Cb refactoring rebase #597
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Bumps [sqlparse](https://github.com/andialbrecht/sqlparse) from 0.4.4 to 0.5.0. - [Changelog](https://github.com/andialbrecht/sqlparse/blob/master/CHANGELOG) - [Commits](andialbrecht/sqlparse@0.4.4...0.5.0) --- updated-dependencies: - dependency-name: sqlparse dependency-type: indirect ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [tqdm](https://github.com/tqdm/tqdm) from 4.66.1 to 4.66.3. - [Release notes](https://github.com/tqdm/tqdm/releases) - [Commits](tqdm/tqdm@v4.66.1...v4.66.3) --- updated-dependencies: - dependency-name: tqdm dependency-type: indirect ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [werkzeug](https://github.com/pallets/werkzeug) from 3.0.1 to 3.0.3. - [Release notes](https://github.com/pallets/werkzeug/releases) - [Changelog](https://github.com/pallets/werkzeug/blob/main/CHANGES.rst) - [Commits](pallets/werkzeug@3.0.1...3.0.3) --- updated-dependencies: - dependency-name: werkzeug dependency-type: indirect ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [jinja2](https://github.com/pallets/jinja) from 3.1.3 to 3.1.4. - [Release notes](https://github.com/pallets/jinja/releases) - [Changelog](https://github.com/pallets/jinja/blob/main/CHANGES.rst) - [Commits](pallets/jinja@3.1.3...3.1.4) --- updated-dependencies: - dependency-name: jinja2 dependency-type: indirect ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [mlflow](https://github.com/mlflow/mlflow) from 2.10.1 to 2.12.1. - [Release notes](https://github.com/mlflow/mlflow/releases) - [Changelog](https://github.com/mlflow/mlflow/blob/master/CHANGELOG.md) - [Commits](mlflow/mlflow@v2.10.1...v2.12.1) --- updated-dependencies: - dependency-name: mlflow dependency-type: direct:development ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [gunicorn](https://github.com/benoitc/gunicorn) from 21.2.0 to 22.0.0. - [Release notes](https://github.com/benoitc/gunicorn/releases) - [Commits](benoitc/gunicorn@21.2.0...22.0.0) --- updated-dependencies: - dependency-name: gunicorn dependency-type: indirect ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
updated-dependencies: - dependency-name: requests dependency-type: indirect ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* try a simple workflow first * try running on new ubuntu VM * fixes * bump poetry version to 1.8.3 * try removing caching.. * add workflow for testing tsv tools
* try skipping test_tsvtools when PR is in draft mode * trigger CI * add a cpu tag to avoid running cpu tests on gpu machines * run also on refactoring branch
* add test workflow on GPU for train * fix conda path * fix conflicting workdir * only run on non-draft PRs * run also on refactoring branch
* add workflow for testing interpretation task * add workflow for testing random search task * add workflow for testing resume task * add workflow for testing transfer learning task * trigger CI * trigger CI
* add cleaning step to test_tsvtools pipeline * add test_generate pipeline * add test_predict pipeline * add test_prepare_data pipeline * add test_quality_checks pipeline * add refactoring target branch, cpu tag, and draft PR filter * trigger CI
* first commit for creation of a Predict_manager
* creation of the trainer * remove trainer's methods from MAPSManager * creation of the trainer * introduce trainer in ClinicaDL's train and resume functions * small improvements in docstrings * omission * other omissions
* get trainer out of mapsmanager folder * base training config class * task specific config classes * unit test for config classes * changes in cli to have default values from task config objects * ranem and simplify build_train_dict * unit test for train_utils * small modification in training config toml template * rename build_train_dict in the other parts of the project * modify task_launcher to use config objects * Bump sqlparse from 0.4.4 to 0.5.0 (aramis-lab#558) Bumps [sqlparse](https://github.com/andialbrecht/sqlparse) from 0.4.4 to 0.5.0. - [Changelog](https://github.com/andialbrecht/sqlparse/blob/master/CHANGELOG) - [Commits](andialbrecht/sqlparse@0.4.4...0.5.0) --- updated-dependencies: - dependency-name: sqlparse dependency-type: indirect ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * typo * change _network_task attribute * omissions * patches to match CLI data * small modifications * correction * correction reconstruction default loss * add architecture command specific to the task * add use_extracted_features parameter * add VAE parameters in reconstruction * add condition on whether cli arg is default or from user * correct wrong import in resume * validators on assignment * reformat * replace literal with enum * review on CLI options * convert enum to str for train function * correct track exp issue * test for ci --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Creation of GenerateConfig
* add predictConfig and InterpretConfig
* add Task class * rename task_launcher and put it in train_utils + add merge_cli_and_config_file_options function * remove task_utils * add unit tests * put train call in cli files * remove train function
* reorganize train folder
* first commirt to clean last PR * add enum file + adapt prepare-data
* create get_default_from_config_class and get_type_from_config_class * add enum for losses, transformations, metrics and optimizer * add PositiveInt, PositiveFloat, NonNegativeInt and NonNegtiveFloat typing
* create prepare data config
* use config classes in trainer and makes the appropriate changes in classification, regression, reconstruction, from_json, resume and random-search
* use config classes in trainer and make the appropriate changes in classification, regression, reconstruction, from_json, resume and random-search --------- Co-authored-by: thibaultdvx <[email protected]>
camillebrianceau
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May 30, 2024
* rebase refactoring on dev
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