theislab/pertpy issues and pull requests

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

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

#389 - DIALOGUE tutorial is bugged.

Issue - State: closed - Opened by Chengwei94 over 1 year ago - 2 comments
Labels: bug

#388 - E-Distance: Choice whether to square Euclidean Distance

Issue - State: closed - Opened by eroell over 1 year ago - 3 comments
Labels: documentation

#387 - fix naming of example data in doc examples

Pull Request - State: closed - Opened by eroell over 1 year ago - 1 comment
Labels: bug

#386 - wasserstein distance return type float

Pull Request - State: closed - Opened by eroell over 1 year ago - 2 comments

#385 - Wasserstein metric returns np.array instead of float

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

#384 - Probably wrong name of example dataset in Distances tutorial

Issue - State: closed - Opened by eroell over 1 year ago - 2 comments
Labels: bug

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

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

#382 - Adapt refreshes per second for rich progressbars to a lower number

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

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

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

#380 - Rewrite Augur test with a fixture for sc_sim_augur

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

#379 - Implementation of CINEMA-OT for pertpy - follow up

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

#378 - Implementation of CINEMA-OT for pertpy - follow up

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

#377 - Implementation of CINEMA-OT for pertpy

Pull Request - State: closed - Opened by MingzeDong over 1 year ago - 2 comments

#376 - Implementation of CINEMA-OT for pertpy

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

#375 - Documentation examples

Pull Request - State: closed - Opened by Lilly-May over 1 year ago - 2 comments
Labels: enhancement

#374 - Fix stephenson 2021 and refactor

Pull Request - State: closed - Opened by Zethson over 1 year ago
Labels: bug, enhancement

#373 - File not found for stephenson 2021 subsampled dataloader

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

#372 - Index MCPS in DIALOGUE results starting with 0

Pull Request - State: open - Opened by Zethson over 1 year ago - 1 comment
Labels: bug

#371 - DIALOGUE attribution

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

#370 - Speed up tests by subsampling

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

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

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

#368 - DIALOGUE extensions and plots

Pull Request - State: closed - Opened by tessadgreen over 1 year ago
Labels: enhancement, chore

#367 - Mechanism of Action enrichment

Issue - State: open - Opened by Zethson over 1 year ago
Labels: enhancement

#366 - scCODA: add low/high acceptance probability warnings

Pull Request - State: closed - Opened by johannesostner over 1 year ago - 1 comment
Labels: bug

#365 - cog.sanger.ac.uk/cmp/download/gene_identifiers_20191101.csv times out

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

#364 - Implicit modification warnings in cellline tests

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

#363 - Set run nuts random key to 0 by default.

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

#362 - Remove statsannotations

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

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

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

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

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

#359 - Different sign between `Final Parameter` and `log2-fold change` in `coda`

Issue - State: closed - Opened by PauBadiaM over 1 year ago - 3 comments
Labels: bug

#358 - Fix seed for `pt.tl.Sccoda.run_nuts`

Issue - State: closed - Opened by PauBadiaM over 1 year ago
Labels: enhancement, coda

#357 - AttributeError: module 'pertpy.plot' has no attribute 'coda on google colab

Issue - State: closed - Opened by HaleySmith13 over 1 year ago - 7 comments
Labels: bug

#356 - Fix README badges

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

#355 - Move to new numpy.random.Generator

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

#354 - Refactoring

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

#353 - Tutorials in RTD docs not rendering

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

#352 - Get rid of switchlang

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

#351 - Get rid of statannotation

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

#350 - dev -> main

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

#349 - Switch to scverse cookiecutter

Pull Request - State: closed - Opened by Zethson over 1 year ago
Labels: enhancement, chore

#348 - [DEPENDABOT]: Bump sphinx-gallery from 0.13.0 to 0.14.0

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

#347 - [DEPENDABOT]: Bump sphinx from 7.2.0 to 7.2.2

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

#346 - [DEPENDABOT]: 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: DEPENDABOT

#345 - move to scverse cookiecutter

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

#344 - Consider merging a few multimodal datasets into Mudata objects

Issue - State: open - Opened by Zethson over 1 year ago
Labels: enhancement

#343 - palette support for da_neighborhoods

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

#342 - [DEPENDABOT]: Bump pypa/gh-action-pypi-publish from 1.8.8 to 1.8.10

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

#341 - [DEPENDABOT]: Bump mypy from 1.4.1 to 1.5.0

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

#340 - [DEPENDABOT]: Bump coverage from 7.2.7 to 7.3.0

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

#339 - Remove remotezip for metadata

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

#337 - Remove whitespace in bulk RNA expression

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

#336 - Remove whitespace in bulk RNA expression

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

#335 - Dialogue multilevel modeling

Issue - State: open - Opened by tessadgreen over 1 year ago
Labels: bug, DIALOGUE

