Releases: pinellolab/DNA-Diffusion
Releases · pinellolab/DNA-Diffusion
v0.1.1
v0.1.0
Changes
🚀 Features
- feat(sequence generation): add ability to generate specific cell types (#359) @ssenan
- feat(docs): update example notebooks, colab links, and huggingface checkpoint (#355) @ssenan
📚 Documentation
- chore(version): 0.1.0 (#360) @ssenan
- feat(sequence generation): add ability to generate specific cell types (#359) @ssenan
- chore(docs): add table new data to toc (#356) @ssenan
- feat(docs): update example notebooks, colab links, and huggingface checkpoint (#355) @ssenan
- Doc updates for data preprocessing, training, sampling and downloading checkpoint (#353) @ssenan
📦 Dependencies
Contributors
ssenan
Assets 2
v0.0.3
Changes
version change to v0.0.3
v0.0.2
Contributors
ssenan
Assets 2
v0.0.1
Changes
- chore(release): provide tokens for testpypi and pypi (#350) @ssenan
- chore(version): update to 0.0.1 (#345) @ssenan
- fix: add linguist config (#304) @cameronraysmith
- fix bug caused by taking length of itertools.pairwise() (#288) @ssenan
- add contributor graph (#281) @cameronraysmith
- docs: add ssenan as a contributor for ideas, and code (#280) @allcontributors[bot]
- docs: add lucapinello as a contributor for ideas (#278) @allcontributors[bot]
- docs: add LucasSilvaFerreira as a contributor for ideas (#277) @allcontributors[bot]
- fix compare_motif_list location call in motif data frame (#205) @ssenan
- Revert "chore(deps): update codecov/codecov-action action to v4 (#194)" (#196) @cameronraysmith
- Fix formatting after latest PR (#164) @ssenan
- Rename train_hf.py to train.py (#158) @ssenan
- Handle dataset for each split individually (#148) @mansoldm
- Dataset refactor (#147) @mansoldm
- added vq_vae_accelerate notebook and trained vq_vae model model4cells (#101) @ttunja
- adding the kmer metrics (#100) @hssn-20
- Adding notebook for filtering master_dataset (#76) @ssenan
- adding the time warping functionality (#63) @noahweber1
- Update README.md (#73) @Ryams
- DDIM Sampling implemented (#65) @mihirneal
- Resolve contributor list in an independant file (#25) @IhabBendidi
- Fixes formatting in the 'Tasks and Potential Roadmap' section (#1) @jxilt
💥 Breaking Changes
- Update workflows to use uv (missing updates to tests) (#334) @ssenan
- Update training code, remove legacy libraries, provide basic usage instructions (#321) @ssenan
- fix cross_attention, removed unused_parameters flag (#236) @ssenan
- src/dnadiffusion rewrite (#150) @ssenan
🚀 Features
- Update workflows to use uv (missing updates to tests) (#334) @ssenan
- Update training code, remove legacy libraries, provide basic usage instructions (#321) @ssenan
- Add sequence selection notebook (#283) @ssenan
- replace black formatter with ruff (#247) @ssenan
- change logging to be dependent on current step (#238) @ssenan
- fix cross_attention, removed unused_parameters flag (#236) @ssenan
- motif composition metric notebook conversion (#222) @ssenan
- add data preprocessing notebooks into library as scripts (#221) @ssenan
- tests for data_util.py and validate_preprocessing.py (#211) @ssenan
- Data preprocessing scripts for sequence validation dataset (#207) @ssenan
- Fixes cell specific sample generation (#195) @ssenan
- Add heatmap generation functionality for cell specific synthetic sequences (#192) @ssenan
- Fix device allocation in sample.py / simplify sequence generation (#160) @ssenan
- Removes torch dataloader from load_data, adds initial tests to dataloading (#156) @ssenan
- Add load function to train_util to resume training (#152) @ssenan
- src/dnadiffusion rewrite (#150) @ssenan
- add example slurm submission (#133) @cameronraysmith
- pytorch-lightning/hydra-zen integration (#105) @ssenan
- merge codebase changes on main into default (#92) @cameronraysmith
- Fixed script pathing, now works as intended on cluster (#87) @ssenan
