Ecosyste.ms: Issues

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GitHub / OmicsML/dance issues and pull requests

#464 - build(deps): bump tifffile from 2024.2.12 to 2024.8.30

Pull Request - State: open - Opened by dependabot[bot] 5 months ago
Labels: dependencies

#463 - build(deps): bump tifffile from 2024.2.12 to 2024.8.10

Pull Request - State: closed - Opened by dependabot[bot] 5 months ago - 1 comment
Labels: dependencies

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

Pull Request - State: open - Opened by pre-commit-ci[bot] 6 months ago

#461 - build(deps): bump tifffile from 2024.2.12 to 2024.7.24

Pull Request - State: closed - Opened by dependabot[bot] 6 months ago - 1 comment
Labels: dependencies

#460 - build(deps-dev): bump pytest from 8.2.0 to 8.3.2

Pull Request - State: open - Opened by dependabot[bot] 6 months ago
Labels: dependencies

#459 - real_multi_modality

Pull Request - State: open - Opened by xingzhongyu 6 months ago

#458 - build(deps-dev): bump pytest from 8.2.0 to 8.3.1

Pull Request - State: closed - Opened by dependabot[bot] 6 months ago - 1 comment
Labels: dependencies

#457 - Update README.md

Pull Request - State: closed - Opened by JiayuanDing100 6 months ago

#456 - build(deps): bump tifffile from 2024.2.12 to 2024.7.2

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

#454 - build(deps): bump opencv-python from 4.9.0.80 to 4.10.0.84

Pull Request - State: open - Opened by dependabot[bot] 7 months ago
Labels: dependencies

#453 - build(deps): bump tifffile from 2024.2.12 to 2024.6.18

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

#452 - build(deps-dev): bump pytest from 8.2.0 to 8.2.2

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

#451 - build(deps): bump opencv-python from 4.9.0.80 to 4.10.0.82

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

#450 - build(deps): bump leidenalg from 0.10.1 to 0.10.2

Pull Request - State: open - Opened by dependabot[bot] 7 months ago
Labels: dependencies

#449 - build(deps): bump tifffile from 2024.2.12 to 2024.5.22

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

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

Pull Request - State: closed - Opened by pre-commit-ci[bot] 7 months ago

#447 - build(deps): bump networkx from 3.2.1 to 3.3

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

#446 - build(deps): bump kdepy from 1.1.8 to 1.1.9

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

#445 - build(deps-dev): bump pytest-xdist from 3.5.0 to 3.6.1

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

#444 - build(deps): bump h5py from 3.10.0 to 3.11.0

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

#443 - build(deps): bump scanpy from 1.9.8 to 1.10.1

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

#442 - build(deps): bump pyro-ppl from 1.8.6 to 1.9.0

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

#441 - build(deps): bump statsmodels from 0.14.0 to 0.14.2

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

#440 - build(deps): bump scipy from 1.11.4 to 1.13.0

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

#439 - build(deps): bump threadpoolctl from 3.2.0 to 3.5.0

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago - 1 comment
Labels: dependencies

#438 - build(deps-dev): bump pytest from 7.4.3 to 8.2.0

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago - 1 comment
Labels: dependencies

#437 - build(deps): bump pandas from 1.5.3 to 2.2.2

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago - 1 comment
Labels: dependencies

#436 - libcusparse.so.11

Issue - State: closed - Opened by arashyunesi 9 months ago - 2 comments

#435 - ImportError when directly running the code in the terminal

Issue - State: closed - Opened by pujing0215 9 months ago - 1 comment

#434 - update reference of dance paper and survey paper

Pull Request - State: closed - Opened by JiayuanDing100 10 months ago

#433 - Fix a bug in install.sh

Pull Request - State: closed - Opened by HelloWorldLTY 10 months ago - 2 comments

#432 - Tutorial notebook is outdated

Issue - State: open - Opened by wehos 10 months ago - 1 comment

#431 - Errors with Installation

Issue - State: open - Opened by wehos 10 months ago - 2 comments

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

Pull Request - State: closed - Opened by pre-commit-ci[bot] 10 months ago

#429 - build(deps): bump threadpoolctl from 3.2.0 to 3.4.0

Pull Request - State: closed - Opened by dependabot[bot] 10 months ago - 1 comment
Labels: dependencies

#428 - build(deps-dev): bump pytest from 7.4.3 to 8.1.1

Pull Request - State: closed - Opened by dependabot[bot] 11 months ago - 1 comment
Labels: dependencies

#427 - build(deps): bump pandas from 1.5.3 to 2.2.1

Pull Request - State: closed - Opened by dependabot[bot] 11 months ago - 1 comment
Labels: dependencies

#426 - build(deps): bump threadpoolctl from 3.2.0 to 3.3.0

Pull Request - State: closed - Opened by dependabot[bot] 11 months ago - 1 comment
Labels: dependencies

#425 - build(deps-dev): bump pytest from 7.4.3 to 8.0.2

Pull Request - State: closed - Opened by dependabot[bot] 11 months ago - 1 comment
Labels: dependencies

#424 - build(deps): bump numpy from 1.26.3 to 1.26.4

Pull Request - State: closed - Opened by dependabot[bot] 11 months ago - 1 comment
Labels: dependencies

