github.com/OpenMS/OpenMS-1 commits | Ecosyste.ms: OpenCollective

smaller test file

fc68a0592687ff6d4821ca55d3a28800b1a2afe8 authored almost 3 years ago by axelwalter <[email protected]>

fix relative path

cd83df9caa015c346d1ae4f5faa3893a54b89cac authored almost 3 years ago by axelwalter <[email protected]>

add massql test file

76d3387c211f12e4d65362fdc57b17e4c8f4f589 authored almost 3 years ago by axelwalter <[email protected]>

[REFACTOR] function to copy spectrum meta data / settings (#3913)

* [FIX] extract function

* [FIX] also copy unit

* Apply suggestions from code review

* ...

3103eb878971eee038395dfdc88b34f1c25f3c53 authored almost 3 years ago by Hannes Roest <[email protected]>

add fallback if no precursor

14e1887e2ecd2eeec2afb1bef9ec52cb7525884c authored almost 3 years ago by axelwalter <[email protected]>

test of cppcheck action (#5727)

* test of cppcheck action

* Update cppcheck.yml

* Update cppcheck...

c68aec83c212d6151cad6215644510a12911a14b authored almost 3 years ago by Timo Sachsenberg <[email protected]>

performance improvements

3f3879758c1bc263345177be81d87f7a0be65c11 authored almost 3 years ago by axelwalter <[email protected]>

update get_massql_df

f1fb96b6ae9f95c100a170862daff011a39cf493 authored almost 3 years ago by axelwalter <[email protected]>

Merge pull request #5721 from cbielow/layer_refactor

Extend LayerStatistics

fceec07d7ef2b9da225e8d70f05a1631d30d4ae2 authored almost 3 years ago by Chris Bielow <[email protected]>

Merge branch 'develop' into layer_refactor

6c074484e17c3d4eed335d0ed394dff111c67753 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

add massql dataframe export for MSExperiment

63ec9f87764953eafb2503588b0b3379898a9bc9 authored almost 3 years ago by axelwalter <[email protected]>

add rvalue reference (#5685)

* add rvalue reference setter to PId

* Update src/openms/source/METADATA/PeptideIdentificatio...

d7218c71b18f90f96e603da269b81ee1023afbb3 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #4425 from bernt-matthias/topic/CVInspector-mapping-is-mandatory

CVInspector: the mapping_file argument is mandatory

ab1b8ef254f47a9a43b9c7138fafac3b41249726 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

minor fix

3cf74f7c124f4646437dbb0314d1fb6e5a276eba authored almost 3 years ago by Timo Sachsenberg <[email protected]>

rewrite of layerstatistics

enable creation of distributions from LayerStatistics -- remove a lot of duplicate code in Canvas'

b7e62e8b14d717529acc71453516bee4ec6b5bcf authored almost 3 years ago by bielow <[email protected]>

missing rename

d2892621d29aab0539e77142ef75c900a427390b authored almost 3 years ago by Timo Sachsenberg <[email protected]>

reviewer comments

731eb4ea06324475f09e684032f0b46609095cd2 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #5719 from timosachsenberg/fix/compile_warnings

fix compile warnings

23c3063a49644403cb852f932a7bcf633c45d7f4 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

allow for horizontal and vertical layout

14789e2d91bf718b3414ae232275eb941ee77543 authored almost 3 years ago by timosachsenberg <[email protected]>

Use newest version of action

fae01cb874a1de111ec47a75e070f0430dc713e0 authored almost 3 years ago by Julianus Pfeuffer <[email protected]>

Do not use minus in step IDs??

20bc0b7a83b2765a9bc01847b80aa08a831d8110 authored almost 3 years ago by Julianus Pfeuffer <[email protected]>

fix compile warnings

c792d3928031877f27b9cb1232f0d5217a63a74a authored almost 3 years ago by timosachsenberg <[email protected]>

add missing type

6dd17ce7f24d50ff69a0f904bd9f2c55d0fe97bb authored almost 3 years ago by Timo Sachsenberg <[email protected]>

wrong output in clang-format GH action

12656aa640abfdd0efb3611f6c42d09b0d72e239 authored almost 3 years ago by Julianus Pfeuffer <[email protected]>

merge develop

261cfd6774692f9ac3be58bea7e1fc95e594f910 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #5718 from OpenMS/jpfeuffer-patch-5

Only run clang-format if sth was changed

6eadea1e3ecf1df77e6eb432d46446687e3cff52 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

add docs

565ea9b20e40fa97557953d3831824e1499b5e5b authored almost 3 years ago by bielow <[email protected]>

