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

fixes pyopenms visibility and external

b31292c29d91cd8b0912c3ce41602e5bfa8d0277 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

forward declare all svm types (#5762)

* forward declare all svm types

* add missing include

* forward declare svm structs as str...

16a9b45c6405296f598f93d5a433cd49bb576463 authored over 2 years ago by Timo Sachsenberg <[email protected]>

typo fixes (#5763)

* fix typo

* fix #5755

* revert wrong fix

07f980d456ee5fbb70e6afaa41805a0f4428da60 authored over 2 years ago by Chris Bielow <[email protected]>

Fix dir vars

fcac5642588139c55d4b5d2d89452a54638c470e authored over 2 years ago by Julianus Pfeuffer <[email protected]>

fix pyopenms race condition in make. try to fix external test

2e03a2e3785a04386ce981631c67ca1dccc268db authored over 2 years ago by Julianus Pfeuffer <[email protected]>

fix more tests

ffde1c5043da3c71b2d5a4037ada2d05bae9f93b authored over 2 years ago by Julianus Pfeuffer <[email protected]>

fix cmake includes

9050c0ac514c462a7f9e1f5c8497134c3ff1f77d authored over 2 years ago by Julianus Pfeuffer <[email protected]>

I give up. just copy the find module from CMake.

5a02c445b5fec989c3b9039c620ffb82454e3fb6 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Fix tests and potentially HDF5 find

3e3b6466e5f67f339927c208cf4f77ffcb955748 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

upper case boost

5186ec670bc8dbe09dcfb0fe869dfdba2ab41166 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

wrong include from copying

9505bfa40ffd1f1af47fbee663c605657b8d859d authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Readd Xerces find until upstream CMake is merged. Add missing extra links to execs.

a717a0426892f69e3dc8a23e7d16cf404d9f9287 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Update install-linux.doxygen (#5759)

47db3e0ca314219f7693539874c69ca657b32f84 authored over 2 years ago by Timo Sachsenberg <[email protected]>

more fixes

cca3329dcc9b31b719dde59216984c7876a1c882 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

reduce warnings

a5597f19f667e18787a56409949da98cea0a7926 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

more fixes

df88669c5812e57077a1e793872516e82c58b69a authored over 2 years ago by Julianus Pfeuffer <[email protected]>

forgot to remove

8825f6ca413e6d7db7efa893fd24cde3368e86e4 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

forgot to use new var

d2af8b705ad74dd2c612945d9f94c86980133f97 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

more find fixes..

fe60db012457049b461c984ff2e01f90160e6cc7 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Fix superweird FindQt required behaviour. Reduce hdf linking to cpp parts only (also more backwards compat.)

97bc46b3fb3f84e5e07d8acb576a8f686440f559 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Fix PYTHON_EXECUTABLE input

fc685905dc353942bb4d4d530b6fd3c5d39498ee authored over 2 years ago by Julianus Pfeuffer <[email protected]>

forgot to revert path

268a313faab1367bc316524f17ae390894cadaa7 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

fix FindWM5 interface

f3f14e3ee9919bcb318ccd0eb0c0f18821dfa9f7 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Sqlite find override fix?

d56838c4fb98d35b53c636ee02403ea74b2562ed authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Merge branch 'fix/pymacdeps' of https://github.com/jpfeuffer/OpenMS into fix/pymacdeps

b45ccf6dcac6dbeb550a8695a804e1ff245cd15d authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Fixes in finding libs

075d0d31478b3aa7f500e80caed43026b05a2d6e authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Merge branch 'develop' into fix/pymacdeps

caff37fa703f0423a26f54b68fa25727e5a4a789 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Also install and use our find modules

a01a7947fa1e8d721c0ff8d3972ccdc985e83c0c authored over 2 years ago by Julianus Pfeuffer <[email protected]>

finished exporting

e71f608b32c3e325b140f1bc88d049c1a3cbc2e3 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

More major refactor for exporting our libraries

0c2d6c8377ee45008dcbee79f3fbf574ab99faa4 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Finished pyopenms build with CMake

eb3e0abe913131adb1c4691b879b9a78db5e7721 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Changes to py CMakelists after cherrypick

2a732bad6d57eaf5f9114114bf70c63e2f74f339 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

merge changes I had on another branch to build pyopenms from cmake

1305a5ee5cf67f1c0689d4a536d0bf1718914022 authored over 2 years ago by Builder <[email protected]>

Major restructure of CMake due to use of imported targets

70c26f3e2324ec92bd4a0cda95fae47c9e046fd8 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

