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

[fix] make sure all previous uses of LoadExperiment match new signature, remove unused headers

405e5a679a5ec5bc0cf1a357b7035eb7e3125b8f authored over 1 year ago by Samuel Wein <[email protected]>

Merge branch 'develop' into Feature/GenericFileLoad

9b5c8c8abc501197741321e2645dcf47ee21a56e authored over 1 year ago by Samuel Wein <[email protected]>

[fix] fixed bug in SwathFile handling of MZXml

046b9088d4202a1a094209c18fa0bc89cc5efbc5 authored over 1 year ago by Samuel Wein <[email protected]>

[nop] document loadIdentifications~

a54e1bb0a137003a68eb93711cda6e7fabb9a1a0 authored over 1 year ago by Samuel Wein <[email protected]>

[fix] added support for identification options to FileHandler fixed bug in loadIdentifications, added the ability to force type for StoreExperiment

74ab2ab83d23b3b1d5be718e2cbc98c97fe639e9 authored over 1 year ago by Samuel Wein <[email protected]>

[fix] pass parameters to consensus file loader

c3fe6600c5dacc7a3766510c2cbb18f4e191936a authored over 1 year ago by Samuel Wein <[email protected]>

[fix] fixed bug in FileMerger

01f894e0ecc3200230a2df06abc56ef6d6456872 authored over 1 year ago by Samuel Wein <[email protected]>

[fix] be less lazy at documenting

0ba650328e642dcb8b33e8ae3eb8c0836eeb2465 authored over 1 year ago by Samuel Wein <[email protected]>

bug fixes

8f366a28230f9f65793958ada1d20d4d3ec39168 authored over 1 year ago by Samuel Wein <[email protected]>

more fixes

858a7936ffea3ba33c416cd19717048899234361 authored over 1 year ago by Samuel Wein <[email protected]>

update syntax of load and store experiment

7ec7a3fe644fe0c9bce0bb644be6ec35e7d8eea3 authored over 1 year ago by Samuel Wein <[email protected]>

fixed FileHandler_Test

e2f5ff2c17c75a54ee75ef9b4d2cf5b4c15da2aa authored over 1 year ago by Samuel Wein <[email protected]>

Refactor existing loadExperiment calls to match new signature

2b8f1a11f4754cb866297003c9e7a353eb59692d authored over 1 year ago by Samuel Wein <[email protected]>

Update containerdeploy.yml

b598863d5d433e378604fb9bc80c51b17f8713f2 authored over 1 year ago by Julianus Pfeuffer <[email protected]>

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

915b3477ac9996b53faa2837f5075fad0e56dba8 authored over 1 year ago by Samuel Wein <[email protected]>

[fix] Fixed new typesWithProperties test

cf6f1c20b4d5aff2d749e238647eabf1a88a7af1 authored over 1 year ago by Samuel Wein <[email protected]>

Merge branch 'develop' into Feature/GenericFileLoad

f0ab6eb9527a9f8e49da1dccbda155edaefa79de authored over 1 year ago by Samuel Wein <[email protected]>

first pass filetype checking

ee024eebb79fd5f31ac1199bcb349ac7d77ffe2a authored over 1 year ago by Samuel Wein <[email protected]>

change defaults for loadExperiment to match underlying MZML calls

e62e79d5912858dfe5a85d27a4fcdf68770a8729 authored over 1 year ago by Samuel Wein <[email protected]>

rename to clarify types

1c4a7eaac32dd21ffc90c28b157918d22fcddb27 authored over 1 year ago by Samuel Wein <[email protected]>

Merge branch 'develop' into feature/modomicsJSON

6f7ae9d5093f97918ac8874ac9343ec1840cee7c authored over 1 year ago by Samuel Wein <[email protected]>

Merge pull request #6777 from JeeH-K/adding_action_updating_year

Adding git action for updating year number

225cc2b91e2387dddc71beb42b70d78b28f404df authored over 1 year ago by Samuel Wein <[email protected]>

Merge branch 'develop' into adding_action_updating_year

b4675c243df8096235354df48baa28cc4398e9b5 authored over 1 year ago by JihyungKim <[email protected]>

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

e1dd3fcf8b353ee25c6983a136b9b97e6807aa80 authored over 1 year ago by Samuel Wein <[email protected]>

[feature] added `feature` to FileTypes to classify which file formats support which features. Added `haveFeatures` to return a FileTypeList based on requested features

55563173fa47d01c16ff88a6dff5de870d8daa46 authored over 1 year ago by Samuel Wein <[email protected]>

Fix python_versions read in (#6778)

* testing different paths for python_versions file

* testing different paths for python_versi...

