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[DOC] general update #1256

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Merged
Remi-Gau merged 19 commits into from
Jul 3, 2024
Merged

[DOC] general update #1256

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fe25140
improve doc
Remi-Gau Jul 1, 2024
510df05
fix doc errors
Remi-Gau Jul 2, 2024
4312760
clean up doc
Remi-Gau Jul 2, 2024
3086f7c
Merge remote-tracking branch 'upstream/main' into doc
Remi-Gau Jul 2, 2024
3832142
split in sub pages
Remi-Gau Jul 2, 2024
a7542ab
update FAQ
Remi-Gau Jul 2, 2024
f906019
further clen up
Remi-Gau Jul 2, 2024
c935ac3
update readme
Remi-Gau Jul 2, 2024
435d77d
extract moae demos
Remi-Gau Jul 2, 2024
9bcc757
update demo
Remi-Gau Jul 2, 2024
0d2f30f
lint
Remi-Gau Jul 3, 2024
f84218e
reorganize demos
Remi-Gau Jul 3, 2024
2e79ee8
fix demo
Remi-Gau Jul 3, 2024
7ecae50
fix packagin
Remi-Gau Jul 3, 2024
bfd23e9
ignore dead links
Remi-Gau Jul 3, 2024
267862e
fix test
Remi-Gau Jul 3, 2024
4154fdb
rm adds
Remi-Gau Jul 3, 2024
d611b74
silence mypy
Remi-Gau Jul 3, 2024
fa34ea6
try fixing python
Remi-Gau Jul 3, 2024
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380 changes: 190 additions & 190 deletions .circleci/config.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,199 +2,199 @@
version: 2.1

jobs:
build:

machine:
image: ubuntu-2204:2022.10.2
steps:
- checkout
- run: make fix_submodule
- restore_cache:
keys:
- my_cache
- run:
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}" .
mkdir -p "${HOME}/docker"
docker save "${user_name}/${repo_name}" > "${HOME}/docker/image.tar"
docker images
- persist_to_workspace:
root: /home/circleci
paths:
- docker/image.tar

get_data:
machine:
image: ubuntu-2204:2022.10.2
steps:
- checkout
- run:
name: Install dependencies
command: |
sudo apt-get update
sudo apt-get install -y python3 git-annex
python3 -m pip install --upgrade pip setuptools
pip3 install datalad
datalad wtf
- restore_cache:
keys:
- my_cache
- run:
name: Get ds000001
command: |
# Git set up: to keep datalad warnings away
git config --global --add user.name "Ford Escort"
git config --global --add user.email 42@H2G2.com
mkdir -p ${HOME}/data/
datalad install -s ///openneuro/ds000001 ${HOME}/data/ds000001
datalad install -s ///openneuro-derivatives/ds000001-fmriprep ${HOME}/data/ds000001-fmriprep
cd ${HOME}/data/ds000001-fmriprep/
datalad get sub-0[1-2]/anat/*MNI*mask.nii.gz \
sub-0[1-2]/anat/*MNI*T1w.nii.gz \
sub-0[1-2]/func/*MNI*desc-preproc*bold.nii.gz \
sub-0[1-2]/func/*MNI*mask.nii.gz \
sub-*/func/*tsv \
sub-*/func/*json -J 12
datalad status
- save_cache:
key: my_cache
paths:
- ~/data
- persist_to_workspace:
root: /home/circleci
paths:
- data/ds000001
- data/ds000001-fmriprep

test:
machine:
image: ubuntu-2204:2022.10.2

steps:
- attach_workspace:
at: /tmp/workspace
- run: docker load -i /tmp/workspace/docker/image.tar

- run: mkdir -p ${HOME}/outputs/ds000001/derivatives

- run:
name: print version
command: |
user_name=cpplab
repo_name=$(echo "${CIRCLE_PROJECT_REPONAME}" | tr '[:upper:]' '[:lower:]')
docker run -ti --rm \
-v /tmp/workspace/data/ds000001:/bids_dataset \
${user_name}/${repo_name} --version

