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

Update openms_ci_matrix_full.yml

revert tutorial change

9feee9ed147e8a657e53323ecd435ef2ee313096 authored 11 months ago by Samuel Wein <[email protected]>

Update openms_ci_matrix_full.yml

Enable tutorial building update path to download docs artifiact

c16a424dda51f9dccf8f278fa8042e697698d744 authored 11 months ago by Samuel Wein <[email protected]>

Update openms_ci_matrix_full.yml

757fa38914fe69e1a151610bc9f43fae124e4695 authored 11 months ago by Samuel Wein <[email protected]>

Update openms_ci_matrix_full.yml

a46fd83b7521e6eb4752123e7062c2d139c4d7db authored 11 months ago by Samuel Wein <[email protected]>

Update .github/workflows/openms_ci_matrix_full.yml

c09b16cf1a9c76a46cf006fbbc6e87742f6aef15 authored 11 months ago by Julianus Pfeuffer <[email protected]>

Update openms_ci_matrix_full.yml

8e893e06d5e15acb8a1c81d80278238a9df4e216 authored 11 months ago by Samuel Wein <[email protected]>

Update .github/workflows/openms_ci_matrix_full.yml

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

e4d3d91dc9a41de754ee21579d49ceacb5a4c0ca authored 11 months ago by Samuel Wein <[email protected]>

Merge branch 'develop' into GHA-full-fixes

905551da42659da02c6e8274ab6db83b638fb745 authored 11 months ago by Samuel Wein <[email protected]>

Merge pull request #7194 from OpenMS/NSIS-fix-fix

Overwrite 1k NSIS without prompt

cdd723be7fe6bf6dae42ac43569d55ca5adcce04 authored 11 months ago by Samuel Wein <[email protected]>

Update openms_ci_matrix_full.yml

Fixes from suggestions

b103f45c60cdb04231a785110fab4250f52ce74a authored 11 months ago by Samuel Wein <[email protected]>

Overwrite 1k NSIS without prompt

Fix bug where Windows CI failed after 7z refused to overwrite NSIS files.

3327a883f7070a2e3bbff291674f464bc344d182 authored 11 months ago by Samuel Wein <[email protected]>

Update openms_ci_matrix_full.yml

try to upload documentation

dd1c5eab81e4373053ccdda4e1b41d256c6d6405 authored 11 months ago by Samuel Wein <[email protected]>

Update openms_ci_matrix_full.yml

b716cd64dd571619c4c1c91aac24dd6561a25180 authored 11 months ago by Samuel Wein <[email protected]>

Feature/includes (#7191)

* [FIX] Qt include fixes

* [FIX] include fixes

9a9cd68bee74358fa57d836315c43c383d9a347c authored 11 months ago by Hannes Roest <[email protected]>

Win installer: check for correct NSIS version (#7192)

* [GHA] use custom NSIS for Windows installer

* check for correct NSIS version before packaging

1b5e049caf3b2427cb4c665ff2d588204fcc99ea authored 11 months ago by Chris Bielow <[email protected]>

[GHA] use custom NSIS for Windows installer (#7190)

f7f43aa2d3a74a68ed37f4cd173f8b88e67482e3 authored 11 months ago by Chris Bielow <[email protected]>

Merge pull request #7189 from cbielow/fix_win_installer

Fix win installer

fd9af40e9a2428924d98c5576891f6c807279686 authored 11 months ago by Chris Bielow <[email protected]>

remove installation of .NET and VS runtimes as dependency of proteowizard (msconvert): the current pwiz ships all vc-runtimes in its ./bin folder and requires a .NET runtime which is by default installed on every Win10 anyway (see https://learn.microsoft.com/en-us/archive/blogs/astebner/mailbag-what-version-of-the-net-framework-is-included-in-what-version-of-the-os)

302b69fc7d3c0bf802640c78ac435531baff6432 authored 11 months ago by Chris Bielow <[email protected]>

switch to shipping vc redist files inside our ./bin directory (avoid use of shipping and calling vc-redist.exe on the target machine)

