update copyright in help and simplify CI

Remi-Gau · Remi-Gau · commit 3fe37d2b2278 · 2022-11-02T12:10:51.000+01:00
diff --git a/.github/workflows/miss_hit.yml b/.github/workflows/miss_hit.yml
diff --git a/.github/workflows/update-contributors.yml b/.github/workflows/update-contributors.yml
diff --git a/.tributors b/.tributors
diff --git a/requirements.txt b/requirements.txt
@@ -1,5 +1,5 @@
 # linting
-miss_hit==0.9.30
+miss_hit==0.9.35
 pre-commit
 
 # doc
diff --git a/src/atlas/copyAtlasToSpmDir.m b/src/atlas/copyAtlasToSpmDir.m
@@ -13,6 +13,7 @@ function copyAtlasToSpmDir(varargin)
   % :type  verbose: boolean
   %
   %
+
   % (C) Copyright 2022 CPP ROI developers
 
   args = inputParser;
diff --git a/src/atlas/extractRoiByLabel.m b/src/atlas/extractRoiByLabel.m
@@ -14,6 +14,7 @@
   %                     and ``label`` for the corresponding label
   % :type labelStruct: structure
   %
+
   % (C) Copyright 2021 CPP ROI developers
 
   hdr = spm_vol(sourceImage);
diff --git a/src/atlas/extractRoiFromAtlas.m b/src/atlas/extractRoiFromAtlas.m
@@ -16,6 +16,7 @@
   % :type roiName: string
   % :type hemisphere: string
   %
+
   % (C) Copyright 2021 CPP ROI developers
 
   if ~ismember(hemisphere, {'L', 'R'})
diff --git a/src/atlas/getAtlasAndLut.m b/src/atlas/getAtlasAndLut.m
@@ -3,6 +3,7 @@
   % Gets the atlas image and the look up table of a given atlas
   %
   %
+
   % (C) Copyright 2021 CPP ROI developers
 
   lut = getLookUpTable(atlasName);
diff --git a/src/atlas/getAtlasFilename.m b/src/atlas/getAtlasFilename.m
@@ -14,6 +14,7 @@
   %   PMID: 25452571
   %   Probabilistic Maps of Visual Topography in Human Cortex
   %
+
   % (C) Copyright 2021 CPP ROI developers
 
   atlasDir = returnAtlasDir(atlasName);
diff --git a/src/atlas/getLookUpTable.m b/src/atlas/getLookUpTable.m
@@ -10,6 +10,7 @@
   %
   % :returns: - :roiLabelLUT: a structure with the fields ``ROI`` and ``label``
   %
+
   % (C) Copyright 2021 CPP ROI developers
 
   if exist(atlasName, 'file')
diff --git a/src/atlas/labelClusters.m b/src/atlas/labelClusters.m
@@ -21,6 +21,7 @@
   % Adapted from:
   % https://en.wikibooks.org/wiki/SPM/How-to#How_to_remove_clusters_under_a_certain_size_in_a_binary_mask?
   %
+
   % (C) Copyright 2021 CPP ROI developers
 
   default_clusterSize = 0;
diff --git a/src/atlas/unzipAtlas.m b/src/atlas/unzipAtlas.m
@@ -1,5 +1,6 @@
 function unzipAtlas(atlas)
   %
+
   % (C) Copyright 2021 CPP ROI developers
 
   atlasDir = returnAtlasDir();
diff --git a/src/roi/checkRoiOrientation.m b/src/roi/checkRoiOrientation.m
@@ -10,6 +10,7 @@
   % :param imagesToCheck: better if fullfile path
   % :type imagesToCheck: string
   %
+
   % (C) Copyright 2021 CPP ROI developers
 
   % TODO
diff --git a/src/roi/createRoi.m b/src/roi/createRoi.m
@@ -67,6 +67,7 @@
   %        - ``mask.global.XYZmm``
   %
   %
+
   % (C) Copyright 2021 CPP ROI developers
 
   args = inputParser;
diff --git a/src/roi/createRoiName.m b/src/roi/createRoiName.m
@@ -6,6 +6,7 @@
   %
   %     roiName = createRoiName(mask, volumeDefiningImage)
   %
+
   % (C) Copyright 2022 CPP ROI developers
 
   args = inputParser;
diff --git a/src/roi/getPeakCoordinates.m b/src/roi/getPeakCoordinates.m
@@ -17,6 +17,7 @@
   % :type threshold: numerical
   %
   %
+
   % (C) Copyright 2021 CPP ROI developers
 
   % TODO
diff --git a/src/roi/keepHemisphere.m b/src/roi/keepHemisphere.m
@@ -13,6 +13,7 @@
   % :type hemisphere: string
   %
   %
+
   % (C) Copyright 2021 CPP ROI developers
 
