kipoi/kipoi issues and pull requests

#700 - kipoi create environment with path specification

Issue - State: open - Opened by osyafinkelberg 2 months ago
Labels: enhancement

#699 - Fix CI

Pull Request - State: open - Opened by Hoeze 10 months ago

#698 - Fix circleci libmamba solver

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

#697 - Update attrs requirement from <=21.4.0 to <=23.2.0

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

#696 - AttributeError: 'MaxEntModel' object has no attribute 'postprocessing'

Issue - State: open - Opened by jessicakan789 12 months ago
Labels: bug

#695 - DeepBind - can't download model

Issue - State: open - Opened by Toozig about 1 year ago
Labels: bug

#694 - can't create tensorflow2 environment

Issue - State: open - Opened by Siebr about 1 year ago
Labels: bug

#693 - Cannot create env after installking kipoi

Issue - State: open - Opened by guxi798 over 1 year ago
Labels: bug

#692 - Set `zarr` version to 2.12.0

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

#691 - Remove deprecated `conda clean` flag `-s` from circleCI

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

#690 - Update attrs requirement from <=21.4.0 to <=23.1.0

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

#689 - DeepSEA: Similar column names with different values

Issue - State: open - Opened by robertzeibich about 2 years ago - 1 comment
Labels: bug

#688 - Update attrs requirement from <=21.4.0 to <22.2.0

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 4 comments
Labels: dependencies

#687 - Fixed kipoi installation

Pull Request - State: closed - Opened by haimasree over 2 years ago

#686 - Removing dataclasses from setup.py

Pull Request - State: closed - Opened by haimasree over 2 years ago

#685 - Dataclasses is not needed. Conditional requirement for py3.6 or less

Pull Request - State: closed - Opened by ccoulombe over 2 years ago - 2 comments

#684 - Fixing issues with triggering build-release-push workflow of kipoi-containers repo from this repo

Pull Request - State: closed - Opened by haimasree over 2 years ago

#683 - Adding some best practices for model submission

Pull Request - State: closed - Opened by haimasree over 2 years ago

#682 - Fixes to circumvent out of memory error during conda environment creation with python=3.10

Pull Request - State: closed - Opened by haimasree over 2 years ago

#681 - conda oom error during nightly tests on circleci with python=3.10

Issue - State: closed - Opened by haimasree over 2 years ago
Labels: bug

#680 - Fix pytorch-cpu and pysam discrepancies

Pull Request - State: closed - Opened by haimasree over 2 years ago

#679 - channel order for pysam is ignored if pysam is versioned

Issue - State: closed - Opened by haimasree over 2 years ago - 1 comment
Labels: bug

#678 - Discrepancies with pytorch-cpu

Issue - State: closed - Opened by haimasree over 2 years ago
Labels: bug

#677 - Multiple fixes

Pull Request - State: closed - Opened by haimasree over 2 years ago

#676 - Fixed CI

Pull Request - State: closed - Opened by haimasree over 2 years ago

#675 - Issue with tests in test_26_cli_examples with python=3.6

Issue - State: closed - Opened by haimasree over 2 years ago
Labels: bug

#674 - A question on model submission.

Issue - State: closed - Opened by okurman over 2 years ago - 7 comments
Labels: bug

#673 - Pin sorted-nearest to 0.0.33

Pull Request - State: closed - Opened by haimasree over 2 years ago

#672 - Updating apptainer version

Pull Request - State: closed - Opened by haimasree over 2 years ago

#671 - Updating Readme with information about shared environment

Pull Request - State: closed - Opened by haimasree over 2 years ago

#670 - Fixed kipoi installation python >=3.8

Pull Request - State: closed - Opened by haimasree almost 3 years ago

#669 - Attempt to fix flaky tests

Pull Request - State: closed - Opened by haimasree almost 3 years ago

#668 - Fixed coverall error

Pull Request - State: closed - Opened by haimasree almost 3 years ago

#667 - Fixed ci

Pull Request - State: closed - Opened by haimasree almost 3 years ago

#666 - Improved CI

Pull Request - State: closed - Opened by haimasree almost 3 years ago

#665 - Add libmamba solver to ci to help kipoi-conda leverage libmamba solver

Pull Request - State: closed - Opened by haimasree almost 3 years ago

#664 - Suport for libmamba solver

Issue - State: closed - Opened by haimasree almost 3 years ago - 1 comment
Labels: enhancement