0ae53923df6c285ca667caa6994178194988be65 authored over 1 year ago by Matteo Pilz <[email protected]>

Merge branch 'develop' into Feature/GenericFileLoad

16067fb9368563c57e11b9049cec2e5051801c55 authored over 1 year ago by Samuel Wein <[email protected]>

uppercase

38e684658faf96d4d95e7faf8c6d94243acffcd0 authored over 1 year ago by Julianus Pfeuffer <[email protected]>

remove generic loads

ca8137e9a87e0d3401d5367f659ddbd982da3339 authored over 1 year ago by Samuel Wein <[email protected]>

Merge pull request #6779 from poshul/fix/AMinusBions

[fix] fix bugged a-B masses and added tests to prevent recurrance

38bf6433f45b668ac571d0bb0ff95ca79662c605 authored over 1 year ago by Samuel Wein <[email protected]>

use the simpler bool versinon

b07ea6ed102866a8a308b5c77ef5afd14c80a346 authored over 1 year ago by Timo Sachsenberg <[email protected]>

Merge branch 'develop' into adding_action_updating_year

dca655c3301a8151597ba03b8b8a4823a974aedb authored over 1 year ago by JihyungKim <[email protected]>

Add regex in sed command

1ec8e837a51ccfd5c3a23c24170a9b0b209d9836 authored over 1 year ago by JeeH-K <[email protected]>

remove MZML header from CachedMZML

ca4c0c46487fb3c250f498075521e29874337b5c authored over 1 year ago by Samuel Wein <[email protected]>

force use of MZML with CachedMZML

f7d219b8d8c0ad8ec23dab5ff769e634a5103157 authored over 1 year ago by Samuel Wein <[email protected]>

Update NASequence_test.cpp

[nop] whitespace

23f0d5dad79c2e277402ed23e0d5b65494a35d79 authored over 1 year ago by Samuel Wein <[email protected]>

first bunch

07e083b42efb2444d1826fdce27ae55c9dab00fc authored over 1 year ago by Samuel Wein <[email protected]>

genericized file loader where possible

588e88f8972defadb6453ca0b1a6aaebc22d507c authored over 1 year ago by Samuel Wein <[email protected]>

Merge branch 'develop' into feature/modomicsJSON

f76836e7b8c40bddc018f27cf16b7d2ac703d7a9 authored over 1 year ago by Samuel Wein <[email protected]>

Merge branch 'develop' into fix/AMinusBions

72bc28bd4984d6e23484d9693fde23fe2bcbab2a authored over 1 year ago by Samuel Wein <[email protected]>

[fix] fix bugged a-B masses and added tests to prevent recurrance

0df5f1fe9016cc6676cae571ae5b6c3c4870aba5 authored over 1 year ago by Samuel Wein <[email protected]>

try to change exec name inside CTD

de3db20811a764815c5d67d89bd095d3b923b4a0 authored over 1 year ago by Julianus Pfeuffer <[email protected]>

Update update_year_number.yml

remove trailing space

8e5c75038ae7a4bd031a96b5583c73ad4992b3b2 authored over 1 year ago by Samuel Wein <[email protected]>

Merge remote-tracking branch 'upstream/develop' into adding_action_updating_year

ee8d7968c54afcf4dc10f84bc6b6807bef26d23b authored over 1 year ago by JeeH-K <[email protected]>

change the trigger point as maunal one

7f518f290c4a4bc870a6254e5b4819afa43c2ad5 authored over 1 year ago by JeeH-K <[email protected]>

fix sed command error and add commit section

c0dd13c079f7f4edc9afe67d3a5fedb1b63eab28 authored over 1 year ago by JeeH-K <[email protected]>

fixing syntax error by removing comment

3840d611f230f5f3da8033041472444ce8a2b647 authored over 1 year ago by JeeH-K <[email protected]>

Merge pull request #6775 from OpenMS/UMUI_replace_deprecated

Update NSIS.template.in

7b501cfa77959153d1e3812b49ece34bdddb9b50 authored over 1 year ago by Samuel Wein <[email protected]>

Expose fileConverter both in OpenMS and Thirdparty KNIME plugin

7ffbd64a96156f1a8f3fd62e5c8da2498c0bea70 authored over 1 year ago by Julianus Pfeuffer <[email protected]>

fixing syntax error by removing comment

eab6c5a7b07a139dd858cd9d1d72d750323ad606 authored over 1 year ago by JeeH-K <[email protected]>

fixing syntax error

637740edb1d8e6901a7a5a3d9e74673ce67d2543 authored over 1 year ago by JeeH-K <[email protected]>

Added a git action for updating year number

47b89bc52b522cfc7ec1c538876b773a1e675d0c authored over 1 year ago by JeeH-K <[email protected]>

Forgot to copy binaries.ini to TP KNIME plugin

addbd8a25902e8e5ec8e9d2219830b81ec1c3bcf authored over 1 year ago by Julianus Pfeuffer <[email protected]>

