Update files for next version release (#300)

CHANGELOG

@@ -5,6 +5,75 @@ Main changes to this code/ project are documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## ClinicaDL 1.1.0
+
+### Changed
+
+** Core: **
+
+- Add new VAE models for training.
+- Add multiprocessing for the `extract` task. 
+- Add tests to validate `resume` and `quality-check` functionalities.
+- Update minimal version for first level dependencies: clinica, scikit-learn,
+  scikit-image.
+- Add a new Makefile to the root of the repository in order to facilitate
+  sysadmin frequent tasks. The CI script was also modified.
+
+** Command line:**
+
+- Update of the train command line: now all actions related to training
+  (resume, list models, tasks…) are sub-commands of the command `clinicadl
+  train`. Task is now a sub-command, and not an argument.
+- Add command to list the available models for the training task and the
+  details of each model.
+- Add an option to the command `save-tensor` to save the reconstruction
+  outputs as nifti files.
+- Add command `clinicadl train from_json` to train again the same experiment
+  from a JSON file generated by ClinicaDL.
+
+### Fixed
+
+- Allow the user to choose the optimizer and the metric independently of the
+  performed task.
+- Logger does not display output according to the `--verbose` option during
+  the training tasks. This behavior is fixed.
+- Behavior of `resume` was changed.
+- Reader to request BIDS/CAPS datasets changed its interface in the recent
+  version of Clinica (>=0.5.4). Code using these functions was adapted.
+- Exceptions raised are now more specific and detailed.
+- Documentation was updated.
+
+
+## ClinicaDL 1.0.4
+
+### Changed
+
+** Core: **
+
+Switch to Poetry to manage production and development requirements.
+Update requirements.
+Improve metrics for multi-class settings.
+Remove NaN values in input data.
+Allow to choose the name of the JSON file produced by `extract`.
+Improve logs.
+
+** Command line:**
+Add `selection_metrics` option in `clinicadl train` (already available in TOML file).
+Print help if no argument is given.
+
+### Fixed
+
+Fix label code generation
+Remove all occurences of a group in a MAPS when choosing the `overwriting` option.
+Fix `resume` when the training.tsv file is empty.
+
+## ClinicaDL 1.0.3 (release bugfix)
+
+### Fixed
+
+- Fix import module for VAE architectures.
+
+
 ## ClinicaDL 1.0.2
 
 ### Changed
@@ -35,18 +104,24 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 Welcome in **ClinicaDL 1.0.0** ! 
 
-This is a new version of ClinicaDL with some major changes in the source code. All the main pipelines 
-have been refactored. ClinicaDL now used is now working with classes instead of function for easier maintenance 
-and better scalability. We introduce in this version our new data structure called MAPS to unify ClinicaDL outputs.
-
-This release also include a major command line refactoring with the introduction of [Click](https://click.palletsprojects.com/en/8.0.x/) library.
-Major changes in several pipelines interfaces have been implemented. For instance the preprocessing pipeline has been 
-split. Train pipeline has also been refactored to reduce the number of options. The goal is to make ClinicaDL more easy to use, to maintain, 
-and adapt the command line to the MAPS.
-
-ClinicaDL aim for more reproducibility: some configuration files are saved in the MAPS to reproduce experiments in the same condition 
-(with same environnement and same parameters). In addition we added some options to fix the random processes seed and use Pytorch 
-latest enhancement for a deterministic behavior.
+This is a new version of ClinicaDL with some major changes in the source code.
+All the main pipelines have been refactored. ClinicaDL now used is now working
+with classes instead of function for easier maintenance and better
+scalability. We introduce in this version our new data structure called MAPS
+to unify ClinicaDL outputs.
+
+This release also include a major command line refactoring with the
+introduction of [Click](https://click.palletsprojects.com/en/8.0.x/) library.
+Major changes in several pipelines interfaces have been implemented. For
+instance the preprocessing pipeline has been split. Train pipeline has also
+been refactored to reduce the number of options. The goal is to make ClinicaDL
+more easy to use, to maintain, and adapt the command line to the MAPS.
+
+ClinicaDL aim for more reproducibility: some configuration files are saved in
+the MAPS to reproduce experiments in the same condition (with same
+environnement and same parameters). In addition we added some options to fix
+the random processes seed and use Pytorch latest enhancement for a
+deterministic behavior.
 
 Other improvement and small fix have also been implemented.
 
@@ -56,8 +131,9 @@ Be careful this version breaks the backward compatibility with previous versions
 
 **Pipelines:**
 
-- New `extract` pipeline to convert nifti images in Pytorch tensors. This pipeline now saves a preprocessing json file 
-    with all the information needed for the train pipeline.
+- New `extract` pipeline to convert nifti images in Pytorch tensors. This
+  pipeline now saves a preprocessing json file with all the information needed
+  for the train pipeline.
 
 **Core:**
 
@@ -93,9 +169,13 @@ Be careful this version breaks the backward compatibility with previous versions
 **Other:**
 
 - Console logs enhancement.
-- Replace tensorboardx dependency with torch.utils.tensorboard to remove tensorboardx from requirement.
+- Replace tensorboardx dependency with torch.utils.tensorboard to remove
+  tensorboardx from requirement.
 - GitHub repository name is now ClinicaDL and not AD-DL anymore.
-- We will now use [GitHub discussion](https://github.com/aramis-lab/clinicadl/discussions) instead of [Google Group](https://groups.google.com/g/clinica-user).
+
+- We will now use [GitHub
+discussion](https://github.com/aramis-lab/clinicadl/discussions) instead of
+[Google Group](https://groups.google.com/g/clinica-user).
 
 ### Deprecated
 

clinicadl/VERSION

@@ -1 +1 @@
-1.0.4
+1.1.0

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "clinicadl"
-version = "1.0.4"
+version = "1.1.0"
 description = "Framework for the reproducible processing of neuroimaging data with deep learning methods"
 license = "MIT"
 authors = ["ARAMIS Lab"]