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

Forgot to import new variable to setup.py

b35fe362673626a56ef6156539e715a58d56eadd authored almost 5 years ago by Julianus Pfeuffer <[email protected]>

More cleanup

f7beb18c5707af5738b9341f00e90fcca80ae6d3 authored almost 5 years ago by Julianus Pfeuffer <[email protected]>

[FIX] another occurrence to check for directory

7eb856739b7b356bb3834c2a9311fbb4b4ec0913 authored almost 5 years ago by jpfeuffer <[email protected]>

[FIX] findExecutable should skip directories in Env with same name

Important on Unices.

767da14fa2da121361c0528abe47328ff7f83ca5 authored almost 5 years ago by jpfeuffer <[email protected]>

Merge branch 'feature/FLASHDeconv' of https://github.com/JeeH-K/OpenMS into feature/FLASHDeconv

5a1fdd7aa8000d82122e5af30e12c39bf545cf5d authored almost 5 years ago by JeeK <[email protected]>

[fix] fixed missing path in test

e5964d4e10558e4a8c599fe2724ab8eb10ca5b99 authored almost 5 years ago by poshul <[email protected]>

Merge branch 'develop' into feature/FLASHDeconv

e857af92fdf01e347bd895281629bf7ed969a8fc authored almost 5 years ago by JeeK <[email protected]>

[CodeFactor] Apply fixes

8ee3a93b54c0aeafa1ea106ecead4b2e9a132683 authored almost 5 years ago by codefactor-io <[email protected]>

Revert "Forgot code examples"

This reverts commit 7e3cf2a6eab1cf1d84f54c2cb79a4f6c95c1781c.

3f03a0eea21d3fe50c9e32d5a8e914a640dc0468 authored almost 5 years ago by Julianus Pfeuffer <[email protected]>

Different approach to fix multiple Singleton instances. Put to cpp.

a80e707091eab2af93e0ab6a33dc0ec2f17db3c3 authored almost 5 years ago by Julianus Pfeuffer <[email protected]>

Merge branch 'feature/FLASHDeconv' of https://github.com/JeeH-K/OpenMS into feature/FLASHDeconv

7ea39d67fa4d7286327be2c060a50607eae5656c authored almost 5 years ago by JeeK <[email protected]>

Merge branch 'develop' into feature/FLASHDeconv

63d7f72922afa39681d07258965298e62b0930a2 authored almost 5 years ago by JeeK <[email protected]>

Revert "Try fixing meyers singleton in ElementDB for usage across compile units."

This reverts commit 49e79ff6a4c625372e89f3129fdf3244aca23649.

611cc60b22b2680b78e26e9bf7e5edcc40403554 authored almost 5 years ago by Julianus Pfeuffer <[email protected]>

Cleanup

9d3ee55904c1b7d44d803e818927584187305257 authored almost 5 years ago by Julianus Pfeuffer <[email protected]>

Forgot code examples

7e3cf2a6eab1cf1d84f54c2cb79a4f6c95c1781c authored almost 5 years ago by Julianus Pfeuffer <[email protected]>

Merge remote-tracking branch 'oliveralka/fix/pyopenms_catalina' into fix/meyersSingletonCompUnits

f9c9fdc3a283942b15b2542e42b872fb9da30a18 authored almost 5 years ago by Julianus Pfeuffer <[email protected]>

Try fixing meyers singleton in ElementDB for usage across compile units.

49e79ff6a4c625372e89f3129fdf3244aca23649 authored almost 5 years ago by Julianus Pfeuffer <[email protected]>

Modify error in DBSerachDeconvMass

0c704feb36203457382be7034e29867928e527ad authored almost 5 years ago by JeeK <[email protected]>

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

2b3e07768af8e9a6bc2147515c6609e44649a82f authored almost 5 years ago by JeeK <[email protected]>

Remove debug output

fbbf3a19e5ad25a6e5e9bbebd59f01565f848ed1 authored almost 5 years ago by jpfeuffer <[email protected]>

