OpenMS commits | Ecosyste.ms: OpenCollective

Merge pull request #1 from axelwalter/main

Deployment with two apps

github.com/OpenMS/streamlit-deployment - 71f26af2ac28390cd704dc47e4b76872fa60566e authored about 1 year ago by Timo Sachsenberg <[email protected]>

enable template with TOPP tools

github.com/OpenMS/streamlit-deployment - 46675c4f417f2e1e9bee28834abf42463a90eac2 authored about 1 year ago by axelwalter <[email protected]>

mount workspaces

github.com/OpenMS/streamlit-deployment - 71827bf62589b1a5efddd6e7f74c639a85f878e5 authored about 1 year ago by axelwalter <[email protected]>

update README

github.com/OpenMS/streamlit-deployment - 0d1d5b96605042fdff00ffa806275dbb4db5d51c authored about 1 year ago by axelwalter <[email protected]>

use simple Dockerfile template app for testing

github.com/OpenMS/streamlit-deployment - b0eec562f7d4d69c846b664db28d727a5727601e authored about 1 year ago by axelwalter <[email protected]>

update README

github.com/OpenMS/streamlit-deployment - d0054455b00bb757f29bb8f976b5cef778b3a85f authored about 1 year ago by axelwalter <[email protected]>

rename compose file

github.com/OpenMS/streamlit-deployment - c44cfec8665db9995110924126835f7c3a9883b5 authored about 1 year ago by axelwalter <[email protected]>

update README

github.com/OpenMS/streamlit-deployment - 10cf2a30d025064060c98c5a257a622bc7af01db authored about 1 year ago by axelwalter <[email protected]>

add umetaflow app to compose file

github.com/OpenMS/streamlit-deployment - 8ec6516a3b8b267f9335c87afd1662a6816e49f0 authored about 1 year ago by axelwalter <[email protected]>

add template and umetaflow submodules

github.com/OpenMS/streamlit-deployment - 59647fc0ff5cf39e537743aa2ac941140ce8d891 authored about 1 year ago by axelwalter <[email protected]>

add umetaflow

github.com/OpenMS/streamlit-deployment - 8d976f0919110a46a8051ee8be418f21a474892d authored about 1 year ago by axelwalter <[email protected]>

Merge pull request #7098 from OpenMS/jpfeuffer-patch-5

[FIX] DatabaseName element in MzIdentMLDOMHandler.cpp

github.com/OpenMS/OpenMS - f958a6bc954de76f373ea5bf659c04c11b0fce38 authored about 1 year ago by Julianus Pfeuffer <[email protected]>

[FIX] DatabaseName element in MzIdentMLDOMHandler.cpp

github.com/OpenMS/OpenMS - df938b59eba2ece4f8c7c6379d5d063aa28803ed authored over 1 year ago by Julianus Pfeuffer <[email protected]>

fixed captcha in local mode

github.com/OpenMS/streamlit-template - 70c9d3b36693258a6872ec64dd10a1ace29c3124 authored over 1 year ago by Arslan <[email protected]>

SageAdapter fixes (#7093)

* update sage adapter

- don't report hits outside of charge range
- prefix SAGE subscores

...

github.com/OpenMS/OpenMS - e10059756d609732acf34f869b97c43fa3393b99 authored over 1 year ago by Timo Sachsenberg <[email protected]>

change the function input description

github.com/OpenMS/streamlit-template - 69c6bb649ade09a02e4bb76dd5ba65963cc5c00a authored over 1 year ago by Arslan Siraj <[email protected]>

update Sage to 0.14.1

github.com/OpenMS/THIRDPARTY - e49256892b14c3abbe0e2e30788b143344e4da07 authored over 1 year ago by timosachsenberg <[email protected]>

added review

github.com/OpenMS/streamlit-template - 477652ba79977310cd7a6d3af49f5ec1623413e5 authored over 1 year ago by Arslan <[email protected]>

[ProteomicsLFQ] Parameterize min. proportion for requant. (#7095)

* [ProteomicsLFQ] Parameterize min. proportion for requant.

