Ecosyste.ms: Issues

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

GitHub / pepkit/pipestat issues and pull requests

#209 - Pipestat messaging update suggestions

Issue - State: open - Opened by nsheff about 2 months ago - 1 comment
Labels: docs

#208 - v0.11.0 release

Pull Request - State: closed - Opened by donaldcampbelljr about 2 months ago

#207 - pipeline_name not set correctly

Issue - State: closed - Opened by donaldcampbelljr about 2 months ago
Labels: likely-solved

#205 - make samples type array and nest under items #204

Pull Request - State: closed - Opened by donaldcampbelljr 3 months ago

#204 - proposed schema changes

Issue - State: closed - Opened by donaldcampbelljr 3 months ago - 2 comments
Labels: likely-solved

#203 - v 0.10.2 point release

Pull Request - State: closed - Opened by donaldcampbelljr 3 months ago

#202 - Obtain pephub_url from config file

Issue - State: closed - Opened by donaldcampbelljr 3 months ago
Labels: likely-solved

#201 - v0.10.1 release

Pull Request - State: closed - Opened by donaldcampbelljr 4 months ago

#200 - Dev pephub backend changes

Pull Request - State: closed - Opened by donaldcampbelljr 4 months ago

#198 - v0.10.0 Release

Pull Request - State: closed - Opened by donaldcampbelljr 4 months ago

#197 - 0.9.3 point release

Pull Request - State: closed - Opened by donaldcampbelljr 6 months ago

#195 - Integrating Pipestat Summarize with PEPHub

Issue - State: open - Opened by donaldcampbelljr 6 months ago - 1 comment

#194 - v0.9.2 release

Pull Request - State: closed - Opened by donaldcampbelljr 6 months ago

#193 - add sqlite option if included in config file

Pull Request - State: closed - Opened by donaldcampbelljr 6 months ago

#192 - Support sqlite for db backend

Issue - State: closed - Opened by donaldcampbelljr 6 months ago
Labels: likely-solved

#191 - Add pipestat summarize for PEPhub backend

Issue - State: closed - Opened by donaldcampbelljr 6 months ago - 2 comments

#190 - Pipestat Summarize - stats not reported and objects have inaccurate paths

Issue - State: closed - Opened by donaldcampbelljr 6 months ago
Labels: bug, likely-solved

#189 - Schema validation requires `boolean` when reporting result. `bool` does not validate properly.

Issue - State: closed - Opened by donaldcampbelljr 6 months ago
Labels: likely-solved, priority-low

#188 - Extracting model creation code

Issue - State: open - Opened by nsheff 6 months ago
Labels: question

#187 - Add pephub backend to Pipestat

Pull Request - State: closed - Opened by donaldcampbelljr 7 months ago - 2 comments

#186 - Add more output schemas to https://schema.databio.org/

Issue - State: closed - Opened by donaldcampbelljr 7 months ago - 1 comment
Labels: documentation, good first issue, priority-low

#185 - update badges

Pull Request - State: closed - Opened by donaldcampbelljr 7 months ago

#184 - Refactor reports.py

Issue - State: open - Opened by donaldcampbelljr 7 months ago - 1 comment
Labels: priority-low, refactor

#183 - v0.9.1 release

Pull Request - State: closed - Opened by donaldcampbelljr 7 months ago

#182 - Dev refactor reporting

Pull Request - State: closed - Opened by donaldcampbelljr 7 months ago

#181 - Dependency check causes pytest failures when running individual tests.

Issue - State: closed - Opened by donaldcampbelljr 7 months ago - 4 comments
Labels: bug, likely-solved

#180 - fix #175

Pull Request - State: closed - Opened by donaldcampbelljr 7 months ago

#179 - v0.9.0 Release

Pull Request - State: closed - Opened by donaldcampbelljr 7 months ago

#178 - Create History for Filebackend and DB Backend

Pull Request - State: closed - Opened by donaldcampbelljr 8 months ago - 3 comments

#177 - pipestat should offer the option to include a history of results

Issue - State: closed - Opened by donaldcampbelljr 8 months ago - 4 comments
Labels: likely-solved, priority-high

#176 - Rethink how pipestat returns reported results

Issue - State: closed - Opened by donaldcampbelljr 8 months ago - 2 comments
Labels: likely-solved

#175 - Retrieve is not using the pipestatmanager object record_identifier if none is supplied

Issue - State: closed - Opened by donaldcampbelljr 8 months ago - 1 comment
Labels: bug, likely-solved

#174 - Should retrieve_one include items such as created and modified time, or only reported results?