Only run clang-format if sth was changed

8f3dc5ebe7b76396078f39dc049fc971b4c08cbe authored almost 3 years ago by Julianus Pfeuffer <[email protected]>

set column limit to high value

5caaa89e3f1e7c13909899fb536940c0233a1e55 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #5716 from OpenMS/feature/update_automatic_rebase

Update rebase.yml

60da4736f4f317393f1d91a571ac65b1ef225311 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

Update rebase.yml

d5d245fff3a19fc930fc11a06e1d28e911720e9b authored almost 3 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #5715 from OpenMS/feature/update_clang_format

clang-format version 13

bca0a861ca176d9e551667caffc6fdcae02f6bf0 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

Update openms_clang_format_add_and_commit.yml

faa16d4b6df2f417cdd19df07a7a1378fcb88e26 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

clang-format version 13

b978546713634b7b1a2e2acb3f6bb34c9be5fe95 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #5713 from cbielow/layer_refactor

Layer refactor: StatisticsDialog

d11477e182ca63c34b3f0a314ffd465541c0d65d authored almost 3 years ago by Timo Sachsenberg <[email protected]>

explicitly add `containsDIM()` functions

c1e1ca9c70af4f3ff6e38849d6b67046639d75e5 authored almost 3 years ago by bielow <[email protected]>

hopefully fixed https://github.com/OpenMS/OpenMS/issues/5714

871a48ee30cc3bed7756de1a42db40e909360985 authored almost 3 years ago by bielow <[email protected]>

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

# Conflicts:
# src/openms_gui/include/OpenMS/VISUAL/LayerDataBase.h
# src/openms_gui/include/Ope...

ca16a545d45e5882b8936012b01d963990e77fe8 authored almost 3 years ago by bielow <[email protected]>

- replace manual switching of layer type with Visitor pattern

- cleanup of LayerStatistics (separate model from view)
- visualization improvements (show ints a...

f2268cd4e426e6d64b832efd58a3d0d03dc512b6 authored almost 3 years ago by bielow <[email protected]>

[REFACTOR] New RangeManager (#5703)

* refactor RangeManager

* add Ranges to all Layer types

* Fix bug: set only m/z visible ar...

acaba98aae3c363364f38d0a3dd44e17d714a2b7 authored almost 3 years ago by Chris Bielow <[email protected]>

MapAlignerPoseClustering: print error message and fall back to identity if no data provided (#5711)

* print error message and fall back to identity if no data provided

* Update MapAlignerPoseCl...

5ebaf1dd7f2d3456f6a51687e815e1f783011df1 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

fix (#5712)

574e5c45d04427b3f9a7d2f6ee760ac0ba2f94ba authored almost 3 years ago by Oliver Alka <[email protected]>

use on disc experiment (#5709)

* use on disc experiment

* Update GNPSExport.cpp

6a7a38b0e908e85c9ce54d9d206c020495c910d2 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

Update .clang-format

b49dcf184ff5e8b5572256f882f2a3294e08b855 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

Bug fixed in precursor registration

+ isolation windows crawling implemented in FLASHIda

8836d5ac6a355fcfbf6908f389e85f352e941db6 authored almost 3 years ago by KyowonJeong <[email protected]>

fix chromatogram range

221a8d1aef077a3680f4290f17ab1b3f31112e6f authored almost 3 years ago by bielow <[email protected]>

remove some remnants

c8f346d9705d21cdc1d36aaf9b92622a248cbfc4 authored almost 3 years ago by bielow <[email protected]>

fix python bindings (wrap doc RANT!!)

currently our pyopenms build will include any CPP it finds, even its it not in the build system.....

3dffb3613fd807cf5397dbd479ddcf36e0bc2760 authored almost 3 years ago by bielow <[email protected]>

fix python bindings

90e680301ce859b4172c927db9ed5b8d801e8f69 authored almost 3 years ago by bielow <[email protected]>

fix pyOpenMS build on Windows with multiple threads by adding `if __name__ == '__main__':`. Avoids infinite recursion for spawning new processes

c773dc0951f86e4850bfa5480de3f9ddb77ff065 authored almost 3 years ago by bielow <[email protected]>

Update PULL_REQUEST_TEMPLATE.md

d124416d7654e68762cefb8103dfa3d8ba3ceec8 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

fix range for cf

5ceea76f6ef4dfe6a9e20413d80f8b7e6076e9ba authored almost 3 years ago by bielow <[email protected]>

fix pyopenms script for Windows

dd6e95e96e36d50848ad95b9b2f90231b3b114a5 authored almost 3 years ago by bielow <[email protected]>

adapt clang format (#5706)

