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Remi-GauRemi-Gau
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[FIX] fix push to docker hub on circle CI (#1282)
* fix push to docker hub * update circle ci workflow * typo * try to fix artefacts * fix paths
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‎.circleci/config.yml‎

Lines changed: 101 additions & 51 deletions
Original file line numberDiff line numberDiff line change
@@ -6,26 +6,32 @@ jobs:
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machine:
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image: ubuntu-2204:2022.10.2
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parameters:
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dh_orga:
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type: string
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default: cpplab
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dh_repo:
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type: string
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default: bidspm
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steps:
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- checkout
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- run: make fix_submodule
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- run:
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name: update submodules
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command: make fix_submodule
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- restore_cache:
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keys:
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- my_cache
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- run:
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name: Build Docker image
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name: build Docker image
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command: |
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set -eux -o pipefail
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# make sure we have a lowercase repo
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user_name=cpplab
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repo_name=$(echo "${CIRCLE_PROJECT_REPONAME}" | tr '[:upper:]' '[:lower:]')
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if [[ -e "${HOME}/docker/image.tar" ]]; then
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docker load -i "${HOME}/docker/image.tar"
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fi
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git describe --tags --always > version
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docker build -t "${user_name}/${repo_name}" .
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docker build -t << parameters.dh_orga >>/<< parameters.dh_repo >> .
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mkdir -p "${HOME}/docker"
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docker save "${user_name}/${repo_name}" > "${HOME}/docker/image.tar"
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docker save << parameters.dh_orga >>/<< parameters.dh_repo >> > "${HOME}/docker/image.tar"
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docker images
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- persist_to_workspace:
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root: /home/circleci
@@ -38,7 +44,7 @@ jobs:
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steps:
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- checkout
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- run:
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name: Install dependencies
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name: install dependencies
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command: |
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sudo apt-get update
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sudo apt-get install -y python3 git-annex
@@ -49,7 +55,7 @@ jobs:
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keys:
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- my_cache
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- run:
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name: Get ds000001
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name: get ds000001
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command: |
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# Git set up: to keep datalad warnings away
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git config --global --add user.name "Ford Escort"
@@ -75,26 +81,35 @@ jobs:
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- data/ds000001
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- data/ds000001-fmriprep
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default_model:
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fast:
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# run actions that run quickly
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machine:
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image: ubuntu-2204:2022.10.2
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parameters:
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dh_orga:
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type: string
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default: cpplab
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dh_repo:
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type: string