541a759ffa81f725ab141f263beafeeb16c85cbf authored 11 months ago by Chris Bielow <[email protected]>

check for Qt5.15 to make sure Qt finds its plugins when we run GUI tools after installation on the target machine

f4823ac7a20c694617e44724cdf25ac3ff228385 authored 11 months ago by Chris Bielow <[email protected]>

[DOC] include FLASHDeconv wizard in the list of GUI tools

867c7e957d920933da2ec3e00c10e734e3af4bf4 authored 11 months ago by Chris Bielow <[email protected]>

Update CHANGELOG

4dd4e7b174a993d4259710cc4670c70a78a7e1d8 authored 12 months ago by Timo Sachsenberg <[email protected]>

Merge remote-tracking branch 'origin/refactor_remove_wavelet' into refactor_remove_wavelet

e8795149ce8f475417f86731d3cef24e90971b3d authored 12 months ago by timosachsenberg <[email protected]>

update changelog

da2243c5cddd8c9af18d5f574d3aed67d781b063 authored 12 months ago by timosachsenberg <[email protected]>

Merge branch 'develop' into refactor_remove_wavelet

cb265c5033211a6c44889834ee360742754c0f7b authored 12 months ago by Timo Sachsenberg <[email protected]>

rename peakpcikermrm to peakpickerchromatogram (#7185)

d2ba17623bca3bae6344cb53a55fb6ee2168e399 authored 12 months ago by Timo Sachsenberg <[email protected]>

forgot

e8f4ef5e56205ba0436a4bbd0f9e7a41ad70cac4 authored 12 months ago by timosachsenberg <[email protected]>

removed some remaining terms in docs

1ce58a94b87a2a0b0ef69a435d7df22a6b93d155 authored 12 months ago by timosachsenberg <[email protected]>

remove unused and outdated wavelet code

9c99b829aa38279b5bb36e8a4bdc4717433501bb authored 12 months ago by timosachsenberg <[email protected]>

fix some compile warnings and add sage citation (#7184)

1294a3ffec2be605801284959f7b77f50db100da authored 12 months ago by Timo Sachsenberg <[email protected]>

Update CHANGELOG

d944c3af40959e7201fc0c4e8aaa1e5e5c45fd69 authored 12 months ago by Chris Bielow <[email protected]>

Merge pull request #7183 from cbielow/fix_mzidentml

[DOC] Annotate SpectraMower tools

e660473da8462725f798e0ab3cd13e218ce3c18c authored 12 months ago by Chris Bielow <[email protected]>

clean up SpectraFilter tools

-- remove MarkerMower, since it does absolutely NOTHING
-- add docs for all the others

d208b1d87738e29fa2f2903cdfd873cb26a38c71 authored 12 months ago by Chris Bielow <[email protected]>

Merge pull request #7180 from JeeH-K/fixing_wizard

[FIX] ParamEditor: Move getting-tags-part to avoid error from a node (subsection param)

e3ecff60d0e13b74f659b94bc8305e915d1f157a authored 12 months ago by Chris Bielow <[email protected]>

added a Changelog of fixing the bug on ParamEditor (#7180)

5b86cc122582ca4be1bd2ceebc89cbbada03e92b authored 12 months ago by JeeH-K <[email protected]>

move getting-tags-part to avoid error from a node (subsection param)

0fe11339af1ec6472877a241e0ec32c3af803004 authored 12 months ago by JeeH-K <[email protected]>

Bump src/pyOpenMS/pyopenms-docs from `4bc75aa` to `64016e7` (#7179)

Bumps [src/pyOpenMS/pyopenms-docs](https://github.com/OpenMS/pyopenms-docs) from `4bc75aa` to `6...

f097269669ba508ef28d72ae283606ff15c0491a authored 12 months ago by dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

changed packages_dir to packages-dir (#7175)

dacb404aaf46bf6c9c4dee37938fe6546d0f30c2 authored 12 months ago by Matteo Pilz <[email protected]>

use trapezoid integration (#7177)

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

02f4818467f39d019a7d601600d46291831f1f29 authored 12 months ago by Timo Sachsenberg <[email protected]>

