Ecosyste.ms: Issues

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

GitHub / pepkit/geofetch issues and pull requests

#139 - Release 0.12.7

Pull Request - State: closed - Opened by khoroshevskyi 2 months ago

#138 - Downloading the supplementary files

Issue - State: closed - Opened by Zethson 3 months ago - 2 comments

#137 - remove docs

Pull Request - State: closed - Opened by khoroshevskyi 5 months ago

#136 - how to get GSE information for a SRR run id?

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

#135 - use VersionInHelp parser

Issue - State: open - Opened by nsheff 9 months ago

#134 - Update docs

Issue - State: open - Opened by khoroshevskyi 10 months ago

#133 - Prefetch check

Pull Request - State: closed - Opened by pedro-w 10 months ago

#132 - Release 0.12.6

Pull Request - State: closed - Opened by khoroshevskyi 10 months ago - 1 comment

#131 - Update installation of prefetch in docs

Issue - State: open - Opened by khoroshevskyi 10 months ago
Labels: docs

#130 - fetch_all does not work

Issue - State: closed - Opened by kapedalex 10 months ago - 11 comments
Labels: likely-solved

#129 - Downloading metadata for all GSE

Issue - State: closed - Opened by srp33 10 months ago - 9 comments

#128 - Are Greek letters causing errors ?

Issue - State: open - Opened by khoroshevskyi 12 months ago
Labels: question

#126 - Add GSE number to sample_name if big concatenated project is created

Issue - State: open - Opened by khoroshevskyi 12 months ago
Labels: question, brainstorming

#125 - Release 0.12.5

Pull Request - State: closed - Opened by khoroshevskyi 12 months ago - 1 comment

#124 - PEP description is None

Issue - State: closed - Opened by khoroshevskyi 12 months ago

#123 - Download metadata from SRA

Issue - State: closed - Opened by amnahsiddiqa about 1 year ago - 2 comments

#122 - Release v0.12.4

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

#121 - Make geofetch more efficient

Issue - State: open - Opened by khoroshevskyi over 1 year ago - 4 comments

#120 - v0.12.3

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

#119 - Geofetch should preserve order

Issue - State: closed - Opened by khoroshevskyi over 1 year ago

#118 - No files found and No data to save when trying to download GSE files

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

#117 - fixed docs

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

#116 - Remove test dependencies from actual GEO files

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

#115 - Release 0.12.2

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

#114 - Add max size option / argument for prefetch

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

#113 - Can't download SRRs larger than 50GB

Issue - State: closed - Opened by drejom over 1 year ago - 3 comments

#112 - Report error in downloading SRA data

Issue - State: closed - Opened by GuohuaZhu over 1 year ago - 3 comments

#111 - v0.12.1

Pull Request - State: closed - Opened by khoroshevskyi almost 2 years ago - 1 comment

#110 - V0.12.0

Pull Request - State: closed - Opened by khoroshevskyi almost 2 years ago - 2 comments

#108 - Update pandas version

Issue - State: closed - Opened by khoroshevskyi almost 2 years ago

#107 - V0.11.2

Pull Request - State: closed - Opened by khoroshevskyi almost 2 years ago

#106 - Created PEPs don't contain some of the information

Issue - State: closed - Opened by khoroshevskyi almost 2 years ago
Labels: bug

#104 - geofetch creates unwanted empty folders

Issue - State: closed - Opened by khoroshevskyi almost 2 years ago
Labels: bug

#103 - Dealing with GEO tables

Issue - State: closed - Opened by khoroshevskyi almost 2 years ago

#102 - Disable downloading huge soft files

Issue - State: closed - Opened by khoroshevskyi almost 2 years ago - 5 comments

#101 - release 0.11.1

Pull Request - State: closed - Opened by khoroshevskyi almost 2 years ago

#100 - geofetch produces incorrect link to sra file

Issue - State: closed - Opened by khoroshevskyi almost 2 years ago - 1 comment
Labels: bug

#99 - Error in expanding metadata list

Issue - State: closed - Opened by khoroshevskyi about 2 years ago - 1 comment
Labels: bug

#98 - Error while downloading project

Issue - State: closed - Opened by khoroshevskyi about 2 years ago - 1 comment
Labels: bug

#97 - Bugs and redundancy in requirements

Issue - State: closed - Opened by khoroshevskyi about 2 years ago

#96 - Naming and docstring refactoring

Pull Request - State: closed - Opened by khoroshevskyi about 2 years ago

#95 - Fix of colons in config file

Pull Request - State: closed - Opened by khoroshevskyi about 2 years ago - 2 comments

#94 - Naming and docstring refactoring in geofetch

Issue - State: closed - Opened by khoroshevskyi about 2 years ago - 1 comment

#93 - Release v0.11.0

Pull Request - State: closed - Opened by khoroshevskyi about 2 years ago - 1 comment

#92 - colons in values

Issue - State: closed - Opened by nsheff about 2 years ago - 5 comments

#91 - subsample null

Issue - State: closed - Opened by nsheff about 2 years ago - 2 comments

#90 - Error in producing config file for raw data

Issue - State: closed - Opened by khoroshevskyi about 2 years ago - 1 comment

#89 - Add example to the cli

Issue - State: closed - Opened by khoroshevskyi about 2 years ago

#88 - geofetch after refactoring doesn't download SRA data

Issue - State: closed - Opened by khoroshevskyi about 2 years ago
Labels: bug, priority-high

#87 - Refactoring + improvements in retrieving peppy project + fixed few bugs

Pull Request - State: closed - Opened by khoroshevskyi about 2 years ago - 3 comments