Update NSIS.template.in

Replace deprecated Macro Names

ec6a230e43785a3d10bcc3ca7fed43cf9fbc65a6 authored over 1 year ago by Samuel Wein <[email protected]>

fixed review suggestions, added tests

55136148696ff31d4db6d37ed3302f5abd42f735 authored over 1 year ago by Samuel Wein <[email protected]>

Merge branch 'develop' into feature/modomicsJSON

3c69ca0e7ed3001afd0e6b0accd93db6d17c0e93 authored over 1 year ago by Samuel Wein <[email protected]>

fix ghcr.io login in containerdeploy action

04dc4d4bb7977533a8b5b2eb4413dee4b4dfac65 authored over 1 year ago by Julianus Pfeuffer <[email protected]>

update if syntax

0bde0910f53e6b5fdf4675584af983799359493c authored over 1 year ago by Samuel Wein <[email protected]>

tidy up RiboNucleotideDB

402aebff17e0814bf7562e1bfa7080acefb9198b authored over 1 year ago by Samuel Wein <[email protected]>

add checking for completeness of ribo jsons, calculate mono-mass from formula if not otherwise specified

23e98245a3eb816a93cae95ea4355be984406a89 authored over 1 year ago by Samuel Wein <[email protected]>

Cleanup FIXME's

d13e0cee7c9145944012c5e031a21e224075888c authored over 1 year ago by Samuel Wein <[email protected]>

Merge branch 'develop' into feature/modomicsJSON

ecb077d8411f2d40d3c8aafd2635aa5f22f14ee2 authored over 1 year ago by Samuel Wein <[email protected]>

added feature to changelog

8b707b9e0d72530d01b67da44919d8983eca2c1a authored over 1 year ago by Samuel Wein <[email protected]>

Merge pull request #6763 from OpenMS/fix_action

Update update_version_numbers.yml

c9266ae4f3163050acee22396b43d768641e6cbf authored over 1 year ago by Julianus Pfeuffer <[email protected]>

Merge pull request #6764 from jpfeuffer/fix/knime

[FIX][KNIME] fixup script to handle knime case on macos

498bc040532570569a3429682003045ad862ffe3 authored over 1 year ago by Julianus Pfeuffer <[email protected]>

Merge branch 'develop' into feature/modomicsJSON

bffe329d37b0d41ca15aeca3738c9b87242b4d9a authored over 1 year ago by Samuel Wein <[email protected]>

[fix] move deoxyribo's to Custom_RNA_modifications

32a69a53a5ef1af38af5012ca79a89698bb8c04e authored over 1 year ago by Samuel Wein <[email protected]>

typo

911eb0fc38728cf1c74850f975a2c4b16a8dd2c2 authored over 1 year ago by Julianus Pfeuffer <[email protected]>

comment

567ac1460b65d5f4a0eba100220e8c2db87f20d2 authored over 1 year ago by Julianus Pfeuffer <[email protected]>

fix fixup script to handle knime case on macos

9af85ffeeb8749f7c217047c9ceab7dad8b1d4d8 authored over 1 year ago by Builder <[email protected]>

[fix] fixed bogus Modomics masses

dc374d4bdf173b2dd22bbd13517e5863f6c04eae authored over 1 year ago by Samuel Wein <[email protected]>

Update OpenSwathDIAPreScoring.cpp (#6762)

9d39da058bb4625a3292a0d01ed4f65593050801 authored over 1 year ago by Samuel Wein <[email protected]>

Update update_version_numbers.yml

009d6b2deadf0a7e7d307d2dacadaeec888ee1e5 authored over 1 year ago by Timo Sachsenberg <[email protected]>

[fix] enable adducts in NASE test (#6761)

d076df2058e9a7425779596754568eee5dc61359 authored over 1 year ago by Samuel Wein <[email protected]>

Update pyopenms-wheels.yml

02ec96cf08435e2676c6d94fce51702c4d385f4e authored over 1 year ago by Timo Sachsenberg <[email protected]>

Fixed paths and added optional loading of user specified mods in either tsv or json

8642947711206665feda500241d4cd674d97961b authored over 1 year ago by Samuel Wein <[email protected]>

[feature] add modomics.json fix ambiguities mapping

85621067fc08cda43c07bfccac57538afc7b00c0 authored over 1 year ago by Samuel Wein <[email protected]>

Merge remote-tracking branch 'upstream/develop' into feature/modomicsJSON

7ba46183adb26c2c371fa6ac6e3350f0c6b6c051 authored over 1 year ago by Samuel Wein <[email protected]>

Fix undefined behavior for counting charges in adducts

d2a64a62e870165558a8eebdf761d5bbaa71fae5 authored over 1 year ago by Samuel Wein <[email protected]>

Fix/id mapper (#6758)

* fix TMT IDMapper bug

* update test

---------

Co-authored-by: timosachsenberg <sachsen...

