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

fix docs

c71ce3fa1ceef6a1612da292f69f0da12c651887 authored almost 2 years ago by jpfeuffer <[email protected]>

fix pyopenms

c59093235cec76c890763ec1f7d5185c7cab73b7 authored almost 2 years ago by jpfeuffer <[email protected]>

First crack at adding 18-plex support

73bd096042392c6d2f3516135989f5bf73011062 authored almost 2 years ago by Radu Suciu <[email protected]>

Merge pull request #6408 from OpenMS/hotfix/pyx

Hotfix/pyx

d92400b680de68cca76131b9f44089339fec86a1 authored almost 2 years ago by Julianus Pfeuffer <[email protected]>

FLASHIda inclusive exclusive targeted mode implmented. Target mass bin bug fixed..

de662926d315f042f6c862c901d79db90237a8cb authored almost 2 years ago by KyowonJeong <[email protected]>

FLASHIda inclusive exclusive targeted mode implmented. Target mass bin bug fixed..

1caa47cb06156ac93781b45f2f316a5f6aa4f6bb authored almost 2 years ago by KyowonJeong <[email protected]>

FLASHIda inclusive exclusive targeted mode implmented.

bce0efbf204add13ad5311f5eee92d04844c2c00 authored almost 2 years ago by KyowonJeong <[email protected]>

[HOTFIX] wrong variable pyx files

c50cfaf3e9e5119f6e9d9355ed3cbad9ff762ae0 authored almost 2 years ago by Julianus Pfeuffer <[email protected]>

update updatecheck url to new cs subdomain

37d625ecd662c083d137fcdf2b3a3f0f4d65eb9d authored almost 2 years ago by Timo Sachsenberg <[email protected]>

[HOTFIX] wrong variable pyx files

f749c8a09058759ee4cd2275fe43a61bd623a7d3 authored almost 2 years ago by Julianus Pfeuffer <[email protected]>

Merge branch 'develop' into fix/bump_cmake_min

78cd4734d021f304d5ce292b3973d3ffbd5d4ff1 authored almost 2 years ago by Samuel Wein <[email protected]>

[UPD] Bumped min cmake version to 3.15 to match with pyopenms

805750ecc5c010afbbb32e6e8958a5790c96cb48 authored almost 2 years ago by Samuel Wein <[email protected]>

Merge pull request #6406 from OpenMS/poshul-patch-1

Update openms-ci.yml

2876447dcbd52d0c703af381de4d82e0342ade83 authored almost 2 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #6369 from rahul799/fix-docstrings-2

fixing docstrings - 2

432a4d0c5fca4b407df600cdd9179e10f99ebbea authored almost 2 years ago by Julianus Pfeuffer <[email protected]>

Merge branch 'develop' into refact_toppview

c2185daba568f6f93f04e9db65fcbe3429549b5b authored almost 2 years ago by Chris Bielow <[email protected]>

extra line chr removed

f426b4dce2e77246a3cc8d6981c4a77fcc1cc1e2 authored almost 2 years ago by rahul799 <[email protected]>

Update pyopenms-wheels.yml

update actions

25f20bd3442a46ef409293b8cb1bb8c6bbcb7e4a authored almost 2 years ago by Samuel Wein <[email protected]>

Update openms_clang_format_add_and_commit.yml

update actions

c02074fed48f5d38b6e240888c092678c64c8bdc authored almost 2 years ago by Samuel Wein <[email protected]>

Update openms_clang_format.yml

update actiona

e57db2b172e3809c8593c6f8e109e2392b7b33d8 authored almost 2 years ago by Samuel Wein <[email protected]>

update fingerid test

3a86233e9c640dab066feccb8a683ed4af01cfdc authored almost 2 years ago by axelwalter <[email protected]>

