[INFRA] updates for 1.0.0 release

.github/workflows/miss_hit.yml → .github/workflows/miss_hit_quality.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_style.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/run_system_tests.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 "initCppSpm; savepath();"       
-
-    - name: Prepare data
-      run: |
-        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
-
+
     - name: Run system tests
       run: |
-        cd demos/MoAE
-        octave $OCTFLAGS --eval "MoAEpilot_run"                  
+        cd manualTests/
+        octave $OCTFLAGS --eval "systemTestMoAE"                  
 

.github/workflows/run_tests.yml

@@ -78,7 +78,7 @@ jobs:
 
     - 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)         
 

.gitignore

@@ -29,6 +29,7 @@ docs/build/*
 
 # ignore virtual env
 cpp_spm/*
+env/*
 
 # visual studio code stuff
 .vscode

README.md

@@ -35,7 +35,7 @@ This is a set of functions to MRI analysis on a
 
 ## Installation
 
-TODO
+<!-- TODO -->
 
 We strongly recommend using the CPP fMRI analysis template repository (INSERT
 URL) to use CPP_SPM.
@@ -114,6 +114,14 @@ Please see our
 [documentation](https://cpp-bids-spm.readthedocs.io/en/latest/index.html) for
 more info.
 
+## Octave compatibility
+
+The following features do not yet work with Octave:
+
+-   anatomicalQA
+-   functionalQA
+-   slice_display toolbox
+
 ## Contributing
 
 Feel free to open issues to report a bug and ask for improvements.
@@ -125,6 +133,18 @@ or you get stuck: it is more likely we did not do good enough a job at
 explaining things. So do not hesitate to open an issue, just to ask for
 clarification.
 
+### Style guidelines
+
+These are some of the guidelines we try to follow.
+
+We use `camelCase` to name functions and variables for the vast majority of the
+code in this repository.
+
+Scripts names in general and as well functions related to the demos use a
+`snake_case`.
+
+Constant are written in `UPPERCASE`.
+
 ## Contributors
 
 Thanks goes to these wonderful people

demos/MoAE/dowload_MoAE_ds.m → demos/MoAE/download_moae_ds.m

@@ -1,6 +1,6 @@
-% (C) Copyright 2021 Remi Gau
-
-function dowload_MoAE_ds(downloadData)
+function download_moae_ds(downloadData)
+  %
+  % (C) Copyright 2021 Remi Gau
 
   if downloadData
 

demos/MoAE/MoAE_create_roi_extract_data.m → demos/MoAE/moae_create_roi_extract_data.m

@@ -6,7 +6,7 @@
 % we are going to extract the value from.
 %
 
-run MoAE_run.m;
+run moae_run.m;
 
 subLabel = '01';
 

demos/MoAE/MoAE_getOption.m → demos/MoAE/moae_get_option.m

@@ -1,8 +1,9 @@
-% (C) Copyright 2019 Remi Gau
-
-function opt = MoAE_getOption()
+function opt = moae_get_option()
+  %
   % returns a structure that contains the options chosen by the user to run
   % slice timing correction, pre-processing, FFX, RFX.
+  %
+  % (C) Copyright 2019 Remi Gau
 
   opt = [];
 

demos/MoAE/MoAE_run.m → demos/MoAE/moae_run.m

@@ -18,32 +18,35 @@
 run ../../initCppSpm.m;
 
 %% Set options
-opt = MoAE_getOption();
+opt = moae_get_option();
 
-dowload_MoAE_ds(downloadData);
+download_moae_ds(downloadData);
 
 %% Run batches
 reportBIDS(opt);
 bidsCopyRawFolder(opt, 1);
 
 % In case you just want to run segmentation and skull stripping
-
-bidsSegmentSkullStrip(opt);
-
+% bidsSegmentSkullStrip(opt);
+%
 % NOTE: skull stripping is also included in 'bidsSpatialPrepro'
 
 bidsSTC(opt);
 
 bidsSpatialPrepro(opt);
 
 % The following do not run on octave for now (because of spmup)
-% anatomicalQA(opt);
-% bidsResliceTpmToFunc(opt);
-% functionalQA(opt);
+anatomicalQA(opt);
+bidsResliceTpmToFunc(opt);
+functionalQA(opt);
 
 bidsSmoothing(FWHM, opt);
 