- Adding subscripts created from original single script (#84) @ssenan
- refactor: (minor) vq-vae (#61) @SauravMaheshkar
- Adding the modified NB (#60) @noahweber1
🪲 Fixes
- Fix version number on release drafter (#348) @ssenan
- Allow uv sync to jointly resolve python version and dependencies (#337) @ssenan
- Provide more detailed documentation about debugging with subset of original DNA-Diffusion dataset (#330) @ssenan
- fix num samples outputted equal to user input (#162) @ssenan
- Fixing build and doc errors after PR merge (#154) @ssenan
- Changes all import lightning to import pytorch_lightning (#127) @ssenan
- Comment out config.py to resolve pre-commit parsing error (#99) @ssenan
🚨 Testing
- Update the unit tests (#71) @jamesthesnake
👷 Continuous Integration
- refactor: separate pypi and conda containers (#230) @cameronraysmith
- update conda environment to torch
2.1.0(#228) @ssenan - feat: automate queue for merge (#190) @cameronraysmith
- make release depend on build and docker (#129) @cameronraysmith
- add release workflows (#125) @cameronraysmith
- Comment out config.py to resolve pre-commit parsing error (#99) @ssenan
- add actions/stale for issues and prs (#82) @cameronraysmith
- add pre-commit configuration (#80) @cameronraysmith
📚 Documentation
- Generalize acceptable GPU types in README and more descriptive list of cell lines used to train the model (#331) @lucapinello
- Provide more detailed documentation about debugging with subset of original DNA-Diffusion dataset (#330) @ssenan
- Update training code, remove legacy libraries, provide basic usage instructions (#321) @ssenan
- adding the specification, makefile and test env (#137) @noahweber1
- use smaller README image (#131) @cameronraysmith
- add documentation (#119) @cameronraysmith
- update metadata (#112) @cameronraysmith
- add actions/stale for issues and prs (#82) @cameronraysmith
- add contributor covenant code of conduct (#78) @cameronraysmith
🔨 Refactoring
- fix(tests): remove outdated motif metric code and associated tests (#342) @ssenan
- Fix flags for gimme motifs to capture more motif hits (#166) @ssenan
- src/dnadiffusion rewrite (#150) @ssenan
- Removed validation metrics from sampling metrics (#108) @ssenan
- merge codebase changes on main into default (#92) @cameronraysmith
- Fixed script pathing, now works as intended on cluster (#87) @ssenan
- Adding subscripts created from original single script (#84) @ssenan
- refactor: (minor) vq-vae (#61) @SauravMaheshkar
- Adding the modified NB (#60) @noahweber1
📦 Dependencies
- feat(release): allow uv to manage build, release, and publish (#347) @ssenan
- Resolve formatting error in build workflow config (#344) @ssenan
- fix(docs): update pyproject.toml to allow for python handlers in docs (#341) @ssenan
- fix(uv.lock): update uv to 0.7.2 & update lock file (#339) @ssenan
- Allow uv sync to jointly resolve python version and dependencies (#337) @ssenan
- Update workflows to use uv (missing updates to tests) (#334) @ssenan
- Update training code, remove legacy libraries, provide basic usage instructions (#321) @ssenan
- chore(deps): update dependency torchvision to v0.19.0 (#301) @renovate[bot]
- chore(deps): update dependency torchvision to v0.18.1 (#265) @renovate[bot]
- chore(deps): update dependency mypy to v1.10.0 (#261) @renovate[bot]
- chore(deps): update dependency torch to v2.3.1 (#264) @renovate[bot]
- Bump codecov to v4 (#294) @ssenan
- ignore ruff rule related to pairwise preference over zip (#290) @ssenan
- chore(deps): update dependency jupyterlab to v4.0.9 (#269) @renovate[bot]
- chore(deps): update dependency ruff to v0.1.6 (#268) @renovate[bot]
- chore(deps): update dependency matplotlib to v3.8.1 (#255) @renovate[bot]
- chore(deps): update dependency accelerate to v0.24.1 (#253) @renovate[bot]
- chore(deps): update dependency types-tqdm to v4.66.0.4 (#251) @renovate[bot]
- chore(deps): update dependency pandas to v2.1.3 (#262) @renovate[bot]