* Update src/topp/ProteomicsLFQ.c...

github.com/OpenMS/OpenMS - acf8b460227636d5dde62f64627e506115449978 authored over 1 year ago by Julianus Pfeuffer <[email protected]>

fix local

github.com/OpenMS/streamlit-template - e1d0cec2e305e0300c08e7f4840428beecd00387 authored over 1 year ago by Arslan <[email protected]>

add subprocess/ fix captcha / annotate code

github.com/OpenMS/streamlit-template - 46d14b3baa8dff43ad5d5d9c7940f7ee28309f41 authored over 1 year ago by Arslan <[email protected]>

make UBSan errors to fail tests (#7094)

github.com/OpenMS/OpenMS - f98a5d49b120d6aa1bcc7b7570efba6aa2a99953 authored over 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...

github.com/OpenMS/OpenMS - 3b5408e9eb70c496315c72db8c1f7109e460d38a authored over 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...

github.com/OpenMS/OpenMS - e97cf3bc57c2b6df9a54d6c468b7444f83df5590 authored over 1 year ago by Timo Sachsenberg <[email protected]>

fix ASAN bug in MapAlignmentAlgorithmIdentification.h (#7089)

* fix ASAN bug in MapAlignmentAlgorithmIdentification.h

* Update SqliteConnector.cpp

github.com/OpenMS/OpenMS - 83a31ae70335408efb83138c067cbad56375fa25 authored over 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...

github.com/OpenMS/OpenMS - 6728962b3622eea8dd73ef2d191477a9c3b8d93f authored over 1 year ago by Timo Sachsenberg <[email protected]>

UBSan fixes (#7087)

* UBSan fix for feature

* Update TransitionExperiment.h

* Update ROCCurve.h

github.com/OpenMS/OpenMS - 5e92e3e58e8cb7123614533210d44d6fb903c91a authored over 1 year ago by Timo Sachsenberg <[email protected]>

Update SemanticValidator.h (#7086)

github.com/OpenMS/OpenMS - fe5c81396e1eef1bb05bfdb3c6905a13b9ef9f10 authored over 1 year ago by Timo Sachsenberg <[email protected]>

Delete Fido directory (#103)

* Delete Linux/64bit/Fido directory

* Delete MacOS/64bit/Fido directory

* Delete Windows/6...

github.com/OpenMS/THIRDPARTY - a3e6ffb171127ae4fb3484524e5a567ce580b956 authored over 1 year ago by Timo Sachsenberg <[email protected]>

[cleanup] remove FIDOAdapter (#7009)

* remove FIDOAdapter

* update doc

---------

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

github.com/OpenMS/OpenMS - 07ff91419871f53ae462954cd78555549cbfb402 authored over 1 year ago by Timo Sachsenberg <[email protected]>

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

github.com/OpenMS/OpenMS - a627a6fd208d42ff2803f1648e35533b5d722032 authored over 1 year ago by Chris Bielow <[email protected]>

Update AddressSanitizer.cmake (#7081)

github.com/OpenMS/OpenMS - 5e4854c9212847baf683981fe114f08f3534041f authored over 1 year ago by Timo Sachsenberg <[email protected]>

Update ProteomicsLFQ.cpp (#7078)

github.com/OpenMS/OpenMS - ecfd8431856a16f04d21d001191294005ebe7745 authored over 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...

github.com/OpenMS/OpenMS - d91d74e53356c36028e0b1d517109cae9755c11b authored over 1 year ago by Timo Sachsenberg <[email protected]>

Docs toppas (#210)

* fix keyboard shortcut (amends
https://github.com/OpenMS/OpenMS/pull/6703)

* linking to TOP...

github.com/OpenMS/OpenMS-docs - de5e6d1d2248755dade26a24bb1d283e6aa50206 authored over 1 year ago by Chris Bielow <[email protected]>

update installer win (#201)

* add Windows defender warning to install instructions

* add image

* Update docs/openms-ap...

github.com/OpenMS/OpenMS-docs - d88c71b7530a53231cbcd303954f1046c3bce74c authored over 1 year ago by Chris Bielow <[email protected]>

Fix broken links (#209)

* fix broken links

* circumvent wrong SSL certificate

* get rid of h...

github.com/OpenMS/OpenMS-docs - 2f132d7335dcfdcc4d26fe10022e4729050935ba authored over 1 year ago by Matteo Pilz <[email protected]>

fix a few links (#203)

* fix a few links

* a few more

---------

Co-authored-by: Timo Sachsenberg <timo.sachsen...

github.com/OpenMS/OpenMS-docs - 32b0c8c3c45475c70710e6a0d8e8800f2158e753 authored over 1 year ago by Chris Bielow <[email protected]>

