Ecosyste.ms: OpenCollective

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github.com/OpenMS/OpenMS

The codebase of the OpenMS project
https://github.com/OpenMS/OpenMS

Merge pull request #5923 from Amit0617/develop

[FIX] Warning: unused variables

f60857e912d76053be64b8eee490becca8cf8d57 authored over 2 years ago by Julianus Pfeuffer <[email protected]>
converting group uid to size_t with stoull

19342a1d7c9cfed59db5c70a5c4fc4c2657476ca authored over 2 years ago by axelwalter <[email protected]>
Merge branch 'OpenMS:develop' into develop

108995ec9f72958ffa609e71bfa9753c512ed09a authored over 2 years ago by AMIT KUMAR MISHRA <[email protected]>
[FIX] Warning: unused variables

0aba16a8902bd34a2f9f3d74218dcb3c607add08 authored over 2 years ago by amit0617 <[email protected]>
Merge pull request #5919 from OpenMS/update_pyopenms_wheel_cmake

Update pyopenms-wheels.yml

5655547d8c21ee832401e0cb4468fdec4ab8eb65 authored over 2 years ago by Timo Sachsenberg <[email protected]>
Update pyopenms-wheels.yml

6a4ee8f379bc9d606afe687318c27c6286ca1d1b authored over 2 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #5916 from Amit0617/develop

[FIX] isnan error

d54a36841436c3533da66047065a8bd7a3efc5be authored over 2 years ago by Timo Sachsenberg <[email protected]>
fix error with filtered ConsensusMap

1c0dfcdf226a67e840d90a92a2567d04a6bb4d92 authored over 2 years ago by axelwalter <[email protected]>
Add parentheses

Co-authored-by: Hannes Roest <[email protected]>

4c326565a2672709d5da643b5e0942323a37c7b7 authored over 2 years ago by M Bernt <[email protected]>
Update MQEvidenceExporter.cpp

removed include duplicates

8bd42e7d799e4c1f8c0dfb1d79c60254384a17fd authored over 2 years ago by AMIT KUMAR MISHRA <[email protected]>
fix: 5864, isnan error

9264cfd89cd55dd58898f29b0ea83e1235e43490 authored over 2 years ago by amit0617 <[email protected]>
Merge pull request #5844 from OpenMS/remove_Map

[REFACTOR] replace Map with std::map

3cd3db31efef6241030830388dbceccb3d6ffd4e authored over 2 years ago by Timo Sachsenberg <[email protected]>
update to contrib that removes zlib from boost

5dc6b1d5f15f25a813649443386602766a426d64 authored over 2 years ago by Timo Sachsenberg <[email protected]>
FLASHDeconv 2.0 beta++ version + target_mass option added, thanks to Dave Tabb.

1bf55cd58fd5fc6d07a3cbbfba0a1d6874a84196 authored over 2 years ago by kyowonjeong <[email protected]>
update contrib

5e802dd8220d7d0beec083d2ab0826a11b51a187 authored over 2 years ago by Timo Sachsenberg <[email protected]>
update contrib with zlib patch

35b868af13fe5f8c3ae7e3502526517303cb1457 authored over 2 years ago by Timo Sachsenberg <[email protected]>
clang formatting

0fc35efa85e6e6082e627afa052993f3e500e98c authored over 2 years ago by Matthias Bernt <[email protected]>
use output-prefix for more tools

66dee6ac90396f03760d10f134afe5507567ee0d authored over 2 years ago by Matthias Bernt <[email protected]>
Merge pull request #5466

- merge 'feature/add_elements' into develop

f3910ff6988b4910ced0787a964a8e48ced9262b authored over 2 years ago by Hannes Roest <[email protected]>
[NOP] cleanup of elements

8254a58fd8ada4fae50e643e2ff9583bb62ad0f1 authored over 2 years ago by Hannes Roest <[email protected]>
FLASHDeconv 2.0 beta++ version + target_mass option added, thanks to Dave Tabb.

fc9168a1ea90eb4864358a958b415968d82665b3 authored over 2 years ago by kyowonjeong <[email protected]>
update GNPS tests

3f508b4e7f924bf8b6071745eb3eac097d9d4a8f authored over 2 years ago by axelwalter <[email protected]>
add score for supplementary table

a403c6336c7778595af945c7a0eef713b9bcedd0 authored over 2 years ago by axelwalter <[email protected]>
use static methods for IIMN

61ae95e15ba1627cf48a792ca74b234ad9af3a67 authored over 2 years ago by axelwalter <[email protected]>
change vertex.uid from String to size_t

b7caf6d89e2b105cdcea00ae028799420abb56f0 authored over 2 years ago by axelwalter <[email protected]>
add IIMN to GNPSExport

e9cdebad3eb3bec5176aabff731b76a03c9f8d89 authored over 2 years ago by axelwalter <[email protected]>
add method to write supplementary pairs table

