Ecosyste.ms: Issues

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

GitHub / bigbio/sdrf-pipelines issues and pull requests

#183 - ignore case in original extension

Pull Request - State: closed - Opened by daichengxin 9 days ago - 3 comments
Labels: Review effort [1-5]: 2

#182 - Fix column order validation

Pull Request - State: closed - Opened by levitsky 27 days ago - 3 comments
Labels: Bug fix, Review effort [1-5]: 2

#181 - Version increased for release

Pull Request - State: closed - Opened by ypriverol 28 days ago

#180 - Add permissions for black

Pull Request - State: closed - Opened by levitsky 28 days ago - 4 comments
Labels: Review effort [1-5]: 1, configuration changes

#179 - Add setuptools dependency

Pull Request - State: closed - Opened by levitsky 28 days ago - 4 comments
Labels: dependencies, Review effort [1-5]: 1

#178 - Fix ValueError on enzyme validation

Pull Request - State: closed - Opened by levitsky 28 days ago - 3 comments
Labels: Bug fix, Review effort [1-5]: 2

#177 - The column technology typecannot be before the assay name -- ERROR

Issue - State: closed - Opened by levitsky 28 days ago - 2 comments

#176 - Validation error for enzyme information encoded by fragpipe

Issue - State: closed - Opened by levitsky 28 days ago - 1 comment

#175 - ImprtError on Python 3.12 due to missing pkg_resouces

Issue - State: closed - Opened by levitsky 28 days ago

#173 - Allow missing/NA-filled columns for sdrf2openms conversion

Issue - State: open - Opened by jpfeuffer about 1 month ago
Labels: enhancement

#172 - Validation fails with some repeated columns

Issue - State: open - Opened by ypriverol 3 months ago - 1 comment
Labels: bug

#171 - skip ols internet check, use instead local parquet files

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

#170 - skip OLS query option, only check locally

Issue - State: closed - Opened by ypriverol 3 months ago
Labels: documentation, enhancement

#169 - Big PR with multiple validations - [DO NOT MERGE YET]

Pull Request - State: closed - Opened by ypriverol 3 months ago - 2 comments

#168 - OLS refactoring.

Pull Request - State: closed - Opened by ypriverol 4 months ago - 1 comment

#166 - Better error message with SDRF to OpenMS

Issue - State: closed - Opened by ypriverol 7 months ago

#165 - Update openms.py

Pull Request - State: closed - Opened by ypriverol 7 months ago - 1 comment

#164 - Error When converting to OpenMS enzymes

Issue - State: closed - Opened by ypriverol 7 months ago
Labels: bug

#163 - small changes realted with OLS.

Pull Request - State: closed - Opened by ypriverol 8 months ago - 1 comment

#162 - Major changes and bug fixing

Pull Request - State: closed - Opened by ypriverol 8 months ago - 1 comment

#161 - Searching for a term found as substring in OLS.

Issue - State: closed - Opened by ypriverol 8 months ago
Labels: enhancement, high-priority

#160 - OLS search terms pagination error

Issue - State: closed - Opened by ypriverol 8 months ago
Labels: bug, high-priority

#159 - Proposal for refactoring & higher maintainability

Issue - State: open - Opened by di-hardt 9 months ago - 6 comments
Labels: documentation, enhancement, question

#158 - Free text validation

Issue - State: open - Opened by TineClaeys 9 months ago - 1 comment

#157 - Decide the main developer behind version 0.0.25 in sdrf-pipelines

Issue - State: closed - Opened by ypriverol 10 months ago - 1 comment
Labels: high-priority

#156 - sdrf pipelines version 0.0.25

Issue - State: open - Opened by ypriverol 10 months ago
Labels: high-priority

#155 - Validate file duplications if not multiplexing is available

Issue - State: open - Opened by ypriverol 11 months ago
Labels: bug, high-priority

#154 - Validator option for the different flavors

Issue - State: open - Opened by jpfeuffer 11 months ago

#153 - The empty cells validation is not good

Issue - State: open - Opened by ypriverol 11 months ago

#152 - Problems understanding TMT label in sdrf file

Issue - State: open - Opened by MetteBoge 11 months ago

#151 - Moving to OLS4 is needed

Issue - State: closed - Opened by ypriverol about 1 year ago

#150 - PLEASE DO NOT MERGE Fix minor issues for the terms validation

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

#149 - Refactor testing and arbitrary extension handling

Pull Request - State: closed - Opened by jspaezp about 1 year ago - 2 comments

#148 - Conversion bruker data

Pull Request - State: closed - Opened by ypriverol about 1 year ago - 13 comments

#146 - Fixed some errors introduced before in #PR 44

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

#145 - [Pitch] Partial keep raw in OpenMS

Issue - State: closed - Opened by jspaezp about 1 year ago - 14 comments

#144 - Check to see if key is present *and* values are set

Pull Request - State: closed - Opened by lazear over 1 year ago - 3 comments

#143 - Fix if-else branch in column name validation

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

#142 - Flexible key-value pair location

Pull Request - State: closed - Opened by WangHong007 over 1 year ago

#141 - Why are these elements private?

