Merge pull request #28 from cpp-lln-lab/dev

[REL] 0.2.0

.github/release-drafter.yml

@@ -0,0 +1,5 @@
+template: |
+  ## Release Notes
+
+  ## CHANGES
+  $CHANGES

.github/workflows/miss_hit_quality.yml

@@ -3,7 +3,9 @@ name: miss_hit_quality
 on:
   push:
     branches:
+      - main
       - master
+      - dev
   pull_request:
     branches: ['*']
 
@@ -14,7 +16,8 @@ jobs:
 
     steps:
 
-    - uses: actions/checkout@v2
+    - name: Install CPP_ROI
+      uses: actions/checkout@v3
       with:
         submodules: true
         fetch-depth: 1
@@ -28,8 +31,6 @@ jobs:
       run: |
         python -m pip install --upgrade pip setuptools
         pip3 install -r requirements.txt
-        cd tests
-        make data
 
     - name: MISS_HIT Metrics
       run: |

.github/workflows/miss_hit_style.yml

@@ -3,9 +3,11 @@ name: miss_hit_style
 on:
   push:
     branches:
+      - main
       - master
+      - dev
   pull_request:
-    branches: '*'
+    branches: ['*']
 
 jobs:
   build:
@@ -14,7 +16,8 @@ jobs:
 
     steps:
 
-    - uses: actions/checkout@v2
+    - name: Install CPP_ROI
+      uses: actions/checkout@v3
       with:
         submodules: true
         fetch-depth: 1
@@ -28,8 +31,6 @@ jobs:
       run: |
         python -m pip install --upgrade pip setuptools
         pip3 install -r requirements.txt
-        cd tests
-        make data
 
     - name: MISS_HIT Code style
       run: |

.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)

.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();

.gitignore

@@ -1,18 +1,18 @@
-
 .DS_Store
 
 *.nii
-
+*.xml
+*.log
 *.asv
 *.m~
 *.mat
 
-<<<<<<< HEAD
+*.html
+
 # files in the demo folder related to running the demo analysis
 # demos/roi
-=======
+
 atlas/visual_topography_probability_atlas/
->>>>>>> 4a2a3830905dfad9b61804bf99e2941a49e4e2fa
 
 # test folder and dummy data
 
@@ -28,3 +28,5 @@ envs/*
 demos/*/*.json
 demos/*/*/*.json
 demos/*/derivatives
+
+atlas/*.json

.pre-commit-config.yaml

@@ -28,7 +28,7 @@ repos:
       additional_dependencies: [miss_hit]
 
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.0.1
+  rev: v4.1.0
   hooks:
     - id: trailing-whitespace
     - id: end-of-file-fixer

README.md

@@ -1,22 +1,13 @@
-<!-- lint disable -->
-
-**Documentation**
-
-**Code quality and style**
-
-**Unit tests and coverage**
-
-**How to cite**
-
-**Contributors**
-
 # CPP ROI
 
-## :warning: :warning: :warning:
+---
+
+## :warning:
 
-**This code is fairly unstable (:boom:) and might still change a lot.**
+**This code is fairly unstable and might still change.**
 
-Also this code currently has 0% test coverage...
+So make sure you "pin" which version or commit you are using for a given
+project, if you don't want your code to break in the future.
 
 ---
 
@@ -57,8 +48,7 @@ as a submodule, and intitialized when running `initCppSpm`.
 
 ### Dependencies
 
-=======
-TODO
+======= TODO
 
 | Dependencies                                               | Used version |
 | ---------------------------------------------------------- | ------------ |
@@ -98,8 +88,4 @@ TODO
 Also includes:
 
 -   Yeo's 7 networks "atlas"
-    -   add REF and URL
-
-## Contributing
-
-## Contributors
+  <!-- add REF and URL -->

src/atlas/returnAtlasDir.m → atlas/returnAtlasDir.m

@@ -10,7 +10,7 @@
   %
   % (C) Copyright 2021 CPP ROI developers
 
-  atlasDir = fullfile(fileparts(mfilename('fullpath')), '..', '..', 'atlas');
+  atlasDir = fileparts(mfilename('fullpath'));
 
   if nargin > 0