github.com/OpenMS/OpenMS-1 commits | Ecosyste.ms: OpenCollective

Update CHANGELOG

b9744c6b2cae4517fc7c547fc198f75272f140ab authored almost 3 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #5633 from emilpaulitz/IsoDistrApprox

Isotopic distribution approximation

cceb3d3f27a8603dab7c73609f72905f944027b9 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

change include in pyOpenMS

b225dc3952112ed8376710fa5d251ebb40b8ffd9 authored almost 3 years ago by Vincent Musch <[email protected]>

[FIX] merge issue FeatureMap

1ee4138397609e3ac78bd500112039d0c5be3884 authored almost 3 years ago by oliveralka <[email protected]>

removed uint8_t to fix python binding problem

4477673dd95e8f699ea02aead1ee1631d7f29163 authored almost 3 years ago by emilpaulitz <[email protected]>

Merge branch 'IsoDistrApprox' of https://github.com/emilpaulitz/OpenMS into IsoDistrApprox

a564aff6cab537784c1b07eaf45f20a3146a1160 authored almost 3 years ago by emilpaulitz <[email protected]>

Update python bindings

be7cd82920c55910f04cca034b9ae2bed59c65ca authored almost 3 years ago by emilpaulitz <[email protected]>

fix double_t

f5c6e24240beb1b3aeb33b1b0a2dd00399be20cc authored almost 3 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #5622 from axelwalter/feature/pandas-dataframes

add pandas df conversion

84d15f108c0c15d7f192b11169c9205b9de4129e authored almost 3 years ago by Julianus Pfeuffer <[email protected]>

bug fix for windows

c855df9a829c6d5954c648b56ed384a7fdb0a223 authored almost 3 years ago by Vincent Musch <[email protected]>

skip unidentified in main iteration

8ecb4aaa84670aa805d2635eaf0e7bbd4433c2f1 authored almost 3 years ago by Julianus Pfeuffer <[email protected]>

Merge branch 'develop' into idfile-integration

96308276c15b8d4475ae1f326f0e82413dac07bc authored almost 3 years ago by Oliver Alka <[email protected]>

add TODO for filtering PeptideHits in main iteration

8377fc73edca549ff24e76cacb742da0cb0d189f authored almost 3 years ago by axelwalter <[email protected]>

fix missing values for peptide identification meta values

c5e7cfba64fdcf9a14a317de3d1c5df75f0dd980 authored almost 3 years ago by axelwalter <[email protected]>

delete old mrmscoring from the cmake file

3786b0d6ce9619bd007458cb2a0169d5bec4d081 authored almost 3 years ago by Vincent Musch <[email protected]>

Update CoarseIsotopePatternGenerator.cpp

6f50d8e59ebe60541f029ebe8c5b47dadb96896c authored almost 3 years ago by Timo Sachsenberg <[email protected]>

Update CoarseIsotopePatternGenerator.h

e0ff15e371bd945b8f2b0d82098300f8e11672ca authored almost 3 years ago by Timo Sachsenberg <[email protected]>

Per charge SNR use per charge cosine

2b6e1447a52f053987bafe0a960a2e0a1e4fe948 authored almost 3 years ago by kyowonjeong <[email protected]>

Updated description

a73d9a9332e88866d84037533dca1d2995338c63 authored almost 3 years ago by emilpaulitz <[email protected]>

Fixed faculty overflow issue

By including the running faculty into the double of result, early overflow is not a problem anym...

2c17611d0ec228e685ec2166ef2d069e5b14424d authored almost 3 years ago by emilpaulitz <[email protected]>

Updated types and description

made num_peaks unsigned, approximateIntensities now returns vector<double>, used the OpenMS type...

eab432b84d21df2b9d2e3984b1bcdb63021a1c42 authored almost 3 years ago by emilpaulitz <[email protected]>

Update to m/z calculation

Detailed description and added charge parameter

47182e417847683092ded1b07d03c7112290ff0d authored almost 3 years ago by emilpaulitz <[email protected]>

Fix tool scan on strong machines (#5640)

Should also go into 2.7.1

9a4225030e6a25631d42c83989ed14199773e732 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

MRMScoring nach OpenMS

2f17e30db1079c10ce4d4b5c01ed9997a23b3aa6 authored almost 3 years ago by Vincent Musch <[email protected]>

add test for PeptideIdentifications to df

72eb3f739e06676637d9982e83c833534ff50773 authored almost 3 years ago by axelwalter <[email protected]>

missing charge values to pandas.NA

6bab1a6eaa70c4c643f4eff767f66aea79414644 authored almost 3 years ago by axelwalter <[email protected]>

little fix

d3ee09708dc7e190c24e85672f53879d4511a772 authored almost 3 years ago by Vincent Musch <[email protected]>

delete whitespaces

8ec36273d089516af89c877e358addcb1684c001 authored almost 3 years ago by Vincent Musch <[email protected]>

