Merge branch 'feat/rollout_mocks' of https://github.com/alexvcaron/sc…

…ilpy into pr/AlexVCaron/664

.github/workflows/freeze_requirements.yml

@@ -0,0 +1,32 @@
+name : Freeze release requirements
+
+on: 
+  push:
+    tags:
+      - '*'
+
+jobs:
+  freeze_requirements:
+    runs-on: ubuntu-latest
+    steps:
+      - 
+        name: Checkout scilpy
+        uses: actions/checkout@v3
+      -
+        name: Install python
+        uses: actions/setup-python@v4
+        with:
+          python-version-file: '.python-version'
+          cache: 'pip'
+      -
+        name: Freeze requirements
+        id: requirements-freezer
+        run: |
+          pip install pip-tools
+          pip-compile --no-upgrade --allow-unsafe -o requirements.${{ github.ref_name }}.frozen
+          echo "requirements=$PWD/requirements.${{ github.ref_name }}.frozen" >> $GITHUB_OUTPUT
+      -
+        name: Upload frozen requirements to release
+        uses: softprops/action-gh-release@v1
+        with:
+          files : ${{ steps.requirements-freezer.outputs.requirements }}

.python-version

@@ -0,0 +1 @@
+3.10

Jenkinsfile

@@ -4,12 +4,12 @@ pipeline {
     stages {
         stage('Build') {
             stages {
-                stage('Python3.7') {
+                stage('Python3.10') {
                     steps {
-                        withPythonEnv('CPython-3.7') {
+                        withPythonEnv('CPython-3.10') {
                             sh '''
-                                pip3 install wheel==0.37.*
-                                pip3 install numpy==1.21.*
+                                pip3 install wheel==0.38.*
+                                pip3 install numpy==1.23.*
                                 pip3 install Cython==0.29.*
                                 pip3 install -e .
                             '''
@@ -21,10 +21,10 @@ pipeline {
 
         stage('Test') {
             steps {
-                withPythonEnv('CPython-3.7') {
+                withPythonEnv('CPython-3.10') {
                     sh '''
-                        pip3 install wheel==0.37.*
-                        pip3 install numpy==1.21.*
+                        pip3 install wheel==0.38.*
+                        pip3 install numpy==1.23.*
                         pip3 install -e .
                         export MPLBACKEND="agg"
                         export OPENBLAS_NUM_THREADS=1
@@ -51,7 +51,7 @@ pipeline {
                         pullRequest.createReviewRequests(['arnaudbore'])
                     }
                     else{
-                        pullRequest.createReviewRequests(['GuillaumeTh'])
+                        pullRequest.createReviewRequests(['frheault'])
                     }
                 }
             }

README.md

@@ -9,24 +9,38 @@
 **Scilpy** mainly comprises tools and utilities to quickly work with diffusion MRI. Most of the tools are based
 on or are wrappers of the [DIPY] library, and most of them will eventually be migrated to [DIPY]. Those tools implement the recommended workflows and parameters used in the lab.
 
+The library is now built for Python 3.10 so be sure to create a virtual environnement for Python 3.10. If this version is not installed on your computer:
+```
+sudo add-apt-repository ppa:deadsnakes/ppa
+sudo apt-get install python3.10 python3.10-dev python3.10-venv python3.10-minimal python3.10-tk
+```
+
+Make sure your pip is up-to-date before trying to install:
+```
+pip install --upgrade pip
+```
+
 The library's structure is mostly aligned on that of [DIPY].
 The library and scripts can be installed locally by using:
 ```
 pip install -e .
 ```
+
 On Linux, most likely you will have to install libraries for COMMIT/AMICO
 ```
 sudo apt install libblas-dev liblapack-dev
 ```
-On Ubuntu-20.04, you will have to install libraries for matplotlib
-```
-sudo apt install libfreetype6-dev
-```
+
 While on MacOS you will have to use (most likely)
 ```
 brew install openblas lapack
 ```
 
+On Ubuntu >=20.04, you will have to install libraries for matplotlib
+```
+sudo apt install libfreetype6-dev
+```
+
 Note that using this technique will make it harder to remove the scripts when changing versions.
 We highly recommend working in a [Python Virtual Environment].
 