2694d0d8889e0a8ef82eab01fdb3980f4075fd8a authored over 2 years ago by axelwalter <[email protected]>
add IonIdentityMolecularNetworking::writeFeatureQuantificationTable

d78ecd5565fbb1e684a937ea49ca32a30af6bf4a authored over 2 years ago by axelwalter <[email protected]>
FLASHDeconv 2.0 beta++ version + speed improvement + low charge filtration

c6c23a6adb91c1c0b697dfd74df834adca448604 authored over 2 years ago by kyowonjeong <[email protected]>
add IonIdentitiyMolecularNetworking class with annotateConsensusMap method

48b3a11e7852708bfe4a5e8b41fecd4fd96346a3 authored over 2 years ago by axelwalter <[email protected]>
Apply suggestions from code review

Co-authored-by: Hannes Roest <[email protected]>

a0bc85f001bb9ff073d699d8a6b9917168d39308 authored over 2 years ago by Timo Sachsenberg <[email protected]>
Update src/openms/include/OpenMS/DATASTRUCTURES/sources.cmake

Co-authored-by: Hannes Roest <[email protected]>

9c0dd585078606c20a5a8dc3176f82b8a670c3d6 authored over 2 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #5904 from hroest/feature/fix_monoisotopic

[FIX] test fix after #5891

58eec1738829a7af3a3ec92262bd1508aa5a2b5f authored over 2 years ago by Timo Sachsenberg <[email protected]>
Update AASequence_test.cpp

b5c56edde47b881b45c3b14ddf5d5299bf0332c9 authored over 2 years ago by Timo Sachsenberg <[email protected]>
[FIX] test fix after #5891

- after the change in monoisotopic mass, we have to adjust the test for
monoisotopic mass for se...

0cad5b0ffa21f312517d1f970cd7908f633bce1e authored over 2 years ago by Hannes Roest <[email protected]>
FLASHDeconv 2.0 beta++ version + speed improvement + low charge filtration

4321e5f64cb001b5e0e6376413f66dce46690ced authored over 2 years ago by kyowonjeong <[email protected]>
Revert thirdparty

284b8e477e694b2b916e6d1fbc12b2cc7e9cdc95 authored over 2 years ago by matteopilz <[email protected]>
remove IIMN export in TextExporter

fa2316c49625d878d66e4892e610f1a55a7ca1c4 authored over 2 years ago by axelwalter <[email protected]>
Merge pull request #5898 from hroest/fix/residue

Recalculate average and mono weight in Residue setFormula

ccd08ee5b2c9a53130d5ed46171edf43d707dddc authored over 2 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #5899 from hroest/feature/doc

[DOC] documentation of OpenSwath

d451edd7d8f7a27a59967c525da250694daed85a authored over 2 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #5896 from OpenMS/fix_5894

Fixes 5894

fdd6ec85a191e740abedf8c63263d20770f4b1b1 authored over 2 years ago by Timo Sachsenberg <[email protected]>
[DOC] documentation of OpenSwath

f53e2ce2cf278d34603ee3b4d92d276b8f442739 authored over 2 years ago by Hannes Roest <[email protected]>
[TEST] add test

8e6d3c3a668b74f369fcb069d1e4463f21e57bc2 authored over 2 years ago by Hannes Roest <[email protected]>
fix

0644c0e5fa72bef1b152f0f1030190c4608e825a authored over 2 years ago by Hannes Roest <[email protected]>
FLASHDeconv 2.0 beta++ version + a bit of speed improve

559469cccdd85f87e48189ecf551c557fa2bb87c authored over 2 years ago by kyowonjeong <[email protected]>
[FIX] update weights after formula changes

95956a1aa8da4b707012c154a0c14de2539abc44 authored over 2 years ago by Hannes Roest <[email protected]>
[DOC] add documentation

ea72a3b0fa63eabb49e2baffd7baff9d1ce7edd1 authored over 2 years ago by Hannes Roest <[email protected]>
FLASHDeconv 2.0 beta++ version + a bit of speed improve

d969bbe5a64de732c793872e56ae20718106eee4 authored over 2 years ago by kyowonjeong <[email protected]>
proper -test mode for FFMetaboID

09265b0094af95b0d92f9086e9b331df8eef1699 authored over 2 years ago by Timo Sachsenberg <[email protected]>
add raw file to FFMetaboID

b662fd70c578ef2702a09da0243b274392602b08 authored over 2 years ago by Timo Sachsenberg <[email protected]>
Update src/pyOpenMS/addons/ADD_TO_ALL.pyx

