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Changelog

(unreleased)

  • Ready now. [jkobject]

1.1.2 (2024-09-04)

  • Release: version 1.1.2 🚀 [jkobject]

1.1.1 (2024-09-04)

  • Release: version 1.1.1 🚀 [jkobject]
  • Adding a term in the test. [jkobject]
  • Ready for releases. [jkobject]

1.1.0 (2024-09-04)

  • Release: version 1.1.0 🚀 [jkobject]
  • Merge branch 'main' of https://github.com/jkobject/scPRINT into main. [jkobject]
  • Release: version 🚀 [jkobject]
  • Debug2. [jkobject]
  • Debug. [jkobject]
  • Nothing really. [jkobject]
  • Nothing really. [jkobject]
  • Wip on tests. [jkobject]
  • Merge branch 'main' of https://github.com/jkobject/scPRINT into main. [jkobject]
  • Lmprovements. [jkobject]
  • Adding better linting and removing RNABERT. [jkobject]
  • Update README.md. [Jérémie Kalfon]
  • Update README.md. [Jérémie Kalfon]
  • Tiny updates. [jkobject]
  • Add more info. [jkobject]
  • Merge remote-tracking branch 'origin/dev' into main. [jkobject]
  • Update README.md. [Jérémie Kalfon]
  • Adding gitignore. [jkobject]
  • Improving readme. [jkobject]

1.0.15 (2024-08-14)

  • Release: version 1.0.15 🚀 [jkobject]
  • Debug of test. [jkobject]
  • Huggingfacehub. [jkobject]

1.0.14 (2024-08-14)

  • Release: version 1.0.14 🚀 [jkobject]
  • Debug and update. [jkobject]
  • Merge branch 'main' of https://github.com/jkobject/scPRINT into main. [jkobject]
  • Update README.md. [Jérémie Kalfon]
  • Triton update and lamin update. [jkobject]
  • Merge branch 'main' of https://github.com/jkobject/scPRINT into main. [jkobject]
  • Update README.md. [Jérémie Kalfon]
  • Update README.md. [Jérémie Kalfon]
  • Cleanup and adding info in readme. [jkobject]
  • Oups. [jkobject]
  • Trying something else. [jkobject]
  • Not doing large packages or swap. [jkobject]
  • Need matrix. [jkobject]
  • Needs. [jkobject]
  • Free disk space. [jkobject]
  • Adding lock. [jkobject]
  • 3.10. [jkobject]
  • Python 3.10 for tests. [jkobject]
  • Now testing scprint. [jkobject]
  • Merge branch 'main' of https://github.com/jkobject/scPRINT into main. [jkobject]
  • Add to gititgnore. [jkobject]
  • Debug. [jkobject]
  • Adding tests. [jkobject]
  • Improving docs. [jkobject]
  • Debugging docs. [jkobject]
  • Merge branch 'dev' into main. [jkobject]
  • Finishing doc. [jkobject]

1.0.0 (2024-08-07)

  • Release: version 1.0.0 🚀 [jkobject]

  • Finishing doc. [jkobject]

  • Starting cleanup and removing scDataLoader. [jkobject]

    Also making it work with CLI

  • Merge remote-tracking branch 'origin/HEAD' into dev. [jkobject]

  • Merge pull request #4 from jkobject/dependabot/github_actions/codecov/codecov-action-4. [Jérémie Kalfon]

    Bump codecov/codecov-action from 3 to 4

  • Bump codecov/codecov-action from 3 to 4. [dependabot[bot]]

    Bumps codecov/codecov-action from 3 to 4.

    updated-dependencies:

    • dependency-name: codecov/codecov-action dependency-type: direct:production update-type: version-update:semver-major ...

  • Merge pull request #5 from jkobject/dependabot/github_actions/softprops/action-gh-release-2. [Jérémie Kalfon]

    Bump softprops/action-gh-release from 1 to 2

  • Bump softprops/action-gh-release from 1 to 2. [dependabot[bot]]

    Bumps softprops/action-gh-release from 1 to 2.

    updated-dependencies:

    • dependency-name: softprops/action-gh-release dependency-type: direct:production update-type: version-update:semver-major ...