docs/source/documentation/btensor_scripts.rst

@@ -0,0 +1,20 @@
+Instructions for tensor-valued dMRI scripts (b-tensor)
+======================================================
+
+
+The scripts for multi-encoding multi-shell multi-tissue CSD (memsmt-CSD) are based on P. Karan et al., Bridging the gap between constrained spherical deconvolution and diffusional variance decomposition via tensor-valued diffusion MRI. Medical Image Analysis (2022). We recommend reading it to understand the scope of the memsmt-CSD problem.
+
+If you want to do CSD with b-tensor data, you should start by computing the fiber response functions. This script should run fast (less than 5 minutes on a full brain).
+::
+
+    scil_compute_memsmt_frf.py wm_frf.txt gm_frf.txt csf_frf.txt --in_dwis dwi_linear.nii.gz dwi_planar.nii.gz dwi_spherical.nii.gz --in_bvals dwi_linear.bval dwi_planar.bval dwi_spherical.bval --in_bvecs dwi_linear.bvec dwi_planar.bvec dwi_spherical.bvec --in_bdeltas 1 -0.5 0 --mask mask.nii.gz --mask_wm wm_mask.nii.gz --mask_gm gm_mask.nii.gz --mask_csf csf_mask.nii.gz -f
+
+Then, you should compute the fODFs and volume fractions. The following command will save a fODF file for each tissue and a volume fractions file. This script should run in about 1-2 hours for a full brain.
+::
+
+    scil_compute_memsmt_fodf.py wm_frf.txt gm_frf.txt csf_frf.txt --in_dwis dwi_linear.nii.gz dwi_planar.nii.gz dwi_spherical.nii.gz --in_bvals dwi_linear.bval dwi_planar.bval dwi_spherical.bval --in_bvecs dwi_linear.bvec dwi_planar.bvec dwi_spherical.bvec --in_bdeltas 1 -0.5 0 --mask mask.nii.gz --processes 8 -f
+
+If you want to do DIVIDE with b-tensor data, you should use the following command. It will save files for the MD, uFA, OP, MK_I, MK_A and MK_T. This script should run in about 1-2 hours for a full brain.
+::
+
+    scil_compute_divide.py --in_dwis dwi_linear.nii.gz dwi_planar.nii.gz dwi_spherical.nii.gz --in_bvals dwi_linear.bval dwi_planar.bval dwi_spherical.bval --in_bvecs dwi_linear.bvec dwi_planar.bvec dwi_spherical.bvec --in_bdeltas 1 -0.5 0 --mask mask.nii.gz --fa fa.nii.gz --processes 8 -f

pytest.ini

@@ -23,9 +23,6 @@ filterwarnings =
     once:::cvxpy
     once:::dmri-amico
 
-usefixtures =
-    apply_mocks
-
 required_plugins =
-    pytest_console_scripts
+    pytest-console-scripts
     pytest-mock

requirements.txt

@@ -1,41 +1,44 @@
+bids-validator==1.9.*
+bctpy==0.5.*
 bz2file==0.98.*
-coloredlogs==10.0.*
-cycler==0.10.*
-Cython==0.29.*
-dipy==1.5.*
-docopt==0.6.2
-fury==0.7.*
-future==0.17.*
-h5py==2.10.*
-joblib==1.1.0
-kiwisolver==1.0.*
-matplotlib==2.2.*
-nibabel==3.0.*
-nilearn==0.6.*
-numpy==1.21.*
-Pillow==9.0.1
-bids-validator==1.6.0
+coloredlogs==15.0.*
+cvxpy==1.3.*
+cycler==0.11.*
+Cython==0.29.*, !=0.29.29
+# dipy==1.6.*
+dmri-amico==1.5.*
+dmri-commit==1.6.*
+docopt==0.6.*
+formulaic==0.3.*
+fury==0.8.*
+future==0.18.*
+h5py==3.7.*
+joblib==1.2.*
+kiwisolver==1.4.*
+matplotlib==3.6.*
+nibabel==4.0.*
+nilearn==0.9.*
+numpy==1.23.*
+openpyxl==3.0.*
+Pillow==9.3.*
 pybids==0.15.*
-pyparsing==2.2.*
+pyparsing==3.0.*
 PySocks==1.7.*
-python-dateutil==2.7.*
-pytz==2018.4.*
-scikit-learn==0.22.*
-scipy==1.4.*
-setuptools==46.1.*
-six==1.15.*
-vtk>=8.0.0,<10.0.0
-trimeshpy==0.0.*
-coloredlogs==10.0.*
-nilearn==0.6.*
-pytest==5.3.*
-pytest_console_scripts==0.2.*
+pytest==7.2.*
+pytest-console-scripts==1.3.*
 pytest-mock==3.10.*
-requests==2.23.*
-bctpy==0.5.*
-statsmodels==0.11.*
-dmri-commit==1.4.*
-openpyxl==2.6.*
-cvxpy==1.1.*
-dmri-amico==1.2.*
-formulaic==0.2.4
+python-dateutil==2.8.*
+pytz==2022.6.*
+requests==2.28.*
+scikit-learn==1.2.*
+scipy==1.9.*
+six==1.16.*
+spams==2.6.*
+statsmodels==0.13.*
+trimeshpy==0.0.2
+vtk==9.2.*
+# Dipy requirements
+h5py>=2.8.0
+packaging>=19.0
+tqdm>=4.30.0
+-e git+https://github.com/scilus/[email protected]#egg=dipy