OmicsML/dance issues and pull requests

#364 - build(deps): bump numba from 0.58.0 to 0.58.1

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

#363 - build(deps): bump networkx from 3.1 to 3.2

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

#362 - build(deps): bump igraph from 0.10.8 to 0.11.2

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

#361 - build(deps): bump numpy from 1.25.2 to 1.26.1

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

#360 - build(deps): bump h5py from 3.9.0 to 3.10.0

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

#359 - build(deps-dev): bump pre-commit from 3.4.0 to 3.5.0

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

#358 - new datasets, additional preprocessing methods, and graph constructions

Pull Request - State: closed - Opened by xingzhongyu over 1 year ago
Labels: enhancement, Priority-P0

#357 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago

#356 - fix readme: conda activation; closes #354

Pull Request - State: closed - Opened by RemyLau over 1 year ago

#355 - build(deps): bump tables from 3.8.0 to 3.9.1

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

#354 - Questions about conda installing

Issue - State: closed - Opened by HelloWorldLTY over 1 year ago - 1 comment
Labels: documentation

#353 - readme: action runner script with instruction

Pull Request - State: closed - Opened by RemyLau over 1 year ago

#352 - fix: remove pyro-ppl from direct deps to prevent install torch early

Pull Request - State: closed - Opened by RemyLau over 1 year ago

#351 - build(deps): bump numpy from 1.25.2 to 1.26.0

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

#350 - build(deps): bump opencv-python from 4.8.0.76 to 4.8.1.78

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

#349 - upgrade tox test; create lint workflow

Pull Request - State: closed - Opened by RemyLau over 1 year ago

#348 - build(deps): bump scipy from 1.11.2 to 1.11.3

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

#347 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago

#346 - build(deps): bump scikit-learn from 1.3.0 to 1.3.1

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

#345 - build(deps): bump numba from 0.57.1 to 0.58.0

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

#344 - build(deps): bump pandas from 2.1.0 to 2.1.1

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

#343 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago

#342 - build(deps): bump igraph from 0.10.6 to 0.10.8

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

#341 - expfeat: implement anndata transform adaptor

Pull Request - State: closed - Opened by RemyLau over 1 year ago

#340 - build(deps-dev): bump tox from 4.11.1 to 4.11.3

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

#339 - build(deps-dev): bump pytest from 7.4.1 to 7.4.2

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

#338 - build(deps): bump scanpy from 1.9.4 to 1.9.5

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 6 comments
Labels: dependencies

