Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / AlexsLemonade/refinebio-py issues and pull requests

#89 - 88 - Quantile Normalize Default Inconsistency

Pull Request - State: closed - Opened by avrohomgottlieb 3 months ago - 1 comment

#88 - Investigate bug with QN being skipped

Issue - State: closed - Opened by avrohomgottlieb 4 months ago

#87 - Add pyrate-limiter to setup.py

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

#85 - unexpected keyword argument 'genetic_information'

Issue - State: closed - Opened by jashapiro about 1 year ago - 1 comment

#84 - Add API request rate limit

Pull Request - State: closed - Opened by arkid15r over 1 year ago

#83 - Handling throttled requests

Issue - State: closed - Opened by jashapiro over 1 year ago - 2 comments

#82 - bump tested versions

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

#81 - Initialize contributed_keywords

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

#80 - submit refinebio-py to bioconda

Issue - State: open - Opened by jashapiro over 2 years ago

#78 - Github Documentation + Github Actions

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

#77 - Parsing API responses

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

#76 - Sample API response + kwargs

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

#73 - Set user-agent header in all requests

Issue - State: open - Opened by kurtwheeler about 3 years ago

#72 - Attempt to add extract_dir specification

Pull Request - State: open - Opened by cansavvy about 3 years ago - 2 comments

#71 - `extract` argument didn't work as expected

Issue - State: open - Opened by cansavvy about 3 years ago - 1 comment

#70 - Add docs link to pypi

Pull Request - State: open - Opened by kurtwheeler about 3 years ago

#69 - Change compendia-version to compendium-version.

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

#68 - Catch all 5xx errors.

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

#67 - Handle errors due to non-json responses

Pull Request - State: closed - Opened by kurtwheeler over 3 years ago

#66 - Fix lazy loading for original files

Pull Request - State: closed - Opened by kurtwheeler over 3 years ago - 1 comment

#65 - Adds downloadable_organism_names to experiment class.

Pull Request - State: closed - Opened by kurtwheeler over 3 years ago

#64 - Handles a connection error with the API.

Pull Request - State: closed - Opened by kurtwheeler over 3 years ago

#63 - Add `quant_sf_only` to the hlf.download_dataset args

Pull Request - State: closed - Opened by wvauclain over 3 years ago

#62 - Fix the lazy loading of files for jobs and samples, and results for tx indices.

Pull Request - State: closed - Opened by kurtwheeler over 3 years ago - 1 comment

#61 - Add ram_amount to DownloaderJob and SurveyJob.

Pull Request - State: closed - Opened by kurtwheeler over 3 years ago

#60 - Makes the client work with the new model changes

Pull Request - State: closed - Opened by kurtwheeler over 3 years ago

#59 - Change the email behavior to opt-in

Pull Request - State: closed - Opened by wvauclain over 3 years ago - 1 comment

#58 - Make Emails Opt-in

Issue - State: closed - Opened by wvauclain over 3 years ago - 1 comment

#57 - Add pytimeparse as a dependency for pypi package

Pull Request - State: closed - Opened by kurtwheeler over 3 years ago

#56 - Fix `--skip-quantile-normalization`

Pull Request - State: closed - Opened by wvauclain over 3 years ago

#55 - Add a timeout to downloading a dataset and stop waiting if the job fails

Pull Request - State: closed - Opened by kurtwheeler over 3 years ago - 1 comment

#54 - Rename the BASE_URL env var to REFINEBIO_BASE_URL

Pull Request - State: closed - Opened by kurtwheeler over 3 years ago

#53 - Link to github repo from the documentation

Issue - State: open - Opened by kurtwheeler over 3 years ago

#52 - CI/CD for docs

Issue - State: open - Opened by bug-sam over 3 years ago
Labels: documentation

#50 - Formatting the docs

Pull Request - State: closed - Opened by bug-sam over 3 years ago - 2 comments

#49 - Get missing data for objects fetched via list endpoints

Pull Request - State: closed - Opened by bug-sam over 3 years ago

#48 - remove OriginalFile download method

Pull Request - State: closed - Opened by bug-sam over 3 years ago

#47 - Typo in documentation about high-level function for downloading compendia

Issue - State: closed - Opened by jaclyn-taroni over 3 years ago - 3 comments

#45 - High Level Token Function

Pull Request - State: closed - Opened by bug-sam over 3 years ago

#44 - Sets up sponsor button for repo.

Pull Request - State: closed - Opened by kurtwheeler almost 4 years ago

#43 - adding has_compendia and has_quantfile_compendia python client side

Pull Request - State: closed - Opened by bug-sam almost 4 years ago

#42 - Improving the Docs!

