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[DOC] general update (#1256)
* improve doc * fix doc errors * clean up doc * split in sub pages * update FAQ * further clen up * update readme * extract moae demos * update demo * lint * reorganize demos * fix demo * fix packagin * ignore dead links * fix test * rm adds * silence mypy * try fixing python
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‎.circleci/config.yml‎

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Original file line numberDiff line numberDiff line change
@@ -2,199 +2,199 @@
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version: 2.1
33

44
jobs:
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build:
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machine:
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image: ubuntu-2204:2022.10.2
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steps:
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- checkout
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- run: make fix_submodule
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- restore_cache:
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keys:
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- my_cache
15-
- run:
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name: Build Docker image
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command: |
18-
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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mkdir -p "${HOME}/docker"
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docker save "${user_name}/${repo_name}" > "${HOME}/docker/image.tar"
29-
docker images
30-
- persist_to_workspace:
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root: /home/circleci
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paths:
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- docker/image.tar
34-
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get_data:
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machine:
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image: ubuntu-2204:2022.10.2
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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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command: |
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sudo apt-get update
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sudo apt-get install -y python3 git-annex
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python3 -m pip install --upgrade pip setuptools
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pip3 install datalad
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datalad wtf
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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: 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"
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git config --global --add user.email [email protected]
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mkdir -p ${HOME}/data/
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datalad install -s ///openneuro/ds000001 ${HOME}/data/ds000001
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datalad install -s ///openneuro-derivatives/ds000001-fmriprep ${HOME}/data/ds000001-fmriprep
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cd ${HOME}/data/ds000001-fmriprep/
61-
datalad get sub-0[1-2]/anat/*MNI*mask.nii.gz \
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sub-0[1-2]/anat/*MNI*T1w.nii.gz \
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sub-0[1-2]/func/*MNI*desc-preproc*bold.nii.gz \
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sub-0[1-2]/func/*MNI*mask.nii.gz \
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sub-*/func/*tsv \
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sub-*/func/*json -J 12
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datalad status
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- save_cache:
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key: my_cache
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paths:
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- ~/data
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- persist_to_workspace:
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root: /home/circleci
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paths:
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- data/ds000001
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- data/ds000001-fmriprep
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test:
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machine:
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image: ubuntu-2204:2022.10.2
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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: mkdir -p ${HOME}/outputs/ds000001/derivatives
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- run:
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name: print version
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command: |
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user_name=cpplab
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repo_name=$(echo "${CIRCLE_PROJECT_REPONAME}" | tr '[:upper:]' '[:lower:]')
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docker run -ti --rm \
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-v /tmp/workspace/data/ds000001:/bids_dataset \
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${user_name}/${repo_name} --version
97-
98-
- run:
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name: smooth
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command: |
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user_name=cpplab
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repo_name=$(echo "${CIRCLE_PROJECT_REPONAME}" | tr '[:upper:]' '[:lower:]')
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docker run -ti --rm \
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-v /tmp/workspace/data/ds000001-fmriprep:/bids_dataset \
105-
-v ${HOME}/outputs:/outputs \
106-
${user_name}/${repo_name} \
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/bids_dataset \
108-
/outputs/ds000001 \
109-
subject \
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--action smooth \
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--task balloonanalogrisktask \
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--participant_label 01 02 \
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--space MNI152NLin2009cAsym \
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--fwhm 8 \
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--verbosity 2
116-
no_output_timeout: 6h
5+
build:
6+
7+
machine:
8+
image: ubuntu-2204:2022.10.2
9+
steps:
10+
- checkout
11+
- run: make fix_submodule
12+
- restore_cache:
13+
keys:
14+
- my_cache
15+
- run:
16+
name: Build Docker image
17+
command: |
18+
set -eux -o pipefail
19+
# make sure we have a lowercase repo
20+
user_name=cpplab
21+
repo_name=$(echo "${CIRCLE_PROJECT_REPONAME}" | tr '[:upper:]' '[:lower:]')
22+
if [[ -e "${HOME}/docker/image.tar" ]]; then
23+
docker load -i "${HOME}/docker/image.tar"
24+
fi
25+
git describe --tags --always > version
26+
docker build -t "${user_name}/${repo_name}" .