Update openms-ci.yml

update jwlawson/actions-setup-cmake for node 16

e62e56246e1baaa2aaf3159964c7a7ae942a0664 authored almost 2 years ago by Samuel Wein <[email protected]>

turn SIRIUS test off

local test will fail without login

5a23c04f679afbc5d51efbc8b45e012e95179db6 authored almost 2 years ago by axelwalter <[email protected]>

Update dockerdeploy.yml

update actions

3428c29de09276be47726163292325df2c6c9c02 authored almost 2 years ago by Samuel Wein <[email protected]>

Update cppcheck.yml

update cppcheck versions

4101d32ee34eb1a3f966e6a9c9b84669bf455f20 authored almost 2 years ago by Samuel Wein <[email protected]>

Update openms-ci.yml

Bump `actions/cache` and `actions/checkout` to v3

3465b9775e5afc2f0a720dfa2d34ddc780fbc55b authored almost 2 years ago by Samuel Wein <[email protected]>

Merge pull request #6393 from poshul/feature/new_cyclophosphate

[feature] enable 3' cyclophosphate as a RNA mod

348b4ad6b5c6da7026f668a3f9aac3b0e44ba342 authored almost 2 years ago by Samuel Wein <[email protected]>

fix nightlies

2f63f3f3418fe174d3673b6f627667f64ad7c233 authored almost 2 years ago by Timo Sachsenberg <[email protected]>

Merge branch 'develop' into refact_toppview

d55a2dbe9d1e53053c640b14b41e275fd3cadc5b authored almost 2 years ago by Chris Bielow <[email protected]>

Merge pull request #6396 from OpenMS/feature/count_ics

Feature/count_ics

be3cbd39d26e7d94dd21b4aef59a89feb9519403 authored almost 2 years ago by Samuel Wein <[email protected]>

Merge pull request #6401 from OpenMS/fix/pyxWarnings

[FIX] fixes some signedness comparison warnings in pyx files

1b50da23dbe7ab3e81fb5c6b3e43ccd31f180829 authored almost 2 years ago by Samuel Wein <[email protected]>

Merge pull request #6402 from cbielow/fix_dtor

add d'tor to fix LNK2001: unresolved external symbol "public: virtual…

350762eb38e603a33608d6604a64410576556d81 authored almost 2 years ago by Samuel Wein <[email protected]>

Merge branch 'develop' into fix_dtor

23f13d89b03416c3d6dbdd025fcb696b0a0fe042 authored almost 2 years ago by Chris Bielow <[email protected]>

add d'tor to fix LNK2001: unresolved external symbol "public: virtual void * __cdecl OpenMS::MSExperiment::`scalar deleting destructor'

some code rearrangements
some docs

961a198047ae248c0fade14fd6e1f7412bc794cb authored almost 2 years ago by bielow <[email protected]>

Update src/pyOpenMS/pxds/EnzymaticDigestion.pxd

Co-authored-by: Julianus Pfeuffer <[email protected]>

5666786c16f03c75bd450af54cf58a04f4da4548 authored almost 2 years ago by Timo Sachsenberg <[email protected]>

[nop] Removed lots of commented out code, a lot of this looks probably worthwhile to keep on a separate branch, but should not be merged

bc849f2cd70a542b052c1ab0ebd3d938b7e3b947 authored almost 2 years ago by Samuel Wein <[email protected]>

minor C17 refresh

b56ec1b38b0c084f30d92d15a9348ac6fe50f4f9 authored almost 2 years ago by bielow <[email protected]>

use new (colored) gradient for log-intensity

687dc948c1374d04d0e353cd1a71f0893ed21b75 authored almost 2 years ago by bielow <[email protected]>

unused parameters

6424eb3caeca429355b86ccf473cda719443b94e authored almost 2 years ago by bielow <[email protected]>

move write-summaries command to the end

54323bfda53658cc6b21b716162e6ebedc6082b2 authored almost 2 years ago by axelwalter <[email protected]>

