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

Update README

Remove old ref to svn

dd23a811af786dd89911e693823985c718d86d5c authored 12 months ago by Samuel Wein <[email protected]>

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

# Conflicts:
# src/topp/PeakPickerHiRes.cpp
# src/topp/PeptideIndexer.cpp
# src/topp/ProteinQuan...

4e787d78af306004abd6f66a1f212553804f9d75 authored 12 months ago by Chris Bielow <[email protected]>

enable WARN_AS_ERROR in doxygen

25c6a13188f7c0519294aaa438827f326bedf2bb authored 12 months ago by Chris Bielow <[email protected]>

leave one error in

e8d0b01d352e3354368a27320f6b768bf8bc46c4 authored 12 months ago by Chris Bielow <[email protected]>

fix remaining doxygen warnings

a779f32c9eb2f12a2877a8c29efef0d2488a71dd authored 12 months ago by Chris Bielow <[email protected]>

docs and better/faster implementation

9d9f6c585ccb879839bfe9f6ca77b238f0e52f16 authored 12 months ago by Chris Bielow <[email protected]>

remove useless critical section

e1536e4ce25abee3c4be831e07df5c7b44b7afd6 authored 12 months ago by Chris Bielow <[email protected]>

doygen warning fixes

53b9b6b3eee6c21cc7e7042ab673be1f1da27536 authored 12 months ago by Chris Bielow <[email protected]>

prepare for markdown support in doxygen (indents are problematic)

2da05f50fa77b6da9c3800e4f04b7450c8c2df42 authored 12 months ago by Chris Bielow <[email protected]>

a lot more doxygen fixes

4eb9aa2d2d4e862a08da8458c647371f3b8a3d06 authored 12 months ago by Chris Bielow <[email protected]>

fix doxygen warnings

1cd7dbe723840fbefa4d7f97d83e875fd005245b authored 12 months ago by Chris Bielow <[email protected]>

fix more doxygen warnings

df8f43c6503468a3597ae9a922c96f3fd1783372 authored 12 months ago by Chris Bielow <[email protected]>

a first brush over developer tutorial; readding conding conventions from Wiki

2f6ea25d3e996c5ce79fd172cc7e3636bb15f3d2 authored 12 months ago by Chris Bielow <[email protected]>

updated user FAQ

6cef09742d10ab4983ef51b8da738a0afd11b414 authored 12 months ago by Chris Bielow <[email protected]>

remove references to PeakPickerWavelet

23789e1403f07b8640cc1cde8936548a55350e5c authored 12 months ago by Chris Bielow <[email protected]>

more doxygen fixes

b8b8d1463fcc31f569022b34422ad070961b9338 authored 12 months ago by Chris Bielow <[email protected]>

fix undetected writing to bad filestream

add/fix class instantatiations

f88ca90637140ebcd6452ef46ea0299dfec760dc authored 12 months ago by Chris Bielow <[email protected]>

more doxygen fixes

aef65f5e1f8946c17308efa5eeac8e4971687e8e authored 12 months ago by Chris Bielow <[email protected]>

add missing DefaultParamHandler' derived classes to doc

f4c874c2238b96127503acff7f892e68ca089d28 authored 12 months ago by Chris Bielow <[email protected]>

better handling of missing DOT (doxygen):

- avoid doxygen warning when its missing

676b5a1945567f418207e00cc60fe5488fb99192 authored 12 months ago by Chris Bielow <[email protected]>

not derived from DefaultParamHandler... thus no params to document

4d534b264a9d49282c3dac1fd567a98f0eb82fae authored 12 months ago by Chris Bielow <[email protected]>

more doxygen fixes

a38d610804407872630cf71308252300f816054c authored 12 months ago by Chris Bielow <[email protected]>

Merge pull request #7209 from enetz/feature/csv_comments

Feature/csv comments

60e2905a7571d7b6a479dcd69141dfd2ea220b66 authored almost 1 year ago by Timo Sachsenberg <[email protected]>

