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

make UBSan errors to fail tests (#7094)

f98a5d49b120d6aa1bcc7b7570efba6aa2a99953 authored about 1 year ago by Timo Sachsenberg <[email protected]>

Keep main score in PercolatorAdapter (#7090)

* Keep main score in PercolatorAdapter

* compile fix

* Update src/topp/PercolatorAdapter.c...

3b5408e9eb70c496315c72db8c1f7109e460d38a authored about 1 year ago by Julianus Pfeuffer <[email protected]>

expose error in ResidueDB code (#7080)

* expose error in ResidueDB code

* fix residuedb

* search for viable Protein and Peptide t...

e97cf3bc57c2b6df9a54d6c468b7444f83df5590 authored about 1 year ago by Timo Sachsenberg <[email protected]>

fix ASAN bug in MapAlignmentAlgorithmIdentification.h (#7089)

* fix ASAN bug in MapAlignmentAlgorithmIdentification.h

* Update SqliteConnector.cpp

83a31ae70335408efb83138c067cbad56375fa25 authored about 1 year ago by Timo Sachsenberg <[email protected]>

Fix asan bug in SageAdapter.cpp (#7085)

* Fix asan bug in SageAdapter.cpp

* Update SageAdapter.cpp

* U...

6728962b3622eea8dd73ef2d191477a9c3b8d93f authored about 1 year ago by Timo Sachsenberg <[email protected]>

UBSan fixes (#7087)

* UBSan fix for feature

* Update TransitionExperiment.h

* Update ROCCurve.h

5e92e3e58e8cb7123614533210d44d6fb903c91a authored about 1 year ago by Timo Sachsenberg <[email protected]>

Update SemanticValidator.h (#7086)

fe5c81396e1eef1bb05bfdb3c6905a13b9ef9f10 authored about 1 year ago by Timo Sachsenberg <[email protected]>

[cleanup] remove FIDOAdapter (#7009)

* remove FIDOAdapter

* update doc

---------

Co-authored-by: timosachsenberg <sachsenb@i...

07ff91419871f53ae462954cd78555549cbfb402 authored about 1 year ago by Timo Sachsenberg <[email protected]>

fix empty ms-levels which lead to exception (#7082)

a627a6fd208d42ff2803f1648e35533b5d722032 authored about 1 year ago by Chris Bielow <[email protected]>

Update AddressSanitizer.cmake (#7081)

5e4854c9212847baf683981fe114f08f3534041f authored about 1 year ago by Timo Sachsenberg <[email protected]>

Update ProteomicsLFQ.cpp (#7078)

ecfd8431856a16f04d21d001191294005ebe7745 authored about 1 year ago by Timo Sachsenberg <[email protected]>

Prot quant comment lines (#7079)

* fix: number of columns depend on number of summarized samples and not file x labels

* add a...

d91d74e53356c36028e0b1d517109cae9755c11b authored about 1 year ago by Timo Sachsenberg <[email protected]>

Merge pull request #7076 from cbielow/feat_TOPPAS_docs

restore TOPPAS tutorial

5f2869cf16201bfd909807f8923071db84c07c91 authored about 1 year ago by Chris Bielow <[email protected]>

include UndefinedBehaviorSanitizer (#7077)

b2f74363c34203ad354ed65cbf58baedc77c5261 authored about 1 year ago by Timo Sachsenberg <[email protected]>

fix ProteinQuantifier (#7072)

* fix experimental design mapping bug

* ignore extensions

* faster lookup

* Update src/...

1710a5f28da2831c672e4001aeb6f659f154ff5c authored about 1 year ago by Timo Sachsenberg <[email protected]>

add changelog

9700bf38242bedba10e0d44f1da16d47f65e8b4d authored about 1 year ago by Chris Bielow <[email protected]>

switch to SPDX license with

grep -lr --include="*.doxygen" "// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE." . | xargs sed -i -...

e18978ff383afb5e103a97f435754b740dc10aa7 authored about 1 year ago by Chris Bielow <[email protected]>

revive TOPPAS tutorial

d0a724b250dc9c35b57f4d43b795ba56c8c2bb5e authored about 1 year ago by Chris Bielow <[email protected]>

rename some of the old UTIL tests to TOPP tests (#7073)

Co-authored-by: timosachsenberg <[email protected]>

4d8fa137781d2d1e3896ee185ad464f9b7342ae0 authored about 1 year ago by Timo Sachsenberg <[email protected]>

fix some remaining occurances of util (#7074)

* renamed some of the doc links

* last fixes?