set sirius compound and tree timeouts to 100s

aa0b7468d4bc1166c05e70143d72bb43c90f8b30 authored almost 2 years ago by axelwalter <[email protected]>

add flag for uncompressed sirius project space

cbdfd46c7629ab58f539040b4bf8ce8de1253d65 authored almost 2 years ago by axelwalter <[email protected]>

update THIRDPARTY with sirius 5.6.1

59a7615ca571a1469ad15c132bd4aaf8b6f5a283 authored almost 2 years ago by axelwalter <[email protected]>

use correct SIRIUS default parameters in SiriusAdapter

652a80b66ec7bfab859c5c6b126d8526cbd8bffe authored almost 2 years ago by axelwalter <[email protected]>

update tests

whitelist compound with varying sum formula results

2b2a3c1188dd69605acff67531a5c593e8871370 authored almost 2 years ago by axelwalter <[email protected]>

update parameters

empty string and -1 for not passing parameter to command need to be in valid range

6a294ba73a30fab92fa85454d97ce8ecba8b8828 authored almost 2 years ago by axelwalter <[email protected]>

add sirius:candidates parameter to tests

f715b01afc09dd437a63022a5b8385a2caf2edda authored almost 2 years ago by axelwalter <[email protected]>

use original sirius 5.6 parameters

write only deviating parameters to sirius CLI tool

84250f12c6abc9d39619b53db874caa13683b10a authored almost 2 years ago by axelwalter <[email protected]>

adapt to changes in fingerid

- number of candidates for sirius and fingerid are the same now
- fingerid done with fingerprint ...

f92256fe9b5d2b6e5a54534eb498f5d184fcec2d authored almost 2 years ago by axelwalter <[email protected]>

removing obsolete FingerID parameters

355a488eb7b7d156e69389fad0d14db2a8d6f834 authored almost 2 years ago by axelwalter <[email protected]>

CSI:FingerID name changed from fingerid to fingerprint

be6d6c92d4e17170eec01c3198ed166173ef3f48 authored almost 2 years ago by axelwalter <[email protected]>

update tests

0973f552d502ae3da49d8b9c8fef2045a0c9a4cc authored almost 2 years ago by axelwalter <[email protected]>

[nop] finished reordering of imports

bdef9f8ce95a6c2408e938331be704e31fd72cbb authored almost 2 years ago by Samuel Wein <[email protected]>

Merge pull request #6398 from OpenMS/fix/newpyomsapi

[FIX] some fixes for reduced pyopenms API

d4bc09f7ae97d3115997ade2b05ec9defb92df93 authored almost 2 years ago by Julianus Pfeuffer <[email protected]>

[FIX] fixes some signedness comparison warnings in pyx files

01de5285ddb27e94480af82a0bd37fda9298e2ff authored almost 2 years ago by Julianus Pfeuffer <[email protected]>

[fix] patched values for DeconvolutedSpectrum_test. THIS SHOULD BE CHECKED

d01409335e996a6d61c419dcc9266a11aa345e9b authored almost 2 years ago by Samuel Wein <[email protected]>

[nop] removed phantom parameter and added move assignment iterator

5509750086166114d51e1319b5a74de8579af665 authored almost 2 years ago by Samuel Wein <[email protected]>

[nop] reorder imports

643041c0838def71974408601aad7744dadc5255 authored almost 2 years ago by Samuel Wein <[email protected]>

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

14f962759b71c578f8845c58daf4386790c56c84 authored almost 2 years ago by bielow <[email protected]>

Merge pull request #6395 from cbielow/feat

enable unused_variable warning as error on Windows

cb20f950bbd4f2d65e231f8124227899d87c25d7 authored almost 2 years ago by Chris Bielow <[email protected]>

[nop] cleanup

a2e1fb16612e3603ca92fd80b38fd007738bbeb6 authored almost 2 years ago by Samuel Wein <[email protected]>

