ -49,7 +55,7 @@ jobs:
keys:
- my_cache
- run:
name: Get ds000001
name: get ds000001
command: |
# Git set up: to keep datalad warnings away
git config --global --add user.name "Ford Escort"
Expand All @@ -75,26 +81,35 @@ jobs:
- data/ds000001
- data/ds000001-fmriprep

default_model:
fast:
# run actions that run quickly
machine:
image: ubuntu-2204:2022.10.2

parameters:
dh_orga:
type: string
default: cpplab
dh_repo:
type: string
default: bidspm
steps:
- attach_workspace:
at: /tmp/workspace
- run: docker load -i /tmp/workspace/docker/image.tar
- run:
name: load docker image
command: docker load -i /tmp/workspace/docker/image.tar

- run: mkdir -p ${HOME}/outputs/ds000001/derivatives
- run:
name: create output directory
command: mkdir -p /home/circleci/outputs/ds000001/derivatives

- run:
name: default model subject level
command: |
user_name=cpplab
repo_name=$(echo "${CIRCLE_PROJECT_REPONAME}" | tr '[:upper:]' '[:lower:]')
docker run -ti --rm \
-v /tmp/workspace/data/ds000001:/bids_dataset \
-v ${HOME}/outputs:/outputs \
${user_name}/${repo_name} \
-v /home/circleci/outputs:/outputs \
<< parameters.dh_orga >>/<< parameters.dh_repo >> \
/bids_dataset \
/outputs/ds000001 \
subject \
Expand All @@ -103,17 +118,15 @@ jobs:
--space MNI152NLin2009cAsym \
--verbosity 3

cat ${HOME}/outputs/ds000001/derivatives/models/*.json
cat /home/circleci/outputs/ds000001/derivatives/models/*.json

- run:
name: default model dataset level
command: |
user_name=cpplab
repo_name=$(echo "${CIRCLE_PROJECT_REPONAME}" | tr '[:upper:]' '[:lower:]')
docker run -ti --rm \
-v /tmp/workspace/data/ds000001:/bids_dataset \
-v ${HOME}/outputs:/outputs \
${user_name}/${repo_name} \
-v /home/circleci/outputs:/outputs \
<< parameters.dh_orga >>/<< parameters.dh_repo >> \
/bids_dataset \
/outputs/ds000001 \
dataset \
Expand All @@ -122,28 +135,58 @@ jobs:
--space MNI152NLin2009cAsym \
--verbosity 3

cat ${HOME}/outputs/ds000001/derivatives/models/*.json
cat /home/circleci/outputs/ds000001/derivatives/models/*.json

- store_artifacts:
path: /home/circleci/outputs

- run:
name: create roi
command: |
docker run -ti --rm \
-v /tmp/workspace/data/ds000001:/bids_dataset \
-v /home/circleci/outputs:/outputs \
<< parameters.dh_orga >>/<< parameters.dh_repo >> \
/outputs/ds000001 \
/outputs/ds000001 \
dataset \
--action create_roi \
--roi_atlas wang \
--roi_name V1v V1d \
--space IXI549Space \
--verbosity 3

- store_artifacts:
path: /home/circleci/outputs

stats:
machine:
image: ubuntu-2204:2022.10.2

parameters:
dh_orga:
type: string
default: cpplab
dh_repo:
type: string
default: bidspm
steps:
- attach_workspace:
at: /tmp/workspace
- run: docker load -i /tmp/workspace/docker/image.tar
- run:
name: load docker image
command: docker load -i /tmp/workspace/docker/image.tar

- run: mkdir -p ${HOME}/outputs/ds000001/derivatives
- run:
name: create output directory
command: mkdir -p /home/circleci/outputs/ds000001/derivatives