  • Merge pull request #6 from cantinilab/main. [Jérémie Kalfon]

    nothing really

  • Merge branch 'jkobject:main' into main. [Jérémie Kalfon]

  • Final edits. [jkobject]

  • Improved and refined README.md. [Daniele Capocefalo]

    corrected phrasing ansd spellinh mistakes, corrected scPRINT naming across the README for consistency!

  • Cleanup. [jkobject]

  • Final-ish version of the notebooks. [jkobject]

  • Finishing notebooks cancer. [jkobject]

  • Final-ish version of the notebooks. [jkobject]

  • Finishing notebooks cancer. [jkobject]

  • Debug on macos. [jkobject]

  • Latest version of submodule. [jkobject]

  • Commit submodules. [jkobject]

  • Cleanup further. [jkobject]

  • Merge remote-tracking branch 'origin/dev' [jkobject]

  • Update LICENSE. [Jérémie Kalfon]

  • Merge pull request #3 from jkobject/dependabot/github_actions/actions/setup-python-5. [Jérémie Kalfon]

    Bump actions/setup-python from 4 to 5

  • Bump actions/setup-python from 4 to 5. [dependabot[bot]]

    Bumps actions/setup-python from 4 to 5.

    updated-dependencies:

    • dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-major ...

  • Nothing really. [jkobject]

  • Final-ish version of the notebooks. [jkobject]

  • Finishing notebooks cancer. [jkobject]

  • Merge branch 'dev' of https://github.com/jkobject/scPRINT into dev. [jkobject]

  • Running more and debug. [maestro-jk]

  • Debugging a couple issues. [maestro-jk]

  • Removing these. [maestro-jk]

  • Cleanup. [maestro-jk]

  • From prev commit. [maestro-jk]

  • Latest notebooks version. [maestro-jk]

  • Improving the readme and the notebooks. [jkobject]

  • Merge branch 'dev' of https://github.com/jkobject/scPRINT into dev. [jkobject]

  • Running the notebooks. [maestro-jk]

  • Attention bias. [maestro-jk]

  • Update notebooks and running tests. [maestro-jk]

  • Merge branch 'dev' of https://github.com/jkobject/scPRINT into dev. [jkobject]

  • Wip attention bais. [maestro-jk]

  • Finished tests. [maestro-jk]

  • Merge branch 'dev' of https://github.com/jkobject/scPRINT into dev. [maestro-jk]

  • Nothing really. [maestro-jk]

  • Merge branch 'dev' of https://github.com/jkobject/scPRINT into dev. [maestro-jk]

  • Moving the test function. [maestro-jk]

  • De not commit notebooks except GN. [jkobject]

  • Finishing denoising and classification. [jkobject]

  • Debugging attention comp. [jkobject]

  • Merge branch 'dev' of https://github.com/jkobject/scPRINT into dev. [jkobject]

  • Merge branch 'dev' of https://github.com/jkobject/scPRINT into dev. [maestro-jk]

  • Novel run results. [maestro-jk]

  • Renaming and running notebooks. [maestro-jk]

  • Finished denoising and testing new emb. [jkobject]

  • Merge branch 'dev' of https://github.com/jkobject/scPRINT into dev. [jkobject]

  • Merge branch 'dev' of https://github.com/jkobject/scPRINT into dev. [maestro-jk]

  • Merge branch 'dev' of https://github.com/jkobject/scPRINT into dev. [maestro-jk]

  • Wip. [maestro-jk]

  • Final debug. [jkobject]

  • Cleanup and some debugs. [jkobject]

  • Merge remote-tracking branch 'origin/temp' into dev. [jkobject]

  • Merge remote-tracking branch 'origin/dev' into temp. [jkobject]

  • Still a wip. [maestro-jk]