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default: bidspm
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steps:
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- attach_workspace:
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at: /tmp/workspace
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- run: docker load -i /tmp/workspace/docker/image.tar
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- run:
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name: load docker image
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command: docker load -i /tmp/workspace/docker/image.tar
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87-
- run: mkdir -p ${HOME}/outputs/ds000001/derivatives
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- run:
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name: create output directory
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command: mkdir -p /home/circleci/outputs/ds000001/derivatives
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- run:
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name: default model subject level
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command: |
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user_name=cpplab
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repo_name=$(echo "${CIRCLE_PROJECT_REPONAME}" | tr '[:upper:]' '[:lower:]')
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docker run -ti --rm \
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-v /tmp/workspace/data/ds000001:/bids_dataset \
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-v ${HOME}/outputs:/outputs \
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${user_name}/${repo_name} \
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-v /home/circleci/outputs:/outputs \
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<< parameters.dh_orga >>/<< parameters.dh_repo >> \
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/bids_dataset \
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/outputs/ds000001 \
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subject \
@@ -103,17 +118,15 @@ jobs:
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--space MNI152NLin2009cAsym \
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--verbosity 3
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cat ${HOME}/outputs/ds000001/derivatives/models/*.json
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cat /home/circleci/outputs/ds000001/derivatives/models/*.json
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- run:
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name: default model dataset level
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command: |
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user_name=cpplab
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repo_name=$(echo "${CIRCLE_PROJECT_REPONAME}" | tr '[:upper:]' '[:lower:]')
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docker run -ti --rm \
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-v /tmp/workspace/data/ds000001:/bids_dataset \
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-v ${HOME}/outputs:/outputs \
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${user_name}/${repo_name} \
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-v /home/circleci/outputs:/outputs \
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<< parameters.dh_orga >>/<< parameters.dh_repo >> \
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/bids_dataset \
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/outputs/ds000001 \
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dataset \
@@ -122,28 +135,58 @@ jobs:
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--space MNI152NLin2009cAsym \
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--verbosity 3
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cat ${HOME}/outputs/ds000001/derivatives/models/*.json
138+
cat /home/circleci/outputs/ds000001/derivatives/models/*.json
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140+
- store_artifacts:
141+
path: /home/circleci/outputs
142+
143+
- run:
144+
name: create roi
145+
command: |
146+
docker run -ti --rm \
147+
-v /tmp/workspace/data/ds000001:/bids_dataset \
148+
-v /home/circleci/outputs:/outputs \
149+
<< parameters.dh_orga >>/<< parameters.dh_repo >> \
150+
/outputs/ds000001 \
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/outputs/ds000001 \
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dataset \
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--action create_roi \
154+
--roi_atlas wang \
155+
--roi_name V1v V1d \
156+
--space IXI549Space \
157+
--verbosity 3
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159+
- store_artifacts:
160+
path: /home/circleci/outputs
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127162
stats:
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machine:
129164
image: ubuntu-2204:2022.10.2
130-
165+
parameters:
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dh_orga:
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type: string
168+
default: cpplab
169+
dh_repo:
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type: string
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default: bidspm
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steps:
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- attach_workspace:
133174
at: /tmp/workspace
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- run: docker load -i /tmp/workspace/docker/image.tar
