Reorganize architecture

.github/workflows/test_cli.yml

@@ -36,12 +36,12 @@ jobs:
           python-version: ${{ env.PYTHON_VERSION }}
       - name: Run CLI tests
         run: |
-          make env.conda
           source /builds/miniconda3/etc/profile.d/conda.sh
+          make env.conda
           conda activate "${{ github.workspace }}"/env
           make install
           cd tests
-          poetry run pytest --verbose \
+          poetry run pytest \
           --junitxml=./test-reports/test_cli_report.xml \
           --disable-warnings \
           --verbose \

.github/workflows/test_generate.yml

@@ -36,12 +36,12 @@ jobs:
           python-version: ${{ env.PYTHON_VERSION }}
       - name: Run tests for generate task
         run: |
-          make env.conda
           source /builds/miniconda3/etc/profile.d/conda.sh
+          make env.conda
           conda activate "${{ github.workspace }}"/env
           make install
           cd tests
-          poetry run pytest --verbose \
+          poetry run pytest \
           --junitxml=./test-reports/test_generate_report.xml \
           --disable-warnings \
           --verbose \

.github/workflows/test_interpret.yml

@@ -36,12 +36,12 @@ jobs:
           python-version: ${{ env.PYTHON_VERSION }}
       - name: Run tests for Interpret task on GPU
         run: |
-          make env.conda
           source "${HOME}/miniconda3/etc/profile.d/conda.sh"
+          make env.conda
           conda activate "${{ github.workspace }}"/env
           make install
           cd tests
-          poetry run pytest --verbose \
+          poetry run pytest \
           --junitxml=./test-reports/test_interpret_report.xml \
           --disable-warnings \
           --verbose \

.github/workflows/test_predict.yml

@@ -36,12 +36,12 @@ jobs:
           python-version: ${{ env.PYTHON_VERSION }}
       - name: Run tests for predict task
         run: |
-          make env.conda
           source /builds/miniconda3/etc/profile.d/conda.sh
+          make env.conda
           conda activate "${{ github.workspace }}"/env
           make install
           cd tests
-          poetry run pytest --verbose \
+          poetry run pytest \
           --junitxml=./test-reports/test_predict_report.xml \
           --disable-warnings \
           --verbose \

.github/workflows/test_prepare_data.yml

@@ -36,12 +36,12 @@ jobs:
           python-version: ${{ env.PYTHON_VERSION }}
       - name: Run tests for prepare data task
         run: |
-          make env.conda
           source /builds/miniconda3/etc/profile.d/conda.sh
+          make env.conda
           conda activate "${{ github.workspace }}"/env
           make install
           cd tests
-          poetry run pytest --verbose \
+          poetry run pytest \
           --junitxml=./test-reports/test_prepare_data_report.xml \
           --disable-warnings \
           --verbose \

.github/workflows/test_quality_checks.yml

@@ -36,12 +36,12 @@ jobs:
           python-version: ${{ env.PYTHON_VERSION }}
       - name: Run tests for Quality Check
         run: |
-          make env.conda
           source /builds/miniconda3/etc/profile.d/conda.sh
+          make env.conda
           conda activate "${{ github.workspace }}"/env
           make install
           cd tests
-          poetry run pytest --verbose \
+          poetry run pytest \
           --junitxml=./test-reports/test_quality_check_report.xml \
           --disable-warnings \
           --verbose \

.github/workflows/test_random_search.yml

@@ -36,12 +36,12 @@ jobs:
           python-version: ${{ env.PYTHON_VERSION }}
       - name: Run Random Search tests on GPU
         run: |
-          make env.conda
           source "${HOME}/miniconda3/etc/profile.d/conda.sh"
+          make env.conda
           conda activate "${{ github.workspace }}"/env
           make install
           cd tests
-          poetry run pytest --verbose \
+          poetry run pytest \
           --junitxml=./test-reports/test_random_search_report.xml \
           --disable-warnings \
           --verbose \

.github/workflows/test_resume.yml

@@ -36,12 +36,12 @@ jobs:
           python-version: ${{ env.PYTHON_VERSION }}
       - name: Run resume tests on GPU
         run: |
-          make env.conda
           source "${HOME}/miniconda3/etc/profile.d/conda.sh"
+          make env.conda
           conda activate "${{ github.workspace }}"/env
           make install
           cd tests
-          poetry run pytest --verbose \
+          poetry run pytest \
           --junitxml=./test-reports/test_resume_report.xml \
           --disable-warnings \
           --verbose \

