Test to merge hugues caps dataset in maelys caps output #644
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* Moved logwriter to utils root * Changed logger formatter and handler * Created sub loggers for different modules of ClinicaDL * Update clinicadl/utils/maps_manager/__init__.py Co-authored-by: mdiazmel <[email protected]> * Fix of logging pr * Moved logger to avoid circular import * Fixed formatter Co-authored-by: mdiazmel <[email protected]>
Bumps [oauthlib](https://github.com/oauthlib/oauthlib) from 3.2.0 to 3.2.1. - [Release notes](https://github.com/oauthlib/oauthlib/releases) - [Changelog](https://github.com/oauthlib/oauthlib/blob/master/CHANGELOG.rst) - [Commits](oauthlib/oauthlib@v3.2.0...v3.2.1) --- updated-dependencies: - dependency-name: oauthlib dependency-type: indirect ... Signed-off-by: dependabot[bot] <[email protected]> Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [protobuf](https://github.com/protocolbuffers/protobuf) from 3.19.4 to 3.19.5. - [Release notes](https://github.com/protocolbuffers/protobuf/releases) - [Changelog](https://github.com/protocolbuffers/protobuf/blob/main/generate_changelog.py) - [Commits](protocolbuffers/protobuf@v3.19.4...v3.19.5) --- updated-dependencies: - dependency-name: protobuf dependency-type: indirect ... Signed-off-by: dependabot[bot] <[email protected]> Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
[MAINT] Upgrade joblib to `1.2.0`
* change diagnosis into group and subgroup * change diagnosis into group and subgroup * change diagnosis into group and subgroup * change diagnosis into group and subgroup * Update tsvtools tests * Update tsvtools tests * simplify kfold and split * update doc * Add docs and add some changes * Update tests * update tests * update getlabels * Update tsvtools * update docs * update jenkins * update tests * Update test tsvtools * test * update Jenkins * update * update * update docs * update docs * update kfold * add get_metadata function * add tests * Changes 30/09 * Update * update * update * Update clinicadl/tsvtools/analysis/analysis_cli.py Co-authored-by: mdiazmel <[email protected]> * update * update * update * update after review * update tests * update tests * Update clinicadl/tsvtools/get_metadata/get_metadata.py Co-authored-by: mdiazmel <[email protected]> * Update clinicadl/tsvtools/get_metadata/get_metadata.py Co-authored-by: mdiazmel <[email protected]> * Update clinicadl/tsvtools/get_progression/get_progression_cli.py Co-authored-by: mdiazmel <[email protected]> * Update clinicadl/tsvtools/get_progression/get_progression_cli.py Co-authored-by: mdiazmel <[email protected]> * Update clinicadl/tsvtools/split/split.py Co-authored-by: mdiazmel <[email protected]> * Update clinicadl/tsvtools/split/split.py Co-authored-by: mdiazmel <[email protected]> * couple of changes before merging Co-authored-by: mdiazmel <[email protected]>
* Update test tsvtools * Revert "Update test tsvtools" This reverts commit 33bac6f. * update tests * refactoring data ci * tests update * update tests * delete data in tests folder * Add working dir * Add working dir * Add working dir * Add temporary dict * Add temporary directory * update * update jenkins * add test for new tsvtools functions * Update Jenkinsfile * Update Jenkinsfile * Update Jenkinsfile * Update Jenkinsfile * fix predict tests * update jenkins * update * update jenkins * update jenkins * update jenkins * update jenkins * update jenkins * update jenkins * update jenkins * update jenkins * update * update * update jenkins * update * update tests * update tests * update tests * update tests * tests * Update .jenkins/Jenkinsfile Co-authored-by: mdiazmel <[email protected]> * Update .jenkins/Jenkinsfile Co-authored-by: mdiazmel <[email protected]> * Update tests/test_tsvtools.py Co-authored-by: mdiazmel <[email protected]> * Update tests/test_tsvtools.py Co-authored-by: mdiazmel <[email protected]> * Update tests/test_tsvtools.py Co-authored-by: mdiazmel <[email protected]> * Update tests/test_tsvtools.py Co-authored-by: mdiazmel <[email protected]> * Update tests/test_tsvtools.py