19321c9005290c684aa7da2a686965dc3f94bf8e authored almost 3 years ago by Timo Sachsenberg <[email protected]>

fixes, more docs from review

2e9f22df672a3d8e205680f7c7fb8f0817ee1969 authored almost 3 years ago by bielow <[email protected]>

[FEATURE] add python compatible get precursor spectrum (#5704)

* [FEATURE] add python compatible get precursor spectrum

* Update MSExperiment.pxd

6005e498335b6ce95ac51ce3590bdc14ea5fd23b authored almost 3 years ago by Timo Sachsenberg <[email protected]>

[ADD] GitHub Action Clang Format (#5577)

* test_clang_format

* Add path to actions_checkout

* [FIX] style

* Ren...

6612e16d9fd8f38af415a88cb28135beb8a7d50a authored almost 3 years ago by Oliver Alka <[email protected]>

extend test; fix last remnants

ca25bacdb28db9b65871051232fedc71231495c2 authored almost 3 years ago by bielow <[email protected]>

Fix bug: set only m/z visible area, not mz+intensity

f1aff7e94b9c504c7697ca8a8a985830b5bad3a3 authored almost 3 years ago by bielow <[email protected]>

add Ranges to all Layer types

3d0b984a3bb762bcf1129bd2dd0b84d31e00ac8e authored almost 3 years ago by bielow <[email protected]>

fix imputation bug on single peak mass traces (#5702)

72ff959c8050b23a607d96f0bb043677621956ac authored almost 3 years ago by Timo Sachsenberg <[email protected]>

Correct a-B fragment masses for DNA (#5587)

* [fix] correct a-B ion masses for deoxy ribo nucleotides

* [fix] fix bone-headed syntax erro...

0810ebf7269532e6bbef7acc0114d89cd3ac0c44 authored almost 3 years ago by Samuel Wein <[email protected]>

refactor RangeManager

66d5fe3ddc58703811769fad8279b7222097120e authored almost 3 years ago by bielow <[email protected]>

[INTERNAL] OMSFileStore: wrap SQLite interaction in transactions to improve runtime

a8150b3ef0af9e2b99d9a7e803c821b469d8a2db authored almost 3 years ago by Hendrik Weisser <[email protected]>

[FIX] fixed merge error in (Metabolite)FeatureDeconvolution

1536f259b0e8b61b19a9a2f8ea8f6180dad977a8 authored almost 3 years ago by Hendrik Weisser <[email protected]>

Merge branch 'idfile-integration' of https://github.com/hendrikweisser/OpenMS into idfile-integration

8f93f1f52de7716a803cc9214a6fb0d364fe7d75 authored almost 3 years ago by Hendrik Weisser <[email protected]>

[INTERNAL] store prepared SQL queries in 'OMSFileStore' to avoid recreating them, improve runtime

a9a6f1440b87921a9edaa7af00237f7282ae4fa3 authored almost 3 years ago by Hendrik Weisser <[email protected]>

[FEATURE] increased fault tolerance in 'IdentificationDataConverter::importIDs' to allow converting problematic idXML

fd184779e5970aba01d1ebb91634d2608d720c15 authored almost 3 years ago by Hendrik Weisser <[email protected]>

Merge branch 'develop' into idfile-integration

c75d04657b279b499ce0f96bb9edf8784353e387 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

Bug in mass determination... fixed and being tested

9cd4ff2dd1f1cb5d70db6e38e89a90c0d2385daf authored almost 3 years ago by KyowonJeong <[email protected]>

New harmonic removal added (after deconvolution, in monoisotopic mass level) in FLASHDeconvAlgorithm.cpp removeHarmonics function

ba3c536e3475badc4d782c2cf376b300e496a0f6 authored almost 3 years ago by KyowonJeong <[email protected]>

New harmonic removal added (after deconvolution, in monoisotopic mass level) in FLASHDeconvAlgorithm.cpp removeHarmonics function

0b55bd659f1cb87de0529daba05026eaa1f915ea authored almost 3 years ago by KyowonJeong <[email protected]>

[INTERNAL] use function 'addMetaValues' where appropriate

a836527e6b65fde46e686ed24a7e85dec0d4eee0 authored almost 3 years ago by Hendrik Weisser <[email protected]>

[COMMENT] removed unhelpful comment

a270793a7b2ee4f7ae8a66cf6336a1f1c21b90e7 authored almost 3 years ago by Hendrik Weisser <[email protected]>

