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

Fix mac runner brew issues

This fixes an issue where brew updates packages already present on the runner after we install p...

285c7f8b48d15e9a9e1e8dd4fe91572fa104eb35 authored 8 months ago by Samuel Wein <[email protected]>

Update openms_ci_matrix_full.yml

force GHA to not update preinstalled packages in brew

fbe93b15625a27074bfc87b2d4bd04202c57dfbd authored 8 months ago by Samuel Wein <[email protected]>

Update openms_ci_matrix_full.yml

8368f1851bfbdd8d82ab1ec18a95ce1e8936be9f authored 8 months ago by Samuel Wein <[email protected]>

Update openms_ci_matrix_full.yml

trying to not specify python3 version

e92bb25faf80c8ff450c4ce60ccb725cb7675929 authored 8 months ago by Samuel Wein <[email protected]>

Update openms_ci_matrix_full.yml

fix two more sha issues

0d9ffcd39239b14b4fade8d2eb79c43e53d2ad13 authored 8 months ago by Samuel Wein <[email protected]>

Update openms_ci_matrix_full.yml

748771bdafe8554a9e91ec44d30726f8b29bb8f3 authored 8 months ago by Samuel Wein <[email protected]>

Update openms_ci_matrix_full.yml

1f1fa4e392ffc1b2aa9bc25ef513c5ecdf767176 authored 8 months ago by Samuel Wein <[email protected]>

Update openms_ci_matrix_full.yml

78ef5d49680d813e0086510b81c24b6425bb4c6c authored 8 months ago by Samuel Wein <[email protected]>

Merge pull request #7334 from OpenMS/poshul-patch-1

Update update_nightly.yml

cb0ad99bc9a78d5d1beb073c5b7747d9e42e260e authored 8 months ago by Samuel Wein <[email protected]>

Merge branch 'develop' into poshul-patch-1

a3195baa0949f91766fc4f6e26edf81ea9081be6 authored 8 months ago by Samuel Wein <[email protected]>

Update update_nightly.yml

add description of how to fix nightly ahead of develop

f3ce46eca19f8a9c833303a18ac0f261a33d4630 authored 8 months ago by Samuel Wein <[email protected]>

fix: installation of examples directory in unnecessary sub-folder (#7337)

91648980641c445b0d87e9a632752b074a259641 authored 8 months ago by Radu Suciu <[email protected]>

Update openms_ci_matrix_full.yml

c1db93fbb3016b60b08cbe4b5983dce3e8d751d3 authored 9 months ago by Samuel Wein <[email protected]>

Merge branch 'develop' into poshul-patch-1

015e4cc6f39ae9f444c24f2da937ac9fb7cbc689 authored 9 months ago by Samuel Wein <[email protected]>

Merge pull request #7332 from cbielow/more_doc

[DOC] Developer guide cleanup

1c07f3cb3a70e5c4796adfcaee3268e782351aac authored 9 months ago by Chris Bielow <[email protected]>

Update doc/doxygen/public/Main.doxygen

Co-authored-by: Timo Sachsenberg <[email protected]>

23850c44d90a478042a40746b10619d94cb21b08 authored 9 months ago by Chris Bielow <[email protected]>

Update update_nightly.yml

Don't use external action for pushing, check if Nightly has work not in develop and throw an error.

d3bd9c6519dd8a4bf008c4d5cadf3b9085d38283 authored 9 months ago by Samuel Wein <[email protected]>

Update openms_ci_matrix_full.yml

2abe0280256e199c2316bcee91292a4fb9b410a3 authored 9 months ago by Samuel Wein <[email protected]>

[DOC] a word on clang-format

67788273be97ee1f515b092343ebef11901d6239 authored 9 months ago by Chris Bielow <[email protected]>

[DOC] fix CMake bug, when using Doxygen 1.10, which compares lexicographically less to 1.8.;; using VERSION_LESS to fix

66319fb02718fe41d30c46d0c40d87884822956b authored 9 months ago by Chris Bielow <[email protected]>

amend to moving tutorial

f698e23b0e006d8746dcc78bdca7bfdbc09fb976 authored 9 months ago by Chris Bielow <[email protected]>

[DOC] some refactoring of topics

14b36b2b4d2d3fb7cf03479f75f3837f5b9f6ec3 authored 9 months ago by Chris Bielow <[email protected]>

Break out linking as latest

bash chokes on variables that may or may not exist (like inputs.mark_as_latest) refactor the beh...