#423 - Celltype annotation automl

Pull Request - State: closed - Opened by xingzhongyu 11 months ago

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

Pull Request - State: closed - Opened by pre-commit-ci[bot] 11 months ago

#419 - build(deps-dev): bump pre-commit from 3.6.0 to 3.6.1

Pull Request - State: closed - Opened by dependabot[bot] 11 months ago - 1 comment
Labels: dependencies

#418 - build(deps): bump tifffile from 2023.7.10 to 2024.2.12

Pull Request - State: closed - Opened by dependabot[bot] 11 months ago - 1 comment
Labels: dependencies

#417 - build(deps): bump tqdm from 4.66.1 to 4.66.2

Pull Request - State: closed - Opened by dependabot[bot] 11 months ago - 1 comment
Labels: dependencies

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

Pull Request - State: closed - Opened by pre-commit-ci[bot] 11 months ago

#415 - build(deps): bump sphinx-rtd-theme from 1.3.0 to 2.0.0

Pull Request - State: closed - Opened by dependabot[bot] 11 months ago - 1 comment
Labels: dependencies

#414 - build(deps): bump opencv-python from 4.8.1.78 to 4.9.0.80

Pull Request - State: closed - Opened by dependabot[bot] 11 months ago - 1 comment
Labels: dependencies

#413 - build(deps): bump scanpy from 1.9.6 to 1.9.8

Pull Request - State: closed - Opened by dependabot[bot] 11 months ago - 1 comment
Labels: dependencies

#411 - Complete wrapped functions

Pull Request - State: closed - Opened by xingzhongyu 12 months ago

#410 - drop py38 support

Pull Request - State: closed - Opened by RemyLau 12 months ago

#409 - build(deps): bump numba from 0.58.0 to 0.59.0

Pull Request - State: closed - Opened by dependabot[bot] 12 months ago - 2 comments
Labels: dependencies

#408 - implement several wrapped preprocessing functions from `sc.pp`

Pull Request - State: closed - Opened by xingzhongyu 12 months ago

#407 - Random `segfault` when running pipeline tuning with `wandb` on certain machines

Issue - State: open - Opened by RemyLau 12 months ago
Labels: bug, help wanted

#405 - build(deps): bump tables from 3.9.1 to 3.9.2

Pull Request - State: closed - Opened by dependabot[bot] 12 months ago - 1 comment
Labels: dependencies

#404 - __init__.py missing from dance/metadata

Issue - State: open - Opened by cwilson51 12 months ago

#403 - build(deps): bump pandas from 1.5.3 to 2.2.0

Pull Request - State: closed - Opened by dependabot[bot] 12 months ago - 4 comments
Labels: dependencies

#403 - build(deps): bump pandas from 1.5.3 to 2.2.0

Pull Request - State: open - Opened by dependabot[bot] 12 months ago
Labels: dependencies

#402 - build(deps): bump scikit-misc from 0.3.0 to 0.3.1

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

#401 - add_transform_test

Pull Request - State: open - Opened by xingzhongyu about 1 year ago - 4 comments

#400 - build(deps): bump numpy from 1.25.2 to 1.26.3

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

#399 - build(deps-dev): bump pytest-xdist from 3.3.1 to 3.5.0

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

#398 - feat: pipeline tuning `wandb` integration

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

#397 - feat: implement ``PipelinePlaner``

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

#396 - build(deps): bump tifffile from 2023.7.10 to 2023.12.9

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

#395 - feat: pipeline resolve

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

#394 - register datasets

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

#393 - register existing transforms

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

#392 - build(deps): bump scanpy from 1.9.5 to 1.9.6

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

#390 - feat: implement `config`, `registry`, and `pipeline`

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

#389 - fix: register `skip_count_check` attr for `FilterGenesRegression`

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

#388 - patchfix: disable windows lint test due to faulty windows img from github action

Pull Request - State: closed - Opened by RemyLau about 1 year ago
Labels: wontfix

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

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

#386 - create CHANGELOG.md

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

#385 - add note about setting up scheduled jobs with crontab

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

#384 - Config support

Issue - State: open - Opened by RemyLau about 1 year ago

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

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

#382 - build(deps-dev): bump pre-commit from 3.5.0 to 3.6.0

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago - 3 comments
Labels: dependencies

#381 - build(deps): bump pandas from 1.5.3 to 2.1.4

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

#380 - fix: align `obs_names` of mod2 to mod1 when necessary

Pull Request - State: closed - Opened by xingzhongyu about 1 year ago
Labels: bug

#378 - Feature: sanity checks

Issue - State: open - Opened by RemyLau about 1 year ago

#377 - bumpversion: 1.0.1 -> 1.1.0.dev

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

#376 - bumpversion: 1.0.1.dev -> 1.0.1

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

#375 - build(deps-dev): bump pytest from 7.4.2 to 7.4.3

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

#374 - build(deps): bump scipy from 1.11.3 to 1.11.4

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

#373 - fix: tests

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

#372 - fix: rtd config

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

#371 - DANCE V1.0.0 benchmark production

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

#370 - build(deps): bump igraph from 0.10.8 to 0.11.3

Pull Request - State: open - Opened by dependabot[bot] about 1 year ago - 7 comments
Labels: dependencies

#369 - build(deps): bump numpy from 1.25.2 to 1.26.2

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

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

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

#366 - build(deps): bump scikit-learn from 1.3.1 to 1.3.2

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

#365 - build(deps): bump networkx from 3.1 to 3.2.1

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