Merge branch 'master' into dev

Remi-Gau · Remi-Gau · commit a0ad9e860100 · 2022-11-02T17:03:23.000+01:00
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -2,7 +2,12 @@
 # https://docs.github.com/en/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
 version: 2
 updates:
-  - package-ecosystem: "github-actions"
-    directory: "/"
+  - package-ecosystem: 'github-actions'
+    directory: '/'
     schedule:
-      interval: "weekly"
+      interval: 'monthly'
+
+  - package-ecosystem: 'gitsubmodule'
+    directory: '/'
+    schedule:
+      interval: 'monthly'
diff --git a/.github/workflows/run_tests_matlab.yml b/.github/workflows/run_tests_matlab.yml
@@ -19,13 +19,13 @@ jobs:
     steps:
 
       - name: Install MATLAB
-        uses: matlab-actions/setup-matlab@v1.0.1
+        uses: matlab-actions/setup-matlab@v1.2.2
         with:
           # MATLAB release to set up R2020a
           release: R2020a
 
       - name: Clone spm_2_bids
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           submodules: true
           fetch-depth: 2
@@ -36,11 +36,10 @@ jobs:
           git clone https://github.com/MOcov/MOcov.git --depth 1
 
       - name: get bids-matlab and JSONio
-        run: |
-          make install_dev
+        run: make install_dev
 
       - name: Run commands
-        uses: matlab-actions/run-command@v1.0.1
+        uses: matlab-actions/run-command@v1.1.1
         with:
           command: cd(fullfile(getenv('GITHUB_WORKSPACE'), '.github', 'workflows')); run tests_matlab;
 
@@ -50,7 +49,7 @@ jobs:
           bash <(curl -s https://codecov.io/bash)
 
       - name: Code coverage
-        uses: codecov/codecov-action@v1
+        uses: codecov/codecov-action@v3
         with:
           file: coverage.xml # optional
           flags: unittests # optional
diff --git a/.github/workflows/run_tests_octave.yml b/.github/workflows/run_tests_octave.yml
@@ -0,0 +1,38 @@
+name: tests_octave
+
+on:
+  push:
+    branches:
+      - master
+      - dev
+  pull_request:
+    branches: ['*']
+
+jobs:
+  test:
+
+    runs-on: ubuntu-20.04
+
+    steps:
+
+    - name: Install dependencies
+      run: |
+        sudo apt-get -y -qq update
+        sudo apt-get -y install octave liboctave-dev
+
+    - name: Clone spm_2_bids
+      uses: actions/checkout@v3
+      with:
+        submodules: true
+        fetch-depth: 2
+
+    - name: get bids-matlab and JSONio
+      run: make install_dev_octave
+
+    - name: MOxUnit Action
+      uses: joergbrech/moxunit-action@v1.2.0
+      with:
+        tests: tests
+        src: src src/defaults src/utils
+        ext: lib/JSONio lib/bids-matlab tests/utils
+        with_coverage: false
diff --git a/.github/workflows/validate_cff.yml b/.github/workflows/validate_cff.yml
@@ -0,0 +1,26 @@
+name: validate CITATION.cff
+
+on:
+  push:
+    branches: ['*']
+    paths:
+      - 'CITATION.cff'
+  pull_request:
+    branches: ['*']
+    paths:
+      - 'CITATION.cff'
+
+jobs:
+
+  validate_cff:
+
+    runs-on: ubuntu-latest
+
+    steps:
+
+    - uses: actions/checkout@v3
+
+    - name: Check whether the citation metadata from CITATION.cff is valid
+      uses: citation-file-format/cffconvert-github-action@2.0.0
+      with:
+        args: "--validate"
diff --git a/.gitignore b/.gitignore
@@ -3,6 +3,7 @@
 .vscode
 
 *.json
+mapping.md
 
 env/
 
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -28,7 +28,7 @@ repos:
       additional_dependencies: [miss_hit]
 
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.2.0
+  rev: v4.3.0
   hooks:
     - id: trailing-whitespace
     - id: end-of-file-fixer
diff --git a/init_spm_2_bids.m b/init_spm_2_bids.m
@@ -62,7 +62,7 @@ function init_spm_2_bids(add_dev)
     pth = fileparts(mfilename('fullpath'));
     addpath(genpath(fullfile(pth, 'src')));
 
-    disp('Correct matlab/octave verions and added to the path!');
+    disp('Correct matlab/octave versions and added to the path!');
 
 end
 
diff --git a/miss_hit.cfg b/miss_hit.cfg
@@ -17,5 +17,5 @@ copyright_entity: "spm_2_bids developers"
 # metric for code quality
 metric "cnest": limit 5
 metric "file_length": limit 500
-metric "cyc": limit 16
+metric "cyc": limit 15
 metric "parameters": limit 6
diff --git a/src/Mapping.m b/src/Mapping.m
@@ -102,26 +102,26 @@
             % filter.ext
             %
 