Modify FLASHDeconv name in ToolHander.cpp

b9d2dea9e39e13cfb49241c96b95b9eea20c48b4 authored almost 5 years ago by JeeK <[email protected]>

[feature] added TOPP tests to test new mass trace quantitation method

9529b3deb39d7345e47c3a4bc186f4c8e1b243ca authored almost 5 years ago by poshul <[email protected]>

[PARAM] added option to store original RTs as meta data to MapAlignerIdentification

e31b10a3f852d2dde8e296db7b2d038f94147c51 authored almost 5 years ago by Hendrik Weisser <[email protected]>

[INTERNAL] more efficient way of updating RTs in IdentificationData

4191d142d3dbc5adcf0de5eee856e4b2be2d28fc authored almost 5 years ago by Hendrik Weisser <[email protected]>

Merge pull request #4395 from cbielow/develop

[FIX] QCCalculator throws an error if fragment masses cannot be infer…

9aaa3705935d53b9b11db52419e645d0e341bb1d authored almost 5 years ago by Chris Bielow <[email protected]>

internal doc

b060f312d72ce797de21d8131cbc015fc33d747a authored almost 5 years ago by Chris Bielow <[email protected]>

[TEST] added test for .oms files in MapAlignerIdentification

89adec3547849db9f16d952e20538ab8a7e761bc authored almost 5 years ago by Hendrik Weisser <[email protected]>

[FEATURE,IO] added support for .oms (database file) input and output to MapAlignerIdentification

f3e2db0d0437e8b00ab269d2dc3a3c9e8518b96f authored almost 5 years ago by Hendrik Weisser <[email protected]>

[FEATURE] added support for RT-transforming data queries in IdentificationData

bc14d0073f6e8e5317e65a799885eaed7c6fb5cc authored almost 5 years ago by Hendrik Weisser <[email protected]>

[FEATURE] added 'empty' function to IdentificationData; changed storage of data queries to enable updates to them

db1bf828593d7ea0c9f783c5ba54f3b8a34f0260 authored almost 5 years ago by Hendrik Weisser <[email protected]>

[DOC] slight documentation improvement

f48b42cf0f7454bd255d4bd5641a1f3c11afa7aa authored almost 5 years ago by Hendrik Weisser <[email protected]>

[FEATURE] added functions to get most recent score and number of scores in ScoredProcessingResult

b252479d2a3c30293c53eb842d06fbb5eb901e04 authored almost 5 years ago by Hendrik Weisser <[email protected]>

[FIX] QCCalculator throws an error if fragment masses cannot be inferred from data

db1038ee2fa61ccc388ce3225c6413dd49300d3c authored almost 5 years ago by Chris Bielow <[email protected]>

[FEATURE] added function to return string representation of the molecule in MoleculeQueryMatch

7c01d1f4eca157804021d98149746e2d8c3a421f authored almost 5 years ago by Hendrik Weisser <[email protected]>

[API] added option to AppliedProcessingStep::getScoresInOrder to only return the top score

109ba91e923ddd7e5abdcc2843d9a88276d959ed authored almost 5 years ago by Hendrik Weisser <[email protected]>

[NOP] removed trailing newlines

8081f62f1e64529842a7f1b6ed2b1112da0d96cb authored almost 5 years ago by Hendrik Weisser <[email protected]>

[feature] add tests for new QuantMethod

a437a268005a2801aafc2a0e1021360d9e9f9a9a authored almost 5 years ago by poshul <[email protected]>

[FIX?] Remove static from ElementDB::getInstance to make it consistent across compile units?

e6ac9efeaa1393ba05e2018bfbe466d5ea2fa64c authored almost 5 years ago by jpfeuffer <[email protected]>

[FIX] SQLite file format for ID data (OMSFile): fix definition of meta info table

48d7f460a1f21ac50bd1e3581fc9d3b0af5b6cea authored almost 5 years ago by Hendrik Weisser <[email protected]>

[FIX] SQLite file format for ID data (OMSFile): fix definition of meta info table

ce76c8eaaeaa69eeec2a1e246f240e788eaeac14 authored almost 5 years ago by Hendrik Weisser <[email protected]>