Merge pull request #7076 from cbielow/feat_TOPPAS_docs

restore TOPPAS tutorial

github.com/OpenMS/OpenMS - 5f2869cf16201bfd909807f8923071db84c07c91 authored over 1 year ago by Chris Bielow <[email protected]>

include UndefinedBehaviorSanitizer (#7077)

github.com/OpenMS/OpenMS - b2f74363c34203ad354ed65cbf58baedc77c5261 authored over 1 year ago by Timo Sachsenberg <[email protected]>

fix ProteinQuantifier (#7072)

* fix experimental design mapping bug

* ignore extensions

* faster lookup

* Update src/...

github.com/OpenMS/OpenMS - 1710a5f28da2831c672e4001aeb6f659f154ff5c authored over 1 year ago by Timo Sachsenberg <[email protected]>

add changelog

github.com/OpenMS/OpenMS - 9700bf38242bedba10e0d44f1da16d47f65e8b4d authored over 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 -...

github.com/OpenMS/OpenMS - e18978ff383afb5e103a97f435754b740dc10aa7 authored over 1 year ago by Chris Bielow <[email protected]>

revive TOPPAS tutorial

github.com/OpenMS/OpenMS - d0a724b250dc9c35b57f4d43b795ba56c8c2bb5e authored over 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]>

github.com/OpenMS/OpenMS - 4d8fa137781d2d1e3896ee185ad464f9b7342ae0 authored over 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...

github.com/OpenMS/OpenMS - 7bf38f0b7572241ce133def85d55863f9384b055 authored over 1 year ago by Timo Sachsenberg <[email protected]>

Update Dockerfile

github.com/OpenMS/contrib - 69e61f28afe3209daae3182da03253c2fcabada8 authored over 1 year ago by Timo Sachsenberg <[email protected]>

Update Dockerfile

github.com/OpenMS/dockerfiles - 36cbd4f087fe88a10136492a3392659888ef5339 authored over 1 year ago by Timo Sachsenberg <[email protected]>

fixes bug in string conversion (#7070)

* Update IDMapper.cpp

github.com/OpenMS/OpenMS - ac2849fccd599d5a033ab71d5886fc6e686cf193 authored over 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...

github.com/OpenMS/OpenMS - b6fcb0d0328b8054d9ec1ee80acf7a67bdb45ccb authored over 1 year ago by Chris Bielow <[email protected]>

Update Main.doxygen (#7068)

github.com/OpenMS/OpenMS - 0671d2608aa8976185b4478a2901dcd7ee662844 authored over 1 year ago by Timo Sachsenberg <[email protected]>

Merge pull request #7067 from cbielow/feat_SPDX_license

Switch to SPDX license format

github.com/OpenMS/OpenMS - 336eb46ddad509393812e07ecd00568b78292c9c authored over 1 year ago by Chris Bielow <[email protected]>

change to SPDX in all .h and .cpp

github.com/OpenMS/OpenMS - 0cc30f9b98054a1cf12b789b64bf0b26687d5e9c authored over 1 year ago by Chris Bielow <[email protected]>

add SPDX template

github.com/OpenMS/OpenMS - 78d588651e42d52a22eb17aba0801984a58d82e6 authored over 1 year ago by Chris Bielow <[email protected]>

manually do tutorials which have special formatting

github.com/OpenMS/OpenMS - e7cc1cca52c8d41b1054c889026239fe6b2b112f authored over 1 year ago by Chris Bielow <[email protected]>

switch to SPDX in other files

github.com/OpenMS/OpenMS - 036213ea371684498b1d067ade238dc00bee9d54 authored over 1 year ago by Chris Bielow <[email protected]>

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

github.com/OpenMS/OpenMS - 63a9fee01fd5a4d3619c1415b0acec656cec96a0 authored over 1 year ago by Chris Bielow <[email protected]>

Merge pull request #117 from OpenMS/fix_redirect_KNIME

redirects for KNIME

github.com/OpenMS/OpenMS-website - 22a44586abd77d7844708ca051320f9e59e7f272 authored over 1 year ago by Chris Bielow <[email protected]>

Merge pull request #7065 from cbielow/fix_filesystem

fix #7051 (repairs #7035)

github.com/OpenMS/OpenMS - 39b6fd45a20c39aa34359d56eb93c41da303eb9b authored over 1 year ago by Chris Bielow <[email protected]>

Merge pull request #116 from matteopilz/main

Fix redirects

github.com/OpenMS/OpenMS-website - 208cba5297048389550f2a7f187e1a78c67e452a authored over 1 year ago by Julianus Pfeuffer <[email protected]>