   % TODO change the hemi entity
diff --git a/src/roi/plotDataInRoi.m b/src/roi/plotDataInRoi.m
@@ -52,6 +52,7 @@
   %     plotDataInRoi(data, mask);
   %
   %
+
   % (C) Copyright 2022 CPP ROI developers
 
   defaultNbBins = 100;
diff --git a/src/roi/renameNeuroSynth.m b/src/roi/renameNeuroSynth.m
@@ -16,6 +16,7 @@
   %     fullfile(pwd, 'space-MNI_label-neurosynthMotion_probseg.nii.gz');
   %
   %
+
   % (C) Copyright 2021 CPP ROI developers
 
   basename = spm_file(inputImage, 'basename');
diff --git a/src/roi/resliceRoiImages.m b/src/roi/resliceRoiImages.m
@@ -15,6 +15,7 @@
   % :param dryRun: Returns the matlabbatch without running it.
   % :type dryRun: logical
   %
+
   % (C) Copyright 2021 CPP ROI developers
 
   % TODO
diff --git a/src/roi/thresholdToMask.m b/src/roi/thresholdToMask.m
@@ -16,6 +16,7 @@
   %
   % :returns: - :outputImage: (string)
   %
+
   % (C) Copyright 2021 CPP ROI developers
 
   % TODO
diff --git a/src/utils/cppRoiRoot.m b/src/utils/cppRoiRoot.m
@@ -6,6 +6,7 @@
   %   pth = cppRoiRoot()
   %
   %
+
   % (C) Copyright 2022 CPP ROI developers
 
   pth = fullfile(fileparts(mfilename('fullpath')), '..', '..');
diff --git a/src/utils/getClusters.m b/src/utils/getClusters.m
@@ -11,6 +11,7 @@
   %
   % See also labelClusters, sortAndLabelClusters
   %
+
   % (C) Copyright 2021 CPP ROI developers
 
   hdr = spm_vol(inputImage);
diff --git a/src/utils/isBinaryMask.m b/src/utils/isBinaryMask.m
@@ -1,5 +1,6 @@
 function status = isBinaryMask(image)
   %
+
   % (C) Copyright 2022 CPP ROI developers
 
   status = true;
diff --git a/src/utils/optimizeSubplotNumber.m b/src/utils/optimizeSubplotNumber.m
@@ -1,5 +1,6 @@
 function [m, n] = optimizeSubplotNumber(mn)
   %
+
   % (C) Copyright 2022 CPP ROI developers
 
   % Optimizes the number of subplot to have on a figure
diff --git a/src/utils/removePrefix.m b/src/utils/removePrefix.m
@@ -1,5 +1,6 @@
 function image = removePrefix(image, prefix)
   %
+
   % (C) Copyright 2019 CPP ROI developers
 
   basename = spm_file(image, 'basename');
diff --git a/src/utils/sortAndLabelClusters.m b/src/utils/sortAndLabelClusters.m
@@ -12,6 +12,7 @@
   %
   % See also: getClusters, labelClusters
   %
+
   % (C) Copyright 2021 CPP ROI developers
 
   % refactor with sortAndThresholdClusters
diff --git a/src/utils/sortAndThresholdClusters.m b/src/utils/sortAndThresholdClusters.m
@@ -1,5 +1,6 @@
 function vol = sortAndThresholdClusters(l2, num, clusterSize)
   %
+
   % (C) Copyright 2020 CPP ROI developers
 
   [n, ni] = sort(histc(l2(:), 0:num), 1, 'descend');

Original file line number	Diff line number	Diff line change
`@@ -13,6 +13,7 @@ function copyAtlasToSpmDir(varargin)`
`13`	`13`	`% :type verbose: boolean`
`14`	`14`	`%`
`15`	`15`	`%`
	`16`	`+`
`16`	`17`	`% (C) Copyright 2022 CPP ROI developers`
`17`	`18`
`18`	`19`	`args = inputParser;`
Original file line number	Diff line number	Diff line change
`@@ -14,6 +14,7 @@`
`14`	`14`	% and ``label`` for the corresponding label
`15`	`15`	`% :type labelStruct: structure`
`16`	`16`	`%`
	`17`	`+`
`17`	`18`	`% (C) Copyright 2021 CPP ROI developers`
`18`	`19`
`19`	`20`	`hdr = spm_vol(sourceImage);`
Original file line number	Diff line number	Diff line change
`@@ -16,6 +16,7 @@`
`16`	`16`	`% :type roiName: string`
`17`	`17`	`% :type hemisphere: string`
`18`	`18`	`%`
	`19`	`+`
`19`	`20`	`% (C) Copyright 2021 CPP ROI developers`
`20`	`21`
`21`	`22`	`if ~ismember(hemisphere, {'L', 'R'})`
Original file line number	Diff line number	Diff line change
`@@ -3,6 +3,7 @@`
`3`	`3`	`% Gets the atlas image and the look up table of a given atlas`
`4`	`4`	`%`
`5`	`5`	`%`
	`6`	`+`
`6`	`7`	`% (C) Copyright 2021 CPP ROI developers`
`7`	`8`
`8`	`9`	`lut = getLookUpTable(atlasName);`
Original file line number	Diff line number	Diff line change
`@@ -10,6 +10,7 @@`
`10`	`10`	`%`
`11`	`11`	% :returns: - :roiLabelLUT: a structure with the fields ``ROI`` and ``label``
`12`	`12`	`%`
	`13`	`+`
`13`	`14`	`% (C) Copyright 2021 CPP ROI developers`
`14`	`15`
`15`	`16`	`if exist(atlasName, 'file')`