Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Run unittets and cleaning #620

Merged
merged 63 commits into from
Jun 14, 2024
Merged

Conversation

thibaultdvx
Copy link
Collaborator

@thibaultdvx thibaultdvx commented Jun 7, 2024

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)

---
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
…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 draft June 12, 2024 08:19
@thibaultdvx thibaultdvx marked this pull request as ready for review June 12, 2024 08:30
@thibaultdvx thibaultdvx added refactoring ClinicaDL refactoring 2024 labels Jun 12, 2024
@thibaultdvx thibaultdvx marked this pull request as draft June 12, 2024 08:48
@thibaultdvx thibaultdvx marked this pull request as ready for review June 12, 2024 09:12
@thibaultdvx thibaultdvx marked this pull request as draft June 12, 2024 09:20
@thibaultdvx thibaultdvx marked this pull request as ready for review June 12, 2024 09:24
Copy link
Collaborator

@camillebrianceau camillebrianceau left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

LGTM !

Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Maybe we can add mood24 branch, WDYT?

Copy link
Collaborator Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Good idea, I will make the change directly on mood24!

@thibaultdvx thibaultdvx merged commit 3547ca1 into aramis-lab:refactoring Jun 14, 2024
21 checks passed
@thibaultdvx thibaultdvx deleted the cleaning branch June 14, 2024 07:53
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
refactoring ClinicaDL refactoring 2024
Projects
None yet
Development

Successfully merging this pull request may close these issues.

4 participants