.github/workflows/test_train.yml

@@ -36,12 +36,12 @@ jobs:
           python-version: ${{ env.PYTHON_VERSION }}
       - name: Run tests for Train on GPU
         run: |
-          make env.conda
           source "${HOME}/miniconda3/etc/profile.d/conda.sh"
+          make env.conda
           conda activate "${{ github.workspace }}"/env
           make install
           cd tests
-          poetry run pytest --verbose \
+          poetry run pytest \
           --junitxml=./test-reports/test_train_report.xml \
           --disable-warnings \
           --verbose \

.github/workflows/test_transfer_learning.yml

@@ -36,12 +36,12 @@ jobs:
           python-version: ${{ env.PYTHON_VERSION }}
       - name: Run tests for Transfer Learning on GPU
         run: |
-          make env.conda
           source "${HOME}/miniconda3/etc/profile.d/conda.sh"
+          make env.conda
           conda activate "${{ github.workspace }}"/env
           make install
           cd tests
-          poetry run pytest --verbose \
+          poetry run pytest \
           --junitxml=./test-reports/test_transfer_learning_report.xml \
           --disable-warnings \
           --verbose \

.github/workflows/test_tsvtools.yml

@@ -36,12 +36,12 @@ jobs:
           python-version: ${{ env.PYTHON_VERSION }}
       - name: Run tests for TSV tools
         run: |
-          make env.conda
           source /builds/miniconda3/etc/profile.d/conda.sh
+          make env.conda
           conda activate "${{ github.workspace }}"/env
           make install
           cd tests
-          poetry run pytest --verbose \
+          poetry run pytest \
           --junitxml=./test-reports/test_tsvtools_report.xml \
           --disable-warnings \
           --verbose \

README.md

@@ -33,34 +33,33 @@
 ## About the project
 
 This repository hosts ClinicaDL, the deep learning extension of [Clinica](https://github.com/aramis-lab/clinica), 
-a python library to process neuroimaging data in [BIDS](https://bids.neuroimaging.io/index.html) format.
+a Python library to process neuroimaging data in [BIDS](https://bids.neuroimaging.io/index.html) format.
 
 > **Disclaimer:** this software is **under development**. Some features can
 change between different releases and/or commits.
 
-To access the full documentation of the project, follow the link 
-[https://clinicadl.readthedocs.io/](https://clinicadl.readthedocs.io/). 
+To access the full documentation of the project, follow the link [https://clinicadl.readthedocs.io/](https://clinicadl.readthedocs.io/). 
 If you find a problem when using it or if you want to provide us feedback,
 please [open an issue](https://github.com/aramis-lab/ad-dl/issues) or write on
 the [forum](https://groups.google.com/forum/#!forum/clinica-user).
 
 ## Getting started
+
 ClinicaDL currently supports macOS and Linux.
 
 We recommend to use `conda` or `virtualenv` for the installation of ClinicaDL
-as it guarantees the correct management of libraries depending on common
-packages:
+as it guarantees the correct management of libraries depending on common packages:
 
 ```{.sourceCode .bash}
-conda create --name ClinicaDL python=3.8
+conda create --name ClinicaDL python=3.10
 conda activate ClinicaDL
 pip install clinicadl
 ```
 
-## Tutorial 
-Visit our [hands-on tutorial web
-site](https://aramislab.paris.inria.fr/clinicadl/tuto) to start
-using **ClinicaDL** directly in a Google Colab instance!
+## Tutorial
+
+Visit our [hands-on tutorial web site](https://aramislab.paris.inria.fr/clinicadl/tuto)
+to start using **ClinicaDL** directly in a Google Colab instance!
 
 ## Related Repositories
 

clinicadl/utils/callbacks/callbacks.py → clinicadl/callbacks/callbacks.py

@@ -127,14 +127,14 @@ def on_train_end(self, parameters, **kwargs):
 class Tracker(Callback):
     def on_train_begin(self, parameters, **kwargs):
         if parameters["track_exp"] == "wandb":
-            from clinicadl.utils.tracking_exp import WandB_handler
+            from clinicadl.callbacks.tracking_exp import WandB_handler
 
             self.run = WandB_handler(
                 kwargs["split"], parameters, kwargs["maps_path"].name
             )
 
         if parameters["track_exp"] == "mlflow":
-            from clinicadl.utils.tracking_exp import Mlflow_handler
+            from clinicadl.callbacks.tracking_exp import Mlflow_handler
 
             self.run = Mlflow_handler(
                 kwargs["split"], parameters, kwargs["maps_path"].name

clinicadl/config/config/callbacks.py → clinicadl/callbacks/config.py

@@ -7,8 +7,8 @@
 from pydantic import BaseModel, ConfigDict, computed_field, field_validator
 from pydantic.types import NonNegativeFloat, NonNegativeInt, PositiveFloat, PositiveInt
 