Skip non existent wheels

55329c87dff14893ec0d278cdf7a2899ddbea9ff authored almost 3 years ago by Julianus Pfeuffer <[email protected]>

new computeRanks, only in MIcombinedMatrix

d25139f690f214900fbf0dbc580ba19607c5bdb4 authored almost 3 years ago by Vincent Musch <[email protected]>

Merge branch 'feature/pandas-dataframes' of https://github.com/axelwalter/OpenMS into feature/pandas-dataframes

21a6c04f5b04607b3c77bd7c3d7db34ad3fc32d1 authored almost 3 years ago by axelwalter <[email protected]>

Merge remote-tracking branch 'origin' into feature/pandas-dataframes

050ecb9792be013d563642f1c3bcaf4d3e6135be authored almost 3 years ago by axelwalter <[email protected]>

add MSExperiment().get_df() test

e5001e0ee1c961276975b7883aee90baee4e173b authored almost 3 years ago by axelwalter <[email protected]>

[DOC] update documentation

ec458fbc965e944e316860ee8083373f509e7771 authored almost 3 years ago by Julianus Pfeuffer <[email protected]>

fix python msvc requirements

d35e49f6da53d0a84fca4faa90b9bcd531987387 authored almost 3 years ago by Julianus Pfeuffer <[email protected]>

Merge branch 'feature/pandas-dataframes' of https://github.com/axelwalter/OpenMS into feature/pandas-dataframes

631d179dcc2a8c159c266ab18af61d1bc89533ff authored almost 3 years ago by axelwalter <[email protected]>

add featuremap test

e796a2eda3626ac3d59e8ddffbf3f0661159b408 authored almost 3 years ago by axelwalter <[email protected]>

Add cxml test

bc5a38aac5000c54e687431de3899660e15e26d0 authored almost 3 years ago by Julianus Pfeuffer <[email protected]>

add manual trigger to pyopenms actions

08874bf2f27ee825071c3b7675ad28888e3bb85d authored almost 3 years ago by Julianus Pfeuffer <[email protected]>

new branch

e88b2315a9866ecf873f2c4689033ce7f3461e15 authored almost 3 years ago by Vincent Musch <[email protected]>

test fix

f6113e1613b62720f49bc9dbcda730d60a9c36fb authored almost 3 years ago by Vincent Musch <[email protected]>

Remove UNDOCUMENTED version pin

7fd31044afd1eccb5740144d101cc90fe635497c authored almost 3 years ago by Julianus Pfeuffer <[email protected]>

delete some comments

20f4f50438387d37bf296f30ef60593620b6c9c5 authored almost 3 years ago by Vincent Musch <[email protected]>

Merge branch 'develop' of https://github.com/OpenMS/OpenMS into swath

e0dcb66198367b73bc5d1f931136dafbc354e313 authored almost 3 years ago by Vincent Musch <[email protected]>

[pyopenms] Fix pyopenms int size (on windows) (#5634)

* [pyopenms] proper int type sizes on all platforms

* nop

* Fix import

* autowrap confu...

3b4621603f750919392ffe159f2f8b37277f148e authored almost 3 years ago by Timo Sachsenberg <[email protected]>

Added Tests for approximateIntensities

a38ceb161eddf5910af4a9042f1aa588ea5df0a0 authored almost 3 years ago by emilpaulitz <[email protected]>

Add approximateIntensities

including python bindings and integration into Deisotoper

6ff9758fedb0560062b4c0e28c486f216b868977 authored almost 3 years ago by emilpaulitz <[email protected]>

made num_peaks optional

8f9ed15d9cf53140cd334a1162eb745cf36bc138 authored almost 3 years ago by emilpaulitz <[email protected]>

Added Tests and Python bindings

45aba870c666fdcb310c3e60ec6c46827a0af3e6 authored almost 3 years ago by emilpaulitz <[email protected]>

Added approximation function

8910f94e943c1daf0462fc3b7e99a7aec0b3d837 authored almost 3 years ago by emilpaulitz <[email protected]>

Finished Approximation for use

return 0 instead of inf

6c8e67ad30c19534c284edc63e920433c615021f authored almost 3 years ago by emilpaulitz <[email protected]>

