Releases: MannLabs/alphabase
Releases · MannLabs/alphabase
v1.4.2
Contributors
mschwoer
Assets 2
v1.4.1
What's Changed
Other Changes / unlabeled
- Updating smiles with changes from main by @boopthesnoot in #219
- Peptides SMILES representation by @boopthesnoot in #220
- ENH: hydroxyisobutyryl@K smiles by @boopthesnoot in #223
- Fix missing variable by @sophiamaedler in #224
- add new release workflow and release template by @mschwoer in #226
- Append SpecLibFlat libraries by @GeorgWa in #221
- FIX Sage spec idx by @GeorgWa in #222
- open hdf file "r" mode on read operations by @mschwoer in #225
- Remove installer building from release workflow by @mschwoer in #227
- add support for fixed string arrays by @sophiamaedler in #210
- updated psm-reader settings for maxquant by @GeorgWa in #228
- remove maxquant MBR rows by @GeorgWa in #229
- release 1.4.1 by @GeorgWa in #230
Full Changelog: v1.4.0...v1.4.1
Contributors
GeorgWa, sophiamaedler, and 2 other contributors
Assets 2
alphabase-v1.4.0
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
1.3.0
What's Changed
Breaking Changes
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
Full Changelog: v1.2.5...1.3.0
Contributors
jalew188, GeorgWa, and 2 other contributors
Assets 2
v1.2.5
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
v1.2.4
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
Full Changelog: v.1.1.2...v1.2.4
Contributors
jalew188, GeorgWa, and 4 other contributors
Assets 2
v.1.1.2
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
v1.1.1
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
Full Changelog: v1.0.3...v1.1.1
Contributors
jalew188, GeorgWa, and ammarcsj
Assets 2
v1.0.3
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