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

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]>

Add approximateIntensities

including python bindings and integration into Deisotoper

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

Added Tests for approximateIntensities

a38ceb161eddf5910af4a9042f1aa588ea5df0a0 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]>

Switch Approximation Mode for DeisotopingWithAveragineModel

1858b0ae7bb280c9f601136cb34318b4f4941820 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]>

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]>

[FEATURE] split ConsensusXML and ConsensusXMLHandler

8e3aef384b2ab53f79dd05681a455e96b15c3298 authored almost 3 years ago by Hannes Roest <[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] fix Decharger linking

ebd3482b97b6e8595be63490cf7e80adf6dcb0f7 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]>

[FIX] fix includes

d96079e32956baa6fc6bbf1bcc597b73bd652670 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]>

[FIX] fix binned spectrum interface

9a688c1989f77b7ec652412e365989ef820df15c authored almost 3 years ago by Hannes Roest <[email protected]>

[DOC] improved IM set/get documentation (#5614)

* extended docs

* augment

e75e5e43ef903f10a263501769fe072f184b89cb authored almost 3 years ago by Chris Bielow <[email protected]>

doppelungen in initialize entfernt

a13267384c4b785b803f73be1dc3982fb52e80c0 authored almost 3 years ago by Vincent Musch <[email protected]>

augment

c620b7b3d21377f923eb3d5dac51fdaabee03d72 authored almost 3 years ago by bielow <[email protected]>

extended docs

69bbfbc6243bec07afeb9acd5b03a4133fb65bf7 authored almost 3 years ago by bielow <[email protected]>

fix xcorr_precursor_combined & contrast

73e9cceec5c186d2f88fa0d1a9889f2a44487f1e authored almost 3 years ago by Vincent Musch <[email protected]>

[REVERT] revert changes in MRMAssay

- switching from boost::unordered_map to std::unordered_map breaks the
regression tests due di...

c9bb40cc85c0529eae606961758fa80340d1ed53 authored almost 3 years ago by Hannes Roest <[email protected]>

Merge branch 'develop' into feature/header_cleanup

5fdc6a314babad8842dd00e2aeebb572b7676570 authored almost 3 years ago by Hannes Roest <[email protected]>

const und ref

9f9c7719dda5a92c48af39efd5b92feb02f34073 authored almost 3 years ago by Vincent Musch <[email protected]>

Merge pull request #118 from OpenMS/develop

update to latest

3dfce80cc1143ad362b40fbbc8254f47cdf98bde authored almost 3 years ago by Chris Bielow <[email protected]>

[FIX] remove intermediate storage of transitions in large vector

- lower memory footprint of PQP storage

52d204008174111ef362ff7f900c0b2df9e3932f authored almost 3 years ago by Hannes Roest <[email protected]>

remove problematic progress loggers

4f1d94ca2ab4cb4edb687a5225921a3071d2ea5f authored almost 3 years ago by Hannes Roest <[email protected]>

[FEATURE] DecoyGenerator speedup

c67054e30e98503941a3ceffba8d3aaed775aaab authored almost 3 years ago by Hannes Roest <[email protected]>

[FIX] use set instead of map

bcb62b9aac2a985609b72e2dee3a0f5cc9c81c0a authored almost 3 years ago by Hannes Roest <[email protected]>

[FEATURE] speed improvement in OpenSwathAssayGenerator

5c990cab6f170c9c8ec1ac0989cc73f5b0985a2e authored almost 3 years ago by Hannes Roest <[email protected]>

[FEATURE] add rvalue functions for TargetedExperiment

947d22545b5b7f84b68b3f75b1ccd7277c6d7748 authored almost 3 years ago by Hannes Roest <[email protected]>

[FEATURE] filter in-place

627cb3726211b2b04a40f0da5391b94d8d450980 authored almost 3 years ago by Hannes Roest <[email protected]>

[FEATURE] lower memory footprint

- lower memory footprint of PQP file writing by storing transitions
repeatedly while iterating...

ad698b0b3ebcaa1c9c503ae493032baef321c5ea authored almost 3 years ago by Hannes Roest <[email protected]>

[FEATURE] use rvalue addition

b79b56033cd42fe47db193ae96dc9d896c39153a authored almost 3 years ago by Hannes Roest <[email protected]>

neue Matrixstruktur in MRM Scoring

96c4f65c555af8e4c6a66298ba8c947ea5251c08 authored almost 3 years ago by Vincent Musch <[email protected]>

prep for quick MS1 peak accession for pyOpenMS / numpy (#5606)

* prep for quick MS1 peak accession for pyOpenMS / numpy

* Update MSExperiment.h

* Update ...

62dfd22e9dd91be62422b1752a345ec3e5b9e188 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

Merge branch 'develop' into feature/header_cleanup

a2a61378a369d79561589afe2475e986ee2303a3 authored almost 3 years ago by Hannes Roest <[email protected]>

Merge pull request #5610 from hroest/feature/header_cleanup_inc

Feature/header cleanup inc

c0466511c156b8faf0f8196a85d69df9906732d2 authored almost 3 years ago by Chris Bielow <[email protected]>

[FIX] Windows fix

28f94dbc1b83e8d4b61e48a05837ad2f2e6d1d63 authored almost 3 years ago by Hannes Roest <[email protected]>

[FIX] windows fix?

9d01d505b41ef24af21f25e468074e81863b7b21 authored about 3 years ago by Hannes Roest <[email protected]>

fixes

e9c306ba5d4b3ba26d9ff64b9758eb2174351aed authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] move back to boost (Clang)

db87c9df531375fd3c91b1c34d5676eb3ab8cba7 authored about 3 years ago by Hannes Roest <[email protected]>

Merge branch 'develop' into feature/header_cleanup_inc

51a9b9a9575108a2363e6742d65e87a1baec433b authored about 3 years ago by Hannes Roest <[email protected]>

Update Deisotoper.pxd

a761c325a5bcd4b80300ca4dcff1a425c24f6f83 authored about 3 years ago by Timo Sachsenberg <[email protected]>

[FIX] move MaxLikeliFitter1D to cpp

9b89cde2a6ab8adb00df26882573b32d4d7b87a2 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] move XMLHandler to cpp

- remove STL dependencies

2a2596dbec764e253d6d15bbf7e361a874c19584 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] move FastLowessSmoothing function to cpp

- remove STL dependencies

f0be6f23023c259a7bc337e2f04764626e965336 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] move GaussFilter to cpp (I/O)

- remove LogStream dependencies

eeb120d5f21f6890db7eb319e0088f1e020c3547 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] move TargetedSpectraExtractor to cpp (I/O)

57f594047f21fb0d21dda2c29da700f2a7b6d531 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] move ConsensusMap to cpp (I/O)

115b197d0acfc4faa642f2a0a64ade2cc8b095c4 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] move LevMarqFitter1D to cpp

- remove Eigen dependency from header file

7bf70ed22b5a80b9019c4cf80730922fd9977143 authored about 3 years ago by Hannes Roest <[email protected]>