[FIX] make FileConverter more robust (#7176)

* [FIX] make FileConverter more robust against misuse (i.e. incompatible in/out) to avoid produc...

a2a75fb2b95d113a8de1457206cb8e9dbfd2f1c2 authored 12 months ago by Chris Bielow <[email protected]>

augment CHANGELOG

1e52378b9eb98304f1a21af3b88c91c252002d1d authored 12 months ago by Chris Bielow <[email protected]>

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

19c724331ea4d76a87161dc83221f15647e52ef6 authored 12 months ago by Chris Bielow <[email protected]>

[FIX] make FileConverter more robust against misuse (i.e. incompatible in/out) to avoid producing empty output containers (metadata makes it non-empty) or even no output file.

752a440bb103272220c0e53fb1299dc5dca81cff authored 12 months ago by Chris Bielow <[email protected]>

Bump src/pyOpenMS/pyopenms-docs from `b44adfe` to `4bc75aa` (#7173)

Bumps [src/pyOpenMS/pyopenms-docs](https://github.com/OpenMS/pyopenms-docs) from `b44adfe` to `4...

eed11154aa30d4c7bcb9dc4b873d2da699b4c0bc authored 12 months ago by dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

update test file (#7170)

e0d185ff7855ce47c40ec45156b6f833e40358aa authored 12 months ago by Timo Sachsenberg <[email protected]>

Merge pull request #7172 from cbielow/fix_clang

fix compile error in MzQCFile.cpp for clang11(linux)

24e0cd14628def9e2d4978d14428e77ea2931670 authored 12 months ago by Chris Bielow <[email protected]>

fix compile error in MzQCFile.cpp for clang11(linux)

2998adf0ae12062b61f364ce1e8b6974e8b432fd authored 12 months ago by Chris Bielow <[email protected]>

Only load MS1 in EICExtractor (#7169)

95f98eeb169081c09b06630d02782cbf732282fb authored 12 months ago by Timo Sachsenberg <[email protected]>

Bump THIRDPARTY from `e492568` to `947b56a` (#7167)

Bumps [THIRDPARTY](https://github.com/OpenMS/THIRDPARTY) from `e492568` to `947b56a`.
- [Releas...

bdef32704d6111e96bdd9f2976efd0a807957ea2 authored 12 months ago by dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Bump contrib from `3d8710c` to `69e61f2` (#7166)

Bumps [contrib](https://github.com/OpenMS/contrib) from `3d8710c` to `69e61f2`.
- [Commits](htt...

0b5888f23af3aa2c339a584d5b45964b78c4fc33 authored 12 months ago by dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Merge pull request #7163 from cbielow/fix_clang

Fix some bugs and warnings

15bc66986055b812545a07c448db61fcd73691de authored 12 months ago by Timo Sachsenberg <[email protected]>

Merge branch 'develop' into fix_clang

17fd9e49c7e6082601c739d438fc1ec1fa73c309 authored 12 months ago by Chris Bielow <[email protected]>

fix error in concatenation

57282835baf9f6a7f456d8807527155c809d8190 authored 12 months ago by Chris Bielow <[email protected]>

Merge pull request #7153 from cbielow/fix_mzidentml

[FIX] mzIdentML improvements (cvParam parsing and more)

254ea4f8ee832f4cad48f0143a51a2880c607050 authored 12 months ago by Chris Bielow <[email protected]>

Merge branch 'develop' into fix_mzidentml

fd4155a0a22706011297f94aa73803cf0dc7ebec authored 12 months ago by Chris Bielow <[email protected]>

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

66aea004130e32900801f8374bb730d7b2361eaf authored 12 months ago by Chris Bielow <[email protected]>

fix clang warnings

ce2b1339749f9c0e128ce8424ddd6c752687c7fd authored 12 months ago by Chris Bielow <[email protected]>

Merge pull request #7161 from matteopilz/fix-ubuntu-wheels-test

Fix ubuntu wheels test

996f4fb128bebd7bd554b83bc61581e5cfd92fc8 authored 12 months ago by Samuel Wein <[email protected]>

testing wheel search fix

f8600ec8697ab0aa61fd7d800acaee5b8bc941d4 authored 12 months ago by matteopilz <[email protected]>

