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release: version 0.3.5 🚀
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‎HISTORY.md

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Changelog
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=========
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(unreleased)
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------------
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- Release: version 🚀 [Christophe Bécavin]
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- Fix str2bool erros. [Christophe Bécavin]
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- Release: version 0.3.4 🚀 [Christophe Bécavin]
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- Formatcode for linting. [Christophe Bécavin]
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- Fix many dependencies. [Christophe Bécavin]
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- Release: version 0.3.3 🚀 [Christophe Bécavin]
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- Fix str2bool import. [Christophe Bécavin]
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- Release: version 0.3.2 🚀 [Christophe Bécavin]
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- Release: version 0.3.1 🚀 [Christophe Bécavin]
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- Fix dependencies for bioconda. [Christophe Bécavin]
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- Release: version 0.3.0 🚀 [Christophe Bécavin]
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- Add default hyperparameters. [Christophe Bécavin]
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- Move run.py and run_hp.py to experiment_script.obsolete. [Christophe
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Bécavin]
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- Clean again project. [Christophe Bécavin]
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- Move analysis_notebooks, bash_script, celltype -->> to
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experiment_script/obsolete/ [Christophe Bécavin]
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- Merge branch 'AntoineCollin:main' into main. [Christophe Becavin]
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- Merge pull request #16 from becavin-lab/main. [Christophe Becavin]
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release: version 0.1.20 🚀
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- Clean project. [Christophe Bécavin]
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- Remove workflow_jobs. [Christophe Bécavin]
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- Remove runfiles.yaml. [Christophe Bécavin]
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- Remove obsolete. [Christophe Bécavin]
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- Fix import errors for : import scmusketeers. [Christophe Bécavin]
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- Add init files. [Christophe Bécavin]
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- Release: version 0.2.1 🚀 [Christophe Bécavin]
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- Release: version 0.2.00 🚀 [Christophe Bécavin]
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- Remove pytorch in dependecy. [Christophe Bécavin]
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- Release: version 0.1.24 🚀 [Christophe Bécavin]
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- Release: version 0.1.23 🚀 [Christophe Bécavin]
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- Release: version 0.1.22 🚀 [Christophe Bécavin]
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- Release: version 0.1.21 🚀 [Christophe Bécavin]
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- Modify mkdocs. [Christophe Bécavin]
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- Release: version 0.1.20 🚀 [Christophe Bécavin]
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- Release: version 0.1.13 🚀 [Christophe Bécavin]
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- Release: version 0.1.12 🚀 [Christophe Bécavin]
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- Release: version 0.1.12 🚀 [Christophe Bécavin]
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- Format code. [Christophe Bécavin]
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- Release: version 0.1.11 🚀 [Christophe Bécavin]
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- Format code. [Christophe Bécavin]
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- Release: version 0.1.10 🚀 [Christophe Bécavin]
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- Release: version 0.1.9 🚀 [Christophe Bécavin]
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- Format code. [Christophe Bécavin]
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- Release: version 0.1.9 🚀 [Christophe Bécavin]
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- Format code. [Christophe Bécavin]
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- Small modif tutorial. [Christophe Bécavin]
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- Merge pull request #14 from AntoineCollin/bug_update. [Christophe
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Becavin]
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Bug update
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- Merge from benchmark and bug_update. [Christophe Bécavin]
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- Createmain_temp branch. [Christophe Bécavin]
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- Fixed bug and task 4. [AntoineCollin]
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- Huge debug in permutation.py. [AntoineCollin]
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- Update README.md. [Christophe Becavin]
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- Update README.md. [Christophe Becavin]
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- Update README.md. [Christophe Becavin]
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- Update README.md. [Christophe Becavin]
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- Fix main. [Christophe Bécavin]
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- Update tutorail, add Deprez et al. Lung dataset. [Christophe Bécavin]
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- Change tutorial.sh. [Christophe Bécavin]
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- Create batch_step function (in last commit) [Christophe Bécavin]
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- Modify attributes of workflow, add ae dann and class_param, add
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freeze.py, clean attributes list in workflow. [Christophe Bécavin]
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- Fix the use of neptune_log parameter to disable Neptune.AI.