#663 - Adding apptainer

Pull Request - State: closed - Opened by haimasree almost 3 years ago

#662 - Fixed ci

Pull Request - State: closed - Opened by haimasree almost 3 years ago

#661 - Updating build docs ci

Pull Request - State: closed - Opened by haimasree almost 3 years ago

#660 - Fixed ci

Pull Request - State: closed - Opened by haimasree almost 3 years ago

#659 - Adding a provision to auto update containers when kipoi has a new version release

Pull Request - State: closed - Opened by haimasree almost 3 years ago

#658 - Add provision for updating the containers when a new kipoi version has been released

Issue - State: closed - Opened by haimasree almost 3 years ago
Labels: enhancement

#657 - Attempting to fix coverall

Pull Request - State: closed - Opened by haimasree almost 3 years ago

#656 - Fixed ci

Pull Request - State: closed - Opened by haimasree almost 3 years ago

#655 - Moving some dependencies from pip to conda

Pull Request - State: closed - Opened by haimasree almost 3 years ago

#654 - Removes deprecated modules including future and six

Pull Request - State: closed - Opened by haimasree almost 3 years ago

#653 - Adding tests and support for python 3.10

Pull Request - State: closed - Opened by haimasree almost 3 years ago

#652 - Fixes for python 3.10

Pull Request - State: closed - Opened by haimasree almost 3 years ago

#651 - Adjustments for python 3.10 (collections.abc.Mapping, collections.abc.Sequence)

Pull Request - State: closed - Opened by haimasree almost 3 years ago

#650 - Which Kipoi RNA splicing models can be applied to WGS data?

Issue - State: closed - Opened by robertzeibich almost 3 years ago - 4 comments

#649 - Error in 'BPNet-OSKN'

Issue - State: closed - Opened by IshikaLuthra almost 3 years ago - 18 comments

#648 - Minor bug fix

Pull Request - State: closed - Opened by haimasree almost 3 years ago

#647 - Use a smaller singularity image for tests

Pull Request - State: closed - Opened by haimasree almost 3 years ago

#646 - Idea: make kipoi models importable

Issue - State: open - Opened by Hoeze almost 3 years ago

#645 - Add python classes model and dataloader description that will allow no yaml model representation

Pull Request - State: closed - Opened by haimasree almost 3 years ago - 1 comment

#644 - Introduce python classes for model and description yamls

Issue - State: closed - Opened by haimasree almost 3 years ago - 1 comment
Labels: enhancement

#643 - Drop Python3.6 support

Issue - State: closed - Opened by Hoeze almost 3 years ago - 5 comments

#642 - add support for writing parquet files

Pull Request - State: closed - Opened by Hoeze almost 3 years ago - 1 comment

#641 - How to have multiple dataloaders for the same model?

Issue - State: closed - Opened by Hoeze almost 3 years ago - 3 comments

#640 - Fixed ci

Pull Request - State: closed - Opened by haimasree about 3 years ago

#639 - Add detailed documentation to `test` command

Pull Request - State: closed - Opened by Hoeze about 3 years ago - 1 comment

#638 - Sharing models through Hugging Face Hub

Issue - State: open - Opened by omarespejel about 3 years ago - 18 comments

#637 - Better singularity logging

Pull Request - State: closed - Opened by haimasree about 3 years ago

#636 - Fixing build docs

Pull Request - State: closed - Opened by haimasree about 3 years ago

#635 - Fix sharding bug due to uneven splits of models into chunks

Pull Request - State: closed - Opened by haimasree about 3 years ago

#634 - import kipoiseq automatically run some unrelated python scripts / rerun unrelated jobs in log?

Issue - State: closed - Opened by princeofpotato about 3 years ago - 7 comments

#633 - Bugs related to h5py/python version addressed

Pull Request - State: closed - Opened by haimasree about 3 years ago

#632 - Removing version restriction of h5py and hdf5

Pull Request - State: closed - Opened by haimasree about 3 years ago

#631 - Ading badges and turning on coveralls again

Pull Request - State: closed - Opened by haimasree about 3 years ago

#630 - Add singularity to kipoi-predict and make it compatible with the multi container setup

Pull Request - State: closed - Opened by haimasree about 3 years ago

#629 - Add singularity cli back and make it compatible with the multi container setup

Issue - State: closed - Opened by haimasree about 3 years ago
Labels: enhancement