79cbb0cfc69008835fa3b85397f2afb00b1c30b2 authored 9 months ago by Samuel Wein <[email protected]>

fix conditionals for mark_as_latest to only run if we are a workflow_dispatch

161b5d39dbdcc941ba36028017f6bda771e1904c authored 9 months ago by Samuel Wein <[email protected]>

Exclude some more dlls from packaging (#7331)

* Update package_general.cmake

* Update cmake/package_general.cmake

ab566c7b0dd845dcd2e0e7fd1419f1d56bcea208 authored 9 months ago by Timo Sachsenberg <[email protected]>

Update openms_ci_matrix_full.yml

GHA parser utterly fails to determine where if finds a syntax error. Fixed syntax error

cc2999956068e91db189099388860cdef5d98659 authored 9 months ago by Samuel Wein <[email protected]>

Update openms_ci_matrix_full.yml

6084a296832d50231048320911ec447be1e8a21e authored 9 months ago by Samuel Wein <[email protected]>

Update openms_ci_matrix_full.yml

41266e09dd8aa65923ad2d1f43201098fbae2546 authored 9 months ago by Samuel Wein <[email protected]>

Update openms_ci_matrix_full.yml

Fix duplicate ID from merge

fedab2b5a00fa2470f7e54b0f1ccf6fa150717af authored 9 months ago by Samuel Wein <[email protected]>

Merge branch 'develop' into release/2.9.1-action

d5ad1eb29bc4a8a6acf20d5ed7c38a3c7b8acac8 authored 9 months ago by Samuel Wein <[email protected]>

Bump contrib from `5e42765` to `3a9eba4` (#7330)

Bumps [contrib](https://github.com/OpenMS/contrib) from `5e42765` to `3a9eba4`.
- [Commits](htt...

83e71c755049f4c1e4c611f518850a8c5342d90d authored 9 months ago by dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Stop KNIME site building multiple times on linux in GHA (#7329)

* Set KNIME update site to not build on Ubuntu clang++

* Update openms_ci_matrix_full.yml

...

c71bf632b008aeb285a28bfa6e26ca168c4f1644 authored 9 months ago by Samuel Wein <[email protected]>

[DOC] enable finding the source of OpenMSConfig.h in our buildsystem

c989bbc24bd15057c04e73a5d3c5e032f6d1166b authored 9 months ago by Chris Bielow <[email protected]>

[DOC] update user FAQ

e26b24b68a0b6e5efe61339ddbc6b9d5a151163f authored 9 months ago by Chris Bielow <[email protected]>

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

2c14b0d0bea0fc60a0a364a5609a3d289d9c591f authored 9 months ago by Chris Bielow <[email protected]>

[DOC] rename doxygen files for better structure; move OpenMS developer tutorial to common place; removed 'known dev bugs' since its very outdated.

45cb7b7a8746eed8ecf019752762579ac5ca0d1f authored 9 months ago by Chris Bielow <[email protected]>

Merge pull request #7327 from OpenMS/timosachsenberg-patch-1

Use private key in nightly action to be able to trigger other workflow

aa8bba258640874a472f2b6758b771824610dc04 authored 9 months ago by Timo Sachsenberg <[email protected]>

Update update_nightly.yml

bf6906785dc5358e5e5f2b99abbe7a14401f333d authored 9 months ago by Timo Sachsenberg <[email protected]>