Merge pull request #7286 from OpenMS/license_header

License header

0b7828d3dbbfa6a94b98a7de512881afd7af6653 authored almost 1 year ago by Timo Sachsenberg <[email protected]>

Bump tj-actions/changed-files in /.github/workflows (#7279)

Bumps [tj-actions/changed-files](https://github.com/tj-actions/changed-files) from 34.6.1 to 41....

cdaeb90068ccfcc6c343edbc5d8fbc0af512a574 authored about 1 year ago by dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

wf not needed anymore

0205bb6c3cfcb51bc3dc976931eca3dacc7870ed authored about 1 year ago by Timo Sachsenberg <[email protected]>

update license header. omit end date

d5b97af403971ef65913e064a81eda88da7378d7 authored about 1 year ago by Timo Sachsenberg <[email protected]>

more doxygen fixes

787001e36886176614cc341b08dd42044ca55203 authored about 1 year ago by Chris Bielow <[email protected]>

fix undetected writing to bad filestream

add/fix class instantatiations

67cb0533e13cd03d4eea1e7133a57987bb7a4589 authored about 1 year ago by Chris Bielow <[email protected]>

not derived from DefaultParamHandler... thus no params to document

9c92143685ca37627e74955f64adbba0cf2d6346 authored about 1 year ago by Chris Bielow <[email protected]>

a lot more doxygen fixes

8692173d4863ea18474f46033f409d297b935e05 authored about 1 year ago by Chris Bielow <[email protected]>

add missing DefaultParamHandler' derived classes to doc

da1706b0c13b34a399d4db25d15c3a4d61544cf2 authored about 1 year ago by Chris Bielow <[email protected]>

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

5df2cd5b7e288437a66b2cd3e9fab232353653ba authored about 1 year ago by Chris Bielow <[email protected]>

remove references to PeakPickerWavelet

e47a5687bee79a16a347582f98f6fae0dcbe94c0 authored about 1 year ago by Chris Bielow <[email protected]>

doygen warning fixes

474e6e1d00637de99b7e0608cf4d7761493287ee authored about 1 year ago by Chris Bielow <[email protected]>

better handling of missing DOT (doxygen):

- avoid doxygen warning when its missing

c4ea88dae399f7764b564b0595d0f17adf6048aa authored about 1 year ago by Chris Bielow <[email protected]>

fix more doxygen warnings

f0b3dc74929dc40c2571e2df83807caf35c88f8b authored about 1 year ago by Chris Bielow <[email protected]>

Always set working dir in pyopenms tests (#7282)

fixes #7281

3781a02944ec65ec78069cb93698422203dbef04 authored about 1 year ago by Julianus Pfeuffer <[email protected]>

a first brush over developer tutorial; readding conding conventions from Wiki

a1e85394cc3cd1ab735614bb24cab1a5e1f7a770 authored about 1 year ago by Chris Bielow <[email protected]>

updated user FAQ

67d49b19c24f12c421b9b47816b8c0af9e7b4557 authored about 1 year ago by Chris Bielow <[email protected]>

fix doxygen warnings

494c92d90135c9ce4d2ee1172ff4f30e5cf5477f authored about 1 year ago by Chris Bielow <[email protected]>

prepare for markdown support in doxygen (indents are problematic)

b8afec980da81c9f6bbdfc66b46ece467b211e18 authored about 1 year ago by Chris Bielow <[email protected]>

cmake cleanup (#7277)

* cmake cleanup

* Update multithreading.cmake

c4406b7d8c5b29b89b930723236d14246ca65be5 authored about 1 year ago by Timo Sachsenberg <[email protected]>

add __repr__ (#7265)

* add __repr__

* fix __repr__

0f13cce7c2fce48722bebb14610ada8c98317ae7 authored about 1 year ago by Timo Sachsenberg <[email protected]>

Allow different sizes of compressed output in zlib unit tests (#7274)

* Allow different sizes of compressed output

* Apply suggestions from code review

* Apply ...

da7603ddb84674c7f1bf143ed1ce91ee40edfc5d authored about 1 year ago by Timo Sachsenberg <[email protected]>

Speedup Ion Mobility OpenSwath Processing (#6479)

* First attempt at modifying DIA scores

Try to forgo filtering by ion mobility by
just compu...

