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

Remi-Gau · Remi-Gau · commit 641ceb0e835f · 2022-05-11T20:03:23.000+02:00
diff --git a/.github/release-drafter.yml b/.github/release-drafter.yml
@@ -0,0 +1,5 @@
+template: |
+  ## Release Notes
+
+  ## CHANGES
+  $CHANGES
diff --git a/.github/workflows/miss_hit_quality.yml b/.github/workflows/miss_hit_quality.yml
@@ -16,7 +16,8 @@ jobs:
 
     steps:
 
-    - uses: actions/checkout@v2
+    - name: Install CPP_ROI
+      uses: actions/checkout@v3
       with:
         submodules: true
         fetch-depth: 1
diff --git a/.github/workflows/miss_hit_style.yml b/.github/workflows/miss_hit_style.yml
@@ -16,7 +16,8 @@ jobs:
 
     steps:
 
-    - uses: actions/checkout@v2
+    - name: Install CPP_ROI
+      uses: actions/checkout@v3
       with:
         submodules: true
         fetch-depth: 1
diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml
diff --git a/.github/workflows/run_tests_matlab.yml b/.github/workflows/run_tests_matlab.yml
@@ -0,0 +1,63 @@
+name: tests and coverage with matlab
+
+on:
+  push:
+    branches:
+      - dev
+      - main
+      - master
+  pull_request:
+    branches: ['*']
+  schedule:
+    - cron: "1 1 1 * *"
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-20.04
+
+    steps:
+      - name: Install MATLAB
+        uses: matlab-actions/setup-matlab@v1.0.1
+        with:
+          # MATLAB release to set up R2020a
+          release: R2020a
+
+      - name: Install CPP_ROI
+        uses: actions/checkout@v3
+        with:
+          submodules: true
+          fetch-depth: 1
+
+      - name: Install SPM
+        run: |
+          git clone https://github.com/spm/spm12.git --depth 1
+
+      - name: Install Moxunit and MOcov
+        run: |
+          git clone https://github.com/MOxUnit/MOxUnit.git --depth 1
+          git clone https://github.com/MOcov/MOcov.git --depth 1
+
+      - name: Add bids-matlab
+        run: |
+          git clone https://github.com/bids-standard/bids-matlab.git --depth 1
+
+      - name: Run commands
+        uses: matlab-actions/run-command@v1.0.1
+        with:
+          command: cd(fullfile(getenv('GITHUB_WORKSPACE'), '.github', 'workflows')); run tests_matlab;
+
+      - name: Run tests
+        run: |
+          cat test_report.log | grep 0
+          bash <(curl -s https://codecov.io/bash)
+
+      - name: Code coverage
+        uses: codecov/codecov-action@v1
+        with:
+          file: coverage.xml # optional
+          flags: unittests # optional
+          name: codecov-umbrella # optional
+          fail_ci_if_error: true # optional (default = false)
diff --git a/.github/workflows/tests_matlab.m b/.github/workflows/tests_matlab.m
@@ -0,0 +1,17 @@
+%
+% (C) Copyright 2022 CPP ROI developers
+
+root_dir = getenv('GITHUB_WORKSPACE');
+
+addpath(fullfile(root_dir, 'spm12'));
+addpath(fullfile(root_dir, 'bids-matlab'));
+addpath(fullfile(root_dir, 'MOcov', 'MOcov'));
+
+cd(fullfile(root_dir, 'MOxUnit', 'MOxUnit'));
+run moxunit_set_path();
+
+cd(fullfile(root_dir));
+
+initCppRoi();
+
+run run_tests();
diff --git a/atlas/returnAtlasDir.m b/atlas/returnAtlasDir.m
@@ -10,7 +10,7 @@
   %
   % (C) Copyright 2021 CPP ROI developers
 
-  atlasDir = fullfile(rootDir(), 'atlas');
+  atlasDir = fileparts(mfilename('fullpath'));
 
   if nargin > 0
 
diff --git a/demos/roi/inputs/visual motion_association-test_z_FDR_0.01.nii.gz b/demos/roi/inputs/visual motion_association-test_z_FDR_0.01.nii.gz
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -23,7 +23,7 @@
 author = "the CPP ROI dev team"
 
 # The full version, including alpha/beta/rc tags
-release = "v0.1.0dev"
+release = "v0.2.0dev"
 
 
 # -- General configuration ---------------------------------------------------
diff --git a/initCppRoi.m b/initCppRoi.m
@@ -5,7 +5,7 @@ function initCppRoi()
   global CPP_ROI_INITIALIZED
   global CPP_ROI_PATHS
 
-  if isempty(CPP_ROI_INITIALIZED)
+  if isempty(CPP_ROI_INITIALIZED) || ~CPP_ROI_INITIALIZED
 
     % directory with this script becomes the current directory
     thisDirectory = fileparts(mfilename('fullpath'));
@@ -18,6 +18,8 @@ function initCppRoi()
     CPP_ROI_PATHS = genpath(fullfile(thisDirectory, 'src'));
     CPP_ROI_PATHS = cat(2, CPP_ROI_PATHS, pathSep, ...
                         fullfile(thisDirectory, 'lib', 'marsbar-0.44'));
+    CPP_ROI_PATHS = cat(2, CPP_ROI_PATHS, pathSep, ...
+                        fullfile(thisDirectory, 'atlas'));
     addpath(CPP_ROI_PATHS, '-begin');
 
     marsbar('on');
diff --git a/run_tests.m b/run_tests.m
@@ -8,6 +8,8 @@
 
 testFolder = fullfile(fileparts(mfilename('fullpath')), 'tests');
 
