------------------
- 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](https://github.com/codecov/codecov-action) from 3 to 4.
- [Release notes](https://github.com/codecov/codecov-action/releases)
- [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md)
- [Commits](https://github.com/codecov/codecov-action/compare/v3...v4)
---
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](https://github.com/softprops/action-gh-release) from 1 to 2.
- [Release notes](https://github.com/softprops/action-gh-release/releases)
- [Changelog](https://github.com/softprops/action-gh-release/blob/master/CHANGELOG.md)
- [Commits](https://github.com/softprops/action-gh-release/compare/v1...v2)
---
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](https://github.com/actions/setup-python) from 4 to 5.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v4...v5)
---
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](https://github.com/stefanzweifel/git-auto-commit-action) from 4 to 5.
- [Release notes](https://github.com/stefanzweifel/git-auto-commit-action/releases)
- [Changelog](https://github.com/stefanzweifel/git-auto-commit-action/blob/master/CHANGELOG.md)
- [Commits](https://github.com/stefanzweifel/git-auto-commit-action/compare/v4...v5)
---
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](https://github.com/actions/checkout) from 3 to 4.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](https://github.com/actions/checkout/compare/v3...v4)
---
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](https://github.com/stefanzweifel/git-auto-commit-action) from 4 to 5.
- [Release notes](https://github.com/stefanzweifel/git-auto-commit-action/releases)
- [Changelog](https://github.com/stefanzweifel/git-auto-commit-action/blob/master/CHANGELOG.md)
- [Commits](https://github.com/stefanzweifel/git-auto-commit-action/compare/v4...v5)
---
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](https://github.com/actions/checkout) from 3 to 4.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](https://github.com/actions/checkout/compare/v3...v4)
---
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]