80432dfbd8a539a109f879cc39b40e38ef83f012 authored over 1 year ago by Timo Sachsenberg <[email protected]>

Update test_pyopenms.yml

e8f69f157c875a1d4e8fe0e1a8f8c15c8e5d8902 authored over 1 year ago by Samuel Wein <[email protected]>

Merge pull request #6726 from matteopilz/develop

Add trigger to pyopenms nightlies test / use pyopenms-versions in pyopenms-wheels

64c888738c2365134453d825146b167b36d7ceb4 authored over 1 year ago by Samuel Wein <[email protected]>

Merge pull request #6679 from axelwalter/feature/update-sirius-5.6.3

Update THIRDPARTY with Sirius 5.6.3

ae91f8434e5434d602e9d1822de78e9024647be1 authored over 1 year ago by Samuel Wein <[email protected]>

Merge pull request #6752 from OpenMS/jpfeuffer-patch-5

[FIX][PYOMS] only run mac_fix_deps if wheel includes dependencies

5f4a873ddc7be961a1f4f73b1273c5e0a65f1459 authored over 1 year ago by Julianus Pfeuffer <[email protected]>

Merge pull request #6753 from OpenMS/jpfeuffer-patch-7

[KNIME] also use install_name_dir at build time

eeeafee02103ed945c583491054622cdc230be5e authored over 1 year ago by Julianus Pfeuffer <[email protected]>

[KNIME] also use install_name_dir at build time

c6c4fd2bdce35da647b8d237779a708b5a06376e authored over 1 year ago by Julianus Pfeuffer <[email protected]>

[FIX][PYOMS] only run mac_fix_deps if wheel includes dependencies

important for conda

38516ac88f9f60cac70a5d9fa7c9f881b7ea39ab authored over 1 year ago by Julianus Pfeuffer <[email protected]>

KNIME share and libs now contributed by resource plugins

d05732d30da167ec96de31632ab4340d5295b6d3 authored over 1 year ago by Julianus Pfeuffer <[email protected]>

Use the new OpenMSToolExecutor class to consider the lib plugin at the extension point in KNIME

814f56988587af81c6a947f42a065861a33a091f authored over 1 year ago by Julianus Pfeuffer <[email protected]>

Also use pyopenms as package name on our pypi server (#6749)

* Update setup.py

* always push to your pypi

7eb82ad5ce9be3d09b1695761d12e417d27e762b authored over 1 year ago by Timo Sachsenberg <[email protected]>

Merge branch 'develop' into develop

fe87e42f7a125823795d60b0750ebcff66da79fd authored over 1 year ago by Timo Sachsenberg <[email protected]>

support SVR in SimpleSVM (#6691)

* support SVR in SimpleSVM

* added test for regression

* update doc

* Update SimpleSVM....

63d101a76133b246743238276b2727ee31382b33 authored over 1 year ago by Timo Sachsenberg <[email protected]>

Merge branch 'develop' into feature/update-sirius-5.6.3

f11f0e9c173e3687ae284363f078a66d972c4c2f authored over 1 year ago by axelwalter <[email protected]>

Update citest.cmake

86e6fb1b5a148dca116b647ffef9db2bac662988 authored over 1 year ago by Timo Sachsenberg <[email protected]>

allow percolatoradapter to properly handle a corner cases when same peptide had the same scan number in merged files (#6698)

* allow percolatoradapter to properly handle a corner cases when same peptide had the same scan ...

07d35ff5825203c8f5d2f540029f70350563d23c authored over 1 year ago by Timo Sachsenberg <[email protected]>

Update os_compiler_matrix.tsv

de1552da8c3583aa50a5fa9b949b64399e0ff010 authored over 1 year ago by Julianus Pfeuffer <[email protected]>

disable host certificate check

2d8c149d2f86edf8c5c17a1cb3471925b657b6e8 authored over 1 year ago by Timo Sachsenberg <[email protected]>

ID Datastructure rule of 6 (#6736)

* rule of 6

* shortened code a bit

* fix

* Update src/tests/class_tests/openms/source/I...

3ec84c3d7dcd1312be5d78b5d8ea1538f2667bf3 authored over 1 year ago by Timo Sachsenberg <[email protected]>

changes to version action

d9e1a20721c03ca39c9e2c3960f91186b4ac7713 authored over 1 year ago by Julianus Pfeuffer <[email protected]>

Merge pull request #6737 from JeeH-K/adding_action_updating_version

Adding new git action for updating OpenMS package numbers

1848b813649f9771fefebbebb22b4a324140b9b9 authored over 1 year ago by Julianus Pfeuffer <[email protected]>