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