#334 - Update CellLineMetaData

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

#333 - RTD config

Pull Request - State: closed - Opened by Zethson over 1 year ago
Labels: bug

#332 - add ontology mapping notebook to tutorials preview

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

#331 - [DEPENDABOT]: Bump sphinx from 7.1.1 to 7.1.2

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

#330 - [DEPENDABOT]: Bump ipywidgets from 8.0.7 to 8.1.0

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

#329 - [DEPENDABOT]: Bump rich from 13.5.1 to 13.5.2

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

#328 - Perturbation space - add/subtract

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

#327 - Feature/perturbation space

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

#326 - [DEPENDABOT]: Bump flake8 from 6.0.0 to 6.1.0

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

#325 - [DEPENDABOT]: Bump furo from 2023.5.20 to 2023.7.26

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

#324 - [DEPENDABOT]: Bump pyupgrade from 3.9.0 to 3.10.1

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

#323 - Milo in Pertpy: annotate_nhoods issue

Issue - State: closed - Opened by MaximilianNuber over 1 year ago - 2 comments
Labels: bug

#321 - fixed the output_file_name of frangieh_2021_raw

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

#320 - [DEPENDABOT]: Bump types-requests from 2.31.0.1 to 2.31.0.2

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

#319 - [DEPENDABOT]: Bump plotnine from 0.12.1 to 0.12.2

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

#318 - [DEPENDABOT]: Bump arviz from 0.15.1 to 0.16.0

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

#317 - [DEPENDABOT]: Bump pypa/gh-action-pypi-publish from 1.8.7 to 1.8.8

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

#316 - Perturbation space - pseudobulk, discriminative classifier, clustering

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

#315 - [DEPENDABOT]: Bump ott-jax from 0.4.1 to 0.4.2

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

#314 - [DEPENDABOT]: Bump scvi-tools from 1.0.0 to 1.0.2

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

#313 - [DEPENDABOT]: Bump pyupgrade from 3.8.0 to 3.9.0

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

#312 - Pydantic breaks scvi import?

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

#311 - Docs improvements

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

#310 - sparse array into panda dataframe in _milo.py

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

#309 - ete3 import error

Issue - State: closed - Opened by liuifrec over 1 year ago - 6 comments
Labels: bug

#308 - [DEPENDABOT]: Bump scipy from 1.11.0 to 1.11.1

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

#307 - [DEPENDABOT]: Bump pyupgrade from 3.7.0 to 3.8.0

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

#306 - [DEPENDABOT]: Bump pypa/gh-action-pypi-publish from 1.8.6 to 1.8.7

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

#305 - add n_jobs support for pairwise distance computation

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

#304 - Add new distances

Pull Request - State: closed - Opened by mojtababahrami1993 over 1 year ago - 9 comments

#303 - Fix docs CI

Pull Request - State: closed - Opened by Zethson over 1 year ago
Labels: bug, enhancement

#302 - fix initial MCMC values

Pull Request - State: closed - Opened by johannesostner over 1 year ago - 1 comment
Labels: bug

#301 - unpin scipy

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

#300 - Improve import time

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

#299 - [DEPENDABOT]: Bump mypy from 1.4.0 to 1.4.1

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

#298 - [DEPENDABOT]: Bump scipy from 1.10.1 to 1.11.0

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

#297 - Fix examples syntax

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

#296 - AttributeError: 'Mixscape' object has no attribute 'pert_sign'

Issue - State: closed - Opened by ngvananh2508 over 1 year ago - 6 comments
Labels: bug

#294 - Conda package

Issue - State: open - Opened by Nusob888 over 1 year ago - 5 comments
Labels: enhancement

#293 - [DEPENDABOT]: Bump scvi-tools from 0.20.3 to 1.0.0

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

#292 - [DEPENDABOT]: Bump pyupgrade from 3.6.0 to 3.7.0

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

#291 - Update CellLineMetaData

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

#290 - AttributeError: 'DataFrame' object has no attribute 'append'

Issue - State: closed - Opened by ngvananh2508 over 1 year ago - 6 comments
Labels: bug

#289 - Adding acceptance rate to pertpy 0.4.0

Issue - State: closed - Opened by ngvananh2508 over 1 year ago - 3 comments
Labels: enhancement, wontfix

#288 - Lacking of explanation of generate_sample_level parameter

Issue - State: closed - Opened by ngvananh2508 over 1 year ago - 1 comment
Labels: enhancement

GitHub / theislab/pertpy issues and pull requests