Update EnzymaticDigestion.cpp

4ca4baba46ce30875a5f7bece3a2e83d987c4415 authored almost 2 years ago by Timo Sachsenberg <[email protected]>

[nop] restore more comments

2cae27226dcf3c9b87c75096567b73c28d7846ba authored almost 2 years ago by Samuel Wein <[email protected]>

Merge branch 'feature/FLASHDeconvOnly' of https://github.com/JeeH-K/OpenMS into JeeH/feature/FLASHDeconvOnly

849eaf71a96cbb5bae114643066d16924c655b4a authored almost 2 years ago by Samuel Wein <[email protected]>

[nop] revert some deleted comments,

b5c455834c7e78693e245a7b030ed479a2901cc1 authored almost 2 years ago by Samuel Wein <[email protected]>

[nop] revert seemingly lost comments.

507d7a8f2a87c5dbe0d405193f8664a32f7ddf58 authored almost 2 years ago by Samuel Wein <[email protected]>

[nop] reordered imports, clarified several comments

b2dcbcfb7ca17af186633d01d421ded07a041cde authored almost 2 years ago by Samuel Wein <[email protected]>

[nop] remove comment for constructor that was IMO confusing

2bdf56f7aa90f6ba825d7802e4e40924981fa83e authored almost 2 years ago by Samuel Wein <[email protected]>

[FIX] some fixes for reduced pyopenms API

e99cadc0eaa3f8c0adcfb42db3c837af031a9f7d authored almost 2 years ago by jpfeuffer <[email protected]>

add test

267f78d8685da970e86c832d2614f40f4ee34ca3 authored almost 2 years ago by Timo Sachsenberg <[email protected]>

[FEATURE] count internal cleavage sites

8d15722148621ea23ba32f105e56f48cd1d96943 authored almost 2 years ago by Timo Sachsenberg <[email protected]>

[nop] revert comment

be6769b1d86c4d2dcf9745ae72b0ceb95a5971f9 authored almost 2 years ago by Samuel Wein <[email protected]>

Merge branch 'feature/new_cyclophosphate' of ssh://github.com/poshul/OpenMS into feature/new_cyclophosphate

d445eeff11f3a788ced544c3bb2ec288493109bd authored almost 2 years ago by Samuel Wein <[email protected]>

add test to make sure that we can parse all the ribonucleotide mods

51c6fb96353884b77d227eb7f4e475e8e64feb6f authored almost 2 years ago by Samuel Wein <[email protected]>

Merge branch 'develop' into feat

f4276ee132c6dc150b7e6fef64168635265ff262 authored almost 2 years ago by Samuel Wein <[email protected]>

fix new errors in Release build

722bc1fb49e07dc389f01e06c6c45b5ac54a0700 authored almost 2 years ago by bielow <[email protected]>

Merge branch 'develop' into feature/FLASHDeconvOnly

ce71a54df9f46776fb65fb45a0d20fa79e954656 authored almost 2 years ago by Samuel Wein <[email protected]>

Merge pull request #6377 from poshul/fix/FFMI_segfault

[fix] fix segfault when passing data with no MS1 scans

d977b6c84f196ec90f482936b2769753030b36e6 authored almost 2 years ago by Samuel Wein <[email protected]>

Merge pull request #6387 from OpenMS/fix/deb

Fix deb dependencies for qsql

9d889f247ff7c0695817049d1879e0bc46b729e7 authored almost 2 years ago by Samuel Wein <[email protected]>

enable unused_variable warning as error on Windows

47f40b80c483aefe6b9a1eab6b6d02a8a04a156b authored almost 2 years ago by bielow <[email protected]>

Merge branch 'develop' into feature/new_cyclophosphate

bbb16fb5f543fb8950865150846c4876a5b7c2d5 authored almost 2 years ago by Samuel Wein <[email protected]>

