Releases · MannLabs/alphabase · GitHub

18 Sep 07:19

alphabase-v1.4.0 Latest

What's Changed

Making sure modifications.tsv is up to date by @boopthesnoot in #207
Open hdf files in read mode if read-only is set by @mschwoer in #202
dynamic generation of SMILES for PTMs by @boopthesnoot in #199
#215 add FG.ApexIonMobility for SPN report reader by @jalew188 in #216
Development by @jalew188 in #218

New Contributors

@boopthesnoot made their first contribution in #207

Full Changelog: 1.3.0...v1.4.0

Contributors

jalew188, boopthesnoot, and mschwoer

Assets 2

05 Aug 08:27

What's Changed

Breaking Changes

Fix double modications by @mschwoer in #188
First compatible alphapeptdeep version: > 1.2.1
load modseq by default by @GeorgWa in #196

New Features

#198 a new param save_mod_seq_in_other_df=False in SpecLibBase.save_hdf by @jalew188 in #201
new sage reader by @GeorgWa in #206
new sage reader by @GeorgWa in #206

Bug fixes

#169 FIX modification sites in sage reader by @jalew188 in #193
windowsfix for np.int64 by @machth in #189

Other Changes

FEAT test data downloader by @GeorgWa in #197
auto-fix more linting issues by @mschwoer in #174
More linting ii by @mschwoer in #175
update unimod to tsv by @GeorgWa in #203
#208 comment protein-level decoy out, as no packages use it yet. by @jalew188 in #209

New Contributors

@machth made their first contribution in #189

Full Changelog: v1.2.5...1.3.0

Contributors

jalew188, GeorgWa, and 2 other contributors

Assets 2

14 Jun 20:54

What's Changed

add functionality to specify temp directory location when creating memory mapped temp arrays by @sophiamaedler in #162
Mitigate wrong encoding under windows by @GeorgWa in #182
Development 1.2.5 by @jalew188 in #183

Full Changelog: v1.2.4...v1.2.5

Contributors

jalew188, GeorgWa, and sophiamaedler

Assets 2

29 May 14:39

What's Changed

FIX MannLabs/alphapeptdeep#119; FIX adding fix mods by @jalew188 in #127
Bump version: 1.1.2 → 1.2.0 by @jalew188 in #128
Development by @jalew188 in #130
feat: optimized specLib flattening by @mo-sameh in #133
FIX bugfix in fixed mods by @GeorgWa in #134
Development by @jalew188 in #135
FEAT sage reader by @GeorgWa in #137
SpecLlibFlat to specLibBase conversion by @mo-sameh in #138
feat: remove unused frag_dfs from lib when appending by @mo-sameh in #140
FIX Sage reader bug by @GeorgWa in #139
updated fragment naming convention by @GeorgWa in #141
rename diann spec_idx to diann_spec_idx by @jalew188 in #142
Development by @jalew188 in #144
Add option to specify own config file by @ammarcsj in #136
FIX match only dense dataframes by @GeorgWa in #145
Development by @jalew188 in #148
FIX flat lib remove unsed by @jalew188 in #149
reconnect to existing HDF5 files using tempmmap by @sophiamaedler in #151
introduce explicit function for creating HDF5 for mapping to using mmap arrays. by @sophiamaedler in #152
#153: apply ruff default formatting by @mschwoer in #154
153 add pre commit hook by @mschwoer in #155
156 change which tests are run in ci pipeline by @mschwoer in #157
158 ruff linting (#158) by @mschwoer in #159
158 more pre commit hooks by @mschwoer in #160
FIX run tests when PR and push by @jalew188 in #161
remove all nbdev-related files by @jalew188 in #164
#165 remove scoring module for clean code by @jalew188 in #166
Rm statistics module by @jalew188 in #168
revert back to run reduced set of tests on branches by @mschwoer in #170
Remove noqa by @jalew188 in #171
FIX noqa by using register_reader(), address many side effects by @jalew188 in #172
Remove warning log on module load by @mschwoer in #163
remove settings.ini from .bumpversion by @GeorgWa in #178
Release 1.2.4 by @GeorgWa in #177

New Contributors

@mo-sameh made their first contribution in #133
@mschwoer made their first contribution in #154

Full Changelog: v.1.1.2...v1.2.4

Contributors

jalew188, GeorgWa, and 4 other contributors

Assets 2

25 Dec 21:26

What's Changed

FIX #120 tracing mono in calc_precursor_isotope_intensity() by @jalew188 in #121
Use multiprocessing for decoy generation by @GeorgWa in #123
Add msfragger quantconfig by @ammarcsj in #124
CHORE updated class diagram by @GeorgWa in #125
Release 1.1.2 by @GeorgWa in #126