- 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} \
/bids_dataset \
/outputs/ds000001 \
subject \
--action smooth \
--task balloonanalogrisktask \
--participant_label 01 02 \
--space MNI152NLin2009cAsym \
--fwhm 8 \
--verbosity 2
no_output_timeout: 6h
build:

machine:
image: ubuntu-2204:2022.10.2
steps:
- checkout
- run: make fix_submodule
- restore_cache:
keys:
- my_cache
- run:
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}" .
mkdir -p "${HOME}/docker"
docker save "${user_name}/${repo_name}" > "${HOME}/docker/image.tar"
docker images
- persist_to_workspace:
root: /home/circleci
paths:
- docker/image.tar

get_data:
machine:
image: ubuntu-2204:2022.10.2
steps:
- checkout
- run:
name: Install dependencies
command: |
sudo apt-get update
sudo apt-get install -y python3 git-annex
python3 -m pip install --upgrade pip setuptools
pip3 install datalad
datalad wtf
- restore_cache:
keys:
- my_cache
- run:
name: Get ds000001
command: |
# Git set up: to keep datalad warnings away
git config --global --add user.name "Ford Escort"
git config --global --add user.email 42@H2G2.com
mkdir -p ${HOME}/data/
datalad install -s ///openneuro/ds000001 ${HOME}/data/ds000001
datalad install -s ///openneuro-derivatives/ds000001-fmriprep ${HOME}/data/ds000001-fmriprep
cd ${HOME}/data/ds000001-fmriprep/
datalad get sub-0[1-2]/anat/*MNI*mask.nii.gz \
sub-0[1-2]/anat/*MNI*T1w.nii.gz \
sub-0[1-2]/func/*MNI*desc-preproc*bold.nii.gz \
sub-0[1-2]/func/*MNI*mask.nii.gz \
sub-*/func/*tsv \
sub-*/func/*json -J 12
datalad status
- save_cache:
key: my_cache
paths:
- ~/data
- persist_to_workspace:
root: /home/circleci
paths:
- data/ds000001
- data/ds000001-fmriprep

test:
machine:
image: ubuntu-2204:2022.10.2

steps:
- attach_workspace:
at: /tmp/workspace
- run: docker load -i /tmp/workspace/docker/image.tar

- run: mkdir -p ${HOME}/outputs/ds000001/derivatives

- run:
name: print version
command: |
user_name=cpplab
repo_name=$(echo "${CIRCLE_PROJECT_REPONAME}" | tr '[:upper:]' '[:lower:]')
docker run -ti --rm \
-v /tmp/workspace/data/ds000001:/bids_dataset \
${user_name}/${repo_name} --version

- 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} \
/bids_dataset \
/outputs/ds000001 \
subject \
--action smooth \
--task balloonanalogrisktask \
--participant_label 01 02 \
--space MNI152NLin2009cAsym \
--fwhm 8 \
--verbosity 2
no_output_timeout: 6h

# needed to access the model
- checkout

- run:
name: stats
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 ~/project/demos/openneuro/models:/models \
${user_name}/${repo_name} \
/bids_dataset \
/outputs/ds000001 \
subject \
--action stats \
--preproc_dir /outputs/ds000001/derivatives/bidspm-preproc \
--model_file /models/model-balloonanalogrisktaskDefault_smdl.json \
--ignore slicetiming \
--space MNI152NLin2009cAsym \
--skip_validation \
--fwhm 8 \
--participant_label 01 02 \
--verbosity 2
no_output_timeout: 6h


deploy:

machine:
image: ubuntu-2204:2022.10.2

steps:
- attach_workspace:
at: /tmp/workspace

- run: 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

: "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"

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}"
fi

else
: "No DOCKER_TOKEN, skipping push to DockerHub"
exit 1
fi
- checkout

- run:
name: stats
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 ~/project/demos/openneuro/models:/models \
${user_name}/${repo_name} \
/bids_dataset \
/outputs/ds000001 \
subject \
--action stats \
--preproc_dir /outputs/ds000001/derivatives/bidspm-preproc \
--model_file /models/model-balloonanalogrisktaskDefault_smdl.json \
--ignore slicetiming \
--space MNI152NLin2009cAsym \
--skip_validation \
--fwhm 8 \
--participant_label 01 02 \
--verbosity 2
no_output_timeout: 6h


deploy:

machine:
image: ubuntu-2204:2022.10.2

steps:
- attach_workspace:
at: /tmp/workspace

- run: 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

: "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"

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}"
fi

else
: "No DOCKER_TOKEN, skipping push to DockerHub"
exit 1
fi

workflows:
build-test-deploy:
jobs:
- build
- get_data
- test:
requires:
- build
- get_data
- deploy:
context:
- DOCKER_HUB
requires:
- test
build-test-deploy:
jobs:
- build
- get_data
- test:
requires:
- build
- get_data
- deploy:
context:
- DOCKER_HUB
requires:
- test

# VS Code Extension Version: 1.5.1
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