-            p = inputParser;
+            args = inputParser;
 
-            addParameter(p, 'prefix', obj.default_value);
-            addParameter(p, 'suffix', obj.default_value);
-            addParameter(p, 'entities', obj.default_value);
-            addParameter(p, 'ext', obj.default_value);
-            addParameter(p, 'name_spec', obj.default_value);
+            addParameter(args, 'prefix', obj.default_value);
+            addParameter(args, 'suffix', obj.default_value);
+            addParameter(args, 'entities', obj.default_value);
+            addParameter(args, 'ext', obj.default_value);
+            addParameter(args, 'name_spec', obj.default_value);
 
-            parse(p, varargin{:});
+            parse(args, varargin{:});
 
-            prefix = p.Results.prefix;
+            prefix = args.Results.prefix;
             if ~iscell(prefix)
                 prefix = {prefix};
             end
 
             obj.mapping(end + 1, 1).prefix = prefix;
-            obj.mapping(end, 1).suffix = p.Results.suffix;
-            obj.mapping(end, 1).entities = p.Results.entities;
-            obj.mapping(end, 1).ext = p.Results.ext;
-            obj.mapping(end, 1).name_spec = p.Results.name_spec;
+            obj.mapping(end, 1).suffix = args.Results.suffix;
+            obj.mapping(end, 1).entities = args.Results.entities;
+            obj.mapping(end, 1).ext = args.Results.ext;
+            obj.mapping(end, 1).name_spec = args.Results.name_spec;
 
         end
 
@@ -322,6 +322,8 @@ function print_mapping(obj, filename)
                                  [obj.smooth, obj.norm, obj.unwarp], ...
                                  [obj.smooth, obj.norm, obj.realign] },        obj.cfg.smooth_norm};
 
+            spec_preproc = {{[obj.realign, obj.stc]},                obj.cfg.preproc};
+
             spec_preproc_norm = {{obj.norm, ...
                                   [obj.norm, obj.bias_cor], ...
                                   [obj.norm, obj.stc,     obj.unwarp], ...
@@ -334,6 +336,7 @@ function print_mapping(obj, filename)
                        spec_smooth, ...
                        spec_smooth_norm, ...
                        spec_preproc_norm, ...
+                       spec_preproc, ...
                        spec_mean, ...
                        spec_norm_mean);
 
@@ -353,15 +356,15 @@ function print_mapping(obj, filename)
             %    idx = obj.find_mapping('prefix', str)
             %
 
-            p = inputParser;
+            args = inputParser;
 
-            addParameter(p, 'prefix', @ischar);
+            addParameter(args, 'prefix', @ischar);
 
-            parse(p, varargin{:});
+            parse(args, varargin{:});
 
             available_mapped_prefixes = {obj.mapping.prefix}';
 
-            idx = strcmp(p.Results.prefix, available_mapped_prefixes);
+            idx = strcmp(args.Results.prefix, available_mapped_prefixes);
 
         end
 
diff --git a/src/spm_2_bids.m b/src/spm_2_bids.m
@@ -1,19 +1,22 @@
-function [new_filename, pth, json] = spm_2_bids(file, map, verbose)
+function [new_filename, pth, json] = spm_2_bids(varargin)
     %
     % Provides a bids derivatives name for a file preprocessed with SPM
     %
     % USAGE::
     %
-    %   [new_filename, pth, json] = spm_2_bids(file)
-    %   [new_filename, pth, json] = spm_2_bids(file, map)
+    %   [new_filename, pth, json] = spm_2_bids(file [, map][, verbose])
     %
     % :param file: SPM preprocessed filename (can be fullpath);
     %              for example ``wmsub-01_ses-01_T1w.nii``
     % :type file: string
+    %
     % :param map: optional spm_2_bids map to overwrite the default
     %             map (see Mapping)
     % :param map: Mapping object
     %
+    % :param verbose:
+    % :param verbose: boolean
+    %
     % :returns: - :new_filename: (string) BIDS compatible filename
     %               for example ``sub-01_ses-01_space-IXI549Space_desc-preproc_T1w.nii``;
     %           - :pth: (string) relative BIDS path
@@ -27,15 +30,23 @@
 
     % (C) Copyright 2021 spm_2_bids developers
 
-    if nargin < 2 || isempty(map)
+    args = inputParser;
+
+    addRequired(args, 'file', @ischar);
+    addOptional(args, 'map', []);
+    addOptional(args, 'verbose', true, @islogical);
+
+    parse(args, varargin{:});
+
+    file = args.Results.file;
+    map = args.Results.map;
+    verbose = args.Results.verbose;
+
+    if isempty(map)
         map = Mapping();
         map = map.default();
     end
 