837003498fb4f0fe278c87815dee0bfcb79199d3 authored over 2 years ago by Hannes Roest <[email protected]>
Corrected spelling error

5ef8488f372b824e69ef286d55b4408c4127a5bb authored over 2 years ago by matteopilz <[email protected]>
Merge remote-tracking branch 'upstream/remove_Map' into remove_Map

2144748db34727eba1fd9542019e023643951db9 authored over 2 years ago by matteopilz <[email protected]>
Simplify double negative std::map find

cf9dbb3695c29c998af5d39cc1b5175b63111486 authored over 2 years ago by matteopilz <[email protected]>
Merge remote-tracking branch 'origin/develop' into remove_Map

8f58d948940676899d96b944ebed8766f8528d0c authored over 2 years ago by Timo Sachsenberg <[email protected]>
FLASHDeconv 2.0 beta++ version.

2723ddb3942fbe753d9b482bd116bd359a4f5d0d authored over 2 years ago by kyowonjeong <[email protected]>
Merge pull request #5891 from hroest/feature/iso_fix

[FEATURE] fix monoisotopic definition

637747ce64bd159309dac7f9f6b3ac728a60dd31 authored over 2 years ago by Timo Sachsenberg <[email protected]>
[FEATURE] fix monoisotopic definition

615bb5734de1d6899820d4e8a4afe2871935f148 authored over 2 years ago by Hannes Roest <[email protected]>
Merge pull request #5892 from oliveralka/fix/SA_Test_10

FIX: SiriusAdapter_test_10

68d3f8056c6ba35747065cbd3505d85d5a04d04e authored over 2 years ago by Timo Sachsenberg <[email protected]>
set "output for per spec" to be printed as default

8b5b32827c2dd51e301754de392d8c1e6cdc1cd6 authored over 2 years ago by JeeH-K <[email protected]>
FIX: SiriusAdapter_test_10

4989be179dd5378b0875b41ceb764ef6a1f10dd3 authored over 2 years ago by oliveralka <[email protected]>
SpectraMerger is now merged into FLASHDeconv tool.

Tested with
- Thermo Std
- Ecoli
- Azo
- Feredrik and Loo MS dataset

15b1335ea4cbbcc1c7c04fab8a4ec513e28b68a5 authored over 2 years ago by kyowonjeong <[email protected]>
[NOP] use same notation

8f5c24371ca8f644f09374192fe3c6cecc6e0314 authored over 2 years ago by Hannes Roest <[email protected]>
[FIX] a few more bugfixes

0cb5badaa8f6af04c0c4c804db4cec728eea2cd9 authored over 2 years ago by Hannes Roest <[email protected]>
Merge pull request #5887 from bernt-matthias/update-unimod

Update unimod

2765546ccc1a656bcee9002a85f2a30d6d4cb6a8 authored over 2 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #5883 from Waschi97/fix/TheoSpecDialog

Fix TheoreticalSpectrumGenerationDialog - closes #5787

82c847f41a83d72d34b7951d0f82b72ddd0bb276 authored over 2 years ago by TomW <[email protected]>
Major change in MS2 deconvolution

- added isotope pattern based harmonic detection : both in mass bin and peak levels
- changed the...

c934181a7d42ef0de7c667beccc78810047a5455 authored over 2 years ago by kyowonjeong <[email protected]>
added changes to CHANGELOG

17449fd7e606df2578f89d7c5eadf52701c5d929 authored over 2 years ago by Tom Waschischeck <[email protected]>
Major change in MS2 deconvolution

- added isotope pattern based harmonic detection : both in mass bin and peak levels
- changed the...

4fb05bc59ca01637e3523cac60bf2769fa4e3b32 authored over 2 years ago by kyowonjeong <[email protected]>
add more modifications

xref https://github.com/OpenMS/OpenMS/pull/5887#issuecomment-1059098323

5bebe8b9a526ae7cf69142430267f3882dc6a650 authored over 2 years ago by Matthias Bernt <[email protected]>
Update src/openms/source/ANALYSIS/DECHARGING/ILPDCWrapper.cpp

Co-authored-by: Hannes Roest <[email protected]>

4dfa5e10896270a255a459baf800444bed1a6a4e authored over 2 years ago by Matteo Pilz <[email protected]>
Update src/openms/source/ANALYSIS/DECHARGING/ILPDCWrapper.cpp

Co-authored-by: Hannes Roest <[email protected]>

23772d2f708362dac6eab9e19b91d6046275a4fa authored over 2 years ago by Matteo Pilz <[email protected]>
removed recently added elements with unknown / zero abundance

