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Merge pull request #379 from nipreps/ci/fix-smoke
CI: Fix smoke tests
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -10,7 +10,7 @@ _machine_defaults: &machine_defaults | |
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| _python_defaults: &python_defaults | ||
| docker: | ||
| - image: cimg/python:3.12.1 | ||
| - image: cimg/python:3.12.5 | ||
| auth: | ||
| username: $DOCKER_USER | ||
| password: $DOCKER_PAT | ||
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@@ -160,17 +160,16 @@ jobs: | |
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| get_data: | ||
| docker: | ||
| - image: cimg/python:3.12.1 | ||
| <<: *python_defaults | ||
| working_directory: /home/circleci/data | ||
| steps: | ||
| - restore_cache: | ||
| keys: | ||
| - data-v0-{{ .Branch }}-{{ .Revision }} | ||
| - data-v0--{{ .Revision }} | ||
| - data-v0-{{ .Branch }}- | ||
| - data-v0-master- | ||
| - data-v0- | ||
| - data-v1-{{ .Branch }}-{{ .Revision }} | ||
| - data-v1--{{ .Revision }} | ||
| - data-v1-{{ .Branch }}- | ||
| - data-v1-master- | ||
| - data-v1- | ||
| - run: | ||
| name: Install datalad + git-annex | ||
| command: | | ||
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@@ -180,7 +179,7 @@ jobs: | |
| git config --global filter.annex.process "git-annex filter-process" | ||
| git config --global user.name "Nipreps CI" | ||
| git config --global user.email "[email protected]" | ||
| pip install "datalad<0.18" | ||
| pip install datalad | ||
| fi | ||
| - run: | ||
| name: Get bcp test data | ||
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@@ -334,7 +333,8 @@ jobs: | |
| --output-spaces MNIInfant:cohort-1 func \ | ||
| --sloppy --write-graph --mem-mb 14000 \ | ||
| --nthreads 4 -vv --age-months 2 --sloppy \ | ||
| --derivatives /tmp/data/${DATASET}/derivatives/precomputed \ | ||
| --surface-recon-method infantfs \ | ||
| --derivatives precomputed=/tmp/data/${DATASET}/derivatives/bibsnet \ | ||
| --output-layout bids --anat-only | ||
| - run: | ||
| name: Checking outputs of anatomical nibabies run | ||
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@@ -362,7 +362,8 @@ jobs: | |
| --output-spaces MNIInfant:cohort-1 func \ | ||
| --sloppy --write-graph --mem-mb 14000 \ | ||
| --nthreads 4 -vv --age-months 2 --sloppy \ | ||
| --derivatives /tmp/data/${DATASET}/derivatives/precomputed \ | ||
| --surface-recon-method infantfs \ | ||
| --derivatives precomputed=/tmp/data/${DATASET}/derivatives/bibsnet \ | ||
| --output-layout bids | ||
| - run: | ||
| name: Checking outputs of full nibabies run | ||
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@@ -390,12 +391,7 @@ jobs: | |
| rm -f /tmp/data/${DATASET}-t2only/sub-01/ses-1mo/anat/*_T1w.* | ||
| tree /tmp/data/${DATASET}-t2only | ||
| mkdir -p /tmp/data/${DATASET}-t2only/derivatives | ||
| cp -r /tmp/data/${DATASET}/derivatives/precomputed /tmp/data/${DATASET}-t2only/derivatives | ||
| # rename the derivatives for now - this is only possible since they share the same space | ||
| sudo apt install rename | ||
| rename 's/space-T1w/space-T2w/' /tmp/data/${DATASET}-t2only/derivatives/precomputed/sub-01/ses-1mo/anat/* | ||
| sed -i 's/_T1w./_T2w./g' /tmp/data/${DATASET}-t2only/derivatives/precomputed/sub-01/ses-1mo/anat/*json | ||
| tree /tmp/data/${DATASET}-t2only/derivatives/precomputed | ||
| cp -r /tmp/data/${DATASET}/derivatives/bibsnet /tmp/data/${DATASET}-t2only/derivatives | ||
| - run: | ||
| name: Run nibabies single anatomical workflow | ||
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@@ -412,7 +408,8 @@ jobs: | |
| --output-spaces MNIInfant:cohort-1 func \ | ||
| --sloppy --write-graph --mem-mb 14000 \ | ||
| --nthreads 4 -vv --age-months 2 --sloppy \ | ||
| --derivatives /tmp/data/${DATASET}-t2only/derivatives/precomputed \ | ||
| --surface-recon-method infantfs \ | ||
| --derivatives precomputed=/tmp/data/${DATASET}-t2only/derivatives/bibsnet \ | ||
| --output-layout bids --anat-only | ||
| - run: | ||
| name: Checking outputs of T2-only nibabies anat | ||
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