Merge pull request #30 from Remi-Gau/dev

[INFRA] add octave tests

Author: Remi-Gau

.github/workflows/run_tests_matlab.yml

@@ -25,7 +25,7 @@ jobs:
           release: R2020a
 
       - name: Clone spm_2_bids
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           submodules: true
           fetch-depth: 2
@@ -36,8 +36,7 @@ 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/[email protected]

.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/[email protected]
+      with:
+        tests: tests
+        src: src src/defaults src/utils
+        ext: lib/JSONio lib/bids-matlab tests/utils
+        with_coverage: false

CITATION.cff

@@ -2,7 +2,7 @@ cff-version: 1.2.0
 
 title: "spm_2_bids"
 
-version: 0.2.0
+version: 0.2.0dev
 
 abstract: Toolbox to convert SPM output files to valid BIDS derivatives.
 

README.md

@@ -1,7 +1,8 @@
 [![code quality](https://github.com/cpp-lln-lab/spm_2_bids/actions/workflows/miss_hit_code_quality.yml/badge.svg)](https://github.com/cpp-lln-lab/spm_2_bids/actions/workflows/miss_hit_code_quality.yml)
 [![code style](https://github.com/cpp-lln-lab/spm_2_bids/actions/workflows/miss_hit_code_style.yml/badge.svg)](https://github.com/cpp-lln-lab/spm_2_bids/actions/workflows/miss_hit_code_style.yml)
-[![tests](https://github.com/cpp-lln-lab/spm_2_bids/actions/workflows/run_tests.yml/badge.svg)](https://github.com/cpp-lln-lab/spm_2_bids/actions/workflows/run_tests.yml)
+[![tests and coverage with matlab](https://github.com/cpp-lln-lab/spm_2_bids/actions/workflows/run_tests_matlab.yml/badge.svg)](https://github.com/cpp-lln-lab/spm_2_bids/actions/workflows/run_tests_matlab.yml)
 [![codecov](https://codecov.io/gh/cpp-lln-lab/spm_2_bids/branch/master/graph/badge.svg?token=yaL40GJK9y)](https://codecov.io/gh/cpp-lln-lab/spm_2_bids)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.6564109.svg)](https://doi.org/10.5281/zenodo.6564109)
 
 # spm_2_bids
 

docs/source/conf.py

@@ -22,7 +22,7 @@
 author = "Rémi Gau"
 
 # The full version, including alpha/beta/rc tags
-release = "v0.2.0"
+release = "v0.2.0dev"
 
 
 # -- General configuration ---------------------------------------------------

requirements.txt

@@ -1,4 +1,4 @@
-miss_hit==0.9.27
+miss_hit==0.9.33
 pre-commit
 jupyterlab
 octave_kernel

src/Mapping.m

@@ -367,20 +367,3 @@ function print_mapping(obj, filename)
 
     end
 end
-
-function bf = prepare_for_printing(spec)
-
-    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

src/utils/identify_rawsources.m

@@ -33,9 +33,9 @@
         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
 

src/utils/identify_sources.m

@@ -71,13 +71,13 @@
         return
     end
 
-    if endsWith(derivatives, '_seg8.mat')
+    if bids.internal.ends_with(derivatives, '_seg8.mat')
 
         prefix_based = false;
 
         derivatives = strrep(derivatives, '_seg8.mat', '.nii');
 
-    elseif endsWith(derivatives, '_uw.mat')
+    elseif bids.internal.ends_with(derivatives, '_uw.mat')
 
         prefix_based = false;
 
@@ -102,17 +102,18 @@
         else
             % remove the prefix of the last step
 
-            if startsWith(bf.prefix, 's') || startsWith(bf.prefix, 'u')
+            if bids.internal.starts_with(bf.prefix, 's') || ...
+                bids.internal.starts_with(bf.prefix, 'u')
                 bf.prefix = bf.prefix(2:end);
 
-            elseif startsWith(bf.prefix, 'w')
+            elseif bids.internal.starts_with(bf.prefix, 'w')
                 bf.prefix = bf.prefix(2:end);
                 add_deformation_field = true;
 
-            elseif startsWith(bf.prefix, 'rp_a')
+            elseif bids.internal.starts_with(bf.prefix, 'rp_a')
                 bf.prefix = bf.prefix(4:end);
 
-            elseif startsWith(bf.prefix, 'mean')
+            elseif bids.internal.starts_with(bf.prefix, 'mean')
                 % TODO mean may involve several files from the source (across runs
                 % and sessions
                 %     prefixes = {

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