Mesnage-Org/pgfinder issues and pull requests

#199 - [pre-commit.ci] pre-commit automatically updated.

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago - 1 comment

#198 - refactor(repo): remove obsolete demo files

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

#197 - Remove demo.py and demo_ftrs.py

Issue - State: closed - Opened by ns-rse over 1 year ago
Labels: good first issue

#196 - Retain multiple matches when difference is < 1ppm

Pull Request - State: closed - Opened by TheLostLambda over 1 year ago - 11 comments

#195 - Add support for FTRS files from Byos 5.2

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

#194 - [pre-commit.ci] pre-commit automatically updated.

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago

#193 - fix: remove ~ characters from output

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

#192 - [pre-commit.ci] pre-commit automatically updated.

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago - 1 comment

#191 - Cleaning some files up in the repo

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

#190 - Remove "~" characters in databases (glyco bonds) replace by "-"

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

#189 - Add support for the latest Byos ftrs files

Issue - State: closed - Opened by smesnage over 1 year ago
Labels: JOSS Essential

#188 - Look into Poetry as a build / dependency managment system

Issue - State: closed - Opened by TheLostLambda over 1 year ago - 8 comments

#187 - Fix the processing of MaqQuant files

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

#186 - [pre-commit.ci] pre-commit automatically updated.

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago - 1 comment

#185 - Cleanup old notebook code and dependencies

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

#184 - Re-write of docs/usage.md

Pull Request - State: closed - Opened by ns-rse over 1 year ago - 9 comments
Labels: documentation

#183 - [pre-commit.ci] pre-commit automatically updated.

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago - 1 comment

#182 - [pre-commit.ci] pre-commit automatically updated.

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago - 1 comment

#181 - Fix new issue: no intensity for unmatched masses!

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

#180 - Revise docs/usage.md

Issue - State: closed - Opened by ns-rse over 1 year ago
Labels: documentation, JOSS Essential

#179 - Updates README

Pull Request - State: closed - Opened by ns-rse over 1 year ago - 7 comments

#178 - Readme should signpost documentation more clearly

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

#177 - fix: re-add intensity for unmatched structures

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

#176 - Need to output intensity for unmatched structures

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

#175 - [pre-commit.ci] pre-commit automatically updated.

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago - 1 comment

#174 - [pre-commit.ci] pre-commit automatically updated.

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago - 1 comment

#173 - [pre-commit.ci] pre-commit automatically updated.

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago - 1 comment

#172 - refactor(data): bundle masses libraries with pgfinder

Pull Request - State: closed - Opened by TheLostLambda over 1 year ago - 5 comments

#171 - fix(deps): remove unneeded matplotlib dependency

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

#170 - PGFinder needs sqlite3 as a dependency?

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

#169 - fix: update mass libraries

Pull Request - State: closed - Opened by TheLostLambda over 1 year ago - 9 comments

#168 - Experiment with calculating the offset of unknown ions to known structures

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

#167 - Brooks's Week of the 19th Hackathon Task List

Issue - State: closed - Opened by TheLostLambda over 1 year ago - 8 comments

#166 - Explore Replacing JupyterLite With a Proper Web UI + Pyodide

Issue - State: closed - Opened by TheLostLambda over 1 year ago - 7 comments

#165 - [pre-commit.ci] pre-commit automatically updated.

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago - 1 comment

#164 - Command line error with maxquant

Issue - State: closed - Opened by bobturneruk over 1 year ago - 3 comments
Labels: JOSS Essential

#163 - Remove files not needed

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

#162 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago - 3 comments

#161 - Switching to run JupyterLite Notebooks

Pull Request - State: closed - Opened by ns-rse over 1 year ago - 5 comments

#160 - Remove the ruamel.yaml dependency from pyproject.toml

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

#159 - ruamel.yaml > pyYAML; testing and dev dependencies added

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

#158 - Updating setuptools prior to package build in PyPI workflow

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

#157 - Adding setuptools_scm to pypi dependencies

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

#156 - Correcting typos in usage

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

#155 - Ns rse/gh pages default redirect

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

#154 - Setting the default branch to redirect GH Pages to

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

#153 - Addressing formatting and reverting to wide format

Pull Request - State: closed - Opened by ns-rse almost 2 years ago - 23 comments

#152 - Retain multiple matches when difference is < 1ppm

Issue - State: closed - Opened by ns-rse almost 2 years ago - 6 comments
Labels: JOSS

#151 - v0.0.2 and Notebook running in JupyterLite

Issue - State: closed - Opened by ns-rse almost 2 years ago - 5 comments
Labels: Priority Task

#150 - Bring demo_ftrs.py in line with demo.py

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

#149 - Improve docs

Pull Request - State: closed - Opened by bobturneruk almost 2 years ago - 5 comments