[feature] added max_height as a quantmethod for mass traces

fb2dec20c54db1ba0ae46fac5889cbd5b38ad6a6 authored almost 5 years ago by poshul <[email protected]>

Add visibility=hidden for Mac and fix setup.py missing regex.

be85a1785b5beac55b981366a9f0115f6646d57b authored almost 5 years ago by Builder <[email protected]>

[feature] added skeleton of new mass trace quant method

cde3cea32818d7ad5b16d20c6e52d92d0386159b authored almost 5 years ago by poshul <[email protected]>

Add boost regex needed for pyopenms probably since boost 1.69.

ac876a4de2ce12424fedfc3d34758c5f00d21ec7 authored almost 5 years ago by Builder <[email protected]>

[API] moved function 'isBetterScore' from 'IdentificationData' to 'ScoreType'

ca87f8ae5ef9c70f8bed0eacfc212eed8a37c2ed authored almost 5 years ago by Hendrik Weisser <[email protected]>

[NOP] whitespace/style fixes

d2c8fc18e8fe4fd05ba002ed65aa6ed7c843c308 authored almost 5 years ago by Hendrik Weisser <[email protected]>

Merge pull request #4390 from cbielow/fix-TICCalculator

fix TICCalculator

5e606316a36a2795345a59595715b6287052423e authored almost 5 years ago by Timo Sachsenberg <[email protected]>

fix #4389

fb7a1191a88d574742808d3e0b30be5f15cea866 authored almost 5 years ago by Chris Bielow <[email protected]>

Merge pull request #4388 from cbielow/TOPPBase-minor

remove some dead code in TOPPBase

547e62ffbc4a3cffed046850ab01622e8206ccec authored almost 5 years ago by Oliver Alka <[email protected]>

Merge pull request #4387 from poshul/pyopenmsfix

[fix] explicitly pass language_level=2 to autowrap, fixing issues with compilation

ab216f945dbbaf38e02512882c47ad6dace63ab2 authored almost 5 years ago by Hannes Roest <[email protected]>

remove some dead code

f40c52ee50ea0529aa170fa2cdf37c2114d2cf10 authored almost 5 years ago by Chris Bielow <[email protected]>

[FIX][FEATURE] Use rpath to correctly find frameworks in wheel. Allow extraction of libs from frameworks as alternative in the fix_dependencies.rb

a632baba4e93c34ff8ada7b0a3079ed31591c6c1 authored almost 5 years ago by Builder <[email protected]>

[fix] explicitly pass language_level=2 to autowrap, fixing issues with compilation.

e1323dd24678e1d765df09433f7b4d8b945ff1e0 authored almost 5 years ago by poshul <[email protected]>

[FIX] copy with symlinks into pyopenms, copy recursively into dists

fdca87fd75e2ba2dcca67f90c863ee0a6d127008 authored almost 5 years ago by Builder <[email protected]>

Merge pull request #4381 from OpenMS/jpfeuffer-patch-2

[FIX] use is_Executable for thermoraw and mono

4a1316cdf4dc5bc5a52498f16d5c137de3f081d9 authored almost 5 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #4384 from cbielow/opt_include

Opt include

8b2288ba4fa9f07ce9f24abe7ea8bb32468148a9 authored almost 5 years ago by jpfeuffer <[email protected]>

[FIX] permissions in fixup script for mac and orders in setup.py

c24963b6307b582d82ed40ce424a46506e0eeeae authored almost 5 years ago by Builder <[email protected]>

Merge pull request #4383 from bernt-matthias/topic/remove-wrong-test

remove a myrimatchadapter test

3fe4d7296d78938c36d23a945efbe5268f28d1bd authored almost 5 years ago by Chris Bielow <[email protected]>

Merge pull request #4382 from bernt-matthias/topic/RTPredics-test-excplict

tests make RTPredict parameters explicit

b674a253f29f37d53b97dbd6d2495970ad2122af authored almost 5 years ago by jpfeuffer <[email protected]>

minor rename

0504fd7a0d80c9531e71f52acebcd4296f2d2562 authored almost 5 years ago by Chris Bielow <[email protected]>

fix warning

a2e958af35ee0f8e05d2dd7c1abde78fd38d1731 authored almost 5 years ago by Chris Bielow <[email protected]>

Revert "[API] added String c'tor from 'unsigned char*' for SQLite compatibility"

This reverts commit b7603745adb4a43582ec7754829ae35a66a44a74.