---------

Co-authored-by: timosachsenberg...

7bf38f0b7572241ce133def85d55863f9384b055 authored about 1 year ago by Timo Sachsenberg <[email protected]>

fixes bug in string conversion (#7070)

* Update IDMapper.cpp

ac2849fccd599d5a033ab71d5886fc6e686cf193 authored about 1 year ago by Timo Sachsenberg <[email protected]>

make internal calibration plots more robust (#7064)

* make internal calibration plots more robust (so they work with our BSA examples, which are onl...

b6fcb0d0328b8054d9ec1ee80acf7a67bdb45ccb authored about 1 year ago by Chris Bielow <[email protected]>

Update Main.doxygen (#7068)

0671d2608aa8976185b4478a2901dcd7ee662844 authored about 1 year ago by Timo Sachsenberg <[email protected]>

Merge pull request #7067 from cbielow/feat_SPDX_license

Switch to SPDX license format

336eb46ddad509393812e07ecd00568b78292c9c authored about 1 year ago by Chris Bielow <[email protected]>

change to SPDX in all .h and .cpp

0cc30f9b98054a1cf12b789b64bf0b26687d5e9c authored about 1 year ago by Chris Bielow <[email protected]>

add SPDX template

78d588651e42d52a22eb17aba0801984a58d82e6 authored about 1 year ago by Chris Bielow <[email protected]>

manually do tutorials which have special formatting

e7cc1cca52c8d41b1054c889026239fe6b2b112f authored about 1 year ago by Chris Bielow <[email protected]>

switch to SPDX in other files

036213ea371684498b1d067ade238dc00bee9d54 authored about 1 year ago by Chris Bielow <[email protected]>

prep: correcting misformatted old license headers in .h/cpp files

63a9fee01fd5a4d3619c1415b0acec656cec96a0 authored about 1 year ago by Chris Bielow <[email protected]>

Merge pull request #7065 from cbielow/fix_filesystem

fix #7051 (repairs #7035)

39b6fd45a20c39aa34359d56eb93c41da303eb9b authored about 1 year ago by Chris Bielow <[email protected]>

fixes https://github.com/OpenMS/OpenMS/issues/7051

cda7f5d00888ba28221d75b648a9dc647aa261c1 authored about 1 year ago by Chris Bielow <[email protected]>

Merge pull request #7063 from OpenMS/fix/sageAndSpecRefs

[FIX] Sage charge states and spec refs and general spec ref handling

4ffa5f3731b75c677275459feecf723525c0b1ac authored about 1 year ago by Julianus Pfeuffer <[email protected]>

fix

4ebb354e9a6adb7d09c193b83f285decfe4a16c1 authored about 1 year ago by Julianus Pfeuffer <[email protected]>

possible fix

f54ce633115b4430c0e7a299c83323838c0f45e7 authored about 1 year ago by Julianus Pfeuffer <[email protected]>

Update src/openms/source/QC/FragmentMassError.cpp

1e8a018e40a7d22eabeef500356b0a2d4cf5f9d0 authored about 1 year ago by Julianus Pfeuffer <[email protected]>

[FIX] Sage charge states and spec refs and general spec ref handling

4ddfea0afd9deee6dfb99eece1d25771b6c45f94 authored about 1 year ago by Julianus Pfeuffer <[email protected]>

Update and rename README to README.md

45f80f4a851ba6b588b1d9fe8589fec27f7148ab authored about 1 year ago by Julianus Pfeuffer <[email protected]>

docs SageAdapter.cpp

1bd1cf65b4025850d236419b9a78865492ac06ab authored about 1 year ago by Julianus Pfeuffer <[email protected]>