  • Merge branch 'dev' of https://github.com/jkobject/scPRINT into dev. [maestro-jk]

  • Removing the pdbs. [maestro-jk]

  • Updates. [maestro-jk]

  • Debug of the runs. [maestro-jk]

  • Work in progress on test. [maestro-jk]

  • Merge branch 'dev' of https://github.com/jkobject/scPRINT into dev. [maestro-jk]

  • Some improvements. [maestro-jk]

  • Wip. [maestro-jk]

  • Improving some hyper params. [maestro-jk]

  • Merge branch 'temp' of https://github.com/jkobject/scPRINT into temp. [jkobject]

  • New runs. [maestro-jk]

  • Wip. [jkobject]

  • Update classifier. [jkobject]

  • Update classification. [jkobject]

  • Need to work on this. [maestro-jk]

  • New notebooks. [maestro-jk]

  • Running new notebooks. [maestro-jk]

  • Merge branch 'temp' of https://github.com/jkobject/scPRINT into temp. [maestro-jk]

  • New notebooks. [jkobject]

  • New completed notebooks. [maestro-jk]

  • Commit the notebooks. [jkobject]

  • Work in progress. [jkobject]

  • Current wip. [jkobject]

  • Final debugs and cleanups. [jkobject]

  • Merge branch 'dev' of https://github.com/jkobject/scPRINT into dev. [jkobject]

  • Updating adaloader. [maestro-jk]

  • More training. [maestro-jk]

  • Launched and relaunched many versions. [maestro-jk]

  • Wip but work remains. [maestro-jk]

  • Solutionning loads of tiny issues. [maestro-jk]

  • Merge branch 'dev' of https://github.com/jkobject/scPRINT into dev. [maestro-jk]

  • Better output of test. [maestro-jk]

  • Some apparent changes to push. [maestro-jk]

  • Running loads of update. [jkobject]

  • Lots of additional tests. [jkobject]

  • Great further results and adding some things. [jkobject]

  • Merge branch 'dev' of https://github.com/jkobject/scPRINT into dev. [jkobject]

  • Merge branch 'dev' of https://github.com/jkobject/scPRINT into dev. [maestro-jk]

  • Merge branch 'dev' of https://github.com/jkobject/scPRINT into dev. [jkobject]

  • Another training vlarge version. [maestro-jk]

  • Merge branch 'dev' of https://github.com/jkobject/scPRINT into dev. [jkobject]

  • Another param set and working on loss. [maestro-jk]

  • Trying out stuff. [maestro-jk]

  • Cleanup notebooks, model edge cases, improve tasks. [jkobject]

  • Merge branch 'dev' of https://github.com/jkobject/scPRINT into dev. [jkobject]

  • Nice umap. [maestro-jk]

  • Replacing with base and some more changes. [maestro-jk]

  • Prefering to use base. [maestro-jk]

  • Better auprc. [jkobject]

  • Merge branch 'dev' of https://github.com/jkobject/scPRINT into dev. [maestro-jk]

  • Merge branch 'dev' into dev-temp. [jkobject]

  • Wip. [jkobject]

  • Nothing. [jkobject]

  • Merge branch 'dev' into dev-temp. [jkobject]

  • Work in progress on denoising and finishing all GRN tests. [jkobject]

  • Getting good results now. [jkobject]

  • Nice results. [jkobject]

  • Cleanups. [jkobject]

  • Merge branch 'dev' of https://github.com/jkobject/scPRINT into dev. [jkobject]

  • Merge branch 'dev' of https://github.com/jkobject/scPRINT into dev. [maestro-jk]

  • Ignoring files. [jkobject]

  • Bench GRN finish. [jkobject]

  • Continuing / finishing bench and extractions of GRNs. [jkobject]

  • Merge branch 'dev' of https://github.com/jkobject/scPRINT into dev. [jkobject]

  • Simple masker. [jkobject]

  • State of things. [maestro-jk]

  • Merge branch 'trial_debug' of https://github.com/jkobject/scPRINT into dev. [maestro-jk]