-    if nargin < 3
-        verbose = true;
-    end
-
     mapping = map.mapping;
     cfg = map.cfg;
 
@@ -83,22 +94,7 @@
                          strcmp({mapping.ext}', '*')], 2);
     end
 
-    % we compare the entities-label pairs present in the file
-    % to those required in the mapping (if any)
-    % if no entity requirement anywhere in the mapping then anything goes
-    entitiy_match = true(size(mapping));
-
-    needs_entity_check = ~cellfun('isempty', {mapping.entities}');
-    if any(needs_entity_check)
-
-        entitiy_match = false(size(mapping));
-
-        idx = find(needs_entity_check);
-        for i = 1:numel(idx)
-            status = check_field_content(bf.entities, mapping(idx(i)).entities);
-            entitiy_match(idx(i)) = status;
-        end
-    end
+    entitiy_match = get_entity_match(mapping, bf);
 
     this_mapping = [prefix_match, suffix_match, entitiy_match, ext_match];
 
@@ -117,9 +113,15 @@
     end
 
     if isempty(spec) && verbose
-        % TODO this warning should probably go in the find_mapping methods
-        msg = sprintf('Unknown prefix: %s', bf.prefix);
-        warning('spm_2_bids:unknownPrefix', msg); %#ok<SPWRN>
+        if isnan(str2double(bf.prefix(1))) && ...
+            ~bids.internal.starts_with(bf.prefix, 'c4') && ... % ALI toolbox prefixes
+             ~bids.internal.starts_with(bf.prefix, 'td_') % spmup toolbox truncated prefixes
+
+            % TODO this warning should probably go in the find_mapping methods
+            msg = sprintf('Unknown prefix: %s', bf.prefix);
+            warning('spm_2_bids:unknownPrefix', msg); %#ok<SPWRN>
+
+        end
         return
     end
 
@@ -145,6 +147,25 @@
 
 end
 
+function entitiy_match = get_entity_match(mapping, bf)
+    % we compare the entities-label pairs present in the file
+    % to those required in the mapping (if any)
+    % if no entity requirement anywhere in the mapping then anything goes
+    entitiy_match = true(size(mapping));
+
+    needs_entity_check = ~cellfun('isempty', {mapping.entities}');
+    if any(needs_entity_check)
+
+        entitiy_match = false(size(mapping));
+
+        idx = find(needs_entity_check);
+        for i = 1:numel(idx)
+            status = check_field_content(bf.entities, mapping(idx(i)).entities);
+            entitiy_match(idx(i)) = status;
+        end
+    end
+end
+
 function json = set_metadata(file, map, verbose, bf)
 
     json = bids.derivatives_json(bf.filename);
diff --git a/src/utils/identify_rawsources.m b/src/utils/identify_rawsources.m
@@ -38,9 +38,9 @@
         verbose = true;
     end
 
-    if endsWith(derivatives, '_seg8.mat')
+    if bids.internal.ends_with(derivatives, '_seg8.mat')
         derivatives = strrep(derivatives, '_seg8.mat', '.nii');
-    elseif endsWith(derivatives, '_uw.mat')
+    elseif bids.internal.ends_with(derivatives, '_uw.mat')
         derivatives = strrep(derivatives, '_uw.mat', '.nii');
     end
 
diff --git a/src/utils/identify_sources.m b/src/utils/identify_sources.m
@@ -62,7 +62,7 @@
 
         derivatives = strrep(derivatives, '_seg8.mat', '.nii');
 
-    elseif endsWith(derivatives, '_uw.mat')
+    elseif bids.internal.ends_with(derivatives, '_uw.mat')
 
         prefix_based = false;
 
diff --git a/src/utils/prepare_for_printing.m b/src/utils/prepare_for_printing.m
@@ -0,0 +1,18 @@
+function bf = prepare_for_printing(spec)
+    %
+    % (C) Copyright 2022 spm_2_bids developers
+
+    if isfield(spec, 'suffix') && isempty(spec.suffix) || ...
+        ~isfield(spec, 'suffix')
+        spec.suffix = '*';
+    end
+
+    if isfield(spec, 'ext') && ~isempty(spec.ext)
+        spec.extension = '.*';
+    end
+    if ~isfield(spec, 'extension') || isempty(spec.extension)
+        spec.ext = '.*';
+    end
+
+    bf = bids.File(spec);
+end
diff --git a/tests/test_spm_2_bids.m b/tests/test_spm_2_bids.m

-Original file line number
+Diff line change
 .vscode
 *.json
 +mapping.md
 env/