Merge pull request #341 from cpp-lln-lab/rel_0.3.0

[REL] Release 1.0.0

Author: Remi-Gau

.github/workflows/check_markdown.yml

@@ -1,4 +1,4 @@
-name: miss_hit
+name: miss_hit_quality
 
 on:
   push:
@@ -29,10 +29,6 @@ jobs:
         python -m pip install --upgrade pip setuptools
         pip3 install -r requirements.txt
 
-    - name: MISS_HIT Code style
-      run: |
-        mh_style --process-slx
-
     - name: MISS_HIT Metrics
       run: |
         mh_metric --ci

.github/workflows/miss_hit.yml renamed to .github/workflows/miss_hit_quality.yml

@@ -0,0 +1,35 @@
+name: miss_hit_style
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches: '*'
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+
+    - uses: actions/checkout@v2
+      with:
+        submodules: true
+        fetch-depth: 1
+
+    - name: Set up Python 3.6
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.6
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip setuptools
+        pip3 install -r requirements.txt
+
+    - name: MISS_HIT Code style
+      run: |
+        mh_style
+

.github/workflows/miss_hit_style.yml

@@ -56,20 +56,9 @@ jobs:
          make -C spm12/src PLATFORM=octave install
          octave $OCTFLAGS --eval "addpath(fullfile(pwd, 'spm12')); savepath();"
         
-    - name: Update octave path
-      run: |
-        octave $OCTFLAGS --eval "addpath(genpath(fullfile(pwd, 'lib'))); savepath();"
-        octave $OCTFLAGS --eval "addpath(genpath(fullfile(pwd, 'src'))); savepath();"        
-
-    - name: Prepare data
-      run: |
-        output_folder='demos/MoAE/output/'
-        mkdir $output_folder
-        curl http://www.fil.ion.ucl.ac.uk/spm/download/data/MoAEpilot/MoAEpilot.bids.zip --output $output_folder'MoAEpilot.zip'
-        unzip $output_folder'MoAEpilot.zip' -d $output_folder
-
+    
     - name: Run system tests
       run: |
-        cd demos/MoAE
-        octave $OCTFLAGS --eval "MoAEpilot_run"                  
+        cd manualTests/
+        octave $OCTFLAGS --eval "test_moae"                  
 

.github/workflows/run_system_tests.yml

@@ -62,22 +62,23 @@ jobs:
         
     - name: Update octave path
       run: |
-        octave $OCTFLAGS --eval "addpath(genpath(fullfile(pwd, 'lib'))); savepath();"
-        octave $OCTFLAGS --eval "addpath(genpath(fullfile(pwd, 'src'))); savepath();"        
+        octave $OCTFLAGS --eval "initCppSpm; savepath();"
+        octave $OCTFLAGS --eval "addpath(fullfile(pwd, 'tests', 'utils')); savepath();"        
 
     - name: Prepare data
       run: |
-        output_folder='demos/MoAE/output/'
-        mkdir $output_folder
-        curl http://www.fil.ion.ucl.ac.uk/spm/download/data/MoAEpilot/MoAEpilot.bids.zip --output $output_folder'MoAEpilot.zip'
-        unzip $output_folder'MoAEpilot.zip' -d $output_folder
+        inputs_folder='demos/MoAE/inputs/'
+        mkdir $inputs_folder
+        curl http://www.fil.ion.ucl.ac.uk/spm/download/data/MoAEpilot/MoAEpilot.bids.zip --output $inputs_folder'MoAEpilot.zip'
+        unzip $inputs_folder'MoAEpilot.zip' -d $inputs_folder
+        mv $inputs_folder/MoAEpilot $inputs_folder/raw
         cd tests
         sh createDummyDataSet.sh
         cd ..
 
     - name: Run tests
       run: |
-        octave $OCTFLAGS --eval "runTests"
+        octave $OCTFLAGS --eval "run_tests"
         cat test_report.log | grep 0
         bash <(curl -s https://codecov.io/bash)         
 

.github/workflows/run_tests.yml

@@ -13,27 +13,23 @@ options_task-*date*.json
 onsets*_events.mat
 
 # files in the demo folder related to running the demo analysis
-demos/*/*.zip
-demos/*/derivatives/*
-demos/MoAE/output/*
-demos/spm*/raw
-demos/spm*/source
+demos/*/outputs/
+demos/*/inputs/
+demos/*/*.nii
+demos/*/cfg/*.json
 
 # test folder and dummy data
-tests/sub-01/*
+tests/*.png
 tests/group/*
-tests/models/*.json
-tests/dummyData/derivatives/cpp_spm/sub-*/*/*/*.nii*
-tests/dummyData/derivatives/cpp_spm/sub-*/*/*/*.tsv
-tests/dummyData/derivatives/cpp_spm/sub-*/*/*/*.txt
-tests/dummyData/derivatives/cpp_spm/sub-*/*/*/*.json
-tests/dummyData/derivatives/cpp_spm/sub-*/stats/*/*/*.nii*
+tests/*/*.json
+tests/dummyData/derivatives/cpp_spm*/sub-*/
 
 # ignore content of the build folder of the doc
 docs/build/*
 
 # ignore virtual env
 cpp_spm/*
+env/*
 
 # visual studio code stuff
 .vscode

.gitignore

@@ -4,3 +4,12 @@
 [submodule "lib/spmup"]
 	path = lib/spmup
 	url = https://github.com/CPernet/spmup.git
+[submodule "lib/CPP_ROI"]
+	path = lib/CPP_ROI
+	url = https://github.com/cpp-lln-lab/CPP_ROI.git
+[submodule "lib/slice_display"]
+	path = lib/slice_display
+	url = https://github.com/bramzandbelt/slice_display.git
+[submodule "lib/brain_colours"]
+	path = lib/brain_colours
+	url = https://github.com/CPernet/brain_colours.git

.gitmodules

@@ -31,11 +31,16 @@
       "affiliation": "Université Catholique de Louvain",
       "name": "Gurtubay, Ane",
       "orcid": "0000-0003-3824-2219"
-    },    
+    },
     {
       "affiliation": "Université Catholique de Louvain",
       "name": "Falagiarda, Federica",
       "orcid": "0000-0001-7844-1605"
+    },
+    {
+      "affiliation": "Université de Montréal",
+      "name": "MacLean, Michèle",
+      "orcid": "0000-0002-0174-9326"
     }
   ],
   "keywords": [
@@ -49,4 +54,4 @@
   ],
   "license": "GPL-3",
   "upload_type": "software"
-}
+}