Switch Approximation Mode for DeisotopingWithAveragineModel

1858b0ae7bb280c9f601136cb34318b4f4941820 authored almost 3 years ago by emilpaulitz <[email protected]>

Merge branch 'OpenMS:develop' into develop

bd19a8cfcfa3bc96f58a1d1e605e094e522c5a6e authored almost 3 years ago by emilpaulitz <[email protected]>

fix multiple definition of GumbelDistributionFunctor (#5632)

5c51ad02b833986049f250c1cb46fe02b77b79cc authored almost 3 years ago by Timo Sachsenberg <[email protected]>

Merge branch 'OpenMS:develop' into develop

ebe4ea7a280f6bfa53f2949c449c2cba1afc64ec authored almost 3 years ago by emilpaulitz <[email protected]>

[FIX] MetaboliteSpectralMatcher (#5630)

* [FIX] MetaboliteSpectralMatcher

* Read MS2 only and warn correctly

ca92ae7e33486203c7eeeaef56998805dd2d62b8 authored almost 3 years ago by Julianus Pfeuffer <[email protected]>

Also import PeakMap in python_extras

b14a473466aaf95ed1d55816fb8df6baf63c7ae9 authored almost 3 years ago by Julianus Pfeuffer <[email protected]>

Import peakmap to override it

5733348a4dfced80038c8dcacaeeb63d83a34ca5 authored almost 3 years ago by Julianus Pfeuffer <[email protected]>

[FEATURE] New Deisotoping Algorithm (#5306)

* [FEATURE] New Deisotoping Algorithm

[FEATURE] New Deisotoping Algorithm

This implementat...

795dd7d45b385f9c14425f797f6f9fa0af2c6152 authored almost 3 years ago by emilpaulitz <[email protected]>

Also set the typedef PeakMap to the new subclass

70e3ccfd32abcbcdb11710e6a711e69c521c8c14 authored almost 3 years ago by Julianus Pfeuffer <[email protected]>

Add ability to use copy constructors

e396b71bcc9fa48953d9c5d7e7b2b62fd7b0284f authored almost 3 years ago by Julianus Pfeuffer <[email protected]>

Merge branch 'OpenMS:develop' into develop

fe598de514ee1ae8b8ce46c21ccb968065d4980f authored almost 3 years ago by emilpaulitz <[email protected]>

unpacking directly in return/yield only allowed from py3.8

https://stackoverflow.com/questions/47272460/python-tuple-unpacking-in-return-statement

7fae880bd91d900d19b5a6f821cdf95baf8bc526 authored almost 3 years ago by Julianus Pfeuffer <[email protected]>

[FIX] use static inline for namespace (#5627)

a990efe1489d4055d639469f38214d45f717e5e4 authored almost 3 years ago by Hannes Roest <[email protected]>

return value

e73023bb9a6c78a981b923a6199eafa327521ba8 authored almost 3 years ago by Hannes Roest <[email protected]>

Merge branch 'develop' into feature/separate_interfaces

c7cf75e18f0a1bd14179bf79b0a2a02881923c7a authored almost 3 years ago by Hannes Roest <[email protected]>

Merge pull request #5620 from OpenMS/jpfeuffer-patch-5

Fix msfragger file origin

20b8d47ebdf454a34302026b92b84bae94d0d225 authored almost 3 years ago by Julianus Pfeuffer <[email protected]>

add pandas to requirements

c4af1f08a2ed057e0b4714ac5adc288e770ad0f2 authored almost 3 years ago by axelwalter <[email protected]>

fix for real

6c231a9f3f5f47c81b504c69084c5b7716c1e508 authored almost 3 years ago by Julianus Pfeuffer <[email protected]>

rename dataframes module to lower case

feb6ba8620454f109dfd14c41b85830d7efcb9c8 authored almost 3 years ago by axelwalter <[email protected]>

[ADD] Spectrum Plotting and Spectrum Mirror Plotting Functions (#5615)

* Added spectra plotting functions

* Updated spectra plotting functions

* Updated spectra ...

fd45e0d4bc47a9630a9f5d75311f24ef736f2fdb authored almost 3 years ago by Matteo Pilz <[email protected]>

use get2DPeakDataLong() for MSExperiment DF

6be4d69756036234ab283392a7226df495cc82b2 authored almost 3 years ago by axelwalter <[email protected]>

Update PercolatorInfile.cpp

ea0ac22ae409ff68d8f0dda9ee1ad5af4e0350cf authored almost 3 years ago by Timo Sachsenberg <[email protected]>

import modules from .