[FEATURE] Add imported targets to all find modules and use CMake's where possible. Also fix fix_dep script

56b6a52bac95d7bb4dec872d08f3bf17a282888c authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Update pyopenms-wheels.yml

7a911a4ca2c3b53a77116eb74ce3f42670d7fd5f authored almost 3 years ago by Julianus Pfeuffer <[email protected]>

Update pyopenms-wheels.yml

6d0ab3e36b44cda9d258c1ea37cb9f4fa579f4b0 authored almost 3 years ago by Julianus Pfeuffer <[email protected]>

[PERFORMANCE] add index for peakannotations (#5753)

* [PERFORMANCE] add index for peakannotations

* add primary key to metainfo

07b841aabf7ef92ea1ee6eda6c90b7de453ccdb4 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

Fixup both Qt*.framework/Versions/$V and Current

seems like people change at will which one gets symlinked

1d0ffd9ce224000eb60a7c1c20c8a59a7fe92f7c authored almost 3 years ago by Julianus Pfeuffer <[email protected]>

Update CMakeLists.txt

9c8ac62523dc57a6dd011c1fd73bd9dd2f86f066 authored almost 3 years ago by Julianus Pfeuffer <[email protected]>

Minor fixes + computeRank test fix

6f275ac6a69e74ba7e9f39d7b26afc608b02434f authored almost 3 years ago by khue.nm <[email protected]>

[ADD] MzTabM support for AccurateMassSearch (based on IdentificationData) (#5744)

* Prototyping of novel ID datastructure in accurate mass search

* cleanup and todos

* add ...

aa03c7f187069d9e7aaeca78a3ac453ec4c7c6d6 authored almost 3 years ago by Oliver Alka <[email protected]>

Merge pull request #5751 from jpfeuffer/fix/pymacdeps

[FIX] pyopenms mac fix dependency order

af9cf0dd3d5dd44956700e0465f64c2afdf962f8 authored almost 3 years ago by Julianus Pfeuffer <[email protected]>

Reduce warnings (#5750)

d7c7f7f30aacee1a5d85896a5380f5508a0ecf40 authored almost 3 years ago by Julianus Pfeuffer <[email protected]>

[FIX] pyopenms mac fix dependency order

7d5da7a8dc3be67807f482ce6a3d20ac77d66de1 authored almost 3 years ago by Julianus Pfeuffer <[email protected]>

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

f47b19daa2119c41bc66821a21225e0f5869a0c3 authored almost 3 years ago by bielow <[email protected]>

Merge pull request #5749 from tillenglert/fix/MSFraggerAdapter

Bugfix MSFraggerAdapter

0828c7e836cbab3357cbb11690609431fa28c3e2 authored almost 3 years ago by Julianus Pfeuffer <[email protected]>

Fixed the options of isotope error to match the ones of MSFragger

be6bda8b3918bb7b613e3134b83c45365e289f8a authored almost 3 years ago by tillenglert <[email protected]>

Bugfix of depracated MSFragger parameter

max_modifications_per_mod changed to max_modifications_per_peptide

e770528157d415c44f1c05e63f4be7bd247350c5 authored almost 3 years ago by tillenglert <[email protected]>

[FIX?] pyopenms nightlies. Wrong deps after CMake restructure?

d6c0c72cefc33f92ce729a1b5f6af8c602ebdb8f authored almost 3 years ago by Julianus Pfeuffer <[email protected]>

reduce boost math usage (#5742)

* reduce boost math usage

* removed extra include

* add missing cmath

* add sstream inc...

8c4c988be7339e3332f921e411edada64df8ca61 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

use std::optional (#5723)

* use std::optional

* merge

7671b74fd9ff5bbc66b7f341c5c8bbcc948e19f8 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

Update CMakeLists.txt

890662aa7e9c844c1d92dba2605bb8a525827e8a authored almost 3 years ago by Timo Sachsenberg <[email protected]>

move GNPSExport to lib (#5638)

* move GNPSExport to lib

* rebase

* add documentation

* Update GNPSMGFFile.pxd

* mis...

b8f8567f05e87e70c4fdc833f4c6ab24c9fe7077 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

FLASHIda.cpp and FLASHIda.c PR comments have been addressed

544388a4ef44d3f59ee6ad63e02ddfe8ed3b21e9 authored almost 3 years ago by KyowonJeong <[email protected]>

