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[INFRA] update dockerfiles #420

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Merged
Remi-Gau merged 3 commits into from
Oct 1, 2021
Merged

[INFRA] update dockerfiles #420

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6f5d945
update dockerfiles
Remi-Gau Oct 1, 2021
9e922ca
remove extra getBoldFilename
Remi-Gau Oct 1, 2021
9521e1a
fix test_bidsFFX to adapt to one of the new test models
Remi-Gau Oct 1, 2021
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4 changes: 3 additions & 1 deletion .dockerignore
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Original file line number Diff line number Diff line change
@@ -1,10 +1,12 @@
.vscode
.git
.github
env
binder
coverage_html
demos/*/outputs/
demos/*/inputs/
demos/*/cfg/
env
tests

# ignoring this might speed up build
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2 changes: 1 addition & 1 deletion Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
FROM ubuntu:focal

#TODO how to update this with the content of the current version
LABEL version="1.0.0"
LABEL version="1.1.2"

# basic OS tools install and also octave
RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get -y install \
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13 changes: 6 additions & 7 deletions Dockerfile_dev
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
FROM ubuntu:focal

#TODO how to update this with the content of the current version
LABEL version="1.0.0"
LABEL version="1.1.2dev"

# basic OS tools install and also octave
RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get -y install \
Expand Down Expand Up @@ -36,14 +36,13 @@ RUN octave --no-gui --eval "addpath(\"/opt/spm12\"); savepath ();"

# gets the dev branch CPP BIDS pipeline code

# RUN git clone --depth 1 --recurse-submodule https://github.com/cpp-lln-lab/CPP_SPM.git \
# && cd CPP_SPM \
# && git checkout -b dev \
# && git pull origin dev
RUN git clone --depth 1 --recurse-submodule https://github.com/cpp-lln-lab/CPP_SPM.git \
&& cd CPP_SPM \
&& git checkout -b dev \
&& git pull origin dev

# or get the local code base

COPY . CPP_SPM
# COPY . CPP_SPM

RUN mkdir code output

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2 changes: 1 addition & 1 deletion lib/spm_2_bids
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Submodule spm_2_bids updated 23 files
+30 −31 .github/workflows/run_tests.yml
+0 −4 .gitignore
+1 −9 Makefile
+0 −5 binder/apt.txt
+0 −2 binder/environment.yml
+0 −12 binder/postBuild
+0 −1 docs/.gitignore
+2 −2 docs/README.md
+5 −6 docs/source/conf.py
+2 −9 docs/source/index.rst
+2 −2 init_env.m
+3 −6 miss_hit.cfg
+0 −1 notebooks/.gitignore
+0 −285 notebooks/demo.ipynb
+6 −6 requirements.txt
+4 −0 run_tests.m
+18 −18 src/defaults/Mapping.m
+1 −1 src/defaults/check_cfg.m
+1 −12 src/defaults/get_spm_prefix_list.m
+4 −4 src/spm_2_bids.m
+5 −5 src/utils/check_field_content.m
+1 −1 tests/test_mapping.m
+2 −3 tests/test_spm_2_bids.m
49 changes: 0 additions & 49 deletions src/getBoldFilename.m
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This file was deleted.

10 changes: 5 additions & 5 deletions tests/tests_workflows/test_bidsFFX.m
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@
initTestSuite;
end

function test_bidsFfx_contrasts()
function test_bidsFFX_contrasts()

opt = setOptions('vislocalizer');
opt.space = {'MNI'};
Expand All @@ -18,11 +18,11 @@ function test_bidsFfx_contrasts()

matlabbatch = bidsFFX('contrasts', opt);

assertEqual(numel(matlabbatch{1}.spm.stats.con.consess), 4);
assertEqual(numel(matlabbatch{1}.spm.stats.con.consess), 7);

end

function test_bidsFfx_fmriprep_no_smoothing()
function test_bidsFFX_fmriprep_no_smoothing()

opt = setOptions('fmriprep');

Expand All @@ -47,7 +47,7 @@ function test_bidsFfx_fmriprep_no_smoothing()

end

function test_bidsFfx_mni()
function test_bidsFFX_mni()

task = {'vislocalizer'}; % 'vismotion'

Expand All @@ -66,7 +66,7 @@ function test_bidsFfx_mni()

end

function test_bidsFfx_individual()
function test_bidsFFX_individual()

task = {'vislocalizer'}; % 'vismotion'

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