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[Christophe Bécavin]
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- Modify epoch parameters. [Christophe Bécavin]
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- Release: version 0.1.7 🚀 [Christophe Bécavin]
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- Release: version 0.1.6 🚀 [Christophe Bécavin]
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- Release: version 0.1.5 🚀 [Christophe Bécavin]
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- Continuous integration 🔄 tests-0.1.5. [Christophe Bécavin]
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- Merge branch 'main' of github.com:AntoineCollin/scMusketeers merged.
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[Christophe Bécavin]
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- Update README.md. [Christophe Becavin]
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- Continuous integration 🔄 tests-0.1.4. [Christophe Bécavin]
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- Merge pull request #12 from AntoineCollin/renaming. [Christophe
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Becavin]
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Merge Renaming to Main
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- Update tutorial with CellTypist Lung. [Christophe Bécavin]
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- Update tutorial with CellTypist Lung. [Christophe Bécavin]
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- Merge branch 'renaming' of github.com:AntoineCollin/scMusketeers into
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renaming merge. [Christophe Bécavin]
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- Update README.md. [Christophe Becavin]
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- Update README.md. [Christophe Becavin]
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- Update tutorial with CellTypist Lung. [Christophe Bécavin]
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- Modifiy tutorial to work on CellTypist Lung atlas. [Christophe
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Bécavin]
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- Add jupyter tutorial. [Christophe Bécavin]
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- Test modif git. [Christophe Bécavin]
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- Release: version 0.1.4 🚀 [Christophe Bécavin]
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- Release: version 0.1.3 🚀 [Christophe Bécavin]
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- Release: version 0.1.2 🚀 [Christophe Bécavin]
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- Merge branch 'renaming' of github.com:AntoineCollin/scMusketeers into
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renaming. [Christophe Bécavin]
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- Update README.md. [Christophe Becavin]
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- Update poetry dependencies. [Christophe Bécavin]
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- Format code and linting. [Christophe Bécavin]
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- Fix security alert - dependabot. [Christophe Bécavin]
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- Rename package name : scmusketeers. [Christophe Bécavin]
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- Merge pull request #10 from AntoineCollin/main. [Christophe Becavin]
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Rename executable andd parameters
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- Merge pull request #9 from AntoineCollin/benchmark. [Christophe
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Becavin]
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Rename executable andd parameters
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- Rename executable andd parameters. [Christophe Bécavin]
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- Merge pull request #8 from AntoineCollin/benchmark. [Christophe
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Becavin]
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Merge Benchmark into Main
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- Merge branch 'main' into benchmark. [Christophe Becavin]
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- Update README.md. [AntoineCollin]
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- Update README.md. [Christophe Becavin]
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- Fix poetry, format code. [Christophe Bécavin]
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- Update poetry after renaming to scMusketeers. [Christophe Bécavin]
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- Modify mkdocs for Musketeers. [Christophe Bécavin]
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- Modify make file. [Christophe Bécavin]
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- First tutorial done! [Christophe Bécavin]
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- First tutorial working for cell transfer on one dataset. [Christophe
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Bécavin]
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- Fix tutorial bugs and create jupyter notebook. [Christophe Bécavin]
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- Fix model for publi in optimize_model.py. [Christophe Bécavin]
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- Fix some bug. [Christophe Bécavin]
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- Create tutorial jupyter notebook. [Christophe Bécavin]
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- Update doc. [Christophe Bécavin]
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- Update project name. [Christophe Bécavin]
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- Fix sampling of dataset. [Christophe Bécavin]
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- Add tutoriel.py to create tutorial data, and update tutorial.sh with
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use-cases. [Christophe Bécavin]
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- Add tutoriel.py to create tutorial data, and update tutorial.sh with
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use-cases. [Christophe Bécavin]
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- Add tutoriel.py to create tutorial data, and update tutorial.sh with
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use-cases. [Christophe Bécavin]
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- Correction coquille. [AntoineCollin]
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- Modify tutoriel for Chris. [Christophe Bécavin]
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- Test test tutorial. [Christophe Bécavin]
