Merge branch 'bids_derivatives' of https://github.com/cpp-lln-lab/CPP_ROI into bids_derivatives

Author: Remi-Gau

.github/workflows/run_tests.yml

@@ -1,15 +1,15 @@
 name: tests and coverage
 
 # Uses the cron schedule for github actions
-# 
+#
 # https://docs.github.com/en/free-pro-team@latest/actions/reference/events-that-trigger-workflows#scheduled-events
-# 
+#
 # ┌───────────── minute (0 - 59)
 # │ ┌───────────── hour (0 - 23)
 # │ │ ┌───────────── day of the month (1 - 31)
 # │ │ │ ┌───────────── month (1 - 12 or JAN-DEC)
 # │ │ │ │ ┌───────────── day of the week (0 - 6 or SUN-SAT)
-# │ │ │ │ │                                   
+# │ │ │ │ │
 # │ │ │ │ │
 # │ │ │ │ │
 # * * * * *
@@ -39,7 +39,7 @@ jobs:
         sudo apt-get -y install octave liboctave-dev
         sudo apt-get -y install nodejs npm
 
-    - name: Clone cpp_spm         
+    - name: Clone cpp_spm
       uses: actions/checkout@v2
       with:
         submodules: true
@@ -58,20 +58,19 @@ jobs:
         git clone https://github.com/MOxUnit/MOxUnit.git --depth 1
         make -C MOxUnit install
         git clone https://github.com/MOcov/MOcov.git --depth 1
-        make -C MOcov install    
+        make -C MOcov install
 
     - name: Add bids-matlab
-      run: | 
-        git clone https://github.com/bids-standard/bids-matlab.git --depth 1      
-        
+      run: |
+        git clone https://github.com/bids-standard/bids-matlab.git --depth 1
+
     - name: Update octave path
       run: |
         octave $OCTFLAGS --eval "initCppRoi; savepath();"
-        octave $OCTFLAGS --eval "addpath(fullfile(pwd, 'bids-matlab')); savepath();"        
+        octave $OCTFLAGS --eval "addpath(fullfile(pwd, 'bids-matlab')); savepath();"
 
     - name: Run tests
       run: |
         octave $OCTFLAGS --eval "run_tests"
         cat test_report.log | grep 0
-        bash <(curl -s https://codecov.io/bash)         
-
+        bash <(curl -s https://codecov.io/bash)

.gitignore

@@ -23,6 +23,3 @@ envs/*
 demos/*/*.json
 demos/*/*/*.json
 demos/*/derivatives
-
-
-

.readthedocs.yml

@@ -23,4 +23,4 @@ formats:
 python:
   version: 3.7
   install:
-    - requirements: requirements.txt
+    - requirements: requirements.txt

lib/marsbar-0.44/@mardo/adjusted_data.m

@@ -1,19 +1,19 @@
 function Ya = adjusted_data(D, Ic)
 % Return adjusted data for estimated design and contrast no
 % FORMAT Ya = adjusted_data(D, Ic)
-% 
+%
 % D      - Estimated marsbar design
 % Ic     - Contrast number to adjust for
-% 
+%
 % Outputs
 % Ya     - Adjusted data, N by M, where N is number of time points
 %          and M is number of regions in estimated marsbar design
-% 
+%
 % e.g
 % E = estimate(D, Y);
 % [E Ic] = add_contrasts(E, 'task', 'T', [1 0 0]);
 % Ya = adjusted_data(E, Ic);
-% 
+%
 % Matthew Brett
 
 if nargin < 2

lib/marsbar-0.44/@mardo/betas.m

@@ -1,6 +1,6 @@
 function r = betas(o)
 % method to get estimated betas
-% 
+%
 % $Id$
 
 if ~is_mars_estimated(o)

lib/marsbar-0.44/@mardo/block_mean_cols.m

@@ -1,9 +1,8 @@
 function bmrs = block_mean_rows(D)
 % method returns rows for means for blocks in design
-% 
+%
 % $Id$
 
 bmrs = [];
 SPM =  des_struct(D);
-bmrs = SPM.xX.iB;   
-  
+bmrs = SPM.xX.iB;

lib/marsbar-0.44/@mardo/block_means.m

@@ -1,13 +1,13 @@
 function bms = block_means(D)
 % method returns means for blocks in design
-% 
+%
 % Inputs
 % D        - design object
 %
 % Outputs
 % bms      - means over block.  Returns B x N matrix
 %            where B is number of blocks, and N is number
-%            of ROIs 
+%            of ROIs
 %
 % $Id$
 
@@ -16,5 +16,3 @@
   error('Design does not yet have data');
 end
 bms = summary_block_means(data(D));
-
-

lib/marsbar-0.44/@mardo/cd_images.m

@@ -4,17 +4,17 @@
 %
 % Synopsis
 % D = cd_images(D); % get new path from GUI
-% D = cd_images(D, '/new/root/path'); 
+% D = cd_images(D, '/new/root/path');
 % D = cd_images(D, '/new/root/path', 1); % force byteswap
-% D = cd_images(D, '/new/root/path', 1); % prevent byteswap  
-%  
+% D = cd_images(D, '/new/root/path', 1); % prevent byteswap
+%
 % D          - mardo design
 % newpath    - path to replace common path of files in analysis [GUI]
-% byteswap   - whether to indicate byte swapping in vol structs 
+% byteswap   - whether to indicate byte swapping in vol structs
 %              [determined from images by default]
-%             
+%
 % $Id$
-  
+
 if nargin < 2
   newpath = spm_get(-1, '', 'New directory root for files');
 end
@@ -35,7 +35,7 @@
 n = length(VY);
 strout = strvcat(VY(:).fname);
 msk    = diff(strout+0)~=0; % common path
-d1     = min(find(sum(msk,1))); 
+d1     = min(find(sum(msk,1)));
 d1     = max([find(strout(1,1:d1) == other_filesep | strout(1,1:d1) == filesep) 0]);
 ffnames = strout(:,d1+1:end); % common path removed
 tmp = ffnames == other_filesep; % filesep exchanged for this platform
@@ -48,7 +48,7 @@
 if ~exist(nfnames{1}, 'file')
   error(['Cannot find first file here: ' nfnames{1}]);
 end
-if isempty(byteswap) 
+if isempty(byteswap)
   byteswap = mars_vol_utils('is_swapped_wrong', VY(1));
 end
 
@@ -58,6 +58,6 @@
   if verbose(D)
     disp('Images vols byteswapped');
   end
-end    
+end
 
 D = set_images(D, VY);

lib/marsbar-0.44/@mardo/contrasts.m

@@ -1,8 +1,8 @@
 function r = contrasts(o, xcon)
 % method to get or set contrasts
-% 
+%
 % $Id$
-  
+
 if nargin < 2
   r = get_contrasts(o);
 else

lib/marsbar-0.44/@mardo/data.m

@@ -1,10 +1,10 @@
 function r = data(o, Y)
-% method to get or set data object 
-% 
+% method to get or set data object
+%
 % $Id$
-  
+
 if nargin < 2
   r = get_data(o);
 else
   r = set_data(o, Y);
-end
+end