-% The following crash on Travis CI
+% The following crash on CI
+WD = pwd;
 bidsFFX('specifyAndEstimate', opt, FWHM);
+cd(WD);
 bidsFFX('contrasts', opt, FWHM);
+cd(WD);
 bidsResults(opt, FWHM);
+cd(WD);

demos/MoAE/MoAE_slice_display.m → demos/MoAE/moae_slice_display.m

@@ -1,7 +1,6 @@
 % (C) Copyright 2021 Remi Gau
 
-run MoAE_run.m;
-run MoAE_create_roi_extract_data.m;
+run moae_create_roi_extract_data.m;
 
 close all;
 

demos/MoAE/options/options_task-auditory.json

@@ -1,19 +1,12 @@
 {
-    "STC_referenceSlice": [],
     "anatReference": {
         "type": "T1w",
-        "session": 1
+        "session": ""
     },
-    "contrastList": [],
-    "dataDir": "/home/remi/github/CPP_SPM/demos/MoAE/output/MoAEpilot",
-    "derivativesDir": "/home/remi/github/CPP_SPM/demos/MoAE/derivatives/default",
-    "funcVoxelDims": [],
-    "groups": [""],
+    "dataDir": "./inputs/raw",
+    "derivativesDir": "./outputs/",
     "model": {
-        "file": "/home/remi/github/CPP_SPM/demos/MoAE/models/model-MoAE_smdl.json"
-    },
-    "realign": {
-        "useUnwarp": true
+        "file": "./models/model-MoAE_smdl.json"
     },
     "result": {
         "Steps": {
@@ -41,9 +34,7 @@
     "skullstrip": {
         "threshold": 0.75
     },
-    "sliceOrder": [],
     "space": "MNI",
-    "subjects": [[]],
     "taskName": "auditory",
     "useFieldmaps": true,
     "zeropad": 2

demos/MoAE/options/options_task-auditory_space-individual.json

@@ -1,15 +1,12 @@
 {
-    "STC_referenceSlice": [],
     "anatReference": {
         "type": "T1w",
-        "session": 1
+        "session": ""
     },
-    "contrastList": [],
-    "dataDir": "/home/remi/github/CPP_SPM/demos/MoAE/output/MoAEpilot",
-    "derivativesDir": "/home/remi/github/CPP_SPM/demos/MoAE/derivatives/native",
-    "funcVoxelDims": [],
+    "dataDir": "./inputs/raw",
+    "derivativesDir": "./outputs/",
     "model": {
-        "file": "/home/remi/github/CPP_SPM/demos/MoAE/models/model-MoAE_smdl.json"
+        "file": "./models/model-MoAE_smdl.json"
     },
     "realign": {
         "useUnwarp": true
@@ -40,7 +37,6 @@
     "skullstrip": {
         "threshold": 0.75
     },
-    "sliceOrder": [],
     "space": "individual",
     "taskName": "auditory",
     "useFieldmaps": true,

demos/MoAE/options/options_task-auditory_unwarp-0.json

@@ -1,15 +1,12 @@
 {
-    "STC_referenceSlice": [],
     "anatReference": {
         "type": "T1w",
-        "session": 1
+        "session": ""
     },
-    "contrastList": [],
-    "dataDir": "/home/remi/github/CPP_SPM/demos/MoAE/output/MoAEpilot",
-    "derivativesDir": "/home/remi/github/CPP_SPM/demos/MoAE/derivatives/unwarp-0",
-    "funcVoxelDims": [],
+    "dataDir": "./inputs/raw",
+    "derivativesDir": "./outputs/",
     "model": {
-        "file": "/home/remi/github/CPP_SPM/demos/MoAE/models/model-MoAE_smdl.json"
+        "file": "./models/model-MoAE_smdl.json"
     },
     "realign": {
         "useUnwarp": false
@@ -40,7 +37,6 @@
     "skullstrip": {
         "threshold": 0.75
     },
-    "sliceOrder": [],
     "space": "MNI",
     "taskName": "auditory",
     "useFieldmaps": true,

demos/MoAE/options/options_task-auditory_unwarp-0_space-individual.json

@@ -1,15 +1,12 @@
 {
-    "STC_referenceSlice": [],
     "anatReference": {
         "type": "T1w",
-        "session": 1
+        "session": ""
     },
-    "contrastList": [],
-    "dataDir": "/home/remi/github/CPP_SPM/demos/MoAE/output/MoAEpilot",
-    "derivativesDir": "/home/remi/github/CPP_SPM/demos/MoAE/derivatives/unwarp-0_native",
-    "funcVoxelDims": [],
+    "dataDir": "./inputs/raw",
+    "derivativesDir": "./outputs/",
     "model": {
-        "file": "/home/remi/github/CPP_SPM/demos/MoAE/models/model-MoAE_smdl.json"
+        "file": "./models/model-MoAE_smdl.json"
     },
     "realign": {
         "useUnwarp": false
@@ -40,7 +37,6 @@
     "skullstrip": {
         "threshold": 0.75
     },
-    "sliceOrder": [],
     "space": "individual",
     "taskName": "auditory",
     "useFieldmaps": true,

demos/MoAE/return_normalized_anat_file.m

@@ -1,6 +1,6 @@
-% (C) Copyright 2021 Remi Gau
-
 function [anat_normalized_file, anatRange] = return_normalized_anat_file(opt, subLabel)
+  %
+  % (C) Copyright 2021 Remi Gau
 
   [BIDS, opt] = getData(opt);
   [~, anatDataDir] = getAnatFilename(BIDS, subLabel, opt);