6c34cf258532519f6f3e7cb954d4751617f87952 authored almost 5 years ago by Hendrik Weisser <[email protected]>

fix behaviour of TOPPBase InputFile tags (they are checked now more frequently, i.e. if required or non-empty)

4678f912d6b1758688cdbeee1098ba1926a3ff21 authored almost 5 years ago by Chris Bielow <[email protected]>

fix warnings

75828430086b79b4ddebc83fcc814c05c8161b79 authored almost 5 years ago by Chris Bielow <[email protected]>

Merge branch 'develop' of https://github.com/OpenMS/OpenMS into id-file-format

1fb38da748114941bfc9a790ccfcc40a6683acf2 authored almost 5 years ago by Hendrik Weisser <[email protected]>

[TEST] test for conversion between .oms (SQLite format) and .idXML using IDFileConverter

7eada98262dbd2e13a8e478c2bed25b2fdf6af77 authored almost 5 years ago by Hendrik Weisser <[email protected]>

remove 1 myrimatchadapter test

because the -min_precursor_charge 4 -max_precursor_charge 3 parameters
do not exist it seems not...

634a0f166a664afc15d0a38e8ca35b670dc8b305 authored almost 5 years ago by M Bernt <[email protected]>

tests make RTPredict parameters explicit

explicitly specify `-in_oligo_params` and `-in_oligo_trainset` instead
of implicit by appending ...

aeb2aef4505fa60444f7231ab6492003bdef4e65 authored almost 5 years ago by M Bernt <[email protected]>

[FEATURE] IdentificationData(Converter): sort processing steps (and exported protein ID runs) by date

a28a151b401b52cbb61bb20078c5284f64004203 authored almost 5 years ago by Hendrik Weisser <[email protected]>

[FEATURE] SQLite file format for ID data (OMSFile): support for storing and loading parent molecule groups

62881d1d2fdc8d04cd75f2fa1b9f6e7cfcca47df authored almost 5 years ago by Hendrik Weisser <[email protected]>

[FEATURE] explicit c'tor for IdentificationData::ParentMoleculeGrouping

ca4893339bb9e30e4e1acefd3ba27e7122930ae6 authored almost 5 years ago by Hendrik Weisser <[email protected]>

[FIX] IdentificationDataConverter: don't export empty primary file lists

8d4e0f9629ad8f7e82ca8b4d94e46b6759c3c161 authored almost 5 years ago by Hendrik Weisser <[email protected]>

[TEST] check that dates are preserved by IdentificationDataConverter

0ea29a654356cb753b68894b0dd59f94d55d8d5d authored almost 5 years ago by Hendrik Weisser <[email protected]>

[FIX] fix automation

3281c1c0c7b797089668160eed304c4ac150c8d9 authored almost 5 years ago by oliveralka <[email protected]>

[FIX] use is_Executable for thermoraw and mono

13016aa4da9227a933f82e53f9e0f4f01a5ff5b2 authored almost 5 years ago by jpfeuffer <[email protected]>

Update fix_dependencies.rb

d30f0ac40424805b914124afc4b029dc802e650d authored almost 5 years ago by jpfeuffer <[email protected]>

[NOP] docu and remove debug output

1c698a44156b32194c7b1cfb9e4f88929fd375cb authored almost 5 years ago by jpfeuffer <[email protected]>

[FIX] fix_dep script to also fixup frameworks that are already present. Might solve gatekeeper issues

3dbd9192d902d84373901b754c89a916a4858bd7 authored almost 5 years ago by Builder <[email protected]>

