pinellolab/DNA-Diffusion issues and pull requests

#315 - chore(deps): update dependency matplotlib to v3.10.0

Pull Request - State: open - Opened by renovate[bot] 13 days ago
Labels: dependencies

#314 - chore(deps): update dependency pandas to v2.2.3

Pull Request - State: open - Opened by renovate[bot] 29 days ago
Labels: dependencies

#313 - chore(deps): update dependency mypy to v1.15.0

Pull Request - State: open - Opened by renovate[bot] about 1 month ago
Labels: dependencies

#312 - chore(deps): update dependency einops to v0.8.1

Pull Request - State: open - Opened by renovate[bot] about 1 month ago
Labels: dependencies

#311 - chore(deps): update crazy-max/ghaction-github-labeler action to v5.2.0

Pull Request - State: open - Opened by renovate[bot] about 1 month ago
Labels: dependencies

#310 - chore(deps): update dependency click to v8.1.8

Pull Request - State: open - Opened by renovate[bot] about 1 month ago
Labels: dependencies

#309 - how can i train the unet with ohter seq_len?

Issue - State: open - Opened by GitHUB-ZYD about 1 month ago

#308 - ci(mergify): upgrade configuration to current format

Pull Request - State: open - Opened by mergify[bot] 3 months ago

#307 - ci(mergify): upgrade configuration to current format

Pull Request - State: closed - Opened by mergify[bot] 3 months ago

#306 - chore(deps): update dependency sourmash to v4.8.14

Pull Request - State: open - Opened by renovate[bot] 3 months ago
Labels: dependencies

#305 - Are the embeddings of DNA diffusion meaningful?

Issue - State: closed - Opened by HelloWorldLTY 5 months ago - 2 comments
Labels: stale

#304 - fix: add linguist config

Pull Request - State: closed - Opened by cameronraysmith 7 months ago
Labels: skip-ci

#303 - Fix linguist classification

Issue - State: closed - Opened by cameronraysmith 7 months ago
Labels: bug

#302 - chore(deps): update dependency seaborn to v0.13.2

Pull Request - State: closed - Opened by renovate[bot] 7 months ago - 1 comment
Labels: stale, dependencies

#301 - chore(deps): update dependency torchvision to v0.19.0

Pull Request - State: closed - Opened by renovate[bot] 7 months ago
Labels: dependencies

#300 - Remove accelerate dependency

Issue - State: closed - Opened by ssenan 7 months ago - 2 comments
Labels: codebase, stale

#299 - Use hydra for configs

Issue - State: closed - Opened by ssenan 7 months ago - 5 comments
Labels: enhancement, stale

#298 - Fix pathing to data files

Issue - State: closed - Opened by ssenan 8 months ago - 2 comments
Labels: bug, stale

#297 - chore(deps): update dependency mkdocstrings to v0.27.0

Pull Request - State: closed - Opened by renovate[bot] 8 months ago - 1 comment
Labels: stale, dependencies

#296 - chore(deps): update dependency xdoctest to v1.2.0

Pull Request - State: closed - Opened by renovate[bot] 8 months ago - 1 comment
Labels: stale, dependencies

#295 - Generalize Logging function for more flexibility

Issue - State: closed - Opened by ssenan 8 months ago - 2 comments
Labels: codebase, stale

#294 - Bump codecov to v4

Pull Request - State: closed - Opened by ssenan 8 months ago
Labels: build

#293 - Update codecov action to v4

Issue - State: closed - Opened by ssenan 9 months ago
Labels: dependencies

#292 - Update README to replace proposal with usage instructions

Issue - State: closed - Opened by ssenan 9 months ago - 4 comments
Labels: documentation, stale

#291 - Remove deprecated refactor folder from src package

Issue - State: closed - Opened by ssenan 9 months ago - 4 comments
Labels: codebase, stale

#290 - ignore ruff rule related to pairwise preference over zip

Pull Request - State: closed - Opened by ssenan 9 months ago
Labels: build

#289 - Error during build caused by RUF007

Issue - State: closed - Opened by ssenan 9 months ago
Labels: bug

#288 - fix bug caused by taking length of itertools.pairwise()

