Merge remote-tracking branch 'upstream/master' into clarify_b0_threshold

.coveragerc

@@ -0,0 +1,20 @@
+[run]
+branch = True
+concurrency = multiprocessing
+data_file = .test_reports/.coverage
+source =
+    scilpy/
+    scripts/
+omit =
+    scripts/tests/*.py
+    scilpy/tests/**/*.py
+    scilpy/**/tests/*.py
+    scilpy/**/tests/**/*.py
+    scripts/tests/*.py
+    scripts/tests/**/*.py
+
+[report]
+skip_empty = True
+
+[html]
+title = Scilpy Coverage Report

.gitignore

@@ -51,6 +51,7 @@ htmlcov/
 nosetests.xml
 coverage.xml
 *,cover
+.test*
 
 # Translations
 *.mo

.python-version

@@ -1 +1 @@
-3.10
+3.10

Jenkinsfile

@@ -31,15 +31,22 @@ pipeline {
             steps {
                 withPythonEnv('CPython-3.10') {
                     sh '''
+                        pip3 install pytest-cov pytest-html
                         pip3 install wheel==0.38.*
                         pip3 install numpy==1.23.*
                         pip3 install packaging==23.*
                         pip3 install -e .
                         export MPLBACKEND="agg"
                         export OPENBLAS_NUM_THREADS=1
-                        pytest -v
+                        pytest --cov-report term-missing:skip-covered
                     '''
                 }
+                discoverGitReferenceBuild()
+                recordCoverage(
+                    name: 'Scilpy Coverage Report',
+                    sourceCodeRetention: 'MODIFIED',
+                    tools: [[parser: 'COBERTURA',
+                    pattern: '**/.test_reports/coverage.xml']])
             }
         }
 
@@ -63,6 +70,13 @@ pipeline {
                         pullRequest.createReviewRequests(['frheault'])
                     }
                 }
+                xunit(
+                    checksName: '',
+                    tools: [JUnit(excludesPattern: '', failIfNotNew: false,
+                            pattern: '**/.test_reports/junit.xml',
+                            skipNoTestFiles: true,
+                            stopProcessingIfError: true)]
+                )
             }
         }
         failure {

README.md

@@ -27,16 +27,6 @@ pip install --upgrade pip
 
 The library's structure is mostly aligned on that of [DIPY].
 
-⚠️ Breaking changes alert - scilpy 1.6.0 ⚠️
-
-scilpy 1.6.0 is based on [hot_dipy](https://github.com/scilus/hot_dipy) a fork of dipy locked before release v1.8.0.
-In order to install the library and scripts flawlessly (we hope), please follow these instructions:
-```
-pip install packaging>=19.0
-pip install numpy==1.23.*
-pip install Cython==0.29.*
-```
-
 The library and scripts can be installed locally by using:
 ```
 pip install -e .

docs/pull_request_template.md

@@ -0,0 +1,31 @@
+# Quick description
+
+Please include a summary of the changes and the related issue(s) or improvement(s).
+Please also include relevant motivation and context. List any dependencies that are required for this change if needed.
+
+...
+
+## Type of change
+
+Check the relevant options.
+
+- [ ] Bug fix (non-breaking change which fixes an issue)
+- [ ] New feature (non-breaking change which adds functionality)
+- [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
+- [ ] This change requires a documentation update
+
+## Provide data, screenshots, command line to test (if relevant)
+
+...
+
+# Checklist
+
+- [ ] My code follows the style guidelines of this project (run [autopep8](https://pypi.org/project/autopep8/))
+- [ ] I added relevant citations to scripts, modules and functions docstrings and descriptions
+- [ ] I have performed a self-review of my code
+- [ ] I have commented my code, particularly in hard-to-understand areas
+- [ ] I have made corresponding changes to the documentation
+- [ ] My changes generate no new warnings
+- [ ] I moved all functions from the script file (except the argparser and main) to scilpy modules
+- [ ] I have added tests that prove my fix is effective or that my feature works
+- [ ] New and existing unit tests pass locally with my changes

pytest.ini

@@ -21,4 +21,20 @@ filterwarnings =
     once:::statsmodels
     once:::dmri-commit
     once:::cvxpy
-    once:::dmri-amico
+    once:::dmri-amico
+
+required_plugins =
+    pytest-console-scripts
+    pytest-mock
+    pytest-html
+    pytest-cov
+
+junit_logging = out-err
+
+addopts =
+    --html=.test_reports/pytest.html
+    --cov-report=html:.test_reports/coverage.html
+    --junit-xml=.test_reports/junit.xml
+    --cov-report=xml:.test_reports/coverage.xml
+    --cov=scilpy/
+    --cov=scripts/    

requirements.txt

@@ -1,34 +1,36 @@
-bids-validator==1.9.*
+bids-validator==1.11.*
 bctpy==0.5.*
 bz2file==0.98.*
 coloredlogs==15.0.*
-cvxpy==1.3.*
+cvxpy==1.4.*
 cycler==0.11.*
 Cython==0.29.*, !=0.29.29
-#dipy==1.7.*
+dipy==1.8.*
 deepdiff==6.3.0
-dmri-amico==1.5.*
-dmri-commit==1.6.*
+dmri-amico==2.0.*
+dmri-commit==2.0.*
 docopt==0.6.*
 formulaic==0.3.*
-fury==0.8.*
+fury==0.9.*
 future==0.18.*
 GitPython==3.1.*
 h5py==3.7.*
 joblib==1.2.*
 kiwisolver==1.4.*
 matplotlib==3.6.*
-nibabel==4.0.*
+nibabel==5.2.*
 nilearn==0.9.*
 numpy==1.23.*
 openpyxl==3.0.*
 packaging == 23.2.*
 Pillow==10.0.*
-pybids==0.15.*
+pybids==0.16.*
 pyparsing==3.0.*
 PySocks==1.7.*
 pytest==7.2.*
 pytest-console-scripts==1.3.*
+pytest-cov==4.1.0
+pytest-html==4.1.1
 pytest-mock==3.10.*
 python-dateutil==2.8.*
 pytz==2022.6.*
@@ -40,8 +42,3 @@ spams==2.6.*
 statsmodels==0.13.*
 trimeshpy==0.0.3
 vtk==9.2.*
-# Dipy requirements
-h5py>=2.8.0
-tqdm>=4.30.0
-
--e git+https://github.com/scilus/[email protected]#egg=dipy