+addpath(fullfile(testFolder, 'utils'));
+
 folderToCover = fullfile(testFolder, '..', 'src');
 
 success = moxunit_runtests( ...
diff --git a/src/utils/cppRoiRoot.m b/src/utils/cppRoiRoot.m
@@ -0,0 +1,14 @@
+function pth = cppRoiRoot()
+  %
+  %
+  % USAGE::
+  %
+  %   pth = cppRoiRoot()
+  %
+  %
+  % (C) Copyright 2022 CPP ROI developers
+
+  pth = fullfile(fileparts(mfilename('fullpath')), '..', '..');
+  pth = spm_file(pth, 'cpath');
+
+end
diff --git a/src/utils/rootDir.m b/src/utils/rootDir.m
diff --git a/tests/space-MNI_label-neurosynth motion_probseg.nii.gz b/tests/space-MNI_label-neurosynth motion_probseg.nii.gz
diff --git a/tests/test_getLookUpTable.m b/tests/test_getLookUpTable.m
@@ -23,10 +23,14 @@ function test_lut_wang()
 
 function test_lut_anat_tb()
 
-  lut = getLookUpTable('anatomy_toobox');
+  if ~isGithubCi
 
-  assertEqual(lut.label(1), 7);
-  assertEqual(lut.ROI{1}, 'Interposed Nucleus');
+    lut = getLookUpTable('anatomy_toobox');
+
+    assertEqual(lut.label(1), 7);
+    assertEqual(lut.ROI{1}, 'Interposed Nucleus');
+
+  end
 
 end
 
diff --git a/tests/test_thresholdToMask.m b/tests/test_thresholdToMask.m
@@ -48,7 +48,9 @@ function test_thresholdToMask_cluster()
 
 function inputImage = setUp(image)
 
-  gzImage = spm_file(fullfile(rootDir(), 'demos', 'roi', 'inputs', image), 'cpath');
+  rootDir = fullfile(fileparts(mfilename('fullpath')), '..');
+
+  gzImage = spm_file(fullfile(rootDir, 'demos', 'roi', 'inputs', image), 'cpath');
   [~, basename] = spm_fileparts(gzImage);
   gunzip(gzImage, pwd);
 
diff --git a/tests/test_unit_returnAtlasDir.m b/tests/test_unit_returnAtlasDir.m
@@ -8,27 +8,19 @@
   initTestSuite;
 end
 
-function test_returnAtlasDir_no_input()
-
-  atlasDir = returnAtlasDir();
-
-  assertEqual(atlasDir, baseAtlasDir());
-
-end
-
 function test_returnAtlasDir_default()
 
   atlasDir = returnAtlasDir('neuromorphometric');
 
-  assertEqual(atlasDir, baseAtlasDir());
+  assertEqual(atlasDir, returnAtlasDir());
 
 end
 
 function test_returnAtlasDir_wang()
 
   atlasDir = returnAtlasDir('wang');
 
-  expected = fullfile(baseAtlasDir(),  'visual_topography_probability_atlas');
+  expected = fullfile(returnAtlasDir(),  'visual_topography_probability_atlas');
 
   assertEqual(atlasDir, expected);
 
@@ -43,9 +35,3 @@ function test_returnAtlasDir_anatomy_toobox()
   assertEqual(atlasDir, expected);
 
 end
-
-function baseDir = baseAtlasDir()
-
-  baseDir = spm_file(fullfile(rootDir(), 'atlas'), 'cpath');
-
-end
diff --git a/tests/utils/isGithubCi.m b/tests/utils/isGithubCi.m
@@ -0,0 +1,18 @@
+function [IS_GITHUB, pth] = isGithubCi()
+  %
+  % (C) Copyright 2022 CPP ROI developers
+
+  IS_GITHUB = false;
+
+  GITHUB_WORKSPACE = getenv('HOME');
+
+  if strcmp(GITHUB_WORKSPACE, '/home/runner')
+
+    fprintf(1, '\n WE ARE RUNNING IN GITHUB CI\n');
+
+    IS_GITHUB = true;
+    pth = GITHUB_WORKSPACE;
+
+  end
+
+end
diff --git a/tests/utils/isOctave.m b/tests/utils/isOctave.m
@@ -0,0 +1,21 @@
+function retval = isOctave()
+  %
+  % Returns true if the environment is Octave.
+  % Only in the test folder for testing purposes
+  %
+  % USAGE::
+  %
+  %   retval = isOctave()
+  %
+  % :returns: :retval: (boolean)
+  %
+  % (C) Copyright 2022 CPP ROI developers
+
+  persistent cacheval   % speeds up repeated calls
+
+  if isempty (cacheval)
+    cacheval = (exist ('OCTAVE_VERSION', 'builtin') > 0);
+  end
+
+  retval = cacheval;
+end
diff --git a/tests/utils/rmRetinoAtlas.m b/tests/utils/rmRetinoAtlas.m
diff --git a/version.txt b/version.txt
@@ -1 +1 @@
-v0.1.0dev
+v0.2.0dev

Original file line number	Diff line number	Diff line change
`@@ -10,7 +10,7 @@`
`10`	`10`	`%`
`11`	`11`	`% (C) Copyright 2021 CPP ROI developers`
`12`	`12`
`13`		`- atlasDir = fullfile(rootDir(), 'atlas');`
	`13`	`+ atlasDir = fileparts(mfilename('fullpath'));`
`14`	`14`
`15`	`15`	`if nargin > 0`
`16`	`16`