Pull Request - State: closed - Opened by bug-sam almost 4 years ago

#41 - Update Errors

Pull Request - State: closed - Opened by bug-sam almost 4 years ago

#40 - Pretty Printing for refine.bio Objects

Pull Request - State: closed - Opened by bug-sam almost 4 years ago

#39 - Extract Methods for Downloadable Classes

Pull Request - State: closed - Opened by bug-sam almost 4 years ago

#38 - Download Updates

Pull Request - State: closed - Opened by bug-sam almost 4 years ago

#37 - Rework Config

Pull Request - State: closed - Opened by bug-sam almost 4 years ago

#36 - Add links to refine.bio docs for more info

Issue - State: closed - Opened by dvenprasad almost 4 years ago - 2 comments
Labels: design input

#35 - Documentation improvements

Issue - State: closed - Opened by kurtwheeler almost 4 years ago - 1 comment

#34 - All download functions should return the downloaded object

Issue - State: closed - Opened by kurtwheeler almost 4 years ago

#31 - Paths don't work as might be commonly expected

Issue - State: closed - Opened by kurtwheeler almost 4 years ago - 1 comment

#30 - Rework the way the config file is saved

Issue - State: closed - Opened by kurtwheeler almost 4 years ago

#29 - Improvements for downloading *pendia

Issue - State: closed - Opened by kurtwheeler almost 4 years ago

#28 - Make printing objects more informative

Issue - State: closed - Opened by kurtwheeler almost 4 years ago

#27 - Make a higher level function for getting an activated token

Issue - State: closed - Opened by kurtwheeler almost 4 years ago - 1 comment

#26 - Improve Error messages

Issue - State: closed - Opened by kurtwheeler almost 4 years ago - 6 comments
Labels: design input

#25 - Command Line Client

Pull Request - State: closed - Opened by bug-sam almost 4 years ago - 1 comment

#24 - Readme Updates

Pull Request - State: closed - Opened by bug-sam almost 4 years ago

#23 - Formatting the Docs

Issue - State: closed - Opened by bug-sam almost 4 years ago - 1 comment
Labels: documentation

#22 - Create command line client that uses this python module

Issue - State: closed - Opened by kurtwheeler almost 4 years ago

#21 - Human Readable Intros for Class/Module Documentation

Issue - State: closed - Opened by bug-sam almost 4 years ago
Labels: documentation

#20 - Update PyPI info

Pull Request - State: closed - Opened by bug-sam almost 4 years ago

#19 - Auto-Generated Docs!!

Pull Request - State: closed - Opened by bug-sam almost 4 years ago - 1 comment

#18 - Rework Token

Pull Request - State: closed - Opened by bug-sam almost 4 years ago

#17 - Slicing for PaginatedList

Pull Request - State: closed - Opened by bug-sam almost 4 years ago

#16 - Slices don't seem to work for PaginatedLists

Issue - State: closed - Opened by kurtwheeler almost 4 years ago

#15 - Publishing to PyPI

Pull Request - State: closed - Opened by bug-sam almost 4 years ago

#14 - Tokens are a bit awkward to use

Issue - State: closed - Opened by kurtwheeler almost 4 years ago - 1 comment

#13 - Create documentation page

Issue - State: closed - Opened by kurtwheeler almost 4 years ago - 1 comment

#12 - Create pip package for client!

Issue - State: closed - Opened by kurtwheeler almost 4 years ago

#11 - High Level Functions

Pull Request - State: closed - Opened by bug-sam about 4 years ago

#10 - Handle api's new standardized errors

Pull Request - State: closed - Opened by bug-sam about 4 years ago - 2 comments

#9 - `add_samples()` method for Dataset class

Issue - State: closed - Opened by kurtwheeler about 4 years ago - 4 comments

#8 - Tweak the way the config is saved and deleted

Issue - State: closed - Opened by kurtwheeler about 4 years ago - 1 comment

#7 - Update docstrings

Pull Request - State: closed - Opened by bug-sam about 4 years ago

#6 - Parse datetimes

Pull Request - State: closed - Opened by bug-sam about 4 years ago

#5 - dataset creation download

Pull Request - State: closed - Opened by bug-sam about 4 years ago

#4 - model class tests

Pull Request - State: closed - Opened by bug-sam about 4 years ago

#3 - Use python datetime objects where appropriate

Issue - State: closed - Opened by kurtwheeler about 4 years ago

#2 - Adding Model Classes

Pull Request - State: closed - Opened by bug-sam about 4 years ago

#1 - moving code from alexslemonade/refinebio

Pull Request - State: closed - Opened by bug-sam about 4 years ago