359fab93b3472046a6a874424473e8c439668c2a authored almost 3 years ago by axelwalter <[email protected]>

remove TODO comments

36c6dd5798c1c3b193683b8694db65b12cf957ad authored almost 3 years ago by axelwalter <[email protected]>

fix codefactor error: else after return

91bd3c1ef9bb7295684384b17d8cb3b96e6dfaed authored almost 3 years ago by axelwalter <[email protected]>

Merge pull request #5603 from hroest/feature/header_cleanup

Reduce OpenMS exposure to third-party headers

25b72baec9543f83de74dfe2a21c82c6f91209d7 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

Update MSFraggerAdapter.cpp

c398649411cc7b0c8d55aebea9dee3a92cce1af1 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

fix

45a0bd367d4ad88dd90666f56fd2fc7be4099007 authored almost 3 years ago by Hannes Roest <[email protected]>

logtype

454d5f9a7b5fe87f3ba79d22b2f78e941b6c4323 authored almost 3 years ago by Hannes Roest <[email protected]>

[FEATURE] split ConsensusXML and ConsensusXMLHandler

8e3aef384b2ab53f79dd05681a455e96b15c3298 authored almost 3 years ago by Hannes Roest <[email protected]>

[FIX] fix includes

d96079e32956baa6fc6bbf1bcc597b73bd652670 authored almost 3 years ago by Hannes Roest <[email protected]>

[MOVE] code move to cpp

80d4478b652e239718c6038cec331b341a32b6a2 authored almost 3 years ago by Hannes Roest <[email protected]>

[FEATURE] separate FeatureXML and FeatureXMLHandler

fead073ae1f3096e471982ebfaf1fe1d7878d1bf authored almost 3 years ago by Hannes Roest <[email protected]>

[FEATURE] fix Decharger linking

ebd3482b97b6e8595be63490cf7e80adf6dcb0f7 authored almost 3 years ago by Hannes Roest <[email protected]>

[FIX] use FileHandler interface

0bfb105e9fabfa1c116cce65a9c4f046b7c66b0e authored almost 3 years ago by Hannes Roest <[email protected]>

[FEATURE] FileHandler

36b535ee8c779266e2a1cf910e26e370bc40ea5e authored almost 3 years ago by Hannes Roest <[email protected]>

header cleanup

0b18191334c0f1ab71e796ff4ba9fa9252c68113 authored almost 3 years ago by Hannes Roest <[email protected]>

[FEATURE] replace with FileHandler

edbd4894ee5ceda126846c46736ee2f9a1f00e74 authored almost 3 years ago by Hannes Roest <[email protected]>

[FEATURE] extend FileHandler

e7035db9cb24c014908b2500cc4c85847524aebc authored almost 3 years ago by Hannes Roest <[email protected]>

Update MSFraggerAdapter.cpp

dcca49fe6006723e5f30210f615480a64d7a6eed authored almost 3 years ago by Timo Sachsenberg <[email protected]>

add pandas df conversion

e1b245756154dd87a448760b19a30f56aa15fbfc authored almost 3 years ago by axelwalter <[email protected]>

neue Matritzen, Scoring wird direkt bei der initialisierung berechnet

f3c2b09915cf73f2fb05bd94d6f605cfacef0a03 authored almost 3 years ago by Vincent Musch <[email protected]>

Update MSFraggerAdapter.cpp

e6cea206f4e54558e00210907c62865fa6c2fac8 authored almost 3 years ago by Julianus Pfeuffer <[email protected]>

Update MSFraggerAdapter.cpp

2a6ab367f583bfb71f9c4ec634fea09c901c4cdf authored almost 3 years ago by Julianus Pfeuffer <[email protected]>

Update MSFraggerAdapter.cpp

79f9ccaba070f8e62a57369a8769f6382ceb31ce authored almost 3 years ago by Julianus Pfeuffer <[email protected]>

Update MSFraggerAdapter.cpp

ba5afa68f14c6fc872b628f35f8a10f1ea0d28f5 authored almost 3 years ago by Julianus Pfeuffer <[email protected]>

Better error Message File origin ConsensusID

01a7a8c054d4e2748540ba4d3f9fac9e3c98ae1e authored almost 3 years ago by Julianus Pfeuffer <[email protected]>

Fix msfragger file origin

37a4a49b152e27480398c885b13fa4a398aefc7f authored almost 3 years ago by Julianus Pfeuffer <[email protected]>

fix

8a070a9e8ad498315267fa1b9c5398762b82620f authored almost 3 years ago by Hannes Roest <[email protected]>