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

some comments

59b22c424352f7603a6f51cf9b64be205d4ae479 authored over 2 years ago by Tom Waschischeck <[email protected]>

comments to doxy, some renaming, new enum for seq type, const members

f555d501db180e26c1589d5c4692bc0d71912684 authored over 2 years ago by Tom Waschischeck <[email protected]>

Merge branch 'develop' into feature/FLASHDeconvOnly

b1a4485e50d44b4451bc189d7d24f313a8db25d1 authored over 2 years ago by JihyungKim <[email protected]>

changed isotope probability label

853afd2b56562790843dc26e50d5af5db62268d9 authored over 2 years ago by Tom Waschischeck <[email protected]>

updated CHANGELOG file with FLASHDeconv description

df9ec862fed0771d1d76f57f6f3933cf30a097ae authored over 2 years ago by JeeH-K <[email protected]>

Change used progress logger to OpenMS ProgressLogger

eb4f1966e74a0c4c633fb32b3d0bb13e5675e235 authored over 2 years ago by JeeH-K <[email protected]>

add pyopenms test for IIMN

1667d2153d694b3c096be50679981a188b9df955 authored over 2 years ago by axelwalter <[email protected]>

polish test files

7a2a5d1410f561f8db3777c7cf3461fe244b77d0 authored over 2 years ago by JeeH-K <[email protected]>

test adapted for new data structure, also fully testing new input methode

db1600f2a4e90ba144da0fb7cbcf7b2ba24c12a5 authored over 2 years ago by Tom Waschischeck <[email protected]>

new data structures for checkbox-spinbox-correlation

fb7605c25898de9ca35315a0ca0d9c65ec5119f0 authored over 2 years ago by Tom Waschischeck <[email protected]>

TransformationLinearModel: refactored manual exact solution

8ba9e85caf94edf75a44b6c9ad2d5581e2e22ea8 authored over 2 years ago by Eugen Netz <[email protected]>

Using exact solution instead of least-squares fit

Also added exception in case the solution doesn't work.

573dceedf894176c81c404af7aa51b670f57c402 authored over 2 years ago by Eugen Netz <[email protected]>

[COMMENT] updated authors

4b4842d610d89b522df73b9749aa25ecab990349 authored over 2 years ago by Eugen Netz <[email protected]>

[FIX] added a special case to linear model fitting

Least-squares fitting with `Wm5::HeightLineFit2` can fail with two points that are too close to ...

5eb2d6f60e40538a94f8ae5c4c84a9ab53765d3e authored over 2 years ago by Eugen Netz <[email protected]>

wrap IonIdentityMolecularNetworking

f402d2f825c1f464944196e68e7c47b6403c8bed authored over 2 years ago by axelwalter <[email protected]>

isotope size 0 check added to getApexIndex etc. in FLASHDeconvHelperStructs.cpp

671d045b7fc4271e7b1e43134bca781865bde166 authored over 2 years ago by kyowonjeong <[email protected]>

merging develop

76bfd581a7cac0cb7986ba6c527ebfdde7449047 authored over 2 years ago by Tom Waschischeck <[email protected]>

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

ac4a97ef235f9c27ad89f011b4d35a7ae83710d3 authored over 2 years ago by Tom Waschischeck <[email protected]>

remove rebase action (now provided by github)

114144fe5c0b5ab0b1d623b055a4e45034e194c3 authored over 2 years ago by Timo Sachsenberg <[email protected]>

Update VS22 second try (#6020)

* reset contrib

* array includes

* update contrib to master

6db36146ff779d2b19c79fd8960ebc524cf7f6d7 authored over 2 years ago by TomW <[email protected]>

fix url (#6018)

c4fa7f37d90d5de088ff08639e0a92a4b21c6af4 authored over 2 years ago by M Bernt <[email protected]>

updated SpectraMerger changes from feature/FLASHDeconv

c50de2624ecd2f636cf9339509065e0c7d487c32 authored over 2 years ago by JeeH-K <[email protected]>

Merge branch 'feature/FLASHDeconv' into feature/FLASHDeconvOnly

# Conflicts:
# src/openms/include/OpenMS/ANALYSIS/TOPDOWN/FLASHIda.h
# src/openms/source/ANALYSI...

5789efdd5ff943548db9a573d7a1bd775f8b0260 authored over 2 years ago by JeeH-K <[email protected]>

Timo's comments are being addressed 2

ebcbe883c58733e2c66f79c4c301a1f6455c1876 authored over 2 years ago by kyowonjeong <[email protected]>

Timo's comments are being addressed

7f43eb935e4da8d09c26fe2ebf1a410092372d94 authored over 2 years ago by kyowonjeong <[email protected]>

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

0b9f8a1cd45d60d9302388713a585f83fa3bc23f authored over 2 years ago by Tom Waschischeck <[email protected]>

reset contrib

74c1ac4a8a2a1aa6a622bd8c649b8cce1b53ea50 authored over 2 years ago by Tom Waschischeck <[email protected]>

Cleaning

f8323b568145dc12b354857caff33ae7702ce8c9 authored over 2 years ago by bertrandboudaud <[email protected]>

Deconvoluted -> deconvolved rename done.

