From 77a09b6c32ce44b4c377406a89546a773d673e43 Mon Sep 17 00:00:00 2001 From: jkobject Date: Wed, 7 Aug 2024 14:54:11 +0200 Subject: [PATCH] =?UTF-8?q?release:=20version=201.0.0=20=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- HISTORY.md | 500 +++++++++++++++++++++++++++++++++++++++++++++++- scprint/VERSION | 2 +- 2 files changed, 494 insertions(+), 8 deletions(-) diff --git a/HISTORY.md b/HISTORY.md index 9bf6ef0..4b5231b 100644 --- a/HISTORY.md +++ b/HISTORY.md @@ -2,12 +2,498 @@ Changelog ========= -0.1.2 (2021-08-14) ------------------- -- Fix release, README and windows CI. [Bruno Rocha] -- Release: version 0.1.0. [Bruno Rocha] +(unreleased) +------------ +- 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] -0.1.0 (2021-08-14) ------------------- -- Add release command. [Bruno Rocha] diff --git a/scprint/VERSION b/scprint/VERSION index 6e8bf73..3eefcb9 100644 --- a/scprint/VERSION +++ b/scprint/VERSION @@ -1 +1 @@ -0.1.0 +1.0.0