Merge pull request #5352 from hendrikweisser/idfile-integration

IdentificationData updates, integration with tools, and SQLite-based file format

7f5009cfbabe74c126eece86f86cb9b7a5e4af62 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #5739 from OpenMS/jpfeuffer-patch-5

[FIX] Major error in pyopenms addon MSSpectrum

523b806bd47f11ef67ad86eb0a112142c1d21bbf authored almost 3 years ago by Julianus Pfeuffer <[email protected]>

add dll export (#5738)

d7b2b44494ad59ce4f9ae225853b8fdb69e1d89d authored almost 3 years ago by Timo Sachsenberg <[email protected]>

[FIX] Major error in pyopenms addon MSSpectrum

3d158d7245b1e10985962305a4f991c2f7c750ef authored almost 3 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #5730 from jpfeuffer/feat/betterPyOmsBuild

[FEATURE] Make pyopenms cmake better. And log output better.

738747e5279dd2600c565f6e7bb71f6e827aa585 authored almost 3 years ago by Julianus Pfeuffer <[email protected]>

update autowrap and other ifcases

ed63d87e97130a0c50d17ae527dabe645c1f01d2 authored almost 3 years ago by Julianus Pfeuffer <[email protected]>

[FIX] included MetaInfoInterface in IdentificationData copy c'tor and 'swap' method

d7b6cb79d9e2abefc570122671298ffd91f76aa9 authored almost 3 years ago by Hendrik Weisser <[email protected]>

[FIX] fixed ambiguities when using 'swap' methods (due to multiple inheritance)

e5fce43e520fba2cbf9a1d97a1ccd824f2972ce8 authored almost 3 years ago by Hendrik Weisser <[email protected]>

[API,TEST] added 'swap' method to MetaInfoInterface

a503602cb03274ee4cecf178de8e154ee30dcd8d authored almost 3 years ago by Hendrik Weisser <[email protected]>

Allow overlapping elution profiles in elution peak detection (#5734)

* allow overlaps of neighbors in elution peak detection

* add test

* update tests

* rev...

88f1ebf490d5e4b21bc36bbf8362dc754dcff3d0 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

Normalize intensity before calculating cross correllation

bef4bf8e19831c93c09d8f3667b10906d3e89e00 authored almost 3 years ago by khue.nm <[email protected]>

[FIX] Add MassTrace ctor (#5737)

688c40748f09e191996105d98e983598c98ab0e3 authored almost 3 years ago by Julianus Pfeuffer <[email protected]>

Merge branch 'develop' into idfile-integration

a4b7e8594f458a64dc598c9ee916a33444b41c14 authored almost 3 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #5720 from OpenMS/dhanmoni_gsoc21_toppview

Dhanmoni gsoc21 toppview

88689f58eb50c807b4e82717feb5b6e461f607ca authored almost 3 years ago by Julianus Pfeuffer <[email protected]>

Review comments and fix exit code.

bea90eb2c75e00708844466d1e0fb67e93131e0d authored almost 3 years ago by Julianus Pfeuffer <[email protected]>

Layer refactor (#5733)

* rename function to better describe its purpose

* [DOC, PARAM] improvements for TSGs paramet...

ee6ddd73c548e2c0271c7092fe5652fbc5ec82fb authored almost 3 years ago by Chris Bielow <[email protected]>

Fix overload

700ef15ae60556b75997b8dd65724bddcb4cfd2b authored almost 3 years ago by Julianus Pfeuffer <[email protected]>

restructure call to defaultsToParam_

696ff79f85a6871cd91b78e49abaa84e85a1a0ac authored almost 3 years ago by bielow <[email protected]>

[DOC, PARAM] improvements for TSGs parameters

d6424cdeb5951680d95c82a89f63b689647a749e authored almost 3 years ago by bielow <[email protected]>

rename function to better describe its purpose

842d6d5315e7e2532d50f32a6737a31c74167f60 authored almost 3 years ago by bielow <[email protected]>

allow to retrieve validStrings for a Param

12e52c9e16bdba3a6eaacc156cbc9bcb9876f51f authored almost 3 years ago by bielow <[email protected]>

- replace TheoSpecGen parameter UI with a more generic ParamEditor and make use of automatic parameter copying

- support spectra alignment using PPM instead of Dalton

d4ac008df09cd5890cef6d55b81ce6128a18dad5 authored almost 3 years ago by bielow <[email protected]>

[FIX] Resolve compatibility issues between IDRipper and IDMerger (#4957)

* [FIX] Resolve compatibility issues between IDRipper and IDMerger

* compile fix

Co-author...