#337 - Preprocessing benchmarking

Pull Request - State: closed - Opened by xingzhongyu over 1 year ago

#336 - fix deprecated option

Pull Request - State: closed - Opened by RemyLau over 1 year ago

#335 - build(deps-dev): bump pytest from 7.4.0 to 7.4.1

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

#334 - build(deps-dev): bump tox from 4.10.0 to 4.11.1

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

#333 - build(deps-dev): bump pre-commit from 3.3.3 to 3.4.0

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

#332 - build(deps): bump pandas from 2.0.3 to 2.1.0

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

#331 - add 4 clustering datasets

Pull Request - State: closed - Opened by xingzhongyu over 1 year ago - 1 comment

#330 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago

#329 - build(deps): bump scanpy from 1.9.3 to 1.9.4

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

#328 - add 5 datasets

Pull Request - State: closed - Opened by xingzhongyu over 1 year ago

#327 - build(deps-dev): bump tox from 4.9.0 to 4.10.0

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

#326 - build(deps): bump sphinx-rtd-theme from 1.2.2 to 1.3.0

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

#325 - pin lower version of scipy and scikit-mis version for python 3.8

Pull Request - State: closed - Opened by RemyLau over 1 year ago

#324 - build(deps): bump igraph from 0.10.1 to 0.10.6

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

#323 - build(deps-dev): bump tox from 4.6.4 to 4.9.0

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

#322 - build(deps): bump scipy from 1.11.1 to 1.11.2

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

#321 - build(deps): bump tqdm from 4.65.0 to 4.66.1

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

#320 - build(deps): bump opencv-python from 4.8.0.74 to 4.8.0.76

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

#319 - build(deps-dev): bump tox from 4.6.4 to 4.8.0

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

#318 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago

#317 - build(deps): bump pyro-ppl from 1.8.5 to 1.8.6

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

#316 - build(deps): bump leidenalg from 0.10.0 to 0.10.1

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

#315 - change python-igraph to igraph

Pull Request - State: closed - Opened by szhorvat over 1 year ago - 1 comment

#314 - build(deps): bump threadpoolctl from 3.1.0 to 3.2.0

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

#313 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago

#312 - build(deps): bump scikit-misc from 0.2.0 to 0.3.0

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

#311 - build(deps): bump torchnmf from 0.3.4 to 0.3.5

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

#310 - build(deps-dev): bump tox from 4.6.3 to 4.6.4

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

#309 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago

#308 - build(deps): bump leidenalg from 0.9.1 to 0.10.0

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

#307 - build(deps): bump opencv-python from 4.7.0.72 to 4.8.0.74

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

#306 - build(deps): bump scikit-learn from 1.2.2 to 1.3.0

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

#305 - bump version: v1.0.0 -> v1.0.1-dev

Pull Request - State: closed - Opened by RemyLau over 1 year ago

#304 - build(deps): bump pandas from 2.0.2 to 2.0.3

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

#303 - build(deps): bump scipy from 1.10.1 to 1.11.1

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

#302 - release v1.0.0

Pull Request - State: closed - Opened by RemyLau over 1 year ago

#301 - fix typo in function name

Pull Request - State: closed - Opened by RemyLau over 1 year ago

#300 - link to tutorial repo

Pull Request - State: closed - Opened by RemyLau over 1 year ago

#299 - implement `gex2adt_subset` for modality prediction and matching tasks

Pull Request - State: closed - Opened by RemyLau over 1 year ago

#298 - refactor multi dataset object for joint embedding tasks

Pull Request - State: closed - Opened by RemyLau over 1 year ago

#297 - hotfix: add additional channels depending on the input data type

Pull Request - State: closed - Opened by RemyLau over 1 year ago

#296 - refactor multi dataset object for matching modality tasks

Pull Request - State: closed - Opened by RemyLau over 1 year ago

#295 - fix dataset class attr name: `DATASETS` -> `AVAILABLE_DATA`

Pull Request - State: closed - Opened by RemyLau over 1 year ago

#294 - build(deps): bump sphinx from 6.2.1 to 7.0.1

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

#293 - build(deps): bump sphinx-autodoc-typehints from 1.23.0 to 1.23.2

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

#292 - update datasets doc struct and fix torchvision dep

Pull Request - State: closed - Opened by RemyLau over 1 year ago

#291 - build(deps-dev): bump pytest-subtests from 0.10.0 to 0.11.0

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

#290 - build(deps): bump numba from 0.57.0 to 0.57.1

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

#289 - build(deps): bump h5py from 3.8.0 to 3.9.0

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

#288 - build(deps-dev): bump pytest from 7.3.2 to 7.4.0

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

#287 - build(deps): bump pandas from 2.0.1 to 2.0.2

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

#286 - add version

Pull Request - State: closed - Opened by RemyLau over 1 year ago

#285 - standardize `AVAILABLE_DATA` to list of strings or dicts

Pull Request - State: closed - Opened by RemyLau over 1 year ago

#284 - refactor multi dataset object for predict modality tasks

Pull Request - State: closed - Opened by RemyLau over 1 year ago

#283 - clean up multi dataset objects

Pull Request - State: closed - Opened by RemyLau over 1 year ago

#282 - expose main properties of anndata (or mudata) to base dance data

Pull Request - State: closed - Opened by RemyLau over 1 year ago

#281 - build(deps-dev): bump tox from 4.6.0 to 4.6.3

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

#280 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago

#279 - build(deps-dev): bump pytest from 7.3.1 to 7.3.2

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

#278 - build(deps): bump mudata from 0.2.2 to 0.2.3

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

#277 - build(deps-dev): bump pre-commit from 3.3.2 to 3.3.3

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

#276 - build(deps): bump pyro-ppl from 1.8.4 to 1.8.5

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

#275 - build(deps-dev): bump tox from 4.6.0 to 4.6.2

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

#274 - change get_available_data to class method

Pull Request - State: closed - Opened by RemyLau over 1 year ago

#273 - add dataset availability check function

Pull Request - State: closed - Opened by RemyLau over 1 year ago

#272 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago

#271 - build(deps-dev): bump tox from 4.5.1 to 4.6.0

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

#270 - build(deps): bump requests from 2.30.0 to 2.31.0

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

#269 - build(deps): bump numba from 0.56.2 to 0.57.0

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

#268 - build(deps-dev): bump tox from 4.5.1 to 4.5.2

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

#267 - build(deps-dev): bump pre-commit from 3.2.2 to 3.3.2

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

#266 - build(deps-dev): bump pytest-xdist from 3.2.1 to 3.3.1

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

#265 - imputation module refactor and fixes

Pull Request - State: closed - Opened by RemyLau over 1 year ago - 1 comment

GitHub / OmicsML/dance issues and pull requests