MannLabs/alphabase issues and pull requests

#242 - Refactor readers iii

Pull Request - State: open - Opened by mschwoer 8 days ago - 1 comment

#241 - Fix modifications bug

Pull Request - State: open - Opened by mschwoer 8 days ago - 1 comment

#240 - fix wrong modification mapping introduced in cdb1ddf

Pull Request - State: closed - Opened by mschwoer 8 days ago - 1 comment

#239 - Refactor readers ii

Pull Request - State: open - Opened by mschwoer 11 days ago - 1 comment

#238 - Linting vi

Pull Request - State: open - Opened by mschwoer 11 days ago

#237 - Linting v

Pull Request - State: closed - Opened by mschwoer 11 days ago - 1 comment

#236 - Linting iv

Pull Request - State: open - Opened by mschwoer 11 days ago - 2 comments

#235 - Linting iii

Pull Request - State: open - Opened by mschwoer 11 days ago - 1 comment

#234 - unsafe autofixes

Pull Request - State: open - Opened by mschwoer 11 days ago

#233 - Linting i

Pull Request - State: open - Opened by mschwoer 11 days ago

#232 - Refactor readers i

Pull Request - State: closed - Opened by mschwoer 13 days ago - 2 comments

#231 - Add psm reader tests

Pull Request - State: closed - Opened by mschwoer 14 days ago - 1 comment

#230 - release 1.4.1

Pull Request - State: closed - Opened by GeorgWa 14 days ago - 1 comment

#229 - remove maxquant MBR rows

Pull Request - State: closed - Opened by GeorgWa 21 days ago

#228 - updated psm-reader settings for maxquant

Pull Request - State: closed - Opened by GeorgWa 22 days ago - 1 comment

#227 - Remove installer building from release workflow

Pull Request - State: closed - Opened by mschwoer 26 days ago

#226 - add new release workflow and release template

Pull Request - State: closed - Opened by mschwoer 26 days ago

#225 - open hdf file "r" mode on read operations

Pull Request - State: closed - Opened by mschwoer 27 days ago - 1 comment

#224 - Fix missing variable

Pull Request - State: closed - Opened by sophiamaedler about 1 month ago

#223 - ENH: hydroxyisobutyryl@K smiles

Pull Request - State: closed - Opened by boopthesnoot about 2 months ago - 1 comment

#222 - FIX Sage spec idx

Pull Request - State: closed - Opened by GeorgWa about 2 months ago - 1 comment

#221 - Append SpecLibFlat libraries

Pull Request - State: closed - Opened by GeorgWa about 2 months ago - 1 comment

#220 - Peptides SMILES representation

Pull Request - State: closed - Opened by boopthesnoot 2 months ago - 1 comment

#219 - Updating smiles with changes from main

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

#218 - Development

Pull Request - State: closed - Opened by jalew188 3 months ago - 1 comment

#217 - memory mapped dask arrays

Issue - State: open - Opened by sophiamaedler 3 months ago

#216 - #215 add FG.ApexIonMobility for SPN report reader

Pull Request - State: closed - Opened by jalew188 4 months ago - 3 comments

#215 - Ion mobility column of spectronaut report not being read in by psm_reader

Issue - State: open - Opened by mlorenz49 4 months ago - 1 comment

#214 - GUI with servers crashed due to multiprocessing with torch and mono

Issue - State: open - Opened by jalew188 4 months ago

#213 - Development

Pull Request - State: closed - Opened by jalew188 4 months ago - 5 comments

#212 - Multithreading does not work for isotope calculation

Issue - State: open - Opened by machth 4 months ago - 2 comments

#211 - Loading library from hdf to translate to tsv fails with KeyError

Issue - State: closed - Opened by JuliaS92 4 months ago - 3 comments

#210 - add support for fixed string arrays

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

#209 - #208 comment protein-level decoy out, as no packages use it yet.

Pull Request - State: closed - Opened by jalew188 4 months ago - 1 comment

#208 - Protein-level decoy is not consistant with `DecoyGenerator` class

Issue - State: closed - Opened by jalew188 4 months ago

#207 - Making sure modifications.tsv is up to date

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

#206 - new sage reader

Pull Request - State: closed - Opened by GeorgWa 4 months ago - 2 comments

#205 - 187 tutorial basic settings

Pull Request - State: closed - Opened by jalew188 4 months ago - 1 comment

#203 - update unimod to tsv

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

#202 - Open hdf files in read mode if read-only is set

Pull Request - State: closed - Opened by mschwoer 4 months ago - 4 comments

#201 - #198 a new param save_mod_seq_in_other_df=False in SpecLibBase.save_hdf

Pull Request - State: closed - Opened by jalew188 4 months ago - 1 comment

#200 - smiles extra and decorator for rdkit functions

Pull Request - State: closed - Opened by GeorgWa 4 months ago - 2 comments

#199 - dynamic generation of SMILES for PTMs

Pull Request - State: closed - Opened by boopthesnoot 4 months ago - 8 comments

#198 - Save precursor_df into HDF5 as a single dataframe instead of two

Issue - State: closed - Opened by jalew188 4 months ago

#197 - FEAT test data downloader

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

#196 - load modseq by default

Pull Request - State: closed - Opened by GeorgWa 5 months ago - 1 comment

#195 - Merge Development

Pull Request - State: closed - Opened by jalew188 5 months ago - 1 comment

#194 - Merge Development

Pull Request - State: closed - Opened by jalew188 5 months ago - 1 comment

#193 - #169 FIX modification sites in sage reader

Pull Request - State: closed - Opened by jalew188 5 months ago - 1 comment

#192 - Patch the failing test. Note: this needs a more through solution!