Merge pull request #5696 from cbielow/layer_refactor

Layer refactor #2

ce6a7b71486121ab9b902e0e65e8ce4f6be21126 authored almost 3 years ago by Chris Bielow <[email protected]>

fix include

e1653b1ca792d12964e67fc5f62d9ee5d307b60d authored almost 3 years ago by bielow <[email protected]>

add missing header for gcc/clang

4de63c8be5f2d6fe2b05a19e015ff0ac732fae5f authored almost 3 years ago by bielow <[email protected]>

Revert "simplification"

This reverts commit c1bf0a2fb2b26f6772efbbc7c9a26234ec98b931.

e94c30151730f84304375083ead4fd39ab145742 authored almost 3 years ago by bielow <[email protected]>

simplification

c1bf0a2fb2b26f6772efbbc7c9a26234ec98b931 authored almost 3 years ago by bielow <[email protected]>

avoid superfluous virtual keyword

e0cdd47afcb5b5e9192ea68cf10049d73bd44719 authored almost 3 years ago by bielow <[email protected]>

precompute end. much faster

6d5382e1225f7479443e9eed090d55f68f783c22 authored almost 3 years ago by bielow <[email protected]>

remove needless extension of range (recalculate_ranges_ already extends by 4%)

f84866042066791f5441439a614f9e02ecbf24cb authored almost 3 years ago by bielow <[email protected]>

noop

83909060f5626c33863cd4bc4bf7aa8ab3424f6d authored almost 3 years ago by bielow <[email protected]>

cleanup ctor

ee7486f22937b8bfe6241744fd0fb9f791d0fd4b authored almost 3 years ago by bielow <[email protected]>

[fix] added 3' phosphate gain for unspecific cleavage of nucleotides.… (#5694)

* [fix] added 3' phosphate gain for unspecific cleavage of nucleotides. This is consistant with ...

e03d5848572027d312fda7cca5540fcfb3062127 authored almost 3 years ago by Samuel Wein <[email protected]>

Hide IsoSpec using pimpl and add some clang-tidy performance fixes on top (#5681)

* cppcoreguidelines-virtual-class-destructor,misc-redundant-expression,performance-trivially-des...

48f80b3cda933c4dc5f2d20444d1cabd58f64d34 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

add convenience function

efad1292147aae1e03c3d71d1e7048f6e87d799a authored almost 3 years ago by bielow <[email protected]>

cleanup unused includes

92fae7ac5c68e19532e555c4a21482a476ea52eb authored almost 3 years ago by bielow <[email protected]>

min/maxIntensity moved into function

5f69702381b1e5b26cf3ecb723c94b9d9e54d1d2 authored almost 3 years ago by bielow <[email protected]>

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

cd9cd790e3d52b4bf063f4f74a0ca2b6fd535365 authored almost 3 years ago by bielow <[email protected]>

shorten code

3c981aea6d27ccc267b28338e67e281af9bfddc9 authored almost 3 years ago by bielow <[email protected]>

Merge pull request #5682 from cbielow/layer_refactor

GUI Layer refactoring -- preparations

42d6def5e466714cb0b9a31b9b1b446d92524bbd authored almost 3 years ago by Chris Bielow <[email protected]>

removing non-FLASHDeconv dependant files

ee800acd8041d110bda1b62233b5091723f8a278 authored almost 3 years ago by JeeH-K <[email protected]>

removing non-FLASHDeconv dependant files

66293bde9c2fdaf96720f4a6c0f9f8f294ebe09b authored almost 3 years ago by JeeH-K <[email protected]>

[DOC] improved doc. on merging in IdentificationData

43d709155681de3e7ddbfa4995e029d70d4e84e9 authored almost 3 years ago by Hendrik Weisser <[email protected]>

[DOC] improved doc. related to IdentificationData in BaseFeature and FeatureMap (incl. grouping of functions)

b29508f5169adb1c7eadd6f826d006223ecaa9d7 authored almost 3 years ago by Hendrik Weisser <[email protected]>

[INTERNAL] replaced boost::optional with std::optional in BaseFeature

9b6a68a9439b82626e3207cc3b37ae92c39d3d10 authored almost 3 years ago by Hendrik Weisser <[email protected]>

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

ed4311a2a3d7c04e53649410315b9c1eb8908e80 authored almost 3 years ago by bielow <[email protected]>

remove wrong noexcepts

ab64cf7f28fd2b3363932b38d36203ce54fae576 authored almost 3 years ago by bielow <[email protected]>

[COMMENT] removed outdated comment

e14a39dda07c8455c7b2794c18628b2af323d150 authored almost 3 years ago by Hendrik Weisser <[email protected]>