openproblems-bio / openproblems-v2

Formalizing and benchmarking open problems in single-cell genomics

openproblems-bio/openproblems-v2 Issues

Add spatial decomposition task
Updated a year ago
update SCOT method in multimodal data_integration task
Updated a year ago
update scot in multimodal data integration task
Updated a year ago
[label_projection] seurat_transfer method out of date
Updated a year ago1
Include task description in task READMEs
Closed a year ago1
Create a schema for the required info for method and metric
Closed a year ago
Store metric score file as csv, not anndata
Updated a year ago2
Existing task READMEs do not follow proposed structure
Closed a year ago4
Label Projection
Closed a year ago1
`test_method_check_config` should be more strict
Closed a year ago
bibtex reference that is malformed in the .bib file (see v1)
Closed a year ago2
bibtex reference that is not in the .bib file
Closed a year ago1
Helper script to auto-generate API template
Updated a year ago4
documentation or repository URLs are not accessible
Closed a year ago
Use shared docker containers for methods with identical dependencies
Closed a year ago4
How to share code across components within a task
Closed a year ago2
Unit test logs are hard to read
Updated a year ago3
create_component fails with subtasks
Closed a year ago5
.bib file missing
Closed a year ago1
Make it easy / document how to run just one component of `viash test`
Updated a year ago2
Test mode for methods
Closed a year ago3
How to debug components?
Closed a year ago2
`adata.X is None` in resources_test
Updated a year ago3
Check that `config.yml` arguments and `script.py` par match
Closed a year ago7
`AssertionError: variants not an info field` raised on default config
Closed a year ago
`test_check_method_config` doesn't check if `preferred_normalization` is valid
Closed a year ago
add assertion messages in component unit testing
Closed a year ago
update subprocess.run cmd in unit tests
Closed a year ago
name or pretty_name is identical to any other method in the same task
Updated a year ago
Long and confusing error message on config parse failure
Updated a year ago2
Add singularity compatibility for users without root access
Updated a year ago5
Harmonize nomeclature of "baseline" vs "control" methods
Closed a year ago1
Write generic dataset loader unit test
Closed a year ago1
Align with infra schema in website docs (change image or change path names in v2): TBD
Closed a year ago1
Document non-docker usage
Updated a year ago1
directory structure mixes infrastructure with contributions
Closed a year ago4
Create PULL_REQUEST_TEMPLATE.md
Closed a year ago1
Change `anndata~=0.8` to `anndata~=0.8.0`
Closed a year ago1
create_component assumes script is written in python
Closed a year ago6
Rename `par` -> `params`
Closed a year ago1
Rename terminology
Closed a year ago
Move `common/check_migration_status` and `common/list_git_shas` to the `migration` namespace?
Closed a year ago1
Align `label_projection` task with `openpipelines-bio/openpipelines/src/labels_transfer`
Updated 2 years ago6
Write component that returns the last changed commit sha for each file
Closed 2 years ago
CONTRIBUTING.md instructions not working
Closed 2 years ago3
Methods in Dimensionality reduction lack metadata info
Closed 2 years ago1
high execution times of `rmse` method and `trustworthiness` and `density` metrics at dimensionality reduction
Updated 2 years ago
running out of memory in `RMSE`
Updated 2 years ago1
NeuralEE error when there are some zero-counts observations
Updated 2 years ago
Adapt dataset format
Closed 2 years ago5