2f1082b91af59bad5739e3b22f49d5f40be90208 authored over 2 years ago by kyowonjeong <[email protected]>

Target mass bug for all MS levels

79c4e3d64fe161d862221d920dc12bd963be63f6 authored over 2 years ago by kyowonjeong <[email protected]>

Merge branch 'feature/FLASHDeconv' into feature/FLASHDeconvOnly

feature/FLASHDeconv version: 9e83c9e

6786c987d483e73aa3029bc5cc446d08faea365b authored over 2 years ago by JeeH-K <[email protected]>

Fix failing IM tests (issue #4339) (#6017)

* Fix failing IM tests

IM tests that failed was the one that had 0 MS1 and 0 MS2 transitions
...

4644b57c60a511d448447929e394aa113f3286b8 authored over 2 years ago by Joshua Charkow <[email protected]>

saving preliminary state

ea586499bf479d13ff9984a5dab21bce07dcecab authored over 2 years ago by Tom Waschischeck <[email protected]>

Merge pull request #6016 from OpenMS/fix_external

fix external project

f74f3eed0bdcc4e03f96142f34e7e85efdd6107f authored over 2 years ago by Chris Bielow <[email protected]>

Merge pull request #6002 from Waschi97/feature/TSGDialog/Test

[TEST] GUI test for TheoreticalSpectrumGenerationDialog

c7d2a3490bb411d9c61400cd1c043e6ce4b49ec7 authored over 2 years ago by Chris Bielow <[email protected]>

fix external project

4b17789411fb47f629b81e6f9fd3741b1b8f6b41 authored over 2 years ago by Chris Bielow <[email protected]>

Merge pull request #6015 from OpenMS/jpfeuffer-patch-5

fix and move pyopenms whls before they get deleted again on lnx

aca4ce313076272f318effeb6d25c091c92029bc authored over 2 years ago by Julianus Pfeuffer <[email protected]>

fix and move pyopenms whls before they get deleted again on lnx

db058fb8b137574408df0afa0e6297a5c587322f authored over 2 years ago by Julianus Pfeuffer <[email protected]>

revert romval of arginine loss

9abfbe3eef88ea1c2a948e825c864714e3f60059 authored over 2 years ago by Timo Sachsenberg <[email protected]>

prototype dim_mapper

0dc6351672906d44639379bbb48009c8296f8f11 authored over 2 years ago by bielow <[email protected]>

fix warning

e3ba8d901d01d5f7a21fc27051b53c7fa5dd5ead authored over 2 years ago by bielow <[email protected]>

move noise filtering into canvas

179da72928bc72aab631a48967438ecee8908b91 authored over 2 years ago by bielow <[email protected]>

some simplification

3662f7afbf787bb19f08dda5c50c70287bfd1c55 authored over 2 years ago by bielow <[email protected]>

Merge branch 'update/VS22support' into feature/TSGDialog/EmpiricalSpectra

833817dd7d2340d1df4ccef847b69f243d663d33 authored over 2 years ago by Tom Waschischeck <[email protected]>

fix warning

c52ec9d010f5be8166e4f77290bee6d20397d10d authored over 2 years ago by bielow <[email protected]>

String QString conversion

775ed12de2012761fcfb8509727781d9bcfcd400 authored over 2 years ago by Tom Waschischeck <[email protected]>

Store retention time in msp files

b3754e5fdd433afc92c884fa5e0aaafe99175488 authored over 2 years ago by bertrandboudaud <[email protected]>

Store MSP: do not store spectrum with no peaks.