Issue - State: closed - Opened by donaldcampbelljr 8 months ago - 1 comment
Labels: question, likely-solved

#173 - Schema validation exception messaging

Issue - State: closed - Opened by khoroshevskyi 9 months ago - 3 comments
Labels: likely-solved

#172 - Only show message about specific backend when created.

Issue - State: closed - Opened by donaldcampbelljr 9 months ago
Labels: likely-solved

#171 - Error in retrieving one result in `retrieve_one`

Issue - State: closed - Opened by khoroshevskyi 9 months ago - 2 comments
Labels: bug, likely-solved

#170 - Check if required fields are checked if they actually required

Issue - State: closed - Opened by khoroshevskyi 9 months ago - 3 comments
Labels: likely-solved

#169 - refactor `replace_JSON_refs` function

Issue - State: closed - Opened by khoroshevskyi 9 months ago - 1 comment
Labels: likely-solved, docs

#168 - Specify database schema using python objects instead yaml file

Issue - State: open - Opened by khoroshevskyi 9 months ago - 1 comment
Labels: enhancement, brainstorming, priority-low

#167 - move codecov to base coverage report

Issue - State: closed - Opened by khoroshevskyi 9 months ago - 5 comments

#166 - Disable sqlmodel warning

Issue - State: open - Opened by khoroshevskyi 9 months ago - 4 comments
Labels: wontfix, priority-low

#165 - v0.8.2 release

Pull Request - State: closed - Opened by donaldcampbelljr 9 months ago - 1 comment

#164 - Allow parameterizing via env vars

Issue - State: closed - Opened by nsheff 9 months ago - 2 comments
Labels: likely-solved, brainstorming

#163 - Retrieving embedded values from object results

Issue - State: closed - Opened by nsheff 9 months ago - 2 comments
Labels: docs

#162 - Allow remote schemas. Fix #160

Pull Request - State: closed - Opened by nsheff 9 months ago - 5 comments

#161 - Should force_overwrite default to true?

Issue - State: closed - Opened by nsheff 9 months ago - 3 comments
Labels: question, likely-solved, priority-high

#160 - Allow schema to be remote

Issue - State: closed - Opened by nsheff 9 months ago - 1 comment
Labels: enhancement, likely-solved

#159 - pipestat retrieval breaks with common prefix

Issue - State: closed - Opened by nsheff 9 months ago - 7 comments
Labels: bug, likely-solved

#158 - Pipestat interface suggestions

Issue - State: closed - Opened by nsheff 9 months ago - 5 comments

#157 - No Schema Supplied should offer more information

Issue - State: closed - Opened by donaldcampbelljr 9 months ago - 1 comment
Labels: likely-solved

#156 - What is multi_pipelines and when should it be used?

Issue - State: closed - Opened by nsheff 10 months ago - 2 comments
Labels: docs

#155 - multi pipelines error with only a single pipeline is confusing

Issue - State: closed - Opened by nsheff 10 months ago
Labels: likely-solved

#154 - Fix quickstart example

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

#153 - Quickstart example does not work

Issue - State: closed - Opened by simeoncarstens 10 months ago - 1 comment
Labels: likely-solved

#152 - v0.8.1 release

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

#151 - pipestat summarize: title of the html page is "Looper: None Summary"

Issue - State: closed - Opened by donaldcampbelljr 10 months ago
Labels: likely-solved

#149 - pipestat summarize: log files are not gathered when making a portable report

Issue - State: closed - Opened by donaldcampbelljr 10 months ago
Labels: likely-solved

#148 - pipestat summarize: columns view should only show stats NOT objects

Issue - State: closed - Opened by donaldcampbelljr 10 months ago - 2 comments
Labels: bug, likely-solved

#147 - Adapt yacman v0.9.3

Pull Request - State: closed - Opened by nsheff 10 months ago - 2 comments

#146 - Add warning to pytests if optional dependencies are not installed.