50155fd768c3f8b07560a3beb01b0bfb6a771d93 authored over 2 years ago by Timo Sachsenberg <[email protected]>
[FIX] bugfixes / compile fixes

ab60e312f9b84d701e9407ecc69cca74607fcd71 authored over 2 years ago by Hannes Roest <[email protected]>
update VS version in pyoms GH actions

b2a35be4c747edb19473bc0dc964b2f69d2e0ae0 authored over 2 years ago by Julianus Pfeuffer <[email protected]>
fix debug statement in gh actions

a1a504c565b7772082e5effc72e2662920d958ea authored over 2 years ago by Julianus Pfeuffer <[email protected]>
[FIX] bugfix (new behavior)

6aeecd7096d5d8e14b9b05d27681ae6993d39416 authored over 2 years ago by Hannes Roest <[email protected]>
[FIX] compile fixes

52717546115744515c4ee319ffa784470029d628 authored over 2 years ago by Hannes Roest <[email protected]>
na seq only info from parameter desc to comment

f3fb8e2306d4830235a54b588c535c05ba0599b3 authored over 2 years ago by Tom Waschischeck <[email protected]>
[FIX] compile fixes for DigestionEnzymeDB

b19fa09aa01cb4c0b2f2e7db1df688e7dd8b9f4b authored over 2 years ago by Hannes Roest <[email protected]>
parameter description for nucleic acid only ions updated

d28f662cbb83a6a24a5350cff5810927e1390665 authored over 2 years ago by Tom Waschischeck <[email protected]>
[FIX] conversion providers for CVTerm-maps

126f3f9fe4e81ea0853fab6e318ffbb1bc5de995 authored over 2 years ago by Hannes Roest <[email protected]>
[FIX] compile fixes, remove leftover Map

2e818759e1b51c75f5d8e704886d9fa76c94080b authored over 2 years ago by Hannes Roest <[email protected]>
[FIX] compile fixes

8401b5580844261bb9902af2557dad72101e3d0d authored over 2 years ago by Hannes Roest <[email protected]>
[FIX] compile fixes

e00bf84ff8cc55daa0fed476950e17852960c350 authored over 2 years ago by Hannes Roest <[email protected]>
add cusom modifications

f62172e727dc7825787a307399b212c5407c7be1 authored over 2 years ago by Matthias Bernt <[email protected]>
update unimod.xml

fixes https://github.com/OpenMS/OpenMS/issues/5874

caa230bd1a2834f3abc4f15bbe8d844270957db8 authored over 2 years ago by Matthias Bernt <[email protected]>
check if vertex in graph with map

0df8bc211bea4260cbbd01925162de1a92011515 authored over 2 years ago by axelwalter <[email protected]>
Replace OpenMS::Map with std::map

45bcc8a90deeada033f8201d351f79b5005abdb2 authored over 2 years ago by matteopilz <[email protected]>
parameter description for peptide only ions updated

f5c1f5be5c713932122869315a47f8e37bd33409 authored over 2 years ago by Tom Waschischeck <[email protected]>
hiding instead of disabling, automatic resizing, added myself to authors

028e83c2f4d7a7926b17721b9fbc1cbaf01677ce authored over 2 years ago by Tom Waschischeck <[email protected]>
simplify comparison

93edddbbb0fe1a44886c7b7608bea872257dffca authored over 2 years ago by axelwalter <[email protected]>
use unordered_map for partners

ae8ba1680c30c92ca0c59827c8afe5dbf5726bb1 authored over 2 years ago by axelwalter <[email protected]>
more efficient partner annotation

7f6b23e3ffce6d830c9b761896ac765b39f63e06 authored over 2 years ago by axelwalter <[email protected]>
improve documentation

85ad1cad13da65b66d2352312496b6e10ee88635 authored over 2 years ago by axelwalter <[email protected]>
Merge pull request #5886 from OpenMS/feature/remove_empty_string_restrictions

[FIX, BREAKING] replace empty strings in restrictions with meaningful value

58ac2727f251f14febb1e2ddc063472f4113ee43 authored over 2 years ago by Timo Sachsenberg <[email protected]>
new signal slot syntax

2d6345e44c82cb7cfa00ddf2d6bdb5aa04fd6324 authored over 2 years ago by Tom Waschischeck <[email protected]>
RNA spectrum generation interface with working backend, checkbox datastructures to cpp, return const ref

3495160f80dc6a1b8a5741b774c727d25acb336f authored over 2 years ago by Tom Waschischeck <[email protected]>
Major change in MS2 deconvolution

- added isotope pattern based harmonic detection : both in mass bin and peak levels
- changed the...

62e1340cebc76f1680c5444d34fe4278dbfca99f authored over 2 years ago by kyowonjeong <[email protected]>
Merge remote-tracking branch 'upstream/remove_Map' into remove_Map

b5167e701ccded99b7ed583ce92a407edadcf524 authored over 2 years ago by matteopilz <[email protected]>