79f553adc066425e7bed2c261cdf58cbf46527b2 authored about 1 year ago by Joshua Charkow <[email protected]>

Update openms_ci_matrix_full.yml

ec6aa46f858d741f4ff79ff0bc8a5c20796b3684 authored about 1 year ago by Samuel Wein <[email protected]>

Update openms_ci_matrix_full.yml

why the heck is it workflow_run when the value is workflow_dispatch?

2430fc9fdfc42e539eb11e125346c3104878c5fe authored about 1 year ago by Samuel Wein <[email protected]>

Update openms_ci_matrix_full.yml

b6683178538ccc938908278dcb9b1d96c24b9b83 authored about 1 year ago by Samuel Wein <[email protected]>

Update openms_ci_matrix_full.yml

f416da1ef559555ad615cc8bdd4c5302fce4042a authored about 1 year ago by Samuel Wein <[email protected]>

Update openms_ci_matrix_full.yml

refactor where we check inputs to avoid bash issues. Fix assignment instead of equality test in ...

39d49fecde40a02fc5e63c11b6ceb9889a905ef6 authored about 1 year ago by Samuel Wein <[email protected]>

Update openms_ci_matrix_full.yml

997b612ed337c41dca204b35da0dbed32d440824 authored about 1 year ago by Samuel Wein <[email protected]>

Update openms_ci_matrix_full.yml

c55b30bda7999b8587d102a93774d7adf5034a2b authored about 1 year ago by Samuel Wein <[email protected]>

Update openms_ci_matrix_full.yml

6631511285d428c9673bbc8415e582f3ea23c026 authored about 1 year ago by Samuel Wein <[email protected]>

Update openms_ci_matrix_full.yml

e1a2339c315ff076c2aa10fab18ab132639e95ed authored about 1 year ago by Samuel Wein <[email protected]>

Update openms_ci_matrix_full.yml

030591fb06ba574b676860dd7431aef2d616f24e authored about 1 year ago by Samuel Wein <[email protected]>

Update openms_ci_matrix_full.yml

47e53e867917fe9ea3017e29cf004d130909fc89 authored about 1 year ago by Samuel Wein <[email protected]>

Update openms_ci_matrix_full.yml

Fix bash issue when running as a push

1e8f93e056e8779af2c9877595a6ab88d9f2016b authored about 1 year ago by Samuel Wein <[email protected]>

Merge branch 'develop' into release/2.9.1-action

42a3788747918b37d6471e55bfd439fc59327bc3 authored about 1 year ago by Samuel Wein <[email protected]>

Update openms_ci_matrix_full.yml

Add explicit token

1f3302cfc17c31c7ed685670399372d911a336d9 authored about 1 year ago by Samuel Wein <[email protected]>

fix: remove CWL CI and pregenerated tool description files (#7275)

* fix: remove cwl CI and prebuild workflows

* fix: remove CWL testing

it was comparing aga...

ea6c611d7e1cc4884209fc47bb93846d381940e4 authored about 1 year ago by Simon Gene Gottlieb <[email protected]>

support tools with multiple headers and cpp files (#7262)

* support splitting tools into multiple files

* nop

* Update src/topp/CMakeLists.txt

* ...