27+
mkdir -p "${HOME}/docker"
28+
docker save "${user_name}/${repo_name}" > "${HOME}/docker/image.tar"
29+
docker images
30+
- persist_to_workspace:
31+
root: /home/circleci
32+
paths:
33+
- docker/image.tar
34+
35+
get_data:
36+
machine:
37+
image: ubuntu-2204:2022.10.2
38+
steps:
39+
- checkout
40+
- run:
41+
name: Install dependencies
42+
command: |
43+
sudo apt-get update
44+
sudo apt-get install -y python3 git-annex
45+
python3 -m pip install --upgrade pip setuptools
46+
pip3 install datalad
47+
datalad wtf
48+
- restore_cache:
49+
keys:
50+
- my_cache
51+
- run:
52+
name: Get ds000001
53+
command: |
54+
# Git set up: to keep datalad warnings away
55+
git config --global --add user.name "Ford Escort"
56+
git config --global --add user.email [email protected]
57+
mkdir -p ${HOME}/data/
58+
datalad install -s ///openneuro/ds000001 ${HOME}/data/ds000001
59+
datalad install -s ///openneuro-derivatives/ds000001-fmriprep ${HOME}/data/ds000001-fmriprep
60+
cd ${HOME}/data/ds000001-fmriprep/
61+
datalad get sub-0[1-2]/anat/*MNI*mask.nii.gz \
62+
sub-0[1-2]/anat/*MNI*T1w.nii.gz \
63+
sub-0[1-2]/func/*MNI*desc-preproc*bold.nii.gz \
64+
sub-0[1-2]/func/*MNI*mask.nii.gz \
65+
sub-*/func/*tsv \
66+
sub-*/func/*json -J 12
67+
datalad status
68+
- save_cache:
69+
key: my_cache
70+
paths:
71+
- ~/data
72+
- persist_to_workspace:
73+
root: /home/circleci
74+
paths:
75+
- data/ds000001
76+
- data/ds000001-fmriprep
77+
78+
test:
79+
machine:
80+
image: ubuntu-2204:2022.10.2
81+
82+
steps:
83+
- attach_workspace:
84+
at: /tmp/workspace
85+
- run: docker load -i /tmp/workspace/docker/image.tar
86+
87+
- run: mkdir -p ${HOME}/outputs/ds000001/derivatives
88+
89+
- run:
90+
name: print version
91+
command: |
92+
user_name=cpplab
93+
repo_name=$(echo "${CIRCLE_PROJECT_REPONAME}" | tr '[:upper:]' '[:lower:]')
94+
docker run -ti --rm \
95+
-v /tmp/workspace/data/ds000001:/bids_dataset \
96+
${user_name}/${repo_name} --version
97+
98+
- run:
99+
name: smooth
100+
command: |
101+
user_name=cpplab
102+
repo_name=$(echo "${CIRCLE_PROJECT_REPONAME}" | tr '[:upper:]' '[:lower:]')
103+
docker run -ti --rm \
104+
-v /tmp/workspace/data/ds000001-fmriprep:/bids_dataset \
105+
-v ${HOME}/outputs:/outputs \
106+
${user_name}/${repo_name} \
107+
/bids_dataset \
108+
/outputs/ds000001 \
109+
subject \
110+
--action smooth \
111+
--task balloonanalogrisktask \
112+
--participant_label 01 02 \
113+
--space MNI152NLin2009cAsym \
114+
--fwhm 8 \
115+
--verbosity 2
116+
no_output_timeout: 6h
117117

118118
# needed to access the model
119-
- checkout
120-
121-
- run:
122-
name: stats
123-
command: |
124-
user_name=cpplab
125-
repo_name=$(echo "${CIRCLE_PROJECT_REPONAME}" | tr '[:upper:]' '[:lower:]')
126-
docker run -ti --rm \
127-
-v /tmp/workspace/data/ds000001:/bids_dataset \
128-
-v ${HOME}/outputs:/outputs \
129-
-v ~/project/demos/openneuro/models:/models \
130-
${user_name}/${repo_name} \
131-
/bids_dataset \
132-
/outputs/ds000001 \
133-
subject \
134-
--action stats \
135-
--preproc_dir /outputs/ds000001/derivatives/bidspm-preproc \
136-
--model_file /models/model-balloonanalogrisktaskDefault_smdl.json \
137-
--ignore slicetiming \
138-
--space MNI152NLin2009cAsym \
139-
--skip_validation \
140-
--fwhm 8 \
141-
--participant_label 01 02 \
142-
--verbosity 2
143-
no_output_timeout: 6h
144-
145-
146-
deploy:
147-
148-
machine:
149-
image: ubuntu-2204:2022.10.2
150-
151-
steps:
152-
- attach_workspace:
153-
at: /tmp/workspace
154-