Pull Request - State: closed - Opened by ssenan 9 months ago
Labels: codebase

#287 - Error in training due to len call on itertools.pairwise()

Issue - State: closed - Opened by ssenan 9 months ago
Labels: bug

#286 - TypeError: object of type 'itertools.pairwise' has no len()

Issue - State: closed - Opened by mjleone 10 months ago - 1 comment

#285 - chore(deps): update dependency pytest to v7.4.4

Pull Request - State: closed - Opened by renovate[bot] 11 months ago - 2 comments
Labels: stale, dependencies

#284 - chore(deps): update dependency jupyterlab to v4.2.5 [security]

Pull Request - State: closed - Opened by renovate[bot] about 1 year ago - 2 comments
Labels: stale, dependencies

#283 - Add sequence selection notebook

Pull Request - State: closed - Opened by ssenan about 1 year ago - 1 comment
Labels: enhancement

#282 - Add sequence selection notebook

Issue - State: closed - Opened by ssenan about 1 year ago
Labels: enhancement

#281 - add contributor graph

Pull Request - State: closed - Opened by cameronraysmith about 1 year ago

#280 - docs: add ssenan as a contributor for ideas, and code

Pull Request - State: closed - Opened by allcontributors[bot] about 1 year ago

#279 - docs: add ssenan as a contributor for ideas, and code

Pull Request - State: closed - Opened by allcontributors[bot] about 1 year ago

#278 - docs: add lucapinello as a contributor for ideas

Pull Request - State: closed - Opened by allcontributors[bot] about 1 year ago

#277 - docs: add LucasSilvaFerreira as a contributor for ideas

Pull Request - State: closed - Opened by allcontributors[bot] about 1 year ago

#276 - Contribution Log

Issue - State: closed - Opened by cameronraysmith about 1 year ago - 12 comments
Labels: documentation, stale

#275 - chore(deps): update dependency pytest-asyncio to v0.25.3

Pull Request - State: open - Opened by renovate[bot] about 1 year ago - 1 comment
Labels: dependencies

Pull Request - State: closed - Opened by cameronraysmith about 1 year ago - 3 comments
Labels: enhancement, refactoring, ci, stale, build, dependencies, github_actions, work-in-progress, execute-workflow, skip-ci

#273 - chore(deps): update dependency accelerate to v0.34.2

Pull Request - State: closed - Opened by renovate[bot] about 1 year ago - 2 comments
Labels: stale, dependencies

#272 - support workflow execution from cli

Issue - State: closed - Opened by cameronraysmith about 1 year ago - 3 comments
Labels: enhancement, stale

#271 - chore(deps): update pypa/gh-action-pypi-publish action to v1.12.4

Pull Request - State: open - Opened by renovate[bot] about 1 year ago - 1 comment
Labels: dependencies

#270 - chore(deps): update dependency types-tqdm to v4.66.0.20240106

Pull Request - State: closed - Opened by renovate[bot] about 1 year ago - 2 comments
Labels: stale, dependencies

#269 - chore(deps): update dependency jupyterlab to v4.0.9

Pull Request - State: closed - Opened by renovate[bot] over 1 year ago - 1 comment
Labels: dependencies

#268 - chore(deps): update dependency ruff to v0.1.6

Pull Request - State: closed - Opened by renovate[bot] over 1 year ago - 1 comment
Labels: dependencies

#267 - chore(deps): update dependency matplotlib to v3.8.2

Pull Request - State: closed - Opened by renovate[bot] over 1 year ago - 2 comments
Labels: stale, dependencies

#266 - chore(deps): update dependency mkdocs-material to v9.6.4

Pull Request - State: open - Opened by renovate[bot] over 1 year ago - 1 comment
Labels: dependencies

#265 - chore(deps): update dependency torchvision to v0.18.1

Pull Request - State: closed - Opened by renovate[bot] over 1 year ago - 2 comments
Labels: dependencies

#264 - chore(deps): update dependency torch to v2.3.1

Pull Request - State: closed - Opened by renovate[bot] over 1 year ago
Labels: dependencies