+from clinicadl.preprocessing.preprocessing import read_preprocessing
 from clinicadl.utils.enum import ExperimentTracking
-from clinicadl.utils.preprocessing import read_preprocessing
 
 logger = getLogger("clinicadl.callbacks_config")
 

clinicadl/cmdline.py

@@ -1,17 +1,19 @@
 # coding: utf8
 import click
 
-from clinicadl.generate.generate_cli import cli as generate_cli
-from clinicadl.hugging_face.hugging_face_cli import cli as hf_cli
-from clinicadl.interpret.interpret_cli import cli as interpret_cli
-from clinicadl.predict.predict_cli import cli as predict_cli
-from clinicadl.prepare_data.prepare_data_cli import cli as prepare_data_cli
-from clinicadl.prepare_data.prepare_data_from_bids_cli import (
+from clinicadl.commandline.pipelines.generate.cli import cli as generate_cli
+from clinicadl.commandline.pipelines.interpret.cli import cli as interpret_cli
+from clinicadl.commandline.pipelines.predict.cli import cli as predict_cli
+from clinicadl.commandline.pipelines.prepare_data.prepare_data_cli import (
+    cli as prepare_data_cli,
+)
+from clinicadl.commandline.pipelines.prepare_data.prepare_data_from_bids_cli import (
     cli as prepare_data_from_bids_cli,
 )
+from clinicadl.commandline.pipelines.train.cli import cli as train_cli
+from clinicadl.hugging_face.hugging_face_cli import cli as hf_cli
 from clinicadl.quality_check.qc_cli import cli as qc_cli
 from clinicadl.random_search.random_search_cli import cli as random_search_cli
-from clinicadl.train.train_cli import cli as train_cli
 from clinicadl.tsvtools.cli import cli as tsvtools_cli
 from clinicadl.utils.logger import setup_logging
 

clinicadl/config/options/callbacks.py → clinicadl/commandline/modules_options/callbacks.py

@@ -1,8 +1,8 @@
 import click
 
-from clinicadl.config.config.callbacks import CallbacksConfig
-from clinicadl.utils.config_utils import get_default_from_config_class as get_default
-from clinicadl.utils.config_utils import get_type_from_config_class as get_type
+from clinicadl.callbacks.config import CallbacksConfig
+from clinicadl.config.config_utils import get_default_from_config_class as get_default
+from clinicadl.config.config_utils import get_type_from_config_class as get_type
 
 emissions_calculator = click.option(
     "--calculate_emissions/--dont_calculate_emissions",

clinicadl/config/options/computational.py → clinicadl/commandline/modules_options/computational.py

@@ -1,8 +1,8 @@
 import click
 
 from clinicadl.config.config.computational import ComputationalConfig
-from clinicadl.utils.config_utils import get_default_from_config_class as get_default
-from clinicadl.utils.config_utils import get_type_from_config_class as get_type
+from clinicadl.config.config_utils import get_default_from_config_class as get_default
+from clinicadl.config.config_utils import get_type_from_config_class as get_type
 
 # Computational
 amp = click.option(

clinicadl/config/options/cross_validation.py → clinicadl/commandline/modules_options/cross_validation.py

@@ -1,8 +1,8 @@
 import click
 
 from clinicadl.config.config.cross_validation import CrossValidationConfig
-from clinicadl.utils.config_utils import get_default_from_config_class as get_default
-from clinicadl.utils.config_utils import get_type_from_config_class as get_type
+from clinicadl.config.config_utils import get_default_from_config_class as get_default
+from clinicadl.config.config_utils import get_type_from_config_class as get_type
 
 # Cross Validation
 n_splits = click.option(

clinicadl/config/options/data.py → clinicadl/commandline/modules_options/data.py

@@ -1,8 +1,8 @@
 import click
 
 from clinicadl.config.config.data import DataConfig
-from clinicadl.utils.config_utils import get_default_from_config_class as get_default
-from clinicadl.utils.config_utils import get_type_from_config_class as get_type
+from clinicadl.config.config_utils import get_default_from_config_class as get_default
+from clinicadl.config.config_utils import get_type_from_config_class as get_type
 
