Sc-musketeers

- Continuous integration 🔄 tests-0.1.5. [Christophe Bécavin]
- Merge branch 'main' of github.com:AntoineCollin/scMusketeers merged.
[Christophe Bécavin]
- Update README.md. [Christophe Becavin]
- Continuous integration 🔄 tests-0.1.4. [Christophe Bécavin]
- Merge pull request 12 from AntoineCollin/renaming. [Christophe
Becavin]

Merge Renaming to Main
- Update tutorial with CellTypist Lung. [Christophe Bécavin]
- Update tutorial with CellTypist Lung. [Christophe Bécavin]
- Merge branch 'renaming' of github.com:AntoineCollin/scMusketeers into
renaming merge. [Christophe Bécavin]
- Update README.md. [Christophe Becavin]
- Update README.md. [Christophe Becavin]
- Update tutorial with CellTypist Lung. [Christophe Bécavin]
- Modifiy tutorial to work on CellTypist Lung atlas. [Christophe
Bécavin]
- Add jupyter tutorial. [Christophe Bécavin]
- Test modif git. [Christophe Bécavin]

- Merge branch 'renaming' of github.com:AntoineCollin/scMusketeers into
renaming. [Christophe Bécavin]
- Update README.md. [Christophe Becavin]
- Update poetry dependencies. [Christophe Bécavin]
- Format code and linting. [Christophe Bécavin]
- Fix security alert - dependabot. [Christophe Bécavin]
- Rename package name : scmusketeers. [Christophe Bécavin]
- Merge pull request 10 from AntoineCollin/main. [Christophe Becavin]

Rename executable andd parameters
- Merge pull request 9 from AntoineCollin/benchmark. [Christophe
Becavin]

Rename executable andd parameters
- Rename executable andd parameters. [Christophe Bécavin]
- Merge pull request 8 from AntoineCollin/benchmark. [Christophe
Becavin]

Merge Benchmark into Main
- Merge branch 'main' into benchmark. [Christophe Becavin]
- Update README.md. [AntoineCollin]
- Update README.md. [Christophe Becavin]
- Fix poetry, format code. [Christophe Bécavin]
- Update poetry after renaming to scMusketeers. [Christophe Bécavin]
- Modify mkdocs for Musketeers. [Christophe Bécavin]
- Modify make file. [Christophe Bécavin]
- First tutorial done! [Christophe Bécavin]
- First tutorial working for cell transfer on one dataset. [Christophe
Bécavin]
- Fix tutorial bugs and create jupyter notebook. [Christophe Bécavin]
- Fix model for publi in optimize_model.py. [Christophe Bécavin]
- Fix some bug. [Christophe Bécavin]
- Create tutorial jupyter notebook. [Christophe Bécavin]
- Update doc. [Christophe Bécavin]
- Update project name. [Christophe Bécavin]
- Fix sampling of dataset. [Christophe Bécavin]
- Add tutoriel.py to create tutorial data, and update tutorial.sh with
use-cases. [Christophe Bécavin]
- Add tutoriel.py to create tutorial data, and update tutorial.sh with
use-cases. [Christophe Bécavin]
- Add tutoriel.py to create tutorial data, and update tutorial.sh with
use-cases. [Christophe Bécavin]
- Correction coquille. [AntoineCollin]
- Modify tutoriel for Chris. [Christophe Bécavin]
- Test test tutorial. [Christophe Bécavin]
- Debugging. [AntoineCollin]
- Prepare tutorial. [Christophe Bécavin]
- Modify code for first tutorial scpermut transfer. [Christophe Bécavin]
- Add tutorial for transfer. [Christophe Bécavin]
- Modified transfer for command line usage. [AntoineCollin]
- Create Main. [Christophe Bécavin]
- Add README and update poetry. [Christophe Bécavin]
- Add folders from memoryleak. [Christophe Bécavin]
- Merging with Christophe. [AntoineCollin]
- Added several training scheme and expe. [AntoineCollin]
- Safety commit before adding pseudo labeling. [AntoineCollin]
- Added run & run_hp as well as few experiments scripts. [AntoineCollin]
- Add poetry. [Christophe Bécavin]
- Modif benchmark python files in benchmark folder. [Christophe Bécavin]
- Modif benchmark python files in benchmark folder. [Christophe Bécavin]
- Modif hp_script. [Christophe Bécavin]
- Merge pull request 3 from AntoineCollin/package. [Christophe Becavin]

P.R. Package to Main
- Modif exemple_sbatch_hp_script.sh. [Christophe Bécavin]
- Move workflow main to __main__ [Christophe Bécavin]
- Rename benchmark - pas a jour ? [Christophe Bécavin]
- Fix import. [Christophe Bécavin]
- Clean clean. [Christophe Bécavin]
- Move to obsolete worklow. [Christophe Bécavin]
- DCA to obsolete. [Christophe Bécavin]
- Clean some files. [Christophe Bécavin]
- Bash script for hp working ! [Christophe Bécavin]
- Prepare test bash script - exemple_bego_script.sh. [Christophe
Bécavin]
- Move all python files. [Christophe Bécavin]
- Move files and create folder. [Christophe Bécavin]
- Test. [Christophe Bécavin]
- ScPermut repo migration. [AntoineCollin]
- Minor leak workflow_hp & operational benchmark. [AntoineCollin]
- Added benchmark models. [AntoineCollin]
- Hyperparam from json. [AntoineCollin]
- Last modifs. [Simon Pelletier]
- Separate job debugging. [AntoineCollin]
- Adding fixes for tf data leaks. [AntoineCollin]
- Fixed tensorflow data leaks. [AntoineCollin]
- Gitignore issue fixed. [AntoineCollin]
- Gitignore issue fixed. [AntoineCollin]
- Gitignore issue fixed. [AntoineCollin]
- Adding experiment files. [AntoineCollin]
- Ready to launch ! [AntoineCollin]
- Ready to launch ! [AntoineCollin]
- Ready to launch ! [AntoineCollin]
- Adding hparams optim. [spell00]
- Added early stopping in training loop. [AntoineCollin]
- Added command line launch script. [AntoineCollin]
- Added command line launch script. [AntoineCollin]
- Added command line launch script. [AntoineCollin]
- Added training loop and training scheme, started cleaning
workfflow_hp. [AntoineCollin]
- Added training loop and training scheme, started cleaning
workfflow_hp. [AntoineCollin]
- First commit on new branch. [AntoineCollin]
- Starting subclassing, last version before branching. [AntoineCollin]
- Late commit. [AntoineCollin]
- Added batch_removal_AE, metrics computation, fixed few bugs.
[AntoineCollin]
- Changed computation of metrics to be performed once. Corrected
randomness of permutation.py. Corrected semi_sup in dataset.py.
Corrected contrastive loss. [AntoineCollin]
- Removed useless files. [AntoineCollin]
- Removed useless files. [AntoineCollin]
- Removed useless files. [AntoineCollin]