  • Continuing / finishing bench and extractions of GRNs. [jkobject]

  • Continuing / finishing bench and extractions of GRNs. [jkobject]

  • Nothing. [maestro-jk]

  • Works finally and let's push. [maestro-jk]

  • Works. [maestro-jk]

  • Still works. [maestro-jk]

  • Now it is still working. [maestro-jk]

  • Nothing really. [maestro-jk]

  • This part is still of. [maestro-jk]

  • Now it works. [maestro-jk]

  • WorkingA. [maestro-jk]

  • Commit of last 3 runs. [maestro-jk]

  • Adding do_class. [maestro-jk]

  • Working on the model. [jkobject]

  • Merge branch 'dev' of https://github.com/jkobject/scPRINT into dev. [jkobject]

  • Merge branch 'dev' of https://github.com/jkobject/scPRINT into dev. [maestro-jk]

  • Merge branch 'dev' of https://github.com/jkobject/scPRINT into dev. [maestro-jk]

  • Wip. [maestro-jk]

  • Working on gene embedding and grn. [jkobject]

  • Forgot this one bit. [jkobject]

  • Now multi species. [jkobject]

  • Updates and cleans post function run. [jkobject]

  • Debug classifications. [jkobject]

  • Merge branch 'dev' of https://github.com/jkobject/scPRINT into dev. [jkobject]

  • Tad of improvements. [maestro-jk]

  • Merge branch 'dev' of https://github.com/jkobject/scPRINT into dev. [maestro-jk]

  • New params. [maestro-jk]

  • Debug model & utils. [jkobject]

  • See adata and accuracy. [jkobject]

  • Some bugs to solve with cell embs. [maestro-jk]

  • Starting to improve GRN but now needs the debugged models. [jkobject]

  • Loads of improvements and a couple debugs. [jkobject]

  • Tiny improvements and debug of classification. [jkobject]

  • Merge branch 'dev' of https://github.com/jkobject/scPRINT into dev. [jkobject]

  • Merge branch 'dev' of https://github.com/jkobject/scPRINT into dev. [maestro-jk]

  • Merge branch 'dev' of https://github.com/jkobject/scPRINT into dev. [maestro-jk]

  • Updates to the model. [maestro-jk]

  • Debugging the model wip. [jkobject]

  • Adding adv class, adv batch class, scheduling debug, debug of cce and cleanups. [jkobject]

  • Debug. [jkobject]

  • Working on GRNfer and some more cleanups. [jkobject]

  • Update README.md. [Jérémie Kalfon]

  • Update README.md. [Jérémie Kalfon]

  • Update submodules. [jkobject]

  • Docstring and building a docs. [jkobject]

  • Add back RNABert. [jkobject]

  • Removing RNABERT. [jkobject]

  • Changing gitmodules. [jkobject]

  • Some cleanups and starting the documentation. [jkobject]

  • Merge branch 'dev' of https://github.com/jkobject/scPRINT into dev. [jkobject]

  • Add files via upload. [Jérémie Kalfon]

  • Merge branch 'dev' of https://github.com/jkobject/scPRINT into dev. [jkobject]

  • Mini improvements and new medium training scheme. [maestro-jk]

  • Merge branch 'dev' of https://github.com/jkobject/scPRINT into dev. [maestro-jk]

  • Nothing. [maestro-jk]

  • Wip. [maestro-jk]

  • Merge branch 'dev' of https://github.com/jkobject/scPRINT into dev. [maestro-jk]

  • Some tiny updates. [maestro-jk]

  • Getting attention matrix. [jkobject]

  • Testing that it runs. [jkobject]

  • Test adding wandb log of datamodule. [jkobject]

  • Update the class hierarchy in model and add accuracy in class. [jkobject]

  • Adding expr avg parquet. [jkobject]

  • Applying the stash on updating the embs task. [jkobject]

  • Some improv and more pretraining scripts. [maestro-jk]