Issue - State: closed - Opened by donaldcampbelljr 10 months ago
Labels: likely-solved

#145 - Update docs - ensure readme has correct container information and mention optional dependencies

Issue - State: closed - Opened by donaldcampbelljr 10 months ago - 1 comment
Labels: likely-solved

#144 - Both PyYAML and oyaml in requirements

Issue - State: closed - Opened by vreuter 10 months ago - 5 comments
Labels: enhancement, likely-solved

#143 - Pypiper + pipestat: minimal dependencies set

Issue - State: closed - Opened by vreuter 10 months ago - 2 comments
Labels: question

#142 - v0.8.0 release

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

#140 - Add portable report

Pull Request - State: closed - Opened by donaldcampbelljr 11 months ago - 6 comments

#139 - pipestat summarize: add portability/zipping

Issue - State: closed - Opened by donaldcampbelljr 11 months ago - 4 comments
Labels: enhancement, likely-solved

#137 - pipestat summarize: fastqc links do not work

Issue - State: closed - Opened by donaldcampbelljr 11 months ago - 2 comments

#136 - v0.7.0 release

Pull Request - State: closed - Opened by donaldcampbelljr 11 months ago - 2 comments

#135 - Dev sqlmodel 0 14

Pull Request - State: closed - Opened by donaldcampbelljr 11 months ago - 1 comment

#134 - Dev pipestat iterator 97

Pull Request - State: closed - Opened by donaldcampbelljr 11 months ago - 1 comment

#133 - Objects YAML button does not point to correct file

Issue - State: closed - Opened by donaldcampbelljr 11 months ago
Labels: likely-solved

#132 - Implement fetching schemas from schema.databio.org

Issue - State: closed - Opened by donaldcampbelljr 11 months ago - 1 comment

#131 - Fix reporting in pipestat summarize

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

#130 - pipestat summarize missing some functionality of looper report

Issue - State: closed - Opened by donaldcampbelljr 12 months ago - 2 comments

#129 - naming of optional dependency packages

Issue - State: closed - Opened by nsheff 12 months ago - 3 comments
Labels: likely-solved

#128 - Revert "Fixed #106"

Pull Request - State: closed - Opened by donaldcampbelljr 12 months ago - 2 comments

#127 - Updating to sqlmodel 0.0.14

Issue - State: closed - Opened by nsheff 12 months ago - 3 comments
Labels: enhancement, likely-solved

#126 - Implement output schema fetching from https://schema.databio.org/

Issue - State: closed - Opened by donaldcampbelljr 12 months ago - 1 comment

#125 - Using pipestat to report results to PEPhub

Issue - State: closed - Opened by nsheff 12 months ago - 1 comment
Labels: enhancement, likely-solved

#124 - Make sure pipestat 0.6.0 is working with Refgenie

Issue - State: closed - Opened by khoroshevskyi almost 1 year ago - 3 comments

#122 - jinja2 requirement not declared, refgenie fails to run

Issue - State: closed - Opened by ialbert almost 1 year ago - 4 comments
Labels: bug, likely-solved

#121 - Updated requirements

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

#120 - Pipestat should be able to create a results file for an individual sample.

Issue - State: closed - Opened by donaldcampbelljr about 1 year ago - 1 comment
Labels: likely-solved

#119 - Using JSON schema as output schema breaks pipestat summarize

Issue - State: closed - Opened by donaldcampbelljr about 1 year ago - 1 comment
Labels: likely-solved

#118 - incorrect version bound specification

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

#117 - Installing optional dependencies per docs is not working

Issue - State: closed - Opened by nsheff about 1 year ago - 6 comments
Labels: likely-solved

#116 - Streamline optional dependency sqlmodel

Issue - State: closed - Opened by nsheff about 1 year ago - 2 comments
Labels: likely-solved

#115 - Use RecordNotFoundError exception when record is not found.

Issue - State: closed - Opened by nsheff about 1 year ago - 2 comments
Labels: likely-solved

#114 - Align environment vars to have the same prefix

Issue - State: closed - Opened by donaldcampbelljr about 1 year ago
Labels: likely-solved

#113 - Fix properties

Issue - State: closed - Opened by donaldcampbelljr about 1 year ago - 1 comment
Labels: likely-solved

#112 - Polish pytests with using fixtures and removing redundancy

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

#110 - Clear status needs an implemented pytest

Issue - State: closed - Opened by donaldcampbelljr about 1 year ago - 2 comments
Labels: likely-solved

#109 - Align pipestat output_schema to be a true JSON schema

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

#108 - Dev 99 103 api refactor

Pull Request - State: closed - Opened by donaldcampbelljr about 1 year ago - 6 comments