Merge remote-tracking branch 'openms/develop' into fix-ubuntu-wheels-test

c5a33e3cf3782ceea55a2667f927c8b8ca10ae33 authored 12 months ago by matteopilz <[email protected]>

Merge pull request #7154 from SGSSGene/fix/duplicate_option_names

Remove duplicate option names

fdc30c500ad41dda0468be4c2d347de198dd48ce authored 12 months ago by Samuel Wein <[email protected]>

Merge pull request #7159 from SGSSGene/fix/xvfb_not_starting

fix: xvfb not starting when xvfb is already running

84a0b4ac50b005351ca86403477bfabed85bae80 authored 12 months ago by Timo Sachsenberg <[email protected]>

fix test files

7fe393b210a810d652b7c8ead61c5fc81a711697 authored 12 months ago by Chris Bielow <[email protected]>

fix: rename parameters to avoid duplicates

This fixes duplicates in the applications:
- PeakPickerWavelet `algorithm:optimization` → `algor...

a128f85e88804c1a3025184c03aa9ed415a2649c authored 12 months ago by Simon Gene Gottlieb <[email protected]>

doc: adjusting CHANGELOG

8e7b96158ed9d88555429998a76dab31c623ff28 authored 12 months ago by Simon Gene Gottlieb <[email protected]>

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

# Conflicts:
# src/tests/topp/THIRDPARTY/MSGFPlusAdapter_1_out.idXML

105dcfdd03cd0d96965c6aade1a53588e9f8ec31 authored 12 months ago by Chris Bielow <[email protected]>

fix test

31e008cbf323e6da8b509fc0822b4299eb5232cd authored 12 months ago by Chris Bielow <[email protected]>

Merge branch 'develop' into fix_mzidentml

4a94e96ad7ab8e3d28200731c84e017b0b90f2e7 authored 12 months ago by Chris Bielow <[email protected]>

fix: xvfb not starting when xvfb is already running

1fb835649a86a46c35db41871761f5eaaf5569de authored 12 months ago by Simon Gene Gottlieb <[email protected]>

amend changelog for recent PRs

65b29a6b967309a42fd1dc01dcb870cb0841b5c8 authored 12 months ago by Chris Bielow <[email protected]>

add conversion of XSD::Boolean to parsing cvParams

67dffa01060971b98c000d9b23569129982049b1 authored 12 months ago by Chris Bielow <[email protected]>

use more robust unit conversion in mzIdentML

c77ca7a88db2a337c6541feea935c26318c19035 authored 12 months ago by Chris Bielow <[email protected]>

move value conversion from mzML to more general XMLHandler for use in other classes

81725a57f4f988887b593dc346cf673c2c8ff135 authored 12 months ago by Chris Bielow <[email protected]>

some cleanup

81c21d9f36eb1c2bc57ced0e9d70b6e829a5ef52 authored 12 months ago by Chris Bielow <[email protected]>

Merge pull request #7156 from cbielow/info_solver

[INFO] OpenMSInfo: report which ILP lib we use

bc34c4ae5e8939798c184ecfaf588d767a4dcbe6 authored 12 months ago by Chris Bielow <[email protected]>

Merge pull request #7155 from cbielow/fix_msfragger

[FIX] MSFragger: relative path to database

c5e870bec5a554d1b652472cf0fc646270019441 authored 12 months ago by Chris Bielow <[email protected]>

Merge pull request #7158 from bernt-matthias/topic/tool-descriptions

improve tool descriptions (slightly)

68e0d95863a4c647937211f384ee8c33946242c0 authored 12 months ago by Samuel Wein <[email protected]>

Merge pull request #6780 from poshul/Feature/GenericFileLoad

genericized file loader where possible

5c3c0c148e15dc530a0f2a6ac324c0fbcff64270 authored 12 months ago by Samuel Wein <[email protected]>

improve tool descriptions (slightly)