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

github.com/OpenMS/OpenMS - cda7f5d00888ba28221d75b648a9dc647aa261c1 authored over 1 year ago by Chris Bielow <[email protected]>

added flashida redirect

github.com/OpenMS/OpenMS-website - a7eead4d30ce8be379699d7fc698044d0f11f20d authored over 1 year ago by matteopilz <[email protected]>

redirects for KNIME

open the help page for TOPP Tools in KNIME: it tries to access https://openms.de/documentation/T...

github.com/OpenMS/OpenMS-website - a1b301c68a5ee613f2293d8dbbfaf8966bf4dcd7 authored over 1 year ago by Chris Bielow <[email protected]>

Merge pull request #24 from Arslan-Siraj/app_exe

fixed local

github.com/OpenMS/streamlit-template - 1d345ccbca7e607e2f49994fde533f24f5cb6358 authored over 1 year ago by axelwalter <[email protected]>

fixed local

github.com/OpenMS/streamlit-template - d6e0c85ffaef2e83dcfb6c2ad9abdaa6de9012c6 authored over 1 year ago by Arslan <[email protected]>

Merge pull request #7063 from OpenMS/fix/sageAndSpecRefs

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

github.com/OpenMS/OpenMS - 4ffa5f3731b75c677275459feecf723525c0b1ac authored over 1 year ago by Julianus Pfeuffer <[email protected]>

fix

github.com/OpenMS/OpenMS - 4ebb354e9a6adb7d09c193b83f285decfe4a16c1 authored over 1 year ago by Julianus Pfeuffer <[email protected]>

possible fix

github.com/OpenMS/OpenMS - f54ce633115b4430c0e7a299c83323838c0f45e7 authored over 1 year ago by Julianus Pfeuffer <[email protected]>

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

github.com/OpenMS/OpenMS - 1e8a018e40a7d22eabeef500356b0a2d4cf5f9d0 authored over 1 year ago by Julianus Pfeuffer <[email protected]>

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

github.com/OpenMS/OpenMS - 4ddfea0afd9deee6dfb99eece1d25771b6c45f94 authored over 1 year ago by Julianus Pfeuffer <[email protected]>

Update and rename README to README.md

github.com/OpenMS/OpenMS - 45f80f4a851ba6b588b1d9fe8589fec27f7148ab authored over 1 year ago by Julianus Pfeuffer <[email protected]>

docs SageAdapter.cpp

github.com/OpenMS/OpenMS - 1bd1cf65b4025850d236419b9a78865492ac06ab authored over 1 year ago by Julianus Pfeuffer <[email protected]>

Update openms_ci_matrix_full.yml

github.com/OpenMS/OpenMS - 1995a0367190d5941e7ff6f3abc3c20037761332 authored over 1 year ago by Julianus Pfeuffer <[email protected]>

Merge pull request #7052 from OpenMS/fix/coarseisogen

[FIX] CoarseIsotope generation

github.com/OpenMS/OpenMS - d214ca65bdabb986a4826235f4805c0687225bee authored over 1 year ago by Julianus Pfeuffer <[email protected]>

Merge pull request #7049 from cbielow/fix_apple

fix ARM64 compile error

github.com/OpenMS/OpenMS - 206a0cfb14974bd7203ad6fc51a9128f9ed93b93 authored over 1 year ago by Julianus Pfeuffer <[email protected]>

Merge pull request #23 from Arslan-Siraj/app_exe

App exe

github.com/OpenMS/streamlit-template - 24162c802357fba21a66f06f8595a4b940fd1ea9 authored over 1 year ago by axelwalter <[email protected]>

Merge pull request #22 from axelwalter/main

Include OpenMS shared libraries

github.com/OpenMS/streamlit-template - e5e80a5dc633112087d1954e2f78ade93cd973b7 authored over 1 year ago by axelwalter <[email protected]>