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- run:
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name: load docker image
177+
command: docker load -i /tmp/workspace/docker/image.tar
135178

136-
- run: mkdir -p ${HOME}/outputs/ds000001/derivatives
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- run:
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name: create output directory
181+
command: mkdir -p /home/circleci/outputs/ds000001/derivatives
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138183
- run:
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name: smooth
140185
command: |
141-
user_name=cpplab
142-
repo_name=$(echo "${CIRCLE_PROJECT_REPONAME}" | tr '[:upper:]' '[:lower:]')
143186
docker run -ti --rm \
144187
-v /tmp/workspace/data/ds000001-fmriprep:/bids_dataset \
145-
-v ${HOME}/outputs:/outputs \
146-
${user_name}/${repo_name} \
188+
-v /home/circleci/outputs:/outputs \
189+
<< parameters.dh_orga >>/<< parameters.dh_repo >> \
147190
/bids_dataset \
148191
/outputs/ds000001 \
149192
subject \
@@ -160,14 +203,12 @@ jobs:
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- run:
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name: stats subject level
162205
command: |
163-
user_name=cpplab
164-
repo_name=$(echo "${CIRCLE_PROJECT_REPONAME}" | tr '[:upper:]' '[:lower:]')
165206
docker run -ti --rm \
166207
-v /tmp/workspace/data/ds000001:/bids_dataset \
167-
-v ${HOME}/outputs:/outputs \
208+
-v /home/circleci/outputs:/outputs \
168209
-v ~/project/demos/openneuro/models:/models \
169210
-v ~/project/demos/openneuro/options:/options \
170-
${user_name}/${repo_name} \
211+
<< parameters.dh_orga >>/<< parameters.dh_repo >> \
171212
/bids_dataset \
172213
/outputs/ds000001 \
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subject \
@@ -185,14 +226,12 @@ jobs:
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- run:
186227
name: stats group level
187228
command: |
188-
user_name=cpplab
189-
repo_name=$(echo "${CIRCLE_PROJECT_REPONAME}" | tr '[:upper:]' '[:lower:]')
190229
docker run -ti --rm \
191230
-v /tmp/workspace/data/ds000001:/bids_dataset \
192-
-v ${HOME}/outputs:/outputs \
231+
-v /home/circleci/outputs:/outputs \
193232
-v ~/project/demos/openneuro/models:/models \
194233
-v ~/project/demos/openneuro/options:/options \
195-
${user_name}/${repo_name} \
234+
<< parameters.dh_orga >>/<< parameters.dh_repo >> \
196235
/bids_dataset \
197236
/outputs/ds000001 \
198237
dataset \
@@ -206,38 +245,48 @@ jobs:
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--verbosity 3 \
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--options /options/ds000001.json
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248+
- store_artifacts:
249+
path: /home/circleci/outputs/ds000001/derivatives/bidspm-stats
250+
209251
deploy:
210252

211253
machine:
212254
image: ubuntu-2204:2022.10.2
213-
255+
parameters:
256+
dh_orga:
257+
type: string
258+
default: cpplab
259+
dh_repo:
260+
type: string
261+
default: bidspm
214262
steps:
215263
- attach_workspace:
216264
at: /tmp/workspace
217265

218-
- run: docker load -i /tmp/workspace/docker/image.tar
266+
- run:
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name: load docker image
268+
command: docker load -i /tmp/workspace/docker/image.tar
219269
- run:
220270
name: push to dockerhub
221271
command: |
222272
set -ex -o pipefail
223273
224274
if [[ -n "${DOCKER_TOKEN}" ]]; then
225275
226-
# make sure we have a lowercase repo
227276
user_name=remigau
228-
repo_name=$(echo "${CIRCLE_PROJECT_REPONAME}" | tr '[:upper:]' '[:lower:]')
229277
230-
echo "${DOCKER_TOKEN}" | docker login -u "${DOCKER_USER}" --password-stdin
278+
echo "${DOCKER_TOKEN}" | docker login -u "${user_name}" --password-stdin
231279
232-
: "Pushing to DockerHub ${user_name}/${repo_name}:unstable"
233-
docker tag "${user_name}/${repo_name}" "${user_name}/${repo_name}:unstable"
234-
docker push "${user_name}/${repo_name}:unstable"
280+
: Pushing to DockerHub << parameters.dh_orga >>/<< parameters.dh_repo >>:unstable
281+
docker tag << parameters.dh_orga >>/<< parameters.dh_repo >> << parameters.dh_orga >>/<< parameters.dh_repo >>:unstable
282+
docker push << parameters.dh_orga >>/<< parameters.dh_repo >>:unstable
235283
236284
if [[ -n "${CIRCLE_TAG}" ]]; then
237-
: "Pushing to DockerHub ${user_name}/${repo_name}:${CIRCLE_TAG}"
238-
docker push "${user_name}/${repo_name}:latest"
239-
docker tag "${user_name}/${repo_name}" "${user_name}/${repo_name}:${CIRCLE_TAG}"
240-
docker push "${user_name}/${repo_name}:${CIRCLE_TAG}"
285+
: Pushing to DockerHub << parameters.dh_orga >>/<< parameters.dh_repo >>:"${CIRCLE_TAG}"
286+
docker tag << parameters.dh_orga >>/<< parameters.dh_repo >> << parameters.dh_orga >>/<< parameters.dh_repo >>:latest
287+
docker push << parameters.dh_orga >>/<< parameters.dh_repo >>:latest
288+
docker tag << parameters.dh_orga >>/<< parameters.dh_repo >> << parameters.dh_orga >>/<< parameters.dh_repo >>:"${CIRCLE_TAG}"
289+
docker push << parameters.dh_orga >>/<< parameters.dh_repo >>:"${CIRCLE_TAG}"
241290
fi
242291
243292
else
@@ -250,7 +299,7 @@ workflows:
250299
jobs:
251300
- build
252301
- get_data
253-
- default_model:
302+
- fast:
254303
requires:
255304
- build
256305
- get_data
@@ -263,5 +312,6 @@ workflows:
263312
- DOCKER_HUB
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requires:
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- build
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- fast
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