dnadiffusion - v0.0.3

Changes

version change to v0.0.3

- Python
Published by github-actions[bot] 10 months ago

dnadiffusion - v0.0.2

Changes

• chore: v0.0.2 (#351) @ssenan
• chore(release): provide tokens for testpypi and pypi (#350) @ssenan

:beetle: Fixes

• Fix version number on release drafter (#348) @ssenan

:package: Dependencies

• feat(release): allow uv to manage build, release, and publish (#347) @ssenan

- Python
Published by github-actions[bot] 10 months ago

dnadiffusion - 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 comparemotiflist 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 vqvaeaccelerate 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

:boom: 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 crossattention, removed unusedparameters flag (#236) @ssenan
• src/dnadiffusion rewrite (#150) @ssenan

:rocket: 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 crossattention, removed unusedparameters flag (#236) @ssenan
• motif composition metric notebook conversion (#222) @ssenan
• add data preprocessing notebooks into library as scripts (#221) @ssenan
• tests for datautil.py and validatepreprocessing.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

:beetle: 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

:rotating_light: Testing

• Update the unit tests (#71) @jamesthesnake

:construction_worker: 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

:books: 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

:hammer: 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

:package: 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 torch 2.1.0 (#228) @ssenan
• chore(deps): update dependency wandb to v0.15.12 (#226) @renovate[bot]
• chore(deps): update dependency einops to v0.7.0 (#220) @renovate[bot]
• chore(deps): update dependency seaborn to v0.13.0 (#218) @renovate[bot]
• chore(deps): update dependency wandb to v0.15.11 (#215) @renovate[bot]
• chore(deps): update dependency pandas to v2.1.1 (#214) @renovate[bot]
• chore(deps): update dependency sourmash to v4.8.4 (#209) @renovate[bot]
• chore(deps): update dependency matplotlib to v3.8.0 (#203) @renovate[bot]
• chore(deps): update dependency memory-efficient-attention-pytorch to v0.1.6 (#201) @renovate[bot]
• fix: pin all package versions (#202) @cameronraysmith
• pin to memory-efficient-attention-pytorch to 0.1.2 (#200) @ssenan
• pin memory-efficient-attention-pytorch to final release version (#199) @ssenan
• chore(deps): update codecov/codecov-action action to v4 (#194) @renovate[bot]
• chore(deps): update docker/setup-qemu-action action to v3 (#189) @renovate[bot]
• chore(deps): update docker/setup-buildx-action action to v3 (#188) @renovate[bot]
• chore(deps): update condaforge/mambaforge docker tag to v23 (#179) @renovate[bot]
• chore(deps): update docker/metadata-action action to v5 (#187) @renovate[bot]
• chore(deps): update docker/login-action action to v3 - autoclosed (#186) @renovate[bot]
• chore(deps): update docker/build-push-action action to v5 (#185) @renovate[bot]
• chore(deps): update docker/build-push-action action to v4 (#183) @renovate[bot]
• chore(deps): update crazy-max/ghaction-github-labeler action to v5 (#182) @renovate[bot]
• chore(deps): update actions/upload-pages-artifact action to v2 (#178) @renovate[bot]
• chore(deps): update actions/stale action to v8 (#177) @renovate[bot]
• fix: apply "dependencies" label to renovate PRs (#184) @cameronraysmith
• pin package versions (#181) @ssenan
• chore(deps): update actions/deploy-pages action to v2 (#176) @renovate[bot]
• chore(deps): update actions/checkout action to v4 (#175) @renovate[bot]
• chore(deps): update release-drafter/release-drafter action to v5.24.0 (#174) @renovate[bot]
• chore(deps): update crazy-max/ghaction-github-labeler action to v4.2.0 (#170) @renovate[bot]
• chore(deps): update pypa/gh-action-pypi-publish action to v1.8.10 (#169) @renovate[bot]
• feat: add renovate config (#167) @cameronraysmith
• adding the specification, makefile and test env (#137) @noahweber1
• add docker container (#121) @cameronraysmith
• add build system (#117) @cameronraysmith

- Python
Published by github-actions[bot] 10 months ago

dnadiffusion - v0.0.0.dev0

Changes

• added vqvaeaccelerate 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

:rocket: 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

:beetle: Fixes

• Changes all import lightning to import pytorch_lightning (#127) @ssenan
• Comment out config.py to resolve pre-commit parsing error (#99) @ssenan

:rotating_light: Testing

• Update the unit tests (#71) @jamesthesnake

:construction_worker: 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

:books: 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

:hammer: 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

:package: Dependencies

• add docker container (#121) @cameronraysmith
• add build system (#117) @cameronraysmith

- Python
Published by github-actions[bot] almost 3 years ago