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MNT: Refactor Docker build process #2982

Merged
merged 19 commits into from
Apr 12, 2023
Merged

MNT: Refactor Docker build process #2982

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04de7ee
DOCKER: Switch to conda for FSL
effigies Jan 10, 2023
75eed57
CI: Update build cache
effigies Apr 4, 2023
6ad2ed1
DOCKER: Find PPA for missing libxp
effigies Apr 4, 2023
84e9f80
MNT: Refactor Dockerfile to use micromamba and per-tool stages
effigies Apr 5, 2023
e367c0f
CI: Update build cache, tag stages
effigies Apr 5, 2023
4dd9876
MNT: Downgrade networkx until new nipype is released
effigies Apr 5, 2023
83cd6cf
ENV: Pin libitk 5.2
effigies Apr 5, 2023
731021e
CI: Stash downloader as well
effigies Apr 5, 2023
c6218cb
ENV: Drop graphviz to 6 to avoid conflict with libitk
effigies Apr 5, 2023
c8385be
DOCKER: Create mamba environment in stage, copy
effigies Apr 5, 2023
4f8af2f
CI: Use buildkit, cache from intermediate stages
effigies Apr 5, 2023
be4d701
CI/DOCKER: Try to target just main build
effigies Apr 5, 2023
cce051b
PIN: niworkflows 1.7.9
effigies Apr 11, 2023
b27c122
CI: Bump ds210 cache [skip ds005][skip ds054]
effigies Apr 12, 2023
12f7f57
CI: Remove codecov dependency
effigies Apr 12, 2023
d2292c5
DOCKER: Set base image as build arg
effigies Apr 12, 2023
db1e1a4
DOCKER: Set BASE_IMAGE arg before any build stages
effigies Apr 12, 2023
93a19a1
MNT: pip-compile --extra telemetry --upgrade
effigies Apr 12, 2023
d9743e7
DOCKER: Upgrade base image as we start over
effigies Apr 12, 2023
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71 changes: 53 additions & 18 deletions .circleci/config.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -119,6 +119,8 @@ orbs:
jobs:
build_clean:
<<: *machine_defaults
environment:
DOCKER_BUILDKIT: 1
steps:
- checkout:
path: *src
Expand All @@ -144,17 +146,19 @@ jobs:

build:
<<: *machine_defaults
environment:
DOCKER_BUILDKIT: 1
steps:
- checkout:
path: *src
- run: *check_skip_job
- restore_cache:
keys:
- build-v0-{{ .Branch }}-{{ .Revision }}
- build-v0--{{ .Revision }}
- build-v0-{{ .Branch }}-
- build-v0-master-
- build-v0-
- build-v2-{{ .Branch }}-{{ .Revision }}
- build-v2--{{ .Revision }}
- build-v2-{{ .Branch }}-
- build-v2-master-
- build-v2-
paths:
- /tmp/docker
- /tmp/images
Expand All @@ -172,6 +176,14 @@ jobs:
name: Pull Ubuntu/jammy image
command: |
set +e
# Source layers if available
docker pull localhost:5000/downloader
docker pull localhost:5000/freesurfer
docker pull localhost:5000/afni
docker pull localhost:5000/ants
docker pull localhost:5000/workbench
docker pull localhost:5000/micromamba