- run:
name: smooth
command: |
user_name=cpplab
repo_name=$(echo "${CIRCLE_PROJECT_REPONAME}" | tr '[:upper:]' '[:lower:]')
docker run -ti --rm \
-v /tmp/workspace/data/ds000001-fmriprep:/bids_dataset \
-v ${HOME}/outputs:/outputs \
${user_name}/${repo_name} \
-v /home/circleci/outputs:/outputs \
<< parameters.dh_orga >>/<< parameters.dh_repo >> \
/bids_dataset \
/outputs/ds000001 \
subject \
Expand All @@ -160,14 +203,12 @@ jobs:
- run:
name: stats subject level
command: |
user_name=cpplab
repo_name=$(echo "${CIRCLE_PROJECT_REPONAME}" | tr '[:upper:]' '[:lower:]')
docker run -ti --rm \
-v /tmp/workspace/data/ds000001:/bids_dataset \
-v ${HOME}/outputs:/outputs \
-v /home/circleci/outputs:/outputs \
-v ~/project/demos/openneuro/models:/models \
-v ~/project/demos/openneuro/options:/options \
${user_name}/${repo_name} \
<< parameters.dh_orga >>/<< parameters.dh_repo >> \
/bids_dataset \
/outputs/ds000001 \
subject \
Expand All @@ -185,14 +226,12 @@ jobs:
- run:
name: stats group level
command: |
user_name=cpplab
repo_name=$(echo "${CIRCLE_PROJECT_REPONAME}" | tr '[:upper:]' '[:lower:]')
docker run -ti --rm \
-v /tmp/workspace/data/ds000001:/bids_dataset \
-v ${HOME}/outputs:/outputs \
-v /home/circleci/outputs:/outputs \
-v ~/project/demos/openneuro/models:/models \
-v ~/project/demos/openneuro/options:/options \
${user_name}/${repo_name} \
<< parameters.dh_orga >>/<< parameters.dh_repo >> \
/bids_dataset \
/outputs/ds000001 \
dataset \
Expand All @@ -206,38 +245,48 @@ jobs:
--verbosity 3 \
--options /options/ds000001.json

- store_artifacts:
path: /home/circleci/outputs/ds000001/derivatives/bidspm-stats

deploy:

machine:
image: ubuntu-2204:2022.10.2

parameters:
dh_orga:
type: string
default: cpplab
dh_repo:
type: string
default: bidspm
steps:
- attach_workspace:
at: /tmp/workspace

- run: docker load -i /tmp/workspace/docker/image.tar
- run:
name: load docker image
command: docker load -i /tmp/workspace/docker/image.tar
- run:
name: push to dockerhub
command: |
set -ex -o pipefail

if [[ -n "${DOCKER_TOKEN}" ]]; then

# make sure we have a lowercase repo
user_name=remigau
repo_name=$(echo "${CIRCLE_PROJECT_REPONAME}" | tr '[:upper:]' '[:lower:]')

echo "${DOCKER_TOKEN}" | docker login -u "${DOCKER_USER}" --password-stdin
echo "${DOCKER_TOKEN}" | docker login -u "${user_name}" --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"
: Pushing to DockerHub << parameters.dh_orga >>/<< parameters.dh_repo >>:unstable
docker tag << parameters.dh_orga >>/<< parameters.dh_repo >> << parameters.dh_orga >>/<< parameters.dh_repo >>:unstable
docker push << parameters.dh_orga >>/<< parameters.dh_repo >>: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}:${CIRCLE_TAG}"
: Pushing to DockerHub << parameters.dh_orga >>/<< parameters.dh_repo >>:"${CIRCLE_TAG}"
docker tag << parameters.dh_orga >>/<< parameters.dh_repo >> << parameters.dh_orga >>/<< parameters.dh_repo >>:latest
docker push << parameters.dh_orga >>/<< parameters.dh_repo >>:latest
docker tag << parameters.dh_orga >>/<< parameters.dh_repo >> << parameters.dh_orga >>/<< parameters.dh_repo >>:"${CIRCLE_TAG}"
docker push << parameters.dh_orga >>/<< parameters.dh_repo >>:"${CIRCLE_TAG}"
fi

else
Expand All @@ -250,7 +299,7 @@ workflows:
jobs:
- build
- get_data
- default_model:
- fast:
requires:
- build
- get_data
Expand All @@ -263,5 +312,6 @@ workflows:
- DOCKER_HUB
requires:
- build
- fast

# VS Code Extension Version: 1.5.1
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