Merge branch 'dev'

.git-blame-ignore-rev

@@ -0,0 +1,2 @@
+# Migrate code style to Black
+1645bbf45b6aad3b8ed74975907373fc98bde5fa

.gitignore

@@ -2,7 +2,7 @@
 build/
 dist/
 examples/external-data
-Clinica.egg-info
+clinicadl.egg-info
 *egg-info
 *.log
 *.lock

.pep8speaks.yml

@@ -4,8 +4,8 @@ scanner:
 
 pycodestyle:
     ignore:
+        - E203 # Whitespace before ':'
         - E501 # Line too long
         - W503 # Line break occurred before a binary operator
-        - W504 # Line break occurred after a binary operator
 
 no_blank_comment: True # If True, no comment is made on PR without any errors.

.pre-commit-config.yaml

@@ -0,0 +1,20 @@
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v2.3.0
+    hooks:
+    -   id: check-yaml
+-   repo: https://github.com/psf/black
+    rev: 20.8b0 
+    hooks:
+    -   id: black
+-   repo: https://github.com/pycqa/isort
+    rev: 5.8.0
+    hooks:
+      - id: isort
+        name: isort (python)
+      - id: isort
+        name: isort (cython)
+        types: [cython]
+      - id: isort
+        name: isort (pyi)
+        types: [pyi]      

CHANGELOG

@@ -26,6 +26,27 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Security
 
+## ClinicaDL 0.2.2
+
+### Added
+
+- New functionality `clinicadl random-search analysis` to obtain the histogram
+  of the balanced accuracy over a random search folder.
+- New functionality `clinicadl train from_json` to train a model with
+  parameters defined in a JSON file.
+- New functionality `clinicadl train resume` to resume a prematurely stopped
+  training task.
+- Possibility to learn the grey matter intensities with the binary
+  classification during training, based on `t1-volume` outputs.
+- Refactor code style using Black tool.
+
+### Changed
+
+- Previous `clinicadl random-search` is now `clinicadl random-search generate`
+- Cross-validation and computational arguments of `clinicadl random-search
+  generate` are now defined in `random_search.json`.
+- Remove tensorboardx dependency.
+
 ## ClinicaDL 0.2.1
 
 ### Added
@@ -47,7 +68,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
-- New functionality `clinica interpret`  to generate saliency maps linked
+- New functionality `clinicadl interpret`  to generate saliency maps linked
   to pretrained models based on groups of individual images.
 - New functionality `clinicadl random-search` to sample random networks from a
   predefined hyperparameter space.
@@ -68,4 +89,3 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - Fix broken file when running preprocessing in t1-extensive.
 
-

clinicadl/clinicadl/VERSION

@@ -1 +1 @@
-0.2.1
+0.2.2

clinicadl/clinicadl/__init__.py

@@ -1,9 +1,10 @@
-__all__ = ['__version__']
+__all__ = ["__version__"]
 
 # Load the Clinica package version
-import sys
 import pkgutil
-__version__ = pkgutil.get_data(__package__, 'VERSION').decode('ascii').strip()
+import sys
+
+__version__ = pkgutil.get_data(__package__, "VERSION").decode("ascii").strip()
 version = __version__
 
 # import pkg_resources