  • Done debug. [jkobject]

  • Wip. [jkobject]

  • Some debugs. [maestro-jk]

  • Debug and improv of embs and depth. [jkobject]

  • Merge branch 'dev' of https://github.com/jkobject/scPRINT into dev. [jkobject]

  • Merge branch 'dev' of https://github.com/jkobject/scPRINT into dev. [maestro-jk]

  • Multiple scripts. [maestro-jk]

  • Wip tests and cleanup. [jkobject]

  • Finally found the bug. [jkobject]

  • Update scDataloader. [jkobject]

  • Merge branch 'dev' of https://github.com/jkobject/scPRINT into dev. [maestro-jk]

  • Debug an issue with the model. [jkobject]

  • Cleaning time and removing geert. [maestro-jk]

  • Merge branch 'dev' of https://github.com/jkobject/scPRINT into dev. [maestro-jk]

  • Wip. [jkobject]

  • Merge branch 'dev' of https://github.com/jkobject/scPRINT into dev. [jkobject]

  • Working on mutliple tasks. [jkobject]

  • Improving continuous encoders. [maestro-jk]

  • Merge branch 'dev' of https://github.com/jkobject/scPRINT into dev. [maestro-jk]

  • Merge branch 'dev' of https://github.com/jkobject/scPRINT into dev. [jkobject]

  • Work on cell emb and dropping useless notebooks. [jkobject]

  • Nothing really. [maestro-jk]

  • Some model improvement. [maestro-jk]

  • New version of the loss. [jkobject]

  • Merge branch 'dev' of https://github.com/jkobject/scPRINT into dev. [jkobject]

  • Starting to work on multi gpus. [maestro-jk]

  • Merge branch 'dev' of https://github.com/jkobject/scPRINT into dev. [maestro-jk]

  • Trying out. [maestro-jk]

  • Merge branch 'dev' of https://github.com/jkobject/scPRINT into dev. [maestro-jk]

  • Nothing. [maestro-jk]

  • Updating deps. [maestro-jk]

  • Debugging classification. [jkobject]

  • Seems to work well. [jkobject]

  • Merge branch 'dev' of https://github.com/jkobject/scPRINT into dev. [jkobject]

  • Merge branch 'dev' of https://github.com/jkobject/scPRINT into dev. [maestro-jk]

  • Nothgin. [maestro-jk]

  • Nothing. [jkobject]

  • Config that seems to be working. [jkobject]

  • Merge branch 'dev' of https://github.com/jkobject/scPRINT into dev. [jkobject]

  • Merge branch 'dev' of https://github.com/jkobject/scPRINT into dev. [maestro-jk]

  • Dropping useless stuff. [maestro-jk]

  • Removing ritini. [maestro-jk]

  • Removing ritini. [maestro-jk]

  • Removing logging. [jkobject]

  • Testing many runs and LR tuning. [jkobject]

  • Cleanup of the model file and some tests. [jkobject]

  • Working on submit. [jkobject]

  • Debug cce. [jkobject]

  • Merge branch 'dev' of https://github.com/jkobject/scPRINT into dev. [jkobject]

  • Merge branch 'dev' of https://github.com/jkobject/scPRINT into dev. [maestro-jk]

  • Adding some stuff. [maestro-jk]

  • Working on the package. [jkobject]

  • Starting to add stuff to the model. [jkobject]

  • Adding notebooks. [jkobject]

  • Merge branch 'main' of https://github.com/jkobject/scPRINT into main. [jkobject]

  • Delete .github/rename_project.sh. [Jérémie Kalfon]

  • Update FUNDING.yml. [Jérémie Kalfon]

  • Adding template. [jkobject]

  • Merge pull request #1 from jkobject/dependabot/github_actions/stefanzweifel/git-auto-commit- action-5. [Jérémie Kalfon]

    Bump stefanzweifel/git-auto-commit-action from 4 to 5

  • ✅ Ready to clone and code. [dependabot[bot]]

  • Bump stefanzweifel/git-auto-commit-action from 4 to 5. [dependabot[bot]]

    Bumps stefanzweifel/git-auto-commit-action from 4 to 5.

    updated-dependencies:

    • dependency-name: stefanzweifel/git-auto-commit-action dependency-type: direct:production update-type: version-update:semver-major ...