#86 - Add more tests

Issue - State: closed - Opened by khoroshevskyi about 2 years ago

#85 - Delete old geofetch website

Issue - State: closed - Opened by khoroshevskyi about 2 years ago - 1 comment
Labels: docs

#84 - peppy init and progress bar

Pull Request - State: closed - Opened by khoroshevskyi about 2 years ago - 1 comment

#83 - raw projects don't have subfolders

Issue - State: closed - Opened by khoroshevskyi about 2 years ago
Labels: bug

#82 - Issues in getting sra file with post request

Issue - State: closed - Opened by khoroshevskyi about 2 years ago - 4 comments
Labels: bug

#81 - Create peppy object by using geofetch

Issue - State: closed - Opened by khoroshevskyi over 2 years ago

#80 - `yaml.scanner.ScannerError` when initializing PEP downloaded with `geofetch`

Issue - State: closed - Opened by nleroy917 over 2 years ago - 1 comment

#79 - Switch From `subprocess` and `wget` to `requests` module

Issue - State: closed - Opened by nleroy917 over 2 years ago
Labels: enhancement

#78 - V0.10.1

Pull Request - State: closed - Opened by khoroshevskyi over 2 years ago - 1 comment

#77 - The usage of the eutils must be improved

Issue - State: closed - Opened by khoroshevskyi over 2 years ago

#76 - version 0.10.0

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

#75 - Dev alex

Pull Request - State: closed - Opened by khoroshevskyi over 2 years ago - 1 comment

#74 - Fail to download GSExxxxxx_SRA.csv

Issue - State: closed - Opened by shkao over 2 years ago - 2 comments
Labels: bug, priority-high

#73 - Add progress bar

Issue - State: closed - Opened by khoroshevskyi over 2 years ago - 2 comments
Labels: enhancement

#72 - Gracefully Terminate Child Subprocesses

Pull Request - State: closed - Opened by nleroy917 over 2 years ago - 4 comments

#71 - Sanitize sample names

Issue - State: closed - Opened by nleroy917 over 2 years ago - 3 comments
Labels: likely-solved, priority-low

#70 - Ability create `.pep.yaml` files

Issue - State: closed - Opened by nleroy917 over 2 years ago - 1 comment
Labels: likely-solved

#69 - version 0.9.0

Pull Request - State: closed - Opened by khoroshevskyi over 2 years ago - 23 comments

#68 - make columns case insensitive

Issue - State: closed - Opened by khoroshevskyi over 2 years ago - 2 comments
Labels: enhancement, likely-solved

#67 - Error while using --filter-size

Issue - State: closed - Opened by khoroshevskyi over 2 years ago
Labels: bug, likely-solved

#66 - Disable creating huge combined pep

Issue - State: closed - Opened by nsheff over 2 years ago

#65 - Large, constant sample attributes should be moved to project config

Issue - State: closed - Opened by nsheff over 2 years ago - 2 comments
Labels: priority-high

#64 - Incorrect help --data-source description

Issue - State: closed - Opened by khoroshevskyi over 2 years ago

#63 - Docs build failing

Issue - State: closed - Opened by nsheff over 2 years ago - 1 comment
Labels: docs

#62 - Error giving sample list file

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

#61 - Release version 0.8.0

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

#60 - The argument --acc-anno is not working for processed data

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

#59 - input sample lists are not working for processed data

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

#58 - input sample lists are not working

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

#57 - In series annotation file files are stored in the list

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

#56 - Decouple Geofetcher and argparser

Issue - State: closed - Opened by khoroshevskyi over 2 years ago - 3 comments
Labels: priority-high

#55 - Clean up soft files

Issue - State: closed - Opened by khoroshevskyi over 2 years ago - 1 comment
Labels: enhancement, question, priority-low

#54 - Don't use absolute hard paths in output PEPs

Issue - State: closed - Opened by nsheff over 2 years ago

#53 - Mkdocs build failing

Issue - State: closed - Opened by nsheff over 2 years ago - 4 comments

#52 - Unit tests

Issue - State: closed - Opened by nsheff over 2 years ago - 2 comments

#51 - Incorrect path in PEP to the downloaded files

Issue - State: closed - Opened by khoroshevskyi over 2 years ago - 1 comment

#50 - Code blocking

Pull Request - State: closed - Opened by nsheff over 2 years ago - 4 comments

#49 - bring in latest master changes

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

#48 - Fix PyPI readme formatting

Issue - State: closed - Opened by nsheff over 2 years ago - 6 comments
Labels: docs

#47 - Metadata standardization

Issue - State: open - Opened by khoroshevskyi almost 3 years ago - 3 comments
Labels: wontfix, compatibility

#46 - Integration of geofetch and pephub

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

#45 - Adding filter that separates experiment and sample data

Issue - State: closed - Opened by khoroshevskyi almost 3 years ago - 2 comments
Labels: enhancement

#44 - Add file size filter for processed files

Issue - State: closed - Opened by khoroshevskyi almost 3 years ago - 8 comments
Labels: enhancement

#43 - Geofetch code blocking and improvements

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

#42 - ignore case in filter regex

Issue - State: closed - Opened by stolarczyk about 4 years ago - 1 comment
Labels: enhancement

#41 - NameError: name 'Sys' is not defined

Issue - State: closed - Opened by stolarczyk about 4 years ago - 1 comment
Labels: bug

#40 - update to new pipeline interface

Issue - State: closed - Opened by nsheff about 4 years ago
Labels: priority-low