Merge pull request #7325 from OpenMS/timosachsenberg-patch-1

fix nightly

47433c4a7eca05ab1f13fa72990e9006d8134f38 authored 9 months ago by Timo Sachsenberg <[email protected]>

fix nightly

9e36b63a9c9efefe75586b52bafb20124948c9c9 authored 9 months ago by Timo Sachsenberg <[email protected]>

Merge pull request #7324 from cbielow/more_doc

[DOC] developer documentation update (C++17 etc)

fb896212d7e906e2be549d5cbae1835a0cc244fb authored 9 months ago by Timo Sachsenberg <[email protected]>

Merge branch 'develop' into more_doc

daa12078914aef3b0ae68c6379985b98873527c8 authored 9 months ago by Chris Bielow <[email protected]>

Update executables.cmake (#7322)

0df52d41e2ab20720fe6335d311d54b212e8be53 authored 9 months ago by Timo Sachsenberg <[email protected]>

fix warning

3a1cd959d1462a536d7e69e107766bc9765e35ae authored 9 months ago by Chris Bielow <[email protected]>

update developer FAQ

efe231105f482c8cbd955bb388c5d063cfd80d57 authored 9 months ago by Chris Bielow <[email protected]>

updated coding conventions to reflect C++17

132dd1536a77c4d6ca9e856e8c24925d1a1a7713 authored 9 months ago by Chris Bielow <[email protected]>

Merge pull request #7320 from cbielow/more_doc

More flexible handling of doxygen warnings

70c303bc46d5804ed470a46b71211a2a94955abc authored 9 months ago by Chris Bielow <[email protected]>

[DOC] fix groups

f2a877c4c0b8ec4f589978b139705201019ed822 authored 9 months ago by Chris Bielow <[email protected]>

allow certain warnings in Doxygen_Warning_Checker;

reduce graphs back to 50 nodes max in DOT

526c10184b5c7966bbbf78234200738d2150cad6 authored 9 months ago by Chris Bielow <[email protected]>

Merge pull request #7315 from OpenMS/dependabot/submodules/src/pyOpenMS/pyopenms-docs-6a0aab2

Bump src/pyOpenMS/pyopenms-docs from `229a171` to `6a0aab2`

a093a955f04e7c29a325b898a1cf08049d280b83 authored 9 months ago by Samuel Wein <[email protected]>

Merge branch 'develop' into dependabot/submodules/src/pyOpenMS/pyopenms-docs-6a0aab2

287a2bae557a3a6aac8e81ca34df2af0d9c502c6 authored 9 months ago by Samuel Wein <[email protected]>

Merge pull request #7317 from OpenMS/update-actions-for-node-20

Update GitHub Actions to Latest Versions in CI Workflow

4872b33fcc43f96e8f469a312459f86637bcab80 authored 9 months ago by Samuel Wein <[email protected]>

Bump versions of actions that use Node-16

961d188dc0b011cd0c3f3140eba688ad390a04c4 authored 9 months ago by Samuel Wein <[email protected]>

Merge branch 'develop' into release/2.9.1-action

99809aa3b46edd18f8fd34db7aba280aff32ee3f authored 9 months ago by Samuel Wein <[email protected]>

Update update_nightly.yml

359580928ce62c70ec5fcdb4bdbe036a427cfb3d authored 9 months ago by Samuel Wein <[email protected]>

Merge pull request #7313 from cbielow/fix_ddocs

Enhancements in Documentation and Code Readability

97a6e847cd73728955d8468285a86fabe66571ac authored 9 months ago by Chris Bielow <[email protected]>

Update src/topp/PeptideIndexer.cpp

8b9ba18b1ae5996dd2375b42e8d4b49ece66f16a authored 9 months ago by Timo Sachsenberg <[email protected]>

Bump src/pyOpenMS/pyopenms-docs from `229a171` to `6a0aab2`

Bumps [src/pyOpenMS/pyopenms-docs](https://github.com/OpenMS/pyopenms-docs) from `229a171` to `6...