Update openms_ci_matrix_full.yml

1995a0367190d5941e7ff6f3abc3c20037761332 authored about 1 year ago by Julianus Pfeuffer <[email protected]>

Merge pull request #7052 from OpenMS/fix/coarseisogen

[FIX] CoarseIsotope generation

d214ca65bdabb986a4826235f4805c0687225bee authored about 1 year ago by Julianus Pfeuffer <[email protected]>

Merge pull request #7049 from cbielow/fix_apple

fix ARM64 compile error

206a0cfb14974bd7203ad6fc51a9128f9ed93b93 authored about 1 year ago by Julianus Pfeuffer <[email protected]>

Merge pull request #7053 from OpenMS/jpfeuffer-patch-5

[FIX] PercolatorInfile reading even more

ec74fb2d44364848e9ff0151623cabafff436b4b authored about 1 year ago by Julianus Pfeuffer <[email protected]>

param docs

7177fef34d76eda9ab344fb2dd8c9c3820fdf1c8 authored about 1 year ago by jpfeuffer <[email protected]>

Fix more SageAdapter

fc428d4b23bd1c871623c1d129e3889746291fb8 authored about 1 year ago by jpfeuffer <[email protected]>

Update ProteomicsLFQ.cpp

166fa2368934ad750ef7e84b5174cccc4680abbe authored about 1 year ago by Julianus Pfeuffer <[email protected]>

[GHA] Upload update site subfolder

a5aaf45a2a8c257770e0310320c1577a1b84b654 authored about 1 year ago by Julianus Pfeuffer <[email protected]>

Use more Constants in ProteomicsLFQ.cpp

4e97f256e9c523122a601bd0435cefd79b41d2f3 authored about 1 year ago by Julianus Pfeuffer <[email protected]>

[FIX] PercolatorInfile reading even more

Spectrum references have no business at a PeptideHit!

a20b5e3729cf5bcb1e358a50c43138b0552c74dd authored about 1 year ago by Julianus Pfeuffer <[email protected]>

[FIX] CoarseIsotope generation

5b25d6ea38aa433e3c693877474eed704cdc3787 authored about 1 year ago by jpfeuffer <[email protected]>

Merge pull request #7044 from OpenMS/jpfeuffer-patch-5

Fix PercolatorInfile loading

d93ea58882cb19f57dff6ee3de300ad93d61a0d2 authored about 1 year ago by Julianus Pfeuffer <[email protected]>

Merge pull request #7047 from OpenMS/jpfeuffer-patch-7

GHA Fix Win Thirdparty

2663bdd23c7c77242929199eb9ddbbacc6beb01e authored about 1 year ago by Julianus Pfeuffer <[email protected]>

fix

061c0e67ac26ad7917dbd3181af42b77a33ee170 authored about 1 year ago by jpfeuffer <[email protected]>

fix ARM64 compile error

b52b4a6a804c9980ae497dda58002754fa819be3 authored about 1 year ago by Chris Bielow <[email protected]>

GHA Fix Win Thirdparty?

ef2cb5b3a4d32e933ddd1aca26e25b09055b2a0b authored about 1 year ago by Julianus Pfeuffer <[email protected]>

More fixes to SageAdapter and downstream tools

f0265c99eecf508a4cac9c4aee410d0d90ec2f18 authored about 1 year ago by jpfeuffer <[email protected]>

Merge pull request #7038 from OpenMS/dependabot/submodules/src/pyOpenMS/pyopenms-docs-b44adfe

Bump src/pyOpenMS/pyopenms-docs from `0d5e4f3` to `b44adfe`

db48984105f00067ae43bbc522eeece58acb85dc authored about 1 year ago by Samuel Wein <[email protected]>

Merge branch 'develop' into dependabot/submodules/src/pyOpenMS/pyopenms-docs-b44adfe

85943c8a730bf3f78d1587e3bfb01dca169b2bb8 authored about 1 year ago by Samuel Wein <[email protected]>

Merge pull request #7046 from OpenMS/poshul-patch-1

Update openms_ci_matrix_full.yml

cf21d5a061d47c751c9373a7d2797160004fc1d7 authored about 1 year ago by Samuel Wein <[email protected]>