docker pull localhost:5000/ubuntu
success=$?
set -e
Expand Down Expand Up @@ -219,7 +231,14 @@ jobs:
e=1 && for i in {1..5}; do
docker build --rm \
--cache-from=nipreps/fmriprep \
--cache-from=localhost:5000/downloader \
--cache-from=localhost:5000/freesurfer \
--cache-from=localhost:5000/afni \
--cache-from=localhost:5000/ants \
--cache-from=localhost:5000/workbench \
--cache-from=localhost:5000/micromamba \
-t nipreps/fmriprep:latest \
--target fmriprep \
--build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` \
--build-arg VCS_REF=`git rev-parse --short HEAD` \
--build-arg VERSION="${CIRCLE_TAG:-$THISVERSION}" . \
Expand All @@ -240,12 +259,28 @@ jobs:
echo "BUILT: \"$BUILT_VERSION\""
set -e
test "$BUILT_VERSION" = "$THISVERSION"
- run:
name: Build and tag stages
no_output_timeout: 40m
command: |
docker build -t localhost:5000/downloader --target downloader .
docker build -t localhost:5000/freesurfer --target freesurfer .
docker build -t localhost:5000/afni --target afni .
docker build -t localhost:5000/ants --target ants .
docker build -t localhost:5000/workbench --target workbench .
docker build -t localhost:5000/micromamba --target micromamba .
- run:
name: Docker push to local registry
no_output_timeout: 40m
command: |
docker tag nipreps/fmriprep:latest localhost:5000/fmriprep
docker push localhost:5000/fmriprep
docker push localhost:5000/downloader
docker push localhost:5000/freesurfer
docker push localhost:5000/afni
docker push localhost:5000/ants
docker push localhost:5000/workbench
docker push localhost:5000/micromamba
- run:
name: Docker registry garbage collection
command: |
Expand All @@ -257,7 +292,7 @@ jobs:
paths:
- src/fmriprep
- save_cache:
key: build-v0-{{ .Branch }}-{{ .Revision }}
key: build-v2-{{ .Branch }}-{{ .Revision }}
paths:
- /tmp/docker
- /tmp/images
Expand Down Expand Up @@ -390,7 +425,7 @@ jobs:
at: /tmp
- restore_cache:
keys:
- build-v0-{{ .Branch }}-{{ .Revision }}
- build-v2-{{ .Branch }}-{{ .Revision }}
paths:
- /tmp/docker
- /tmp/images
Expand Down Expand Up @@ -463,7 +498,7 @@ jobs:
at: /tmp
- restore_cache:
keys:
- build-v0-{{ .Branch }}-{{ .Revision }}
- build-v2-{{ .Branch }}-{{ .Revision }}
paths:
- /tmp/docker
- /tmp/images
Expand Down Expand Up @@ -651,7 +686,7 @@ jobs:
at: /tmp
- restore_cache:
keys:
- build-v0-{{ .Branch }}-{{ .Revision }}
- build-v2-{{ .Branch }}-{{ .Revision }}
paths:
- /tmp/docker
- /tmp/images
Expand Down Expand Up @@ -767,7 +802,7 @@ jobs:
at: /tmp
- restore_cache:
keys:
- build-v0-{{ .Branch }}-{{ .Revision }}
- build-v2-{{ .Branch }}-{{ .Revision }}
paths:
- /tmp/docker
- /tmp/images
Expand All @@ -776,11 +811,11 @@ jobs:
- data-v0-{{ .Branch }}-{{ .Revision }}
- restore_cache:
keys:
- ds210-anat-v0-{{ .Branch }}-{{ .Revision }}
- ds210-anat-v0--{{ .Revision }}
- ds210-anat-v0-{{ .Branch }}-
- ds210-anat-v0-master-
- ds210-anat-v0-
- ds210-anat-v1-{{ .Branch }}-{{ .Revision }}
- ds210-anat-v1--{{ .Revision }}
- ds210-anat-v1-{{ .Branch }}-
- ds210-anat-v1-master-
- ds210-anat-v1-
- docker/install-docker-credential-helper
- run: *docker_auth
- run: *setup_docker_registry
Expand Down Expand Up @@ -808,7 +843,7 @@ jobs:
rm -rf /tmp/${DATASET}/work/reportlets
rm -rf /tmp/${DATASET}/derivatives/fmriprep
- save_cache:
key: ds210-anat-v0-{{ .Branch }}-{{ .Revision }}
key: ds210-anat-v1-{{ .Branch }}-{{ .Revision }}
paths:
- /tmp/ds210/work

Expand Down Expand Up @@ -873,7 +908,7 @@ jobs:
fi
- restore_cache:
keys:
- build-v0-{{ .Branch }}-{{ .Revision }}
- build-v2-{{ .Branch }}-{{ .Revision }}
paths:
- /tmp/docker
- /tmp/images
Expand All @@ -896,7 +931,7 @@ jobs:
- run: *check_skip_job
- restore_cache:
keys:
- build-v0-{{ .Branch }}-{{ .Revision }}
- build-v2-{{ .Branch }}-{{ .Revision }}
paths:
- /tmp/docker
- /tmp/images
Expand Down
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