bcb3ff2ffe9efc43c5149af68e2cd3a0bf0f3fa9 authored 9 months ago by dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Merge branch 'develop' into fix_devdocs

f520fba00cbe42da7d30944102132be4cd189ef5 authored 9 months ago by Chris Bielow <[email protected]>

add package to output

7ac16cf88bfcb5779fec7fbb818acb28994d8d4a authored 9 months ago by Chris Bielow <[email protected]>

add package type, so it does not get lost when re-writing the CmakeCache.txt in https://github.com/OpenMS/OpenMS/blob/develop/tools/ci/cibuild.cmake#L139

76d03617cced6ebf078e2db1a6933f480d6e112f authored 9 months ago by Chris Bielow <[email protected]>

debug

cc070bafab6e8c5c0b541d1f8866b74803c6bcb5 authored 9 months ago by Chris Bielow <[email protected]>

better error message for missing NSIS

bdc35894cffa21c1e594cff4316491ff3624f064 authored 9 months ago by Chris Bielow <[email protected]>

Bump src/pyOpenMS/pyopenms-docs from `64016e7` to `229a171` (#7311)

Bumps [src/pyOpenMS/pyopenms-docs](https://github.com/OpenMS/pyopenms-docs) from `64016e7` to `2...

9c12a4e9700544c788777164b239a17df454a5c6 authored 9 months ago by dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Update update_nightly.yml

Update fetch-depth to fetch all changes.

80a4e524defe9e44a9cb3390c6363332afd9a99a authored 9 months ago by Samuel Wein <[email protected]>

Merge branch 'develop' into fix_devdocs

0328f9b23e3ec5c02d9f209447eb292130bf539a authored 9 months ago by Chris Bielow <[email protected]>

fix some more

cee266367d320ce3be036cd26413daedaedd65c2 authored 9 months ago by Chris Bielow <[email protected]>

Update update_nightly.yml (#7307)

* Update update_nightly.yml

Fix version number for action

* Update update_nightly.yml

r...

d9c17f85b8afc13fffec557f3b90b1d7f5298c56 authored 9 months ago by Samuel Wein <[email protected]>

Add action to replace Jenkins at updating the nightly branch every night (#7306)

cd5183f295bd97ae5e7b8198c9b2adc3b2da03b3 authored 9 months ago by Samuel Wein <[email protected]>

disable doc dependency -- CI seems to choke on it

3dc886db036000d4e23c2103e1715f7bd4a23112 authored 9 months ago by Chris Bielow <[email protected]>

try to attach the doxygen-error.log to CDash

e38abd96fec71718c4769e42b819176ce28aefec authored 9 months ago by Chris Bielow <[email protected]>

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

# Conflicts:
# doc/doxygen/parameters/DefaultParamHandlerDocumenter.cpp

cbe8a107ce8906a9f1919f4cb3afb4994386623f authored 9 months ago by Chris Bielow <[email protected]>

add DOXYGEN_VERSION to know which version was used in CI (may explain why it differs from local results)

768f06e1b371b0ceb5b1c63ef692f0b638532ea8 authored 9 months ago by Chris Bielow <[email protected]>

fix more warnings only known to certain doxygen versions

537688ece6cd44cc0a336d638f2a1f56f5a0310f authored 9 months ago by Chris Bielow <[email protected]>

Merge pull request #7305 from OpenMS/fix_DefaultParamHandlerDocumenter

fix compiler issue

d44f5d19425e219366bbbd084911aab241f6baa9 authored 9 months ago by Samuel Wein <[email protected]>