Update openms_ci_matrix_full.yml

Fix permissions for Knime updatesite before uploading.

b773d643a5c6e2b438e33e7641ce27abcbd65683 authored about 1 year ago by Samuel Wein <[email protected]>

Apply suggestions from code review

Co-authored-by: Chris Bielow <[email protected]>

3101a2462ea9436a3630bddf8a3fd568a3695099 authored about 1 year ago by Samuel Wein <[email protected]>

Merge branch 'develop' into poshul-patch-1

ef9dba0be1054b7cca51df88e2d81940cedcc70a authored about 1 year ago by Samuel Wein <[email protected]>

Merge branch 'develop' into Feature/GenericFileLoad

f2ca58362edd6d107ff1451c7299235e17c48c00 authored about 1 year ago by Samuel Wein <[email protected]>

move checkTypes_ logic out of function

ec8ac8d34f8a1ef8f40b51ff63cca59c77024fd8 authored about 1 year ago by Samuel Wein <[email protected]>

fixes #7045 by fixing win paths

9a9a540517a19d3573e0ea40eabbc5439c490d6a authored about 1 year ago by Julianus Pfeuffer <[email protected]>

Update openms_ci_matrix_full.yml

Fix variable for determining where to upload package.

703207eb078dec600ffcd79999d58bc55d1c8ff0 authored about 1 year ago by Samuel Wein <[email protected]>

Merge pull request #7035 from cbielow/xml_stuff

[FEATURE] add reporting for read/write speed for mzML

71bb596cd998d67d2840a96b04f213c8e1337b08 authored about 1 year ago by Chris Bielow <[email protected]>

cleaner numbers/units

835f116e595040f666ee46b1b6914c605c233983 authored about 1 year ago by Chris Bielow <[email protected]>

[nop] remove rogue periods from documentation in FileHandler

59994b0dc445118421944dc4fc6273e3f9488b07 authored about 1 year ago by Samuel Wein <[email protected]>

Merge branch 'develop' into Feature/GenericFileLoad

43a9be3027b4ce4ffe3d50b1f4aec46c68690402 authored about 1 year ago by Samuel Wein <[email protected]>

Merge branch 'Feature/GenericFileLoad' of ssh://github.com/poshul/OpenMS into Feature/GenericFileLoad

1fa7f6c6ae714f77fbf3d266ed9582a748dd1923 authored about 1 year ago by Samuel Wein <[email protected]>

update documentation in FileHandler.h

1e0ea59e8c321fdff51ae65c3a4ed0b188283f83 authored about 1 year ago by Samuel Wein <[email protected]>

better handling for where filename and content disagree

c9877da3a4eb21c5d689243ee04d2131c49b3ec2 authored about 1 year ago by Samuel Wein <[email protected]>

improve failure messages for fileHandler

2e1bd3c78709278da22103487706a288cb117217 authored about 1 year ago by Samuel Wein <[email protected]>

Merge pull request #7042 from OpenMS/poshul-patch-1

Update openms_ci_matrix_full.yml

b13efa775d1bcd0b8dd536306456338c8e4e76f6 authored about 1 year ago by Samuel Wein <[email protected]>

refactor

ac175958932a5a77f65af8b8be436a76b2e56483 authored about 1 year ago by Samuel Wein <[email protected]>

Update src/openms/source/FORMAT/MzMLFile.cpp

Co-authored-by: Chris Bielow <[email protected]>

817a6e31a99bfaef05666a4619c3265f20423baa authored about 1 year ago by Samuel Wein <[email protected]>

convert fileproperties to class

22fd07614fea7b5efacc0f9ca9084cb2fe7543d1 authored about 1 year ago by Samuel Wein <[email protected]>

change unordered_set to vector for filet_types

4005b1de6ee831fe8838384e1c9b5600ddd662a5 authored about 1 year ago by Samuel Wein <[email protected]>

moved tmp file creation to function from macro

4216ca6a027241fe0a7d8ea1f8ef1659e2666b64 authored about 1 year ago by Samuel Wein <[email protected]>

