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Put resume in trainer #612

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merged 37 commits into from
Jun 6, 2024

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thibaultdvx
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  • Creates from_json and from_maps builders in Trainer, in order to create an instance from a json file or a MAPS folder.
  • Puts resume function in the Trainer.
  • Changes resume and from_json CLI to use these new functionalities.

dependabot bot and others added 30 commits April 22, 2024 10:03
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)

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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)

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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)

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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)

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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
…nt in README (aramis-lab#600)

* update python version used for creating conda env in README

* investigate

* fix
* add no-gpu and adapt-base-dir flag
* Update quality_check.py
* add FileNotFound error in tree
@thibaultdvx thibaultdvx marked this pull request as ready for review June 4, 2024 16:36
@thibaultdvx thibaultdvx added the refactoring ClinicaDL refactoring 2024 label Jun 6, 2024
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LGTM !

@thibaultdvx thibaultdvx merged commit 461c2e8 into aramis-lab:refactoring Jun 6, 2024
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camillebrianceau pushed a commit to camillebrianceau/clinicadl that referenced this pull request Jun 10, 2024
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4 participants