[FEATURE] use compile feature instead of fixed CXX standard to require only a minimum

82774a6372dbeae2cc65b8345b0b5f064fa90cb8 authored almost 5 years ago by Julianus Pfeuffer <[email protected]>

[ADD] since Mojave 10.14.0

c1f231bdacfb08786dde41e0e620a54d4a3284c3 authored almost 5 years ago by oliveralka <[email protected]>

[FIX] check variable

024ef7f1661a9c603a290b18a105c7a45e5da66b authored almost 5 years ago by oliveralka <[email protected]>

[FIX] pyopenms macOS catalina

8cb1ee1069c21f24f62fdf0a161d34ee4b5ad187 authored almost 5 years ago by oliveralka <[email protected]>

Merge pull request #4375 from cbielow/opt_include

some QC metric changes

db8f92da535259e3b52841efd739c84861562b3d authored almost 5 years ago by Timo Sachsenberg <[email protected]>

Merge branch 'develop' of https://github.com/OpenMS/OpenMS into id-file-format

abd426521db282dee3bb394bb9207adc279e4e03 authored almost 5 years ago by Hendrik Weisser <[email protected]>

Merge pull request #4372 from OpenMS/fix/4364

make file type explicit in PIS

a9f0e8ed755651d5a5da6e92dffad4139481d1cb authored almost 5 years ago by Timo Sachsenberg <[email protected]>

remove broken binding?

0096afe4e426937798292f6fbb248bf013dd4058 authored almost 5 years ago by Chris Bielow <[email protected]>

Merge pull request #4262 from enetz/feature/deisotoper_precursor_filter

[FEATURE] Deisotoper precursor filter and decreasing model fine tuning

db9b7f521272caf059791f5e4a7d0677f1e7922c authored almost 5 years ago by Timo Sachsenberg <[email protected]>

Minor speed up..

126c7256d93e98231bcf76cd01b44bf45a1de46b authored almost 5 years ago by kyowonjeong <[email protected]>

fix test

83199922e9f9bca3def9b37314d320c0f019de20 authored almost 5 years ago by Chris Bielow <[email protected]>

update Python bindings

f8d32f65f9da68b6ea2fcc40ab9b36b6aa08c95d authored almost 5 years ago by Chris Bielow <[email protected]>

add renamed files

2b7d2bcc0dc4bb2bad475fdbec7e6705c2a553ef authored almost 5 years ago by Chris Bielow <[email protected]>

Paper revision version

2253ccdc268b7c4cb859398da9140201899af428 authored almost 5 years ago by kyowonjeong <[email protected]>

rearrange some QC metrics

c68107e2c981f0ea3bea46024994c056e95bf138 authored almost 5 years ago by Chris Bielow <[email protected]>

[FEATURE] add 'getBasePeak()' and 'getTIC()' to MSSpectrum

89f7fdee7998dcd9cef55767f5e2741d789dccf0 authored almost 5 years ago by Chris Bielow <[email protected]>

For simple, good but a bit noisy...

17e7d6f7395ff178780a8368fd19e3ad3c71a3ad authored almost 5 years ago by kyowonjeong <[email protected]>

Update PrecursorIonSelector.cpp

ab1854f85fdd01a8d7c1db8aa5c1e39dda8393c2 authored almost 5 years ago by Timo Sachsenberg <[email protected]>

Made signing script executable

96aa0d61bb05af16d80a03e4109345eaa4161989 authored almost 5 years ago by Julianus Pfeuffer <[email protected]>

might fix https://github.com/OpenMS/OpenMS/issues/4364

91244097861407980d550bdf69af1b607ecc29d6 authored almost 5 years ago by Timo Sachsenberg <[email protected]>

Update sign_bins_and_libs.rb

11b9775ec6e0005fe6a3ae7bab390b84c15edf40 authored almost 5 years ago by jpfeuffer <[email protected]>

Update package_dragndrop_dmg.cmake

6fcac764934125faed5c2bdb36df3a55973cbbe1 authored almost 5 years ago by jpfeuffer <[email protected]>