  • Merge pull request #2 from jkobject/dependabot/github_actions/actions/checkout-4. [Jérémie Kalfon]

    Bump actions/checkout from 3 to 4

  • ✅ Ready to clone and code. [dependabot[bot]]

  • Bump actions/checkout from 3 to 4. [dependabot[bot]]

    Bumps actions/checkout from 3 to 4.

    updated-dependencies:

    • dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ...

  • ✅ Ready to clone and code. [jkobject]

  • Initial commit. [Jérémie Kalfon]

  • Debugging known issues, adding CLI mode, testing more dataloader. [jkobject]

  • More debugs. [jkobject]

  • Cleanups. [jkobject]

  • Update of the notebooks. [jkobject]

  • And more. [jkobject]

  • More. [jkobject]

  • Debugging. [jkobject]

  • Nothing really. [jkobject]

  • Adding better plots and different depth management. [jkobject]

  • Cleanup. [jkobject]

  • Working on the model and first successfull runs. [jkobject]

  • Testing a first version of scprint. [jkobject]

  • Some more runs. [jkobject]

  • Working on EGT. [jkobject]

  • Some runs. [jkobject]

  • Debug conda env issues. [jkobject]

  • Working on the model and flashattention. [jkobject]

  • Improving explainer. [jkobject]

  • Cleanup model and test EGT. [jkobject]

  • Finalizing the model framework. [jkobject]

  • Working on the model. [jkobject]

  • Removing dataloader. [jkobject]

  • Finish dataloader. [jkobject]

  • Preprocessing. [jkobject]

  • Current. [jkobject]

  • Running rnabert. [jkobject]

  • Starting to debug dataloader. [jkobject]

  • More debugs. [jkobject]

  • Quick update. [jkobject]

  • Adding math.md. [jkobject]

  • Final update RNAbert. [jkobject]

  • Updating rnabert. [jkobject]

  • Commit often. [jkobject]

  • Adding RNABert submodule. [jkobject]

  • Continuing work on scprint. [jkobject]

  • Finishing dataloader and test of scGPT. [jkobject]

  • Adding some stuff. [maestro-jk]

  • Working on the package. [jkobject]

  • Starting to add stuff to the model. [jkobject]

  • Adding notebooks. [jkobject]

  • Merge branch 'main' of https://github.com/jkobject/scPRINT into main. [jkobject]

  • Delete .github/rename_project.sh. [Jérémie Kalfon]

  • Update FUNDING.yml. [Jérémie Kalfon]

  • Adding template. [jkobject]

  • Merge pull request #1 from jkobject/dependabot/github_actions/stefanzweifel/git-auto-commit- action-5. [Jérémie Kalfon]

    Bump stefanzweifel/git-auto-commit-action from 4 to 5

  • ✅ Ready to clone and code. [dependabot[bot]]

  • Bump stefanzweifel/git-auto-commit-action from 4 to 5. [dependabot[bot]]

    Bumps stefanzweifel/git-auto-commit-action from 4 to 5.

    updated-dependencies:

    • dependency-name: stefanzweifel/git-auto-commit-action dependency-type: direct:production update-type: version-update:semver-major ...

  • Merge pull request #2 from jkobject/dependabot/github_actions/actions/checkout-4. [Jérémie Kalfon]

    Bump actions/checkout from 3 to 4

  • ✅ Ready to clone and code. [dependabot[bot]]

  • Bump actions/checkout from 3 to 4. [dependabot[bot]]

    Bumps actions/checkout from 3 to 4.

    updated-dependencies:

    • dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ...

  • ✅ Ready to clone and code. [jkobject]

  • Initial commit. [Jérémie Kalfon]