 # Data
 baseline = click.option(

clinicadl/config/options/dataloader.py → clinicadl/commandline/modules_options/dataloader.py

@@ -1,8 +1,8 @@
 import click
 
 from clinicadl.config.config.dataloader import DataLoaderConfig
-from clinicadl.utils.config_utils import get_default_from_config_class as get_default
-from clinicadl.utils.config_utils import get_type_from_config_class as get_type
+from clinicadl.config.config_utils import get_default_from_config_class as get_default
+from clinicadl.config.config_utils import get_type_from_config_class as get_type
 
 # DataLoader
 batch_size = click.option(

clinicadl/config/options/early_stopping.py → clinicadl/commandline/modules_options/early_stopping.py

@@ -1,8 +1,8 @@
 import click
 
 from clinicadl.config.config.early_stopping import EarlyStoppingConfig
-from clinicadl.utils.config_utils import get_default_from_config_class as get_default
-from clinicadl.utils.config_utils import get_type_from_config_class as get_type
+from clinicadl.config.config_utils import get_default_from_config_class as get_default
+from clinicadl.config.config_utils import get_type_from_config_class as get_type
 
 # Early Stopping
 patience = click.option(

clinicadl/config/options/maps_manager.py → clinicadl/commandline/modules_options/maps_manager.py

@@ -1,7 +1,7 @@
 import click
 
 from clinicadl.config.config.maps_manager import MapsManagerConfig
-from clinicadl.utils.config_utils import get_type_from_config_class as get_type
+from clinicadl.config.config_utils import get_type_from_config_class as get_type
 
 maps_dir = click.argument("maps_dir", type=get_type("maps_dir", MapsManagerConfig))
 data_group = click.option("data_group", type=get_type("data_group", MapsManagerConfig))

clinicadl/config/options/modality.py → clinicadl/commandline/modules_options/modality.py

@@ -5,8 +5,8 @@
     DTIModalityConfig,
     PETModalityConfig,
 )
-from clinicadl.utils.config_utils import get_default_from_config_class as get_default
-from clinicadl.utils.config_utils import get_type_from_config_class as get_type
+from clinicadl.config.config_utils import get_default_from_config_class as get_default
+from clinicadl.config.config_utils import get_type_from_config_class as get_type
 
 tracer = click.option(
     "--tracer",

clinicadl/commandline/modules_options/network.py

@@ -0,0 +1,20 @@
+import click
+
+from clinicadl.config.config_utils import get_default_from_config_class as get_default
+from clinicadl.config.config_utils import get_type_from_config_class as get_type
+from clinicadl.network.config import NetworkConfig
+
+# Model
+multi_network = click.option(
+    "--multi_network/--single_network",
+    default=get_default("multi_network", NetworkConfig),
+    help="If provided uses a multi-network framework.",
+    show_default=True,
+)
+dropout = click.option(
+    "--dropout",
+    type=get_type("dropout", NetworkConfig),
+    default=get_default("dropout", NetworkConfig),
+    help="Rate value applied to dropout layers in a CNN architecture.",
+    show_default=True,
+)

clinicadl/config/options/optimization.py → clinicadl/commandline/modules_options/optimization.py

@@ -1,8 +1,8 @@
 import click
 
-from clinicadl.config.config.optimization import OptimizationConfig
-from clinicadl.utils.config_utils import get_default_from_config_class as get_default
-from clinicadl.utils.config_utils import get_type_from_config_class as get_type
+from clinicadl.config.config_utils import get_default_from_config_class as get_default
+from clinicadl.config.config_utils import get_type_from_config_class as get_type
+from clinicadl.optimizer.optimization import OptimizationConfig
 
 # Optimization
 accumulation_steps = click.option(

clinicadl/config/options/optimizer.py → clinicadl/commandline/modules_options/optimizer.py

@@ -1,8 +1,8 @@
 import click
 
-from clinicadl.config.config.optimizer import OptimizerConfig
-from clinicadl.utils.config_utils import get_default_from_config_class as get_default
-from clinicadl.utils.config_utils import get_type_from_config_class as get_type
+from clinicadl.config.config_utils import get_default_from_config_class as get_default
+from clinicadl.config.config_utils import get_type_from_config_class as get_type
+from clinicadl.optimizer.optimizer import OptimizerConfig
 
 # Optimizer
 learning_rate = click.option(