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rm: wrapper pooch argument
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2 files changed

+3
-18
lines changed

2 files changed

+3
-18
lines changed

.circleci/config.yml

Lines changed: 3 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -214,8 +214,6 @@ jobs:
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- run:
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name: Get intermediate transforms
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command: |
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mkdir -p /tmp/pooch
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cd /tmp/pooch
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# Caching intermediate templates so no need to constantly fetch
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XFM="from-MNI152NLin6Asym_to-MNIInfant+1_xfm.h5"
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echo "Downloading $XFM"
@@ -229,7 +227,6 @@ jobs:
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paths:
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- fslicense
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- bcp/nipype.cfg
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- pooch/*
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test_pytest:
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!!merge <<: *machine_defaults
@@ -348,8 +345,7 @@ jobs:
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--nthreads 4 -vv --age-months 2 --sloppy \
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--surface-recon-method infantfs \
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--derivatives precomputed=/tmp/data/${DATASET}/derivatives/bibsnet \
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--output-layout bids --anat-only \
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--pooch-cache-dir /tmp/pooch
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--output-layout bids --anat-only
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- run:
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name: Checking outputs of anatomical nibabies run
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command: |
@@ -378,8 +374,7 @@ jobs:
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--nthreads 4 -vv --age-months 2 \
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--surface-recon-method infantfs \
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--derivatives precomputed=/tmp/data/${DATASET}/derivatives/bibsnet \
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--output-layout bids \
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--pooch-cache-dir /tmp/pooch
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--output-layout bids
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- run:
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name: Checking outputs of full nibabies run
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command: |
@@ -425,8 +420,7 @@ jobs:
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--nthreads 4 -vv --age-months 2 \
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--surface-recon-method infantfs \
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--derivatives precomputed=/tmp/data/${DATASET}-t2only/derivatives/bibsnet \
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--output-layout bids --anat-only --cifti-output \
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--pooch-cache-dir /tmp/pooch
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--output-layout bids --anat-only --cifti-output
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- run:
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name: Checking outputs of T2-only nibabies anat
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command: |

wrapper/src/nibabies_wrapper/__main__.py

Lines changed: 0 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -476,12 +476,6 @@ def _is_file(path, parser):
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type=os.path.abspath,
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help='Filter file',
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)
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g_wrap.add_argument(
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'--pooch-cache-dir',
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metavar='DIR',
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type=os.path.abspath,
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help='Directory to serve as cache for pooch files'
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)
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# Developer patch/shell options
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g_dev = parser.add_argument_group(
@@ -649,9 +643,6 @@ def main():
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if opts.deriv_filter_file:
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container.add_mount(opts.deriv_filter_file, '/opt/derivative_filters.json')
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unknown_args.extend(['--deriv-filter-file', '/opt/derivative_filters.json'])
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if opts.pooch_cache_dir:
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container.add_mount(opts.pooch_cache_dir, '/tmp/pooch_cache', read_only=False)
654-
container.add_envvar(('NIBABIES_POOCH_DIR', '/tmp/pooch_cache'))
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# Patch derivatives for searching
656647
if opts.derivatives:
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deriv_args = ['--derivatives']

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