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merge dev in refactoring #651

Merged
merged 30 commits into from
Sep 6, 2024
Merged

merge dev in refactoring #651

merged 30 commits into from
Sep 6, 2024

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camillebrianceau
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dependabot bot and others added 30 commits April 22, 2024 10:03
@dependabot
Bump sqlparse from 0.4.4 to 0.5.0 (aramis-lab#558)
a9a23b9 
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>
@dependabot
Bump tqdm from 4.66.1 to 4.66.3 (aramis-lab#569)
36eb46f 
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>
@dependabot
Bump werkzeug from 3.0.1 to 3.0.3 (aramis-lab#570)
fa7f0f1 
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>
@dependabot
Bump jinja2 from 3.1.3 to 3.1.4 (aramis-lab#571)
a05fcd5 
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>
@dependabot
Bump mlflow from 2.10.1 to 2.12.1 (aramis-lab#575)
b2fc3e6 
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>
@dependabot
Bump gunicorn from 21.2.0 to 22.0.0 (aramis-lab#576)
495d5b9 
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>
@dependabot
Bump requests from 2.31.0 to 2.32.0 (aramis-lab#578)
bdd102a 
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>
@NicolasGensollen
[CI] Run tests through GitHub Actions (aramis-lab#573)
beccd4c 
* 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
@NicolasGensollen
[CI] Skip tests when PR is in draft mode (aramis-lab#592)
2861e9d 
* 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
@NicolasGensollen
[CI] Test train workflow on GPU machine (aramis-lab#590)
f5de251 
* add test workflow on GPU for train

* fix conda path

* fix conflicting workdir

* only run on non-draft PRs

* run also on refactoring branch
@NicolasGensollen
[CI] Port remaining GPU tests to GitHub Actions (aramis-lab#593)
69b3538 
* 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
@NicolasGensollen
[CI] Remove GPU pipeline from Jenkinsfile (aramis-lab#594)
c9d9252
@NicolasGensollen
[CI] Port remaining non GPU tests to GitHub Actions (aramis-lab#581)
753f04e 
* 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
@NicolasGensollen
[CI] Remove jenkins related things (aramis-lab#595)
c424d77
@thibaultdvx
Add flags to run CI tests locally (aramis-lab#596)
52d7561
@NicolasGensollen
[CI] Remove duplicated verbose flag in test pipelines (aramis-lab#598)
39d22fd
@NicolasGensollen
[DOC] Update the Python version used for creating the conda environme…
571662c 
…nt in README (aramis-lab#600)

* update python version used for creating conda env in README

* investigate

* fix
@thibaultdvx
Flag for local tests (aramis-lab#608)
d54d59c 
* add no-gpu and adapt-base-dir flag
@HuguesRoy
Update quality_check.py (aramis-lab#609)
f20e7fb 
* Update quality_check.py
@thibaultdvx
Fix issue in compare_folders (aramis-lab#610)
f6f382a 
* add FileNotFound error in tree
@NicolasGensollen
[INFRA] Update the Makefile check.lock target (aramis-lab#603)
52f9492
@NicolasGensollen
[CI] Run unit tests and linter on refactoring branch (aramis-lab#618)
996cdd5 
* run unit tests on refactoring

* run linter on refactoring
@thibaultdvx
Trigger tests when undrafted (aramis-lab#623)
d0d5cd2 
* add ready_for_review event
@dependabot
Bump urllib3 from 1.26.18 to 1.26.19 (aramis-lab#625)
dca3802 
Bumps [urllib3](https://github.com/urllib3/urllib3) from 1.26.18 to 1.26.19.
- [Release notes](https://github.com/urllib3/urllib3/releases)
- [Changelog](https://github.com/urllib3/urllib3/blob/1.26.19/CHANGES.rst)
- [Commits](urllib3/urllib3@1.26.18...1.26.19)

---
updated-dependencies:
- dependency-name: urllib3
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
@dependabot
Bump certifi from 2024.2.2 to 2024.7.4 (aramis-lab#634)
b8d402b 
Bumps [certifi](https://github.com/certifi/python-certifi) from 2024.2.2 to 2024.7.4.
- [Commits](certifi/python-certifi@2024.02.02...2024.07.04)

---
updated-dependencies:
- dependency-name: certifi
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
@dependabot
Bump zipp from 3.17.0 to 3.19.1 (aramis-lab#635)
6dc2956 
Bumps [zipp](https://github.com/jaraco/zipp) from 3.17.0 to 3.19.1.
- [Release notes](https://github.com/jaraco/zipp/releases)
- [Changelog](https://github.com/jaraco/zipp/blob/main/NEWS.rst)
- [Commits](jaraco/zipp@v3.17.0...v3.19.1)

---
updated-dependencies:
- dependency-name: zipp
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
@dependabot
Bump setuptools from 69.0.3 to 70.0.0 (aramis-lab#636)
b30aac8 
Bumps [setuptools](https://github.com/pypa/setuptools) from 69.0.3 to 70.0.0.
- [Release notes](https://github.com/pypa/setuptools/releases)
- [Changelog](https://github.com/pypa/setuptools/blob/main/NEWS.rst)
- [Commits](pypa/setuptools@v69.0.3...v70.0.0)

---
updated-dependencies:
- dependency-name: setuptools
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
@dependabot
Bump sentry-sdk from 1.40.1 to 2.8.0 (aramis-lab#638)
f6d3f25 
Bumps [sentry-sdk](https://github.com/getsentry/sentry-python) from 1.40.1 to 2.8.0.
- [Release notes](https://github.com/getsentry/sentry-python/releases)
- [Changelog](https://github.com/getsentry/sentry-python/blob/master/CHANGELOG.md)
- [Commits](getsentry/sentry-python@1.40.1...2.8.0)

---
updated-dependencies:
- dependency-name: sentry-sdk
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
@nburgos
Update LICENSE.txt to 2024 (aramis-lab#645)
fa85c2c 
Update copyright from 2016-2020 to 2016-2024
@camillebrianceau
merge
62d2713
@camillebrianceau camillebrianceau marked this pull request as ready for review September 6, 2024 12:48
thibaultdvx
thibaultdvx approved these changes Sep 6, 2024
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LGTM

@thibaultdvx thibaultdvx merged commit e4f6f80 into aramis-lab:refactoring Sep 6, 2024
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@camillebrianceau @thibaultdvx @NicolasGensollen @HuguesRoy @nburgos