Pull Request - State: closed - Opened by mschwoer 5 months ago - 2 comments

#190 - Tutorial: Basic functionalities in alphabase

Issue - State: open - Opened by jalew188 5 months ago

#189 - windowsfix for np.int64

Pull Request - State: closed - Opened by machth 5 months ago - 2 comments

#188 - Fix double modications

Pull Request - State: closed - Opened by mschwoer 5 months ago - 3 comments
Labels: breaking-change

#187 - Tutorial: basic settings in alphabase

Issue - State: open - Opened by jalew188 5 months ago - 1 comment

#186 - test

Pull Request - State: closed - Opened by mschwoer 5 months ago - 1 comment

#184 - Tutorial Outline Notebook

Issue - State: closed - Opened by jalew188 5 months ago

#183 - Development 1.2.5

Pull Request - State: closed - Opened by jalew188 6 months ago

#182 - Mitigate wrong encoding under windows

Pull Request - State: closed - Opened by GeorgWa 6 months ago - 2 comments

#181 - ERROR: 'charmap' codec can't decode byte 0x81 in position 4429...

Issue - State: closed - Opened by hcadre 6 months ago - 11 comments
Labels: bug

#180 - Race condition when reading speclib from two instances

Issue - State: open - Opened by mschwoer 6 months ago - 7 comments

#178 - remove settings.ini from .bumpversion

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

#177 - Release 1.2.4

Pull Request - State: closed - Opened by GeorgWa 6 months ago - 1 comment

#176 - Remove import sides effects and wildcard importing

Issue - State: closed - Opened by jalew188 6 months ago

#175 - More linting ii

Pull Request - State: closed - Opened by mschwoer 6 months ago - 1 comment

#174 - auto-fix more linting issues

Pull Request - State: closed - Opened by mschwoer 6 months ago - 4 comments

#173 - Use https://charlesreid1.github.io/python-patterns-the-registry.html for registers

Issue - State: open - Opened by jalew188 6 months ago

#172 - FIX noqa by using register_reader(), address many side effects

Pull Request - State: closed - Opened by jalew188 6 months ago - 1 comment

#171 - Remove noqa

Pull Request - State: closed - Opened by jalew188 6 months ago - 1 comment

#170 - revert back to run reduced set of tests on branches

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

#169 - Modification site bug for SageReader

Issue - State: closed - Opened by jalew188 6 months ago
Labels: bug

#168 - Rm statistics module

Pull Request - State: closed - Opened by jalew188 6 months ago - 2 comments

#167 - Move tests to pytest

Issue - State: closed - Opened by jalew188 6 months ago - 1 comment

#166 - #165 remove scoring module for clean code

Pull Request - State: closed - Opened by jalew188 6 months ago - 1 comment

#165 - Remove non-core parts from alphabase

Issue - State: closed - Opened by jalew188 6 months ago - 2 comments

#164 - remove all nbdev-related files

Pull Request - State: closed - Opened by jalew188 6 months ago - 1 comment

#163 - Remove warning log on module load

Pull Request - State: closed - Opened by mschwoer 6 months ago - 2 comments

#162 - add functionality to specify temp directory location when creating memory mapped temp arrays

Pull Request - State: closed - Opened by sophiamaedler 7 months ago - 6 comments

#161 - FIX run tests when PR and push

Pull Request - State: closed - Opened by jalew188 7 months ago

#160 - 158 more pre commit hooks

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

#159 - 158 ruff linting (#158)

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

#158 - Basic Linting

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

#157 - 156 change which tests are run in ci pipeline

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

#156 - Add more tests to CI pipeline

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

#155 - 153 add pre commit hook

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

#154 - #153: apply ruff default formatting

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

#153 - Code formatting

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

#152 - introduce explicit function for creating HDF5 for mapping to using mmap arrays.

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

#151 - reconnect to existing HDF5 files using tempmmap

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

#150 - DIA-NN .speclib reader

Issue - State: open - Opened by GeorgWa 8 months ago
Labels: enhancement

#149 - FIX flat lib remove unsed

Pull Request - State: closed - Opened by jalew188 8 months ago - 1 comment

#148 - Development

Pull Request - State: closed - Opened by jalew188 8 months ago - 1 comment

#146 - implement SpecLibFlat.remove_unused_fragments()

Issue - State: closed - Opened by GeorgWa 8 months ago - 5 comments
Labels: enhancement

#145 - FIX match only dense dataframes

Pull Request - State: closed - Opened by GeorgWa 8 months ago - 7 comments

#144 - Development

Pull Request - State: closed - Opened by jalew188 9 months ago - 1 comment

#143 - Pandas column is non-writeable on linux

Issue - State: closed - Opened by timheymann 9 months ago - 1 comment

#142 - rename diann spec_idx to diann_spec_idx

Pull Request - State: closed - Opened by jalew188 9 months ago - 4 comments

#141 - updated fragment naming convention

Pull Request - State: closed - Opened by GeorgWa 9 months ago

#140 - feat: remove unused frag_dfs from lib when appending

Pull Request - State: closed - Opened by mo-sameh 9 months ago

#139 - FIX Sage reader bug

Pull Request - State: closed - Opened by GeorgWa 9 months ago - 2 comments

#138 - SpecLlibFlat to specLibBase conversion

Pull Request - State: closed - Opened by mo-sameh 9 months ago - 2 comments

GitHub / MannLabs/alphabase issues and pull requests