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Update deployment and add version notice #77

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merged 11 commits into from
Sep 7, 2023
Merged

Update deployment and add version notice #77

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8478878
Update deployment and add version notice
Shotgunosine Aug 31, 2023
6aab7cf
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Aug 31, 2023
e286c00
fix circle
Shotgunosine Aug 31, 2023
484ef9d
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Aug 31, 2023
889a93e
update docker tagging
Shotgunosine Sep 7, 2023
17a6375
add downlaod instructions to readme
Shotgunosine Sep 7, 2023
c714133
cleanup deploy variable names
Shotgunosine Sep 7, 2023
3ebcb2b
use a large machine for building
Shotgunosine Sep 7, 2023
b9aaf11
use x-large for building
Shotgunosine Sep 7, 2023
2b19f36
use x-large for building
Shotgunosine Sep 7, 2023
e730668
Save time by dropping cache on build action
Shotgunosine Sep 7, 2023
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30 changes: 21 additions & 9 deletions .circleci/config.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -198,20 +198,31 @@ jobs:

# make sure we have a lowercase repo
user_name="bids"
repo_name=$(echo "${CIRCLE_PROJECT_REPONAME}_fs<< parameters.version >>" | tr '[:upper:]' '[:lower:]')
repo_name=$(echo "${CIRCLE_PROJECT_REPONAME}" | tr '[:upper:]' '[:lower:]')
FSMAJORVERSION=<< parameters.version >>
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if [[ FSMAJORVERSION -eq 6 ]]; then
FSVERSION=6.0.1
else
FSVERSION=7.4.1
fi

if [[ -n "${DOCKER_TOKEN}" ]]; then
echo "${DOCKER_TOKEN}" | docker login -u "${DOCKER_USER}" --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"
docker tag "${user_name}/${repo_name}" "${user_name}/${repo_name}:${FSVERSION}-unstable"
docker push "${user_name}/${repo_name}:${FSVERSION}-unstable"

if [[ -n "${CIRCLE_TAG}" ]]; then
: "Pushing to DockerHub ${user_name}/${repo_name}:${FSVERSION}-${CIRCLE_TAG}"
if [[ FSMAJORVERSION -eq 6 ]]; then
docker push "${user_name}/${repo_name}:latest"
fi

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}:${CIRCLE_TAG}"
docker tag "${user_name}/${repo_name}" "${user_name}/${repo_name}:${FSMAJORVERSION}"
docker push ${user_name}/${repo_name}:${FSMAJORVERSION}
docker tag "${user_name}/${repo_name}" "${user_name}/${repo_name}:${FSVERSION}-${CIRCLE_TAG}"
docker push "${user_name}/${repo_name}:${FSVERSION}-${CIRCLE_TAG}"
fi

fi
Expand Down Expand Up @@ -244,6 +255,7 @@ workflows:
only: /.*/

- test:
name: test_<< matrix.version >>
matrix:
parameters:
version: ['6', '7']
Expand All @@ -263,7 +275,7 @@ workflows:
context:
- dockerhub
requires:
- test
- test_<< matrix.version >>
filters:
branches:
ignore: /.*/
Expand Down
17 changes: 13 additions & 4 deletions run.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,7 @@
def run(command, env={}, ignore_errors=False):
merged_env = os.environ
merged_env.update(env)

# DEBUG env triggers freesurfer to produce gigabytes of files
merged_env.pop('DEBUG', None)
process = Popen(command, stdout=PIPE, stderr=subprocess.STDOUT, shell=True, env=merged_env)
Expand All @@ -27,7 +28,17 @@ def run(command, env={}, ignore_errors=False):
if process.returncode != 0 and not ignore_errors:
raise Exception("Non zero return code: %d" % process.returncode)


# warn about freesurfer version
with open(os.path.join(os.environ['FREESURFER_HOME'], 'build-stamp.txt'), 'r') as h:
bs = h.read()
if 'x86_64-7.' in bs:
fsversion=7
else:
fsversion=6
warn("You are using FreeSurver version 6. "
"The FreeSurfer 7 BIDS-App is now available via docker pull bids/freesurfer:v7 . "
"FreeSurfer 7 will become the default version in the FreeSurfer BIDS-App begining in 2024. "
"From that point on, the FreeSurfer 6 BIDS-App will remain available at bids/freesurfer:v6 .")
__version__ = open(os.path.join(os.path.dirname(os.path.realpath(__file__)), 'version')).read()

parser = argparse.ArgumentParser(description='FreeSurfer recon-all + custom template generation.')
Expand Down Expand Up @@ -519,9 +530,7 @@ def run(command, env={}, ignore_errors=False):

# The call to python2 is only required if we're running Freesurfer 6, we'll need to check version
# and modify the calls accordingly.
with open(os.path.join(os.environ['FREESURFER_HOME'], 'build-stamp.txt'), 'r') as h:
bs = h.read()
if '-7.' in bs:
if fsversion == 7:
cmd_start = ''
else:
cmd_start = 'python2 '
Expand Down