Full Changelog: v1.1.1...v.1.1.2

Contributors

jalew188, GeorgWa, and ammarcsj

Assets 2

11 Nov 13:38

What's Changed

resolve unexpected behaviour by @GeorgWa in #108
Quant table reader by @ammarcsj in #105
Quant table reader by @ammarcsj in #109
Development by @jalew188 in #110
annotate precursor df with FASTA by @GeorgWa in #112
include mac OS M1 runner by @GeorgWa in #114
Updated modification handling by @GeorgWa in #113
Handle mod translation failure gracefully by @GeorgWa in #115
Prepare release by @GeorgWa in #116
Release v1.1.1 by @GeorgWa in #117

New Contributors

@ammarcsj made their first contribution in #105

Full Changelog: v1.0.3...v1.1.1

Contributors

jalew188, GeorgWa, and ammarcsj

Assets 2

17 Jul 09:19

What's Changed

fragment nbs by @jalew188 in #1
Basic mass/fragment calculators in alphabase by @jalew188 in #2
NIST elements and re-define AAs by @jalew188 in #5
Io by @swillems in #4
base library class by @jalew188 in #3
quick fix for save_hdf codes by @jalew188 in #6
Rename variable by @jalew188 in #9
Doc and test by @jalew188 in #10
PSM reader by @jalew188 in #11
peptide hash by mmh3 package by @jalew188 in #13
Mq phos fix by @jalew188 in #16
Mmap io by @swillems in #14
More docs / isotope calculation / absolute import by @jalew188 in #18
Isotope & docs by @jalew188 in #19
Mmap arrays by @swillems in #22
Fix spec idx by @jalew188 in #23
Docs for main functions and classes in AlphaBase by @jalew188 in #20
CHORE by @jalew188 in #24
diann CScore by @jalew188 in #25
Development by @jalew188 in #26
Bump version: 0.0.5 → 0.0.6 by @jalew188 in #27
Development by @jalew188 in #28
Nb docs by @jalew188 in #29
Fasta by @jalew188 in #30
Nb docs by @jalew188 in #31
Nb docs by @jalew188 in #32
Development by @jalew188 in #33
Development by @jalew188 in #34
Development by @jalew188 in #35
Development by @jalew188 in #37
Development by @jalew188 in #38
Development by @jalew188 in #39
Development by @jalew188 in #40
LOESS Regression by @GeorgWa in #41
updated weight function by @GeorgWa in #44
Scoring by @jalew188 in #43
rescore by @jalew188 in #51
added fragment handling functionality by @GeorgWa in #47
GeorgW Diann decoy fix by @jalew188 in #54
Flat lib by @jalew188 in #53
Reannotate fragments by @GeorgWa in #57
Sphinx doc by @jalew188 in #56
add nbdev_test to github actions by @jalew188 in #58
Development by @jalew188 in #59
Aligning spectral library names by @GeorgWa in #60
Development by @jalew188 in #61
Development by @jalew188 in #63
Development by @jalew188 in #64
Development by @jalew188 in #65
frag_end_idx->frag_stop_idx by @jalew188 in #66
v0.4.0 by @jalew188 in #67
Uniformly distributed kernels for LOESS regression by @GeorgWa in #69
DiaNN-like supervised Percolator by @jalew188 in #68
v1.0.0 by @jalew188 in #70
Development by @jalew188 in #71
Python=3.9 workspace by @jalew188 in #72
readme by @jalew188 in #73
Development by @jalew188 in #75
rename methods; tutorials for dev by @jalew188 in #76
CHORE: prot decoy by @jalew188 in #77
replace mmh3 with xxhash by @jalew188 in #79
flexible frag representation to add frags by @jalew188 in #81
use flat_frag_start/stop_idx other than frag_start/stop_idx for flatten fragments by @jalew188 in #84
remove is_pd_dataframe attr for DataFrame in hdf by @jalew188 in #86
Development by @jalew188 in #88
Updated Library Handling by @GeorgWa in #91
add possibility to redefine path where tempmmap arrays are saved by @sophiamaedler in #99
New dtype by @jalew188 in #100
msfragger pepxml reader support for c-term modifications by @yangkl96 in #85
Calculate isotope intensity distribution using multiprocessing by @GeorgWa in #104
Validation of pandas dataframes close #96 by @GeorgWa in #101
count and filter by frag count, close #93 by @GeorgWa in #102
Increase layout width for better display of long names by @GeorgWa in #106
Development by @GeorgWa in #107

New Contributors

@jalew188 made their first contribution in #1
@swillems made their first contribution in #4
@GeorgWa made their first contribution in #41
@sophiamaedler made their first contribution in #99
@yangkl96 made their first contribution in #85

Full Changelog: https://github.com/MannLabs/alphabase/commits/v1.0.3

Contributors

jalew188, GeorgWa, and 3 other contributors

Assets 2