Issue - State: closed - Opened by fabianegli over 1 year ago - 1 comment

#140 - wiff supporting and default label modifications

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

#139 - Erroneous TMT label extraction logic

Issue - State: open - Opened by fabianegli about 2 years ago

#138 - Added a few more parameters for generating the maxquant parameter file

Pull Request - State: closed - Opened by veitveit about 2 years ago - 8 comments

#137 - Unimod and ols error

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

#136 - changes by pyupgrade --py36-plus

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

#135 - add boilerplate gitignore items for Python package development

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

#134 - Version option for CLI

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

#133 - use standard pytest file naming convention

Pull Request - State: closed - Opened by fabianegli over 2 years ago
Labels: WIP

#132 - Random minor imporvements

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

#131 - ENH: use TLS by default

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

#130 - [BUG] openms/unimod.py

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

#129 - fix-zumma-zooma

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

#128 - use isort and black

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

#127 - strange method name

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

#126 - CI is failing, probably due to resource location change

Issue - State: closed - Opened by fabianegli over 2 years ago - 3 comments

#125 - Data file distribution

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

#124 - Access to yml and xml files

Issue - State: closed - Opened by veitveit over 2 years ago - 3 comments

#123 - Various fixes and adding conversion to Normalyzer

Pull Request - State: closed - Opened by veitveit over 2 years ago - 7 comments

#122 - [ENH] Have a "--version" parameter to print versions

Issue - State: closed - Opened by jpfeuffer over 2 years ago - 5 comments
Labels: enhancement, high-priority

#120 - pyyaml added to the requirements

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

#119 - [SECURITY] Move from xml to defusedxml for XML parsing

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

#118 - [ENH] Use logging instead of print

Issue - State: closed - Opened by fabianegli over 2 years ago - 1 comment
Labels: enhancement, help wanted

#117 - [MAINT] rename master branch to main

Issue - State: closed - Opened by fabianegli over 2 years ago - 3 comments
Labels: low-priority

#116 - [MAINT] remove validate_sdrfs.sh

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

#114 - [MAINT] ignore formatting commits in blame

Issue - State: open - Opened by fabianegli over 2 years ago - 1 comment

#113 - [DISCUSSION] A more concise CLI that is well behaved

Issue - State: open - Opened by fabianegli over 2 years ago
Labels: help wanted, question

#112 - [ENH] Need for more comprehensive integration testing

Issue - State: open - Opened by fabianegli over 2 years ago - 4 comments
Labels: enhancement, help wanted, high-priority

#111 - [DISCUSSION] Permissive or strict parser?

Issue - State: open - Opened by fabianegli over 2 years ago
Labels: help wanted, question

#110 - [QUESTION] What purpose does the `validate_sdrfs.sh` script have in this repo?

Issue - State: closed - Opened by fabianegli over 2 years ago - 6 comments
Labels: help wanted, question

#109 - [DOC] Link to relevant repos

Issue - State: open - Opened by fabianegli over 2 years ago - 3 comments
Labels: help wanted, question, high-priority

#108 - [ENH] Consistent API input checks with useful feedback on failure

Issue - State: open - Opened by fabianegli over 2 years ago
Labels: enhancement

#107 - [MAINT] Favor pathlib over path string manipulation

Issue - State: open - Opened by fabianegli over 2 years ago - 1 comment
Labels: good first issue, high-priority

#106 - [CODE] Use pandas to parse the SDRF

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

#105 - [ENH] Using some Python coding best practices for open source repositories

Issue - State: open - Opened by fabianegli over 2 years ago - 5 comments
Labels: enhancement, help wanted

#104 - [Feature request] Make parsed SDRF data usable

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

#102 - [DOC] Document how to run tests

Issue - State: open - Opened by fabianegli over 2 years ago - 2 comments
Labels: high-priority

#101 - add acquisition column

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

#100 - Compatible with ITRAQ

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

#98 - retrieve strategy

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

#97 - Update MSstats

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

#96 - Fix bug

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

#95 - Fixed bugs

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

#94 - Fixed bugs

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

#93 - added most of enzymes in PSI-MS for OpenMS

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

#92 - Fixed errors

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

#91 - Fixed errors

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

#90 - maxquant parameter file has typo

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

#87 - Minor bug fixes

Pull Request - State: closed - Opened by jgriss over 3 years ago - 4 comments

#86 - [BUG] TMT16 labels are incorrect in openms.py

Issue - State: closed - Opened by jgriss over 3 years ago

#85 - [Usability] Fix uncaught exception when unsupported labels are used in SDRF file

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

#84 - msstats conversion and factor value validation

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

#83 - Add mandatory replicate column validation

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