#148 - Moving config so binder picks it up

Pull Request - State: closed - Opened by ns-rse almost 2 years ago - 5 comments

#147 - Add parameters.yaml to package_data

Pull Request - State: closed - Opened by ns-rse almost 2 years ago - 6 comments

#146 - Fixing notebooks and add Jupyterlite Notebook

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

#145 - Issue related #81 (Just closed!); new formatting incompatible with consolidation

Issue - State: closed - Opened by smesnage almost 2 years ago - 7 comments
Labels: Priority Task

#144 - Improve column names in output files

Issue - State: closed - Opened by ns-rse almost 2 years ago - 4 comments
Labels: improvement

#143 - Support multiple versions of documentation on GitHub Pages

Issue - State: closed - Opened by ns-rse almost 2 years ago - 3 comments
Labels: documentation, CI/CD

#142 - myBinder Crashes

Issue - State: closed - Opened by bobturneruk almost 2 years ago - 9 comments
Labels: Priority Task

#141 - Calculates diff in PPM between theoretical and observed

Pull Request - State: closed - Opened by ns-rse almost 2 years ago - 4 comments
Labels: needs long format

#140 - Removing dependency on tag to test sphinx build

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

#139 - Docs & readme

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

#138 - Add uploaded filename display in Jupyter Notebook

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

#137 - Jupyter notebook display

Issue - State: closed - Opened by smesnage about 2 years ago - 3 comments

#136 - Running interactive notebook locally

Issue - State: closed - Opened by bobturneruk about 2 years ago - 4 comments
Labels: documentation

#135 - Fix theoretical mass upload problem

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

#134 - Fix mybinder error

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

#133 - Error message in mybinder

Issue - State: closed - Opened by bobturneruk about 2 years ago - 4 comments

#132 - 131 | Correcting PyPI and GH Pages workflows to work on tagged commit…

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

#131 - Correct GitHub Workflows for publishing to PyPI

Issue - State: closed - Opened by ns-rse about 2 years ago
Labels: CI/CD

#130 - Add content needed for JOSS submission

Pull Request - State: closed - Opened by bobturneruk over 2 years ago - 9 comments

#129 - Enable PGFinder to queue searches (multiple FTRS files with one given database)

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

#128 - Versioneer produces version on building

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

#127 - 126 | Switching to pytest-regtest for regression tests

Pull Request - State: closed - Opened by ns-rse over 2 years ago - 3 comments

#126 - Switch to pytest-regtest for regression tests

Issue - State: closed - Opened by ns-rse over 2 years ago
Labels: CI/CD, tests

#125 - Remove unused columns

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

#124 - 120 | sphinx-markdown-tables-0.0.16 released, reverting

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

#123 - 120 | Order matters, install patched sphinx-markdown-tables 1st

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

#122 - Tidying up tests

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

#121 - 120 | Patched version of sphinx-markdown-tables

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

#120 - Documentation building broken

Issue - State: closed - Opened by ns-rse over 2 years ago

#119 - 118 | Including wheel for bdist_wheel building during PyPI release

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

#118 - Fix Workflow for releasing to PyPI

Issue - State: closed - Opened by ns-rse over 2 years ago
Labels: CI/CD

#117 - 116 | Adding email address; including numpydoc for documentation

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

#116 - Add email address to setup.cfg metadata

Issue - State: closed - Opened by ns-rse over 2 years ago

#115 - Tidy up test data

Issue - State: closed - Opened by ns-rse over 2 years ago

#114 - Consistent nomenclature

Issue - State: closed - Opened by ns-rse over 2 years ago - 30 comments

#113 - Iterate over enabled_mod_list.

Issue - State: closed - Opened by ns-rse over 2 years ago - 11 comments
Labels: improvement, refactor

#112 - Delete columns in the matching output (thought it had been done with #65 but it has not!)

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

#111 - Saving matches in long format

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

#110 - Initial long data matching implementation

Pull Request - State: closed - Opened by Ankur-AVP-Patel over 2 years ago - 18 comments

#109 - Submit PGFinder work to JOSS

Issue - State: closed - Opened by smesnage over 2 years ago - 6 comments
Labels: JOSS

#108 - Bulking out documentation, hopefully fixing missing docstrings

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

#107 - Automate release of tagged versions to PyPi and ORDA

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

#106 - Replace database in PGFinder with correct one generated by Masscalc

Issue - State: closed - Opened by smesnage over 2 years ago - 23 comments

#105 - Round out documentation : Introduction

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

#104 - Refactor code to work in "long format"

Issue - State: closed - Opened by ns-rse over 2 years ago - 4 comments
Labels: enhancement

GitHub / Mesnage-Org/pgfinder issues and pull requests