- chore(deps): update dependency xdoctest to v1.1.2 (#248) @renovate[bot]
- chore(deps): update dependency ruff to v0.1.5 (#260) @renovate[bot]
- chore(deps): update dependency wandb to v0.16.0 (#259) @renovate[bot]
- chore(deps): update dependency pandas to v2.1.2 (#249) @renovate[bot]
- chore(deps): update dependency jupyterlab to v4.0.8 (#256) @renovate[bot]
- chore(deps): update dependency mkdocs-material to v9.4.8 (#258) @renovate[bot]
- chore(deps): update dependency ruff to v0.1.4 (#257) @renovate[bot]
- chore(deps): update dependency pytest to v7.4.3 (#246) @renovate[bot]
- chore(deps): update dependency ruff to v0.1.3 (#250) @renovate[bot]
- chore(deps): update dependency mkdocs-material to v9.4.7 (#252) @renovate[bot]
- chore(deps): update dependency mkdocs-material to v9.4.6 (#241) @renovate[bot]
- chore(deps): update dependency accelerate to v0.24.0 (#244) @renovate[bot]
- replace black formatter with ruff (#247) @ssenan
- chore(deps): update dependency mypy to v1.6.1 (#242) @renovate[bot]
- chore(deps): update dependency black to v23.10.1 (#240) @renovate[bot]
- chore(deps): update dependency ruff to v0.1.2 (#243) @renovate[bot]
- chore(deps): update release-drafter/release-drafter action to v5.25.0 (#239) @renovate[bot]
- refactor: separate pypi and conda containers (#230) @cameronraysmith
- chore(deps): update dependency torchvision to v0.16.0 (#227) @renovate[bot]
- chore(deps): update dependency torch to v2.1.0 (#225) @renovate[bot]
- fix: bump dev version
0.0.0.dev1(#229) @cameronraysmith - update conda environment to ...
Contributors
cameronraysmith, lucapinello, and 11 other contributors
Assets 2
v0.0.0.dev0
Changes
- added vq_vae_accelerate notebook and trained vq_vae model model4cells (#101) @ttunja
- adding the kmer metrics (#100) @hssn-20
- Adding notebook for filtering master_dataset (#76) @ssenan
- adding the time warping functionality (#63) @noahweber1
- Update README.md (#73) @Ryams
- DDIM Sampling implemented (#65) @mihirneal
- Resolve contributor list in an independant file (#25) @IhabBendidi
- Fixes formatting in the 'Tasks and Potential Roadmap' section (#1) @jxilt
🚀 Features
- pytorch-lightning/hydra-zen integration (#105) @ssenan
- merge codebase changes on main into default (#92) @cameronraysmith
- Fixed script pathing, now works as intended on cluster (#87) @ssenan
- Adding subscripts created from original single script (#84) @ssenan
- refactor: (minor) vq-vae (#61) @SauravMaheshkar
- Adding the modified NB (#60) @noahweber1
🪲 Fixes
- Changes all import lightning to import pytorch_lightning (#127) @ssenan
- Comment out config.py to resolve pre-commit parsing error (#99) @ssenan
🚨 Testing
- Update the unit tests (#71) @jamesthesnake
👷 Continuous Integration
- make release depend on build and docker (#129) @cameronraysmith
- add release workflows (#125) @cameronraysmith
- Comment out config.py to resolve pre-commit parsing error (#99) @ssenan
- add actions/stale for issues and prs (#82) @cameronraysmith
- add pre-commit configuration (#80) @cameronraysmith
📚 Documentation
- use smaller README image (#131) @cameronraysmith
- add documentation (#119) @cameronraysmith
- update metadata (#112) @cameronraysmith
- add actions/stale for issues and prs (#82) @cameronraysmith
- add contributor covenant code of conduct (#78) @cameronraysmith
🔨 Refactoring
- Removed validation metrics from sampling metrics (#108) @ssenan
- merge codebase changes on main into default (#92) @cameronraysmith
- Fixed script pathing, now works as intended on cluster (#87) @ssenan
- Adding subscripts created from original single script (#84) @ssenan
- refactor: (minor) vq-vae (#61) @SauravMaheshkar
- Adding the modified NB (#60) @noahweber1
📦 Dependencies
- add docker container (#121) @cameronraysmith
- add build system (#117) @cameronraysmith
Contributors
cameronraysmith, Ryams, and 9 other contributors