#263 - chore(deps): update dependency mkdocstrings to v0.24.0

Pull Request - State: closed - Opened by renovate[bot] over 1 year ago - 2 comments
Labels: stale, dependencies

#262 - chore(deps): update dependency pandas to v2.1.3

Pull Request - State: closed - Opened by renovate[bot] over 1 year ago - 1 comment
Labels: dependencies

#261 - chore(deps): update dependency mypy to v1.10.0

Pull Request - State: closed - Opened by renovate[bot] over 1 year ago - 1 comment
Labels: dependencies

#260 - chore(deps): update dependency ruff to v0.1.5

Pull Request - State: closed - Opened by renovate[bot] over 1 year ago - 1 comment
Labels: dependencies

#259 - chore(deps): update dependency wandb to v0.16.0

Pull Request - State: closed - Opened by renovate[bot] over 1 year ago - 1 comment
Labels: dependencies

#258 - chore(deps): update dependency mkdocs-material to v9.4.8

Pull Request - State: closed - Opened by renovate[bot] over 1 year ago - 1 comment
Labels: dependencies

#257 - chore(deps): update dependency ruff to v0.1.4

Pull Request - State: closed - Opened by renovate[bot] over 1 year ago - 1 comment
Labels: dependencies

#256 - chore(deps): update dependency jupyterlab to v4.0.8

Pull Request - State: closed - Opened by renovate[bot] over 1 year ago - 2 comments
Labels: dependencies

#255 - chore(deps): update dependency matplotlib to v3.8.1

Pull Request - State: closed - Opened by renovate[bot] over 1 year ago - 2 comments
Labels: dependencies

#254 - chore(deps): update dependency pytest-asyncio to v0.22.0 - autoclosed

Pull Request - State: closed - Opened by renovate[bot] over 1 year ago - 1 comment
Labels: dependencies

#253 - chore(deps): update dependency accelerate to v0.24.1

Pull Request - State: closed - Opened by renovate[bot] over 1 year ago - 1 comment
Labels: dependencies

#252 - chore(deps): update dependency mkdocs-material to v9.4.7

Pull Request - State: closed - Opened by renovate[bot] over 1 year ago - 1 comment
Labels: dependencies

#251 - chore(deps): update dependency types-tqdm to v4.66.0.4

Pull Request - State: closed - Opened by renovate[bot] over 1 year ago - 2 comments
Labels: dependencies

#250 - chore(deps): update dependency ruff to v0.1.3

Pull Request - State: closed - Opened by renovate[bot] over 1 year ago - 2 comments
Labels: dependencies

#249 - chore(deps): update dependency pandas to v2.1.2

Pull Request - State: closed - Opened by renovate[bot] over 1 year ago - 2 comments
Labels: dependencies

#248 - chore(deps): update dependency xdoctest to v1.1.2

Pull Request - State: closed - Opened by renovate[bot] over 1 year ago - 2 comments
Labels: dependencies

#247 - replace black formatter with ruff

Pull Request - State: closed - Opened by ssenan over 1 year ago - 1 comment
Labels: enhancement, build

#246 - chore(deps): update dependency pytest to v7.4.3

Pull Request - State: closed - Opened by renovate[bot] over 1 year ago - 2 comments
Labels: dependencies

#245 - use ruff instead of black for code formatting

Issue - State: closed - Opened by ssenan over 1 year ago
Labels: enhancement

#244 - chore(deps): update dependency accelerate to v0.24.0

Pull Request - State: closed - Opened by renovate[bot] over 1 year ago - 1 comment
Labels: dependencies

#243 - chore(deps): update dependency ruff to v0.1.2

Pull Request - State: closed - Opened by renovate[bot] over 1 year ago - 1 comment
Labels: dependencies

#242 - chore(deps): update dependency mypy to v1.6.1

Pull Request - State: closed - Opened by renovate[bot] over 1 year ago - 2 comments
Labels: dependencies

#241 - chore(deps): update dependency mkdocs-material to v9.4.6

Pull Request - State: closed - Opened by renovate[bot] over 1 year ago - 1 comment
Labels: dependencies