Co-authored-by: mdiazmel <[email protected]> * Update tests/test_prepare_data.py Co-authored-by: mdiazmel <[email protected]> * Update tests/test_prepare_data.py Co-authored-by: mdiazmel <[email protected]> * Update tests/test_predict.py Co-authored-by: mdiazmel <[email protected]> * tests tsvtools * tests predict * tests predict * tests * tests * tests * tests * QC et randomSearch * fix prepare-experiment * update tests + prepare-exp * tests interpret * last change * tests * prep exp * qc * prepare-data * prepare-data n_procs * prepare-data n_procs * prepare-data n_procs * prepare-data * add tests * tests * jenkins * tests * tests * tests * tests * tests * tests * tests_local * tests * tests * tests * tests * tests * tests and update environment.yml (python 3.8 to 3.9) * tests * tests * tests * tests Co-authored-by: mdiazmel <[email protected]>
DOC: Add badge for monthly downloads
Migrate lock file to version 2
* bump certifi and pillow version * poetry update * bump llvmlite from 0.34.0 to 0.39.1 * tests
* update train, randomSearch, predict, interpret for new tsvtools * modification split /maps manager * new function adapt * fix warning : use pd.concat instead of append * add old get-labels
* fix qc tensor problem * add path to download models * add clinicadl installation with pipx * remove use of CapsDataset * add models.py file * add docstrings
Bumps [future](https://github.com/PythonCharmers/python-future) from 0.18.2 to 0.18.3. - [Release notes](https://github.com/PythonCharmers/python-future/releases) - [Changelog](https://github.com/PythonCharmers/python-future/blob/master/docs/changelog.rst) - [Commits](PythonCharmers/python-future@v0.18.2...v0.18.3) --- updated-dependencies: - dependency-name: future dependency-type: indirect ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
There is now a project called [build](https://pypa-build.readthedocs.io/en/stable/) which is dedicated to building Python package distributions regardless of the project backend (setuptools, poetry, hatch...). The PyPA also publishes an official GH action for releasing to PyPI. This PR combines both.
Bumps [idna](https://github.com/kjd/idna) from 3.6 to 3.7. - [Release notes](https://github.com/kjd/idna/releases) - [Changelog](https://github.com/kjd/idna/blob/master/HISTORY.rst) - [Commits](kjd/idna@v3.6...v3.7) --- updated-dependencies: - dependency-name: idna dependency-type: indirect ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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 (#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
* run unit tests on refactoring * run linter on refactoring
* add ready_for_review event
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>
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>
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>
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>
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>
* add pydantic to dependency (#556) * Creation of a PredictManager from MapsManager (#557) * first commit for creation of a Predict_manager * Creation of the trainer (#559) * 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 * concatenation and stacking of capsdatasets +creation from control file * low level caps dataset class (CapsDatasetImage) * reformat * reformat * Typing * typing : fench to english... * compatibility for patch,roi and slices * Dataloader for paired and unpaired datasets * Update clinicadl/utils/caps_dataset/caps_dataset_refactoring/caps_dataset.py Co-authored-by: Gensollen <[email protected]> * Update clinicadl/utils/caps_dataset/caps_dataset_refactoring/caps_dataset.py Co-authored-by: thibaultdvx <[email protected]> * Update clinicadl/utils/caps_dataset/caps_dataset_refactoring/caps_dataset.py Co-authored-by: Gensollen <[email protected]> * Update concat_dataset.py broken path solved --------- Co-authored-by: thibaultdvx <[email protected]> Co-authored-by: HuguesRoy <[email protected]> Co-authored-by: HuguesRoy <[email protected]> Co-authored-by: Gensollen <[email protected]>
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