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

[FIX] PercolatorInfile reading even more

github.com/OpenMS/OpenMS - ec74fb2d44364848e9ff0151623cabafff436b4b authored over 1 year ago by Julianus Pfeuffer <[email protected]>

hooks/example-data added

github.com/OpenMS/streamlit-template - fa6b8c5de40ef284cf75441de62183295594af31 authored over 1 year ago by Arslan <[email protected]>

captcha functionality added

github.com/OpenMS/streamlit-template - c2e80c7f1a6e7006864d675067f7efbd5492022e authored over 1 year ago by Arslan <[email protected]>

new hook information

github.com/OpenMS/streamlit-template - 0589bfbf88feb42423b255d1ec520526a7434e49 authored over 1 year ago by Arslan Siraj <[email protected]>

param docs

github.com/OpenMS/OpenMS - 7177fef34d76eda9ab344fb2dd8c9c3820fdf1c8 authored over 1 year ago by jpfeuffer <[email protected]>

Fix more SageAdapter

github.com/OpenMS/OpenMS - fc428d4b23bd1c871623c1d129e3889746291fb8 authored over 1 year ago by jpfeuffer <[email protected]>

Update ProteomicsLFQ.cpp

github.com/OpenMS/OpenMS - 166fa2368934ad750ef7e84b5174cccc4680abbe authored over 1 year ago by Julianus Pfeuffer <[email protected]>

[GHA] Upload update site subfolder

github.com/OpenMS/OpenMS - a5aaf45a2a8c257770e0310320c1577a1b84b654 authored over 1 year ago by Julianus Pfeuffer <[email protected]>

include OpenMS shared libraries

github.com/OpenMS/streamlit-template - 7ff0064cdabe24093d37867a2e7f3286ba25d0af authored over 1 year ago by axelwalter <[email protected]>

Merge pull request #21 from axelwalter/download-executable-in-docker

Downloadable Windows executable

github.com/OpenMS/streamlit-template - 6e9b10b56b692f5d6260ffb5b113e1cf0a419507 authored over 1 year ago by axelwalter <[email protected]>

Use more Constants in ProteomicsLFQ.cpp

github.com/OpenMS/OpenMS - 4e97f256e9c523122a601bd0435cefd79b41d2f3 authored over 1 year ago by Julianus Pfeuffer <[email protected]>

[FIX] PercolatorInfile reading even more

Spectrum references have no business at a PeptideHit!

github.com/OpenMS/OpenMS - a20b5e3729cf5bcb1e358a50c43138b0552c74dd authored over 1 year ago by Julianus Pfeuffer <[email protected]>

[FIX] CoarseIsotope generation

github.com/OpenMS/OpenMS - 5b25d6ea38aa433e3c693877474eed704cdc3787 authored over 1 year ago by jpfeuffer <[email protected]>

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

Fix PercolatorInfile loading

github.com/OpenMS/OpenMS - d93ea58882cb19f57dff6ee3de300ad93d61a0d2 authored over 1 year ago by Julianus Pfeuffer <[email protected]>

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

GHA Fix Win Thirdparty

github.com/OpenMS/OpenMS - 2663bdd23c7c77242929199eb9ddbbacc6beb01e authored over 1 year ago by Julianus Pfeuffer <[email protected]>

fix

github.com/OpenMS/OpenMS - 061c0e67ac26ad7917dbd3181af42b77a33ee170 authored over 1 year ago by jpfeuffer <[email protected]>

fix ARM64 compile error

github.com/OpenMS/OpenMS - b52b4a6a804c9980ae497dda58002754fa819be3 authored over 1 year ago by Chris Bielow <[email protected]>

GHA Fix Win Thirdparty?

github.com/OpenMS/OpenMS - ef2cb5b3a4d32e933ddd1aca26e25b09055b2a0b authored over 1 year ago by Julianus Pfeuffer <[email protected]>

More fixes to SageAdapter and downstream tools

github.com/OpenMS/OpenMS - f0265c99eecf508a4cac9c4aee410d0d90ec2f18 authored over 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`

github.com/OpenMS/OpenMS - db48984105f00067ae43bbc522eeece58acb85dc authored over 1 year ago by Samuel Wein <[email protected]>

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

github.com/OpenMS/OpenMS - 85943c8a730bf3f78d1587e3bfb01dca169b2bb8 authored over 1 year ago by Samuel Wein <[email protected]>

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

Update openms_ci_matrix_full.yml

github.com/OpenMS/OpenMS - cf21d5a061d47c751c9373a7d2797160004fc1d7 authored over 1 year ago by Samuel Wein <[email protected]>

Update openms_ci_matrix_full.yml

Fix permissions for Knime updatesite before uploading.

github.com/OpenMS/OpenMS - b773d643a5c6e2b438e33e7641ce27abcbd65683 authored over 1 year ago by Samuel Wein <[email protected]>