Fix PercolatorInfile loading

45e2f89a70f8b46f25ed00d0089ce13877313ff0 authored about 1 year ago by Julianus Pfeuffer <[email protected]>

Update openms_ci_matrix_full.yml

de21f17b7e7250eee8cbbd33689bf3fd4e620828 authored about 1 year ago by Samuel Wein <[email protected]>

Update openms_ci_matrix_full.yml

7807eb570ebf65ab35740f472a049b3dcc256c5b authored about 1 year ago by Samuel Wein <[email protected]>

Update openms_ci_matrix_full.yml

Enable SSH uploading of artifacts.

2694e00c30ad9dfaa53b6d85c92704634d85fb48 authored about 1 year ago by Samuel Wein <[email protected]>

[PKG] Try allow install in user folder

fa0474ee7ce937e6316489fe48b47efe7ce161c0 authored about 1 year ago by Julianus Pfeuffer <[email protected]>

Bump src/pyOpenMS/pyopenms-docs from `0d5e4f3` to `b44adfe`

Bumps [src/pyOpenMS/pyopenms-docs](https://github.com/OpenMS/pyopenms-docs) from `0d5e4f3` to `b...

01a0341801dd5698beecb15922abf0836dfd284a authored about 1 year ago by dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

GUIProgressLogger fix

38b78cd6decfc00f2f7c6fa46be76f18b1c2ccdd authored about 1 year ago by Chris Bielow <[email protected]>

add Changelog

50b3979549cedb8f5d3d8d9ac728287e823c7502 authored about 1 year ago by Chris Bielow <[email protected]>

Added FileHandler function to load a single spectrum from a filetype the only supports single spectra

0811c849fe9f71245898e7b7e4a6ebd74381cbdc authored about 1 year ago by Samuel Wein <[email protected]>

[GHA] minor docs

4c3ee8a35f6b99ff305e6af11c2b94a8c66756c9 authored about 1 year ago by Julianus Pfeuffer <[email protected]>

add I/O speed to mzML parsing/writing

76be12f2896ab1382ae46f9c0c52a461052b3fa3 authored about 1 year ago by Chris Bielow <[email protected]>

refactor and get rid of boost::shared_ptr

0133041d8b73134e514889d08faf7712a7cb0243 authored about 1 year ago by Chris Bielow <[email protected]>

use different gitlastchangedate approach

c424172d651f8ac277dbb850edcc17efedeb0572 authored about 1 year ago by Julianus Pfeuffer <[email protected]>

add example of setting file options

a493d3ae9867bed2e47e70255760afc117ff6e84 authored about 1 year ago by Samuel Wein <[email protected]>

gha fix

69b4c2a6fb9b046b0cbdcaf714025f95b5d868dd authored about 1 year ago by Julianus Pfeuffer <[email protected]>

GHA debug git_lastchangedate

313958f64d2c3227bee011371f880e23392b978e authored about 1 year ago by Julianus Pfeuffer <[email protected]>

Merge pull request #7025 from cbielow/feat_simd_whitespace

More SIMD/SSE2: removeWhitespace

baf6331bc1f2f47378711684009911ddf6d80da9 authored about 1 year ago by Samuel Wein <[email protected]>

Merge pull request #6996 from OpenMS/dependabot/submodules/src/pyOpenMS/pyopenms-docs-0d5e4f3

Bump src/pyOpenMS/pyopenms-docs from `04c8016` to `0d5e4f3`

151249b9295ef8ceae30ad934bdc4db34e3c83a8 authored about 1 year ago by Samuel Wein <[email protected]>

GHA Option order choco

3ed610281708c895fecc81faeb83940386335304 authored about 1 year ago by Julianus Pfeuffer <[email protected]>

GHA clone gkn and make some output more quiet

fcdf73f4b21466215f7ccbf77299df5917adf285 authored about 1 year ago by Julianus Pfeuffer <[email protected]>

download into plugin source directly??

7c4276484834855a218ec8295e16af02e8ceefbb authored about 1 year ago by Julianus Pfeuffer <[email protected]>