198a676845fece78b6e5d2babb79120c0bfa6aff authored about 1 year ago by Timo Sachsenberg <[email protected]>

fix conversion to number (instead of ASCII code, since `operator<<(QString, char)` seems to be used for `int`, which leads to "(exit code: ÿ)." (#7273)

c106320a1374bd1de9f2c97bf61c21520b6156cc authored about 1 year ago by Chris Bielow <[email protected]>

renamed "thirdparty" folder to the more common "extern" (#7268)

3ed1396024f6b039b92ee282a548d4eba67fb40d authored about 1 year ago by Timo Sachsenberg <[email protected]>

Update CHANGELOG

6625421116cae3770fa70de7aa9fb64f6ee639f4 authored about 1 year ago by Chris Bielow <[email protected]>

[FEATURE] Concurrent MSGF+ database indexing (#7272)

* minor update

* add locking to fasta index creation, allowing multiple adapters to run in pa...

d999ae56eb83278f534121bbc2401315cc518b83 authored about 1 year ago by Chris Bielow <[email protected]>

Plotting fix - matched peaks highlighting (#7243)

* Fix plotting.py for existing annotations from SpectrumAnnotator

* remove debug

* added m...

117f7a1d814633432583dfce19db5e73240a495b authored about 1 year ago by Matteo Pilz <[email protected]>

Merge branch 'develop' into release/2.9.1-action

9d776b1a6c51ac909a57ded337560709b60dc2db authored about 1 year ago by Samuel Wein <[email protected]>

Merge pull request #7269 from OpenMS/nightlyfix

Bump brew python to 3.12

7bce5149fe0b9472b0bc62597891f004db1b85fe authored about 1 year ago by Samuel Wein <[email protected]>

Bump brew python to 3.12

2774fcfa2c2cb8418f784b0b5fac0e76fabd57dc authored about 1 year ago by Samuel Wein <[email protected]>

Merge branch 'develop' into release/2.9.1-action

4dda488158d7319999ec6511fbcd01571e7cd539 authored about 1 year ago by Samuel Wein <[email protected]>

Bump contrib from `69e61f2` to `5e42765` (#7267)

Bumps [contrib](https://github.com/OpenMS/contrib) from `69e61f2` to `5e42765`.
- [Commits](htt...

af95149b2d0b2aa24a37da75ade82d7ae6d07cbc authored about 1 year ago by dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Reverted change without an effect and cleaned up unused code

79c67b88f79883a8891107949d02685b7b2ac980 authored about 1 year ago by enetz <[email protected]>

[FEATURE] Optional support for comment lines in TextFile

Moved comment line support from CsvFile to TextFIle as an optional parameter.
CsvFile and Intern...

6d3bda4a169961aa0506dac027c1f45a9fad551a authored about 1 year ago by enetz <[email protected]>

Merge branch 'develop' into release/2.9.1-action

072a28e0d88e20b78febe22c39e615420997ed7e authored about 1 year ago by Samuel Wein <[email protected]>

Merge pull request #7258 from cbielow/doc_toppas

Update TOPPAS tutorial

57817d632cf70d45eeb52817c3f6afc2f54921f4 authored about 1 year ago by Timo Sachsenberg <[email protected]>

update workflows to latest TOPP version

3b3a3a6667d9732efc18d7954367d092eb6c323d authored about 1 year ago by Chris Bielow <[email protected]>

remove references to OMSSA, replace by Comet.

Fix some formatting issues.

36b955e2d5ee449f2874c1ffe273dcece0a74297 authored about 1 year ago by Chris Bielow <[email protected]>

update images to latest TOPPAS version

ffc38209dc8f56133a681481f527bd979e7dc659 authored about 1 year ago by Chris Bielow <[email protected]>

re-index mzML file and avoid CV warning

ca0704238b02e6a4eafb0a7d585ccb029696de26 authored about 1 year ago by Chris Bielow <[email protected]>

fix warning in traml handler (#7253)

e084a3572e9b2b5f7ba24cce567012929b5cea5f authored about 1 year ago by Timo Sachsenberg <[email protected]>

fix doc (#7250)

7903e31382d351232916906b4b6f813d5b111552 authored about 1 year ago by Timo Sachsenberg <[email protected]>

fix wrong OpenMP max_threads in OpenMSInfo TOPP tool (introduced in #7132) (#7247)