Merge branch 'develop' into fix_DefaultParamHandlerDocumenter

376c8f5c86b432629e9dbbe7e9578ac08db0b5d0 authored 9 months ago by Samuel Wein <[email protected]>

fix compiler issue

f9207426905f46d41ffbdfdb99d446b92598bfe7 authored 9 months ago by Samuel Wein <[email protected]>

fix compiler issue with taking the address of RValue

ce88b09cd0ffd768d2341c6cefa89fb84517ab5b authored 9 months ago by Samuel Wein <[email protected]>

avoid doxygen warnings on the console

42d32de8a0624dbcfca632475e3200a56861814f authored 9 months ago by Chris Bielow <[email protected]>

update dependencies

ea210dcf639a77e00b99c34f4ff2c2602d8e53cb authored 9 months ago by Chris Bielow <[email protected]>

fix more warnings

a678c5ade402a0a0e8ad00c81eadbc11a900bd23 authored 9 months ago by Chris Bielow <[email protected]>

Merge branch 'develop' into fix_devdocs

fe0f13f28739f0722064853f9bfe723445b98d75 authored 9 months ago by Chris Bielow <[email protected]>

better readability of output

ced905f741cd853110ef8216eb977501550baad5 authored 9 months ago by Chris Bielow <[email protected]>

fix more doxzgen warnings

1018a02e677334dc9b39719f4beebfd76b7e8fd2 authored 9 months ago by Chris Bielow <[email protected]>

[NOOP] reorder

9cccf23ad193a866d6144fbc07c01d1618b7c173 authored 9 months ago by Chris Bielow <[email protected]>

increase max nodes. if this is too much, we need to filter warnings like 'Included by graph for 'PeptideIdentification.h' not generated, too many nodes (68), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES.' in our Doxygen_warning_checker.cpp

f9c78817a1b764eceadaa0f3067a2e2f0dad8c03 authored 9 months ago by Chris Bielow <[email protected]>

remove class (oversight from last cleanup), yet doxygen generates warnings for it

618f581fe7a1898fc59efb5c7f44fe903a3195bc authored 9 months ago by Chris Bielow <[email protected]>

Update codium-pr-agent.yml

090909d71f9f017b822e8dd5e8d0d0d3e06a8d56 authored 9 months ago by Timo Sachsenberg <[email protected]>

move pr ai reviewer to workflows

8a6d4edb5bf9497a42ae8677cff6a761ec6741ae authored 9 months ago by Timo Sachsenberg <[email protected]>

Rename codium-pr-agent to codium-pr-agent.yml

8dc398bf7940efc8d185e3de5178c606bc4ecfe8 authored 9 months ago by Timo Sachsenberg <[email protected]>

Create codium-pr-agent (#7304)

418a0fe93babe080227783872fb140463355c83b authored 9 months ago by Timo Sachsenberg <[email protected]>

add a test which checks for doxygen warnings

9ff2a0362a0ae2354ed6f435257048948a09d06d authored 9 months ago by Chris Bielow <[email protected]>

fix doxygen warnings

37f261148cb2fa9568823c05cabc19e278c93597 authored 9 months ago by Chris Bielow <[email protected]>

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

90e48a4e7494b58d624f2889bc1ec88daf4cdf18 authored 9 months ago by Chris Bielow <[email protected]>

try enabling doxygen on GHA-Ubuntu per default (not only for packaging)

6bb2ad65894d38fcd25cc8bb8d35d740426ebd3c authored 9 months ago by Chris Bielow <[email protected]>

proper block display

41bfb7f09c97d65aa85caf8b12e7e86ea1a280b4 authored 9 months ago by Chris Bielow <[email protected]>

Merge branch 'develop' into fix_devdocs

30d839b5589ca10adf0600f27294b40d6faaf001 authored 9 months ago by Chris Bielow <[email protected]>

fix compile errors

3a8373f3103ea11cebc44d14534d7d74e6f6c44e authored 9 months ago by Chris Bielow <[email protected]>

fix oversight

499854080a0e4303adf024a3038aecc621acc59b authored 9 months ago by Chris Bielow <[email protected]>

Merge pull request #7301 from OpenMS/poshul-patch-1

Update README

04646126b6c1aa11e83b4a9c3c9745ea99939aaf authored 9 months ago by Timo Sachsenberg <[email protected]>