Merge pull request #6140 from OpenMS/timosachsenberg/filefilter-added-6138

[FEATURE] FileFilter: added option to remove hulls

2d1ec37d9b908eaf4347a39934f1b39d695206fe authored almost 2 years ago by Samuel Wein <[email protected]>

Merge pull request #6364 from OpenMS/pyoms/interface

[PYOPENMS] cleanup interfaces

2bd127070223c54ec146da569cceb8336f6dbb2b authored almost 2 years ago by Samuel Wein <[email protected]>

Merge branch 'develop' into pyoms/interface

024fa484d9f15549e4eb84ebdeac59ee69035e07 authored almost 2 years ago by Samuel Wein <[email protected]>

Merge pull request #6341 from poshul/feature/nase_debug

Feature/nase debug

fce7ae6693d5253bdbad53ef08641f76611f6457 authored almost 2 years ago by Samuel Wein <[email protected]>

Merge branch 'develop' into timosachsenberg/filefilter-added-6138

cf67cfc2308a3c5130a1aeac2bc7fbad8b1ff704 authored almost 2 years ago by Samuel Wein <[email protected]>

Merge branch 'develop' into idfile-json-export

bc9fe006ca1d77b62593f9ca062729ba39896436 authored almost 2 years ago by Samuel Wein <[email protected]>

Merge pull request #6312 from poshul/NASE_charge_fix

[nop] Added documentation for some NASequence functions that needed it.

fec8d6faefccaa459f97bd7ee047346e9424cd00 authored almost 2 years ago by Samuel Wein <[email protected]>

Merge pull request #6388 from axelwalter/feature/ffmid-compound-access-attributes

[Feature] add getters for FFMIDCompound attributes

fc727b6fee5884e1a520835d6c819193955c3d86 authored almost 2 years ago by Samuel Wein <[email protected]>

Merge branch 'develop' into feature/ffmid-compound-access-attributes

58b5ef61f3ea0bdb78eb7b338cf0d72e4b1ac7ee authored almost 2 years ago by Samuel Wein <[email protected]>

Merge branch 'develop' into fix/FFMI_segfault

3be323777a92eed2580c5430bd8b8da097588b79 authored almost 2 years ago by Samuel Wein <[email protected]>

Merge branch 'develop' into fix/deb

0e7cca03bf0a392acc2820efba8954b0a7869acb authored almost 2 years ago by Samuel Wein <[email protected]>

Merge branch 'develop' into feature/new_cyclophosphate

471bad511408aebf51b89d01a28770511d720321 authored almost 2 years ago by Samuel Wein <[email protected]>

Merge remote-tracking branch 'origin/feature/FLASHDeconv' into feature/FLASHDeconvOnly

dee3a16b0037f00a9173e545a6d5b0371e8b918f authored almost 2 years ago by JeeH-K <[email protected]>

Merge remote-tracking branch 'upstream/develop' into feature/FLASHDeconvOnly

84878de9ba6926d82b5f6340431d446d34af7461 authored almost 2 years ago by JeeH-K <[email protected]>

remove unused variables

fe79f05c2f565451f9d08a9ada5f35ece6a4f0cf authored almost 2 years ago by bielow <[email protected]>

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

f0a9431a2943bb2f73a49b299beaade51f167369 authored almost 2 years ago by bielow <[email protected]>

fix tests

f805b52435e7635f3a640cd912480f0b50f47030 authored almost 2 years ago by bielow <[email protected]>

Merge branch 'develop' into refact_toppview

fa29d9d5fe54c9c337a0b02505fe49effe75bf32 authored almost 2 years ago by Samuel Wein <[email protected]>

Merge pull request #6358 from rahul799/fix-docstrings

fixing docstrings

050c33309ab23af3fab217a6bf9867c965323116 authored almost 2 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #6389 from OpenMS/feature/SSE

write identifier in SSE

12477447243f7e6084e00fa06a6054e7994e0d54 authored about 2 years ago by Julianus Pfeuffer <[email protected]>