77d16b62158d404e46eddc19824685d163f66dfa authored about 1 year ago by Chris Bielow <[email protected]>

Update openms_ci_matrix_full.yml

explicitly add write permissions to github.token

194a0a07f1ba3eb49e40279ca2b0cd01adef0f16 authored about 1 year ago by Samuel Wein <[email protected]>

Check if this excludes vcpkg from dependabot.yml updates (#7245)

1ff4cde0264f121202e7c16928d89d4354463f26 authored about 1 year ago by Timo Sachsenberg <[email protected]>

Fix syntax for gh

5b44fdc308182d355362a3d3184074a8e68dac79 authored about 1 year ago by Samuel Wein <[email protected]>

fixed (hopefully) tag syntax

5cbb23dbe089983f5abf10436508e8666a9e475d authored about 1 year ago by Samuel Wein <[email protected]>

correct how we get the shas

dc7f1c59a10951a9c79dd536fd346bd55f6ea872 authored about 1 year ago by Samuel Wein <[email protected]>

fix ref to removed tool

7be700288f3d1d1f47648c1a2c3e63a26717a20b authored about 1 year ago by Samuel Wein <[email protected]>

fix spacing

7668be62b09555aa8056346dfdb11b5345c875f2 authored about 1 year ago by Samuel Wein <[email protected]>

Merge branch 'release/2.9.1-action' of ssh://github.com/OpenMS/OpenMS into release/2.9.1-action

e5674c0f1a4c4078da26b9e7b1787c4b422f7fc0 authored about 1 year ago by Samuel Wein <[email protected]>

move changelog creation up and add checks for nonsensical inputs. Fail if trying to mark_latest on a version that already exists

04ce8680bbdbdbe48740509a1fa75f0ba89aa064 authored about 1 year ago by Samuel Wein <[email protected]>

Merge branch 'develop' into release/2.9.1-action

ede64fc12626383ac5f27437a72aafd0d6cecae6 authored about 1 year ago by Samuel Wein <[email protected]>

more robust precursor purity (PR 3 of X) (#7240)

* minor refactoring

* removed RNPxl

* make precursor purity calculation more robust

* U...

39b23207571ffd9f871d4531b21a6f79412b1c77 authored about 1 year ago by Timo Sachsenberg <[email protected]>

[cleanup] remove outdated RNPxl tool (PR 2 of X) (#7239)

* minor refactoring

* removed RNPxl

* fix pxds

* also remove topp test

---------

...

c3bb6b01a2bc6f3cbf8d4c32293a88e5204f8059 authored about 1 year ago by Timo Sachsenberg <[email protected]>

[refactoring] moving files into more appropriate folders (PR 1 of X) (#7238)

* minor refactoring

* Update HyperScore.pxd

* Update MorpheusScore.pxd

---------

Co-...

795c19f54fecb5ea1004fb7d8de329a0ab909d37 authored about 1 year ago by Timo Sachsenberg <[email protected]>

Merge pull request #7237 from OpenMS/pr-7226

[FEATURE] z* and z' ions for ExD (fixed tests)

9604cfc0e7d5462a5e49845e5fc68158ccc5f4df authored about 1 year ago by Timo Sachsenberg <[email protected]>

Merge pull request #7236 from OpenMS/feature/vcpkg

Added port file to use qt from system libraries, fixed bug in LPWrapper cmake files (thanks Juli...

7ede0c9691e90cb371cdef76b459c52b8d9625a9 authored about 1 year ago by Timo Sachsenberg <[email protected]>

Merge remote-tracking branch 'origin/pr-7226' into pr-7226

b88db9587ca1e986a41ac4a63e2742a7633b4321 authored about 1 year ago by timosachsenberg <[email protected]>

fix pyopenms wrapper

f51ac071b9555e919b14eee9b7f96509c83b01c8 authored about 1 year ago by timosachsenberg <[email protected]>