985d4f8c1a33d02b1f617541427ca063fcc2cf67 authored 12 months ago by Matthias Bernt <[email protected]>

[INFO] report which ILP lib we use

7dabf9decbfb6b9de49932c3f87e8eb38025d2d6 authored 12 months ago by Chris Bielow <[email protected]>

Update FileHandler_test.cpp

2962cc51b4fd4659dc0fb8d5b582f0a05e375ac3 authored 12 months ago by Samuel Wein <[email protected]>

convert relative db names to absolute paths, since msfragger is executed in a new working dir (temp dir)

b1d1c939127ac33d0123e9fac75d4c78dc4065c3 authored 12 months ago by Chris Bielow <[email protected]>

require MSFragger.jar to exist (or whatever the user specified)

e91d75a51249d36c1c2489f72746394400268509 authored 12 months ago by Chris Bielow <[email protected]>

improve error message when input files are not found

8bfd1d767a7f12da2c0f2a0dad5e3faa25d6372e authored 12 months ago by Chris Bielow <[email protected]>

Remove ref to outdate file_property

1821aab90dcf239e98c96aa5a11587a16bb01c38 authored 12 months ago by Samuel Wein <[email protected]>

update Changelog

b10b578c99e2eec9138e1ad7f4a78a359b80b4fc authored 12 months ago by Chris Bielow <[email protected]>

expose out_type as normal user parameter (do not hide it as advanced)

354cf8ead319ba49337ec59850cf9880e25815c0 authored 12 months ago by Chris Bielow <[email protected]>

avoid calling ".toString().toDouble());" on potentially empty DataValue (which would crash)

af31eba9daf7decdf0ac4e76e1b7719a23ae894f authored 12 months ago by Chris Bielow <[email protected]>

augment #7129 (fixes #7099) since the value was read as "" (which will not count as 'isEmpty()' for a DataValue!

b730e1028bae1e66cb2f0d6e68be7b0ec3507b05 authored 12 months ago by Chris Bielow <[email protected]>

some internal docs

ff0c060389ebaab359055038d7173df3d8a339a5 authored 12 months ago by Chris Bielow <[email protected]>

Added new Exception type InvalidFileType

7084ddbe475a5cd87af980fb6faa3408e739f02b authored 12 months ago by Samuel Wein <[email protected]>

Update FileTypes.cpp

e91ef4fe5936488952b649556c0be1960f6127b9 authored 12 months ago by Samuel Wein <[email protected]>

Update FileTypes.h

516d111604eecd26ed7484edc160b6cb82013df2 authored 12 months ago by Samuel Wein <[email protected]>

Merge branch 'develop' into Feature/GenericFileLoad

6bfff75d4ee4f8e5922f3b564706ed2672cb9e88 authored 12 months ago by Samuel Wein <[email protected]>

Merge pull request #7146 from OpenMS/release/3.1.0

Release/3.1.0

443b652db20cf6a61c38b3e3deb4f2154fca3596 authored 12 months ago by Timo Sachsenberg <[email protected]>

Merge pull request #7147 from cbielow/fix_mzquantml

Fix MzQuantMLHandler error when <Modification> element has no "massDelta" attribute)

f9a11f76cec27f9187c38559c71b26e7e21016dd authored 12 months ago by Chris Bielow <[email protected]>

Merge pull request #7148 from bernt-matthias/rm-compnovo-test-files

remove remnant CompNovo test data

7c33681348a14c8434adb0b2563dfdd3d0101c12 authored 12 months ago by Timo Sachsenberg <[email protected]>

Merge branch 'develop' into Feature/GenericFileLoad

9f4b17e84cb7f7f665e466e74afac7d680ffffec authored 12 months ago by Samuel Wein <[email protected]>

remove remnant CompNovo test data

35d56bb1af80cd96c5227296e3d95fe1e8776425 authored 12 months ago by Matthias Bernt <[email protected]>

fix #7145 (MzQuantMLHandler error when <Modification> element has no "massDelta" attribute)

d0643e03fd4017d61bcde0b5b5c4fd8b2b09244d authored 12 months ago by Chris Bielow <[email protected]>