0bc944378b9a0c4f4b9e3685052bdef30a14ddf0 authored over 2 years ago by bertrandboudaud <[email protected]>

Added one option to return unknown feature in searchSpectrum

f221055deb1304a2d70fb5b3ab208db52f7d91ca authored over 2 years ago by bertrandboudaud <[email protected]>

Removed debug traces

a8de3f79492333f381a7693017a00623a0f0b904 authored over 2 years ago by bertrandboudaud <[email protected]>

Removed debug traces

0dbc87d60f7329520c429ff709539a61184fcaed authored over 2 years ago by bertrandboudaud <[email protected]>

Store retention time in msp files

d2dbfcbded04b71e4a28e1a364f92bd1bd11d126 authored over 2 years ago by bertrandboudaud <[email protected]>

storeSpectraTraML renamed constructTransitionsList

429c5f04ee2bfc3f25e9ab08cb67a40821b076d1 authored over 2 years ago by bertrandboudaud <[email protected]>

Added one option to return unknown feature in searchSpectrum

94a8d5250dbffaf816ee4934e7fdb83dd6179f33 authored over 2 years ago by bertrandboudaud <[email protected]>

Store MSP: do not store spectrum with no peaks.

514cd713a0b32efd1df35547749bf12c753a5b53 authored over 2 years ago by bertrandboudaud <[email protected]>

Added new extractSpectra method for DDA

946808467670a3638f4d1e37a991ca1952d300fa authored over 2 years ago by bertrandboudaud <[email protected]>

Fixed doc

9e1a02729a60f3aa61dca691d9fd6ad8a3c86791 authored over 2 years ago by bertrandboudaud <[email protected]>

Merge pull request #6013 from OpenMS/jpfeuffer-patch-5

[FIX] Make plotting.py more robust

4fe1d96c5a03eea86d3059feb967b03dcc439380 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

fixes https://github.com/OpenMS/OpenMS/issues/4448

removed
arginine->addLossName("");
arginine->addLossFormula(EmpiricalFormula("CONH2"));

8464efb2debf9c3be1ca237968a5bcc6c5333c86 authored over 2 years ago by Timo Sachsenberg <[email protected]>

[FIX] Make plotting.py more robust

53dee72d99fb1e8540c72598bf3a31563436394a authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #6007 from OpenMS/pyopenms/typehints

Add type hints to openms conversion providers

13a4908faae4c6e814168ff6617b81bc92edca82 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

fix Typo

fdc1ad28962cd0ec85bdcc84fb30c401e9d9339f authored over 2 years ago by bielow <[email protected]>

some speed improvements in plotting

5b0dcbde3b5bdf6cd1cfd64e52b7aa86d9fabe4e authored over 2 years ago by bielow <[email protected]>

coinor and boost updated

cfadeac691dafe013ce4694e5570666810cc7122 authored over 2 years ago by Tom Waschischeck <[email protected]>

merging TSGTest to adapt it for metabolic input

7309268e91a897802453e8441b59d3574b829548 authored over 2 years ago by Tom Waschischeck <[email protected]>

Merge pull request #6009 from OpenMS/feature/pyomstyping

[FEATURE] package type stubs with pyopenms

78304b740751603ac5c41b618ec95d0c8e48c51c authored over 2 years ago by Julianus Pfeuffer <[email protected]>

[FEATURE] package type stubs with pyopenms

4b59c3408b935145be7fd238b999f19cc1cfe261 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

[pyopenms] fixes some of the newly introduced bugs (#5997)

* Add support for PASEF scans

Previously when processing diaPASEF data with overlapping m/z S...

d39eb52eb4272bcb12190f8496be3cc28d827897 authored over 2 years ago by Timo Sachsenberg <[email protected]>

use contrib_manylinux container from github registry (#6005)

* use contrib_manylinux container from github registry

* also update openms-ci to use new reg...

e0eb614683a4213fa6433344174598c6e1cd8f97 authored over 2 years ago by Timo Sachsenberg <[email protected]>

Update special_autowrap_conversionproviders.py

0c4ce8e9a8bcca1af2662f446df85d7503cf1406 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Add type hints to openms conversion providers

1a8d341cfaaa9803ca51036ae72ab21be29cee98 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

minor comment updates in contrib

1275fe9a1630786e30e0a18c036a9070b87ae73a authored over 2 years ago by Tom Waschischeck <[email protected]>

testing if error message boxes are produced

fb44986de09620f543f61f3be9f326ddab37adf3 authored over 2 years ago by Tom Waschischeck <[email protected]>

[FEATURE] Export annotated spectra from Sirius as mzml

ec7aec3622cfea53a9244f0c63d8538bb9a4d983 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

renamed istope model buttons

75c10eaa66cdb70545b2bb231334bec274669aa5 authored over 2 years ago by Tom Waschischeck <[email protected]>

removed unnecessary vector, some vectors to arrays,'_' for protected members, comments, typos