155-
- run: docker load -i /tmp/workspace/docker/image.tar
156-
- run:
157-
name: push to dockerhub
158-
command: |
159-
set -ex -o pipefail
160-
161-
if [[ -n "${DOCKER_TOKEN}" ]]; then
162-
163-
# make sure we have a lowercase repo
164-
user_name=remigau
165-
repo_name=$(echo "${CIRCLE_PROJECT_REPONAME}" | tr '[:upper:]' '[:lower:]')
166-
167-
echo "${DOCKER_TOKEN}" | docker login -u "${DOCKER_USER}" --password-stdin
168-
169-
: "Pushing to DockerHub ${user_name}/${repo_name}:unstable"
170-
docker tag "${user_name}/${repo_name}" "${user_name}/${repo_name}:unstable"
171-
docker push "${user_name}/${repo_name}:unstable"
172-
173-
if [[ -n "${CIRCLE_TAG}" ]]; then
174-
: "Pushing to DockerHub ${user_name}/${repo_name}:${CIRCLE_TAG}"
175-
docker push "${user_name}/${repo_name}:latest"
176-
docker tag "${user_name}/${repo_name}" "${user_name}/${repo_name}:${CIRCLE_TAG}"
177-
docker push "${user_name}/${repo_name}:${CIRCLE_TAG}"
178-
fi
179-
180-
else
181-
: "No DOCKER_TOKEN, skipping push to DockerHub"
182-
exit 1
183-
fi
119+
- checkout
120+
121+
- run:
122+
name: stats
123+
command: |
124+
user_name=cpplab
125+
repo_name=$(echo "${CIRCLE_PROJECT_REPONAME}" | tr '[:upper:]' '[:lower:]')
126+
docker run -ti --rm \
127+
-v /tmp/workspace/data/ds000001:/bids_dataset \
128+
-v ${HOME}/outputs:/outputs \
129+
-v ~/project/demos/openneuro/models:/models \
130+
${user_name}/${repo_name} \
131+
/bids_dataset \
132+
/outputs/ds000001 \
133+
subject \
134+
--action stats \
135+
--preproc_dir /outputs/ds000001/derivatives/bidspm-preproc \
136+
--model_file /models/model-balloonanalogrisktaskDefault_smdl.json \
137+
--ignore slicetiming \
138+
--space MNI152NLin2009cAsym \
139+
--skip_validation \
140+
--fwhm 8 \
141+
--participant_label 01 02 \
142+
--verbosity 2
143+
no_output_timeout: 6h
144+
145+
146+
deploy:
147+
148+
machine:
149+
image: ubuntu-2204:2022.10.2
150+
151+
steps:
152+
- attach_workspace:
153+
at: /tmp/workspace
154+
155+
- run: docker load -i /tmp/workspace/docker/image.tar
156+
- run:
157+
name: push to dockerhub
158+
command: |
159+
set -ex -o pipefail
160+
161+
if [[ -n "${DOCKER_TOKEN}" ]]; then
162+
163+
# make sure we have a lowercase repo
164+
user_name=remigau
165+
repo_name=$(echo "${CIRCLE_PROJECT_REPONAME}" | tr '[:upper:]' '[:lower:]')
166+
167+
echo "${DOCKER_TOKEN}" | docker login -u "${DOCKER_USER}" --password-stdin
168+
169+
: "Pushing to DockerHub ${user_name}/${repo_name}:unstable"
170+
docker tag "${user_name}/${repo_name}" "${user_name}/${repo_name}:unstable"
171+
docker push "${user_name}/${repo_name}:unstable"
172+
173+
if [[ -n "${CIRCLE_TAG}" ]]; then
174+
: "Pushing to DockerHub ${user_name}/${repo_name}:${CIRCLE_TAG}"
175+
docker push "${user_name}/${repo_name}:latest"
176+
docker tag "${user_name}/${repo_name}" "${user_name}/${repo_name}:${CIRCLE_TAG}"
177+
docker push "${user_name}/${repo_name}:${CIRCLE_TAG}"
178+
fi
179+
180+
else
181+
: "No DOCKER_TOKEN, skipping push to DockerHub"
182+
exit 1
183+
fi
184184
185185
workflows:
186-
build-test-deploy:
187-
jobs:
188-
- build
189-
- get_data
190-
- test:
191-
requires:
192-
- build
193-
- get_data
194-
- deploy:
195-
context:
196-
- DOCKER_HUB
197-
requires:
198-
- test
186+
build-test-deploy:
187+
jobs:
188+
- build
189+
- get_data
190+
- test:
191+
requires:
192+
- build
193+
- get_data
194+
- deploy:
195+
context:
196+
- DOCKER_HUB
197+
requires:
198+
- test
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