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- Debugging. [AntoineCollin]
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- Prepare tutorial. [Christophe Bécavin]
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- Modify code for first tutorial scpermut transfer. [Christophe Bécavin]
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- Add tutorial for transfer. [Christophe Bécavin]
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- Modified transfer for command line usage. [AntoineCollin]
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- Create Main. [Christophe Bécavin]
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- Add README and update poetry. [Christophe Bécavin]
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- Add folders from memoryleak. [Christophe Bécavin]
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- Merging with Christophe. [AntoineCollin]
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- Added several training scheme and expe. [AntoineCollin]
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- Safety commit before adding pseudo labeling. [AntoineCollin]
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- Added run & run_hp as well as few experiments scripts. [AntoineCollin]
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- Add poetry. [Christophe Bécavin]
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- Modif benchmark python files in benchmark folder. [Christophe Bécavin]
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- Modif benchmark python files in benchmark folder. [Christophe Bécavin]
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- Modif hp_script. [Christophe Bécavin]
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- Merge pull request #3 from AntoineCollin/package. [Christophe Becavin]
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P.R. Package to Main
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- Modif exemple_sbatch_hp_script.sh. [Christophe Bécavin]
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- Move workflow main to __main__ [Christophe Bécavin]
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- Rename benchmark - pas a jour ? [Christophe Bécavin]
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- Fix import. [Christophe Bécavin]
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- Clean clean. [Christophe Bécavin]
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- Move to obsolete worklow. [Christophe Bécavin]
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- DCA to obsolete. [Christophe Bécavin]
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- Clean some files. [Christophe Bécavin]
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- Bash script for hp working ! [Christophe Bécavin]
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- Prepare test bash script - exemple_bego_script.sh. [Christophe
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Bécavin]
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- Move all python files. [Christophe Bécavin]
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- Move files and create folder. [Christophe Bécavin]
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- Test. [Christophe Bécavin]
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- ScPermut repo migration. [AntoineCollin]
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- Minor leak workflow_hp & operational benchmark. [AntoineCollin]
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- Added benchmark models. [AntoineCollin]
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- Hyperparam from json. [AntoineCollin]
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- Last modifs. [Simon Pelletier]
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- Separate job debugging. [AntoineCollin]
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- Adding fixes for tf data leaks. [AntoineCollin]
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- Fixed tensorflow data leaks. [AntoineCollin]
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- Gitignore issue fixed. [AntoineCollin]
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- Gitignore issue fixed. [AntoineCollin]
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- Gitignore issue fixed. [AntoineCollin]
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- Adding experiment files. [AntoineCollin]
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- Ready to launch ! [AntoineCollin]
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- Ready to launch ! [AntoineCollin]
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- Ready to launch ! [AntoineCollin]
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- Adding hparams optim. [spell00]
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- Added early stopping in training loop. [AntoineCollin]
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- Added command line launch script. [AntoineCollin]
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- Added command line launch script. [AntoineCollin]
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- Added command line launch script. [AntoineCollin]
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- Added training loop and training scheme, started cleaning
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workfflow_hp. [AntoineCollin]
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- Added training loop and training scheme, started cleaning
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workfflow_hp. [AntoineCollin]
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- First commit on new branch. [AntoineCollin]
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- Starting subclassing, last version before branching. [AntoineCollin]
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- Late commit. [AntoineCollin]
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- Added batch_removal_AE, metrics computation, fixed few bugs.
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[AntoineCollin]
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- Changed computation of metrics to be performed once. Corrected
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randomness of permutation.py. Corrected semi_sup in dataset.py.
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Corrected contrastive loss. [AntoineCollin]
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- Removed useless files. [AntoineCollin]
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- Removed useless files. [AntoineCollin]
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- Removed useless files. [AntoineCollin]
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‎scmusketeers/tools/VERSION

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0.3.5

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