01fd53b5c67efd7ff0bc40b1e536b7a1da25b811 authored over 2 years ago by Tom Waschischeck <[email protected]>

contrib update, fixed some resulting build errors

af5d263af7be6ed7e4e82afa8c1f9243a664a74e authored over 2 years ago by Tom Waschischeck <[email protected]>

forgot to rename function call

9019815158b40fc18bb96db4358b4b03f0f96271 authored over 2 years ago by Tom Waschischeck <[email protected]>

getParam() -> private getParam_()

699bc34503e4bdcc07209d8f903ae2f1d1bc23f2 authored over 2 years ago by Tom Waschischeck <[email protected]>

some variable renaming and another map to vector

f0afcbd533e67084686d6e53d0734b7db7984d2c authored over 2 years ago by Tom Waschischeck <[email protected]>

map to vector for simplicity

34fde278236b8c9a6ce37f9b206cf17289c4d6ac authored over 2 years ago by Tom Waschischeck <[email protected]>

remove unnecessary link libraries

63a7217d719601e85953ff17f24c8859d3d673db authored over 2 years ago by Tom Waschischeck <[email protected]>

PSMFeatureExtractor add tests (#5087)

* PSMFeatureExtractor differentiate list and single file input

The tool has two input modes s...

ae31f310df4ea7a3e319d97aa063762fc432b0d2 authored over 2 years ago by M Bernt <[email protected]>

contrib update

2008f0a535557126b53dafb2d73021037529a8ff authored over 2 years ago by Tom Waschischeck <[email protected]>

name change of GUI elements

373632d6fc615cd38107a9d8d815b5142ef647f5 authored over 2 years ago by Tom Waschischeck <[email protected]>

comments

9dc965fc150f950cedaceaf76e421314d37f7221 authored over 2 years ago by Tom Waschischeck <[email protected]>

shorter delay for faster test

287ed04ce77c57389646f6f0f99d4aa0c87022c7 authored over 2 years ago by Tom Waschischeck <[email protected]>

testing parameters and spectrum generation, function for GUI testing ions and intensities

a12d824e711d147ae1b1d1aa39d1c5c768d77df7 authored over 2 years ago by Tom Waschischeck <[email protected]>

Revert "[FIX] fix memory leak"

This reverts commit c1ac64b0a5e43cdc30764e965bfdcd9ea7603974.

bc87d11b6e248427ed6706e31b6965e30b1560b0 authored over 2 years ago by Hannes Roest <[email protected]>

run github actions CI for every push/PR (#6000)

b9eca03b649d6abb7b167cac6ca2bee1c7a6de9e authored over 2 years ago by Timo Sachsenberg <[email protected]>

CI warning fixes for pr-5819 (#5999)

* swp warm up: some hopefully easy fixes for continious integration

* Added myself to AUTHORS...

7edc15dde7f48b97665ccc603bd27240edd19e35 authored over 2 years ago by Lenny Kovac <[email protected]>

template function to test spin boxes

83370bf52612729565db9ba35b9fb57c8e383915 authored over 2 years ago by Tom Waschischeck <[email protected]>

testing isotope model, ion type and intensity GUI

0a10de26d14e8541b4e37f269ca651729eb034db authored over 2 years ago by Tom Waschischeck <[email protected]>

new slot clicking on list widget item enables/disables it

9ad4bff1845a88b675caf13f056ad08a16463294 authored over 2 years ago by Tom Waschischeck <[email protected]>

[FIX] few left toSet warnings (#5996)

9e8dbe9c50f1d2ffceb432d55ed0a0c05ddf308a authored over 2 years ago by AMIT KUMAR MISHRA <[email protected]>

[FIX] few more toList() left (#5995)

* [FIX] few more left toList()

a8de8e656e8ce35726816e020949c0ab88204b45 authored over 2 years ago by AMIT KUMAR MISHRA <[email protected]>

[FIX] suppress few left skipemptyparts (#5994)

* [FIX] suppress similar skipemptyparts

* [FIX] some more skipemptyparts

16c2d8048bb625872a007ec33fb491719fa42d6a authored over 2 years ago by AMIT KUMAR MISHRA <[email protected]>

Update sources.cmake

ffae8c67c5b631fcb095acf107466226742b1fc3 authored over 2 years ago by Timo Sachsenberg <[email protected]>

Update MzMLHandler.cpp

edd1bc5377fbaaed58e3b4ddeb89ec973a950625 authored over 2 years ago by Timo Sachsenberg <[email protected]>

fix missing file extension

c91d38cb1a5b9e3743ff2653cdc9bbd0972e11e3 authored over 2 years ago by Timo Sachsenberg <[email protected]>