#240 - chore(deps): update dependency black to v23.10.1

Pull Request - State: closed - Opened by renovate[bot] over 1 year ago - 2 comments
Labels: dependencies

#239 - chore(deps): update release-drafter/release-drafter action to v5.25.0

Pull Request - State: closed - Opened by renovate[bot] over 1 year ago - 1 comment
Labels: dependencies

#238 - change logging to be dependent on current step

Pull Request - State: closed - Opened by ssenan over 1 year ago - 1 comment
Labels: enhancement

#237 - change loss logging to global_step instead of current_epoch

Issue - State: closed - Opened by ssenan over 1 year ago
Labels: bug

#236 - fix cross_attention, removed unused_parameters flag

Pull Request - State: closed - Opened by ssenan over 1 year ago - 1 comment
Labels: enhancement, breaking

#235 - cross attention value assignment incorrect

Issue - State: closed - Opened by ssenan over 1 year ago
Labels: bug

#234 - add torch compile flag to training/sampling

Issue - State: closed - Opened by ssenan over 1 year ago
Labels: enhancement

#233 - move downstream validation metrics out of src/dnadiffusion

Issue - State: closed - Opened by ssenan over 1 year ago - 2 comments
Labels: refactoring, stale, dependencies

#232 - integrate enformer helper functions

Issue - State: closed - Opened by ssenan over 1 year ago - 2 comments
Labels: enhancement, stale, metrics

#231 - chore(deps): update python docker tag to v3.12

Pull Request - State: closed - Opened by renovate[bot] over 1 year ago - 1 comment
Labels: dependencies

#230 - refactor: separate pypi and conda containers

Pull Request - State: closed - Opened by cameronraysmith over 1 year ago - 1 comment
Labels: ci, build

#229 - fix: bump dev version `0.0.0.dev1`

Pull Request - State: closed - Opened by cameronraysmith over 1 year ago - 1 comment
Labels: build

#228 - update conda environment to torch `2.1.0`

Pull Request - State: closed - Opened by ssenan over 1 year ago - 1 comment
Labels: ci, build, dependencies

#227 - chore(deps): update dependency torchvision to v0.16.0

Pull Request - State: closed - Opened by renovate[bot] over 1 year ago - 1 comment
Labels: dependencies

#226 - chore(deps): update dependency wandb to v0.15.12

Pull Request - State: closed - Opened by renovate[bot] over 1 year ago - 1 comment
Labels: dependencies

#225 - chore(deps): update dependency torch to v2.1.0

Pull Request - State: closed - Opened by renovate[bot] over 1 year ago
Labels: dependencies

#224 - update environment.yml to include all libraries from additional validation metrics

Issue - State: closed - Opened by ssenan over 1 year ago
Labels: dependencies

#223 - add all validation metrics notebooks to notebooks folder

Issue - State: closed - Opened by ssenan over 1 year ago - 2 comments
Labels: enhancement, stale

#222 - motif composition metric notebook conversion

Pull Request - State: closed - Opened by ssenan over 1 year ago - 1 comment
Labels: enhancement, metrics

#221 - add data preprocessing notebooks into library as scripts

Pull Request - State: closed - Opened by ssenan over 1 year ago - 1 comment
Labels: enhancement

#220 - chore(deps): update dependency einops to v0.7.0

Pull Request - State: closed - Opened by renovate[bot] over 1 year ago - 1 comment
Labels: dependencies

#219 - blat notebook addition to library

Issue - State: closed - Opened by ssenan over 1 year ago - 2 comments
Labels: enhancement, stale, metrics

#218 - chore(deps): update dependency seaborn to v0.13.0

Pull Request - State: closed - Opened by renovate[bot] over 1 year ago - 1 comment
Labels: dependencies

#217 - add filter master data to library

Issue - State: closed - Opened by ssenan over 1 year ago
Labels: enhancement

#216 - add master dataset creation to library

Issue - State: closed - Opened by ssenan over 1 year ago - 1 comment
Labels: enhancement

GitHub / pinellolab/DNA-Diffusion issues and pull requests