1cbde3999d5279d357eca8536bf7cde572a242e0 authored almost 3 years ago by Leon Kuchenbecker <[email protected]>

initial implementation of output prefix parameters (#4527)

* initial implementation of output prefix parameters

as discussed in https://github.com/OpenM...

31228f1d0bd3180b65530988105dcc1b7710d4cf authored almost 3 years ago by M Bernt <[email protected]>

rebuild

be29996ca5858580870374b674138e8fbf06c253 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

Cleanup of Qt warnings. Better table col sizes. Better fallback in JS.

f7c4d3b57d39bf14b46fe2308befdad1216da319 authored almost 3 years ago by Julianus Pfeuffer <[email protected]>

Remove more comments

c6a112f64c7c31e03b16c1ba58eab130f17767b1 authored almost 3 years ago by khue.nm <[email protected]>

Add author name

38862f1bbfe4f717c9a667313abd2bf0a82139b9 authored almost 3 years ago by khue.nm <[email protected]>

[FEATURE] Make pyopenms cmake better. And log output better.

6ec780c02bae4b25e7d8ac2118dceecc5e235636 authored almost 3 years ago by Julianus Pfeuffer <[email protected]>

Merge branch 'develop' of https://github.com/khuenm/OpenMS into swath_merge2

66832364f4a05bdece495a84ca4a203c1e91bd5d authored almost 3 years ago by khue.nm <[email protected]>

Fix seg fault and clean up code

cce5deb2aa84368864de6d2049a58db6c37d34e2 authored almost 3 years ago by khue.nm <[email protected]>

Update GNPSExport.cpp (#5594)

* Update GNPSExport.cpp

I added a few more details on the proposed workflow (command examples...

3c38f4887b5dce2638be08a1e56a7ed4305bfcc0 authored almost 3 years ago by Efi Kontou <[email protected]>

Calculating a Corrected Database Suitability (#4905)

* function in DefaultParamHandler

* meta values written in comet- & msgf+ adapter, test missi...

fc5e2d4af3de16c275058c816d7a59beaff25feb authored almost 3 years ago by TomW <[email protected]>

Merge branch 'develop' into idfile-integration

37dd83b0881cf1b434279730ce45740c39e4d6b8 authored almost 3 years ago by Hendrik Weisser <[email protected]>

[TEST] updated FFId and ProteomicsLFQ tests after revert

92517d070a4ea3de40e4bb9858166874d91a2d91 authored almost 3 years ago by Hendrik Weisser <[email protected]>

[API,IO] revert adaptation of FeatureFinderIdentifiation to new ID data structures (incl. ProteomicsLFQ)

a9990f0cf9ef7643fb4229be78ceecb21449a32a authored almost 3 years ago by Hendrik Weisser <[email protected]>

Merge pull request #5729 from cbielow/layer_refactor

Layer refactor

8eb6bdf92def92a50809d1b732c9cec722bf859b authored almost 3 years ago by Chris Bielow <[email protected]>

Apply suggestions from code review

Co-authored-by: Timo Sachsenberg <[email protected]>

2862f290a5698c7fd257de118ad43babffc31058 authored almost 3 years ago by Chris Bielow <[email protected]>

remove switching based on layer type

8ae673b68d1ff44634ebc0853ac84198fbe51f38 authored almost 3 years ago by bielow <[email protected]>

improve compilation time by removing includes

4d2403569fc298a90dc9c5927033af173d718791 authored almost 3 years ago by bielow <[email protected]>

minor code duplication removed

0531023ab1d8c411d67fab2cedda4b4cbea2de53 authored almost 3 years ago by bielow <[email protected]>

Merge branch 'layer_refactor' of https://github.com/cbielow/OpenMS into layer_refactor

75822449391916597aa35d4f74d0cb5c8a6ecdf2 authored almost 3 years ago by bielow <[email protected]>

some minor fixes

4f5e7c0a2e6a545b797616ae4f75c615fc42cf11 authored almost 3 years ago by bielow <[email protected]>

Fix/activation modes (#4918)

* [FIX] adopt activation modes to new obo

* [FIX] copy-paste error

* Update MzMLHandler.cp...

9b22a2955b45808a148793bd5ceb62df840978fe authored almost 3 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #5722 from axelwalter/feature/massql-export

[Feature] export MSExperiment to data frames for MassQL

beeda3b07f317bdadba2e2089ea18ab54c1468c3 authored almost 3 years ago by axelwalter <[email protected]>