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

Remove duplicated tutorial (#226)

* fix broken links

* relink developer quickstart guide

* update TOPP...

8f1c156d6a6539689f8dd1255f16058e815b0864 authored 8 months ago by Matteo Pilz <[email protected]>

Make introduction_lc.png a more reasonable size

81d2a3f127a3437541de7a6ddf64dc49d8530054 authored 8 months ago by Samuel Wein <[email protected]>

Updated PepConsensusId.png

878002c4587c18fd7275c0ca4bec1756ee36e8d3 authored 8 months ago by Samuel Wein <[email protected]>

Update OpenMS logo

5e0e594df960bea87d1bded1c73c0fea73b6c041 authored 8 months ago by Samuel Wein <[email protected]>

new images

8e1d60a314dfc432f450344a6dac19857167edee authored 8 months ago by Samuel Wein <[email protected]>

Update iPRG_lfq with non-transparent background

1b79648ae1696738f42f58a4f9a5e6874dac8c70 authored 8 months ago by Samuel Wein <[email protected]>

Update KNIME Tutorial (#225)

* fix broken links

* relink developer quickstart guide

* update TOPP...

a5f784d5e82ed1e02f70b1ee429e22a8582d85ac authored 8 months ago by Matteo Pilz <[email protected]>

Prune dead links (#224)

* Update tutorial.md

* Update openms-user-tutorial.md

* Update tut...

b26767ba4812301fd88250b371c8d82afbe5820a authored 8 months ago by Samuel Wein <[email protected]>

cleanup of 3.1 and 3.2

e569a8fcbc3b3fe9e2238140eac948f6b40e4cc3 authored 9 months ago by Samuel Wein <[email protected]>

Cleanup

5bb77360afda4030cfd2ad56815f8b2c700f2628 authored 9 months ago by Samuel Wein <[email protected]>

reorder metanode tutorial. update procedure for column type assignment and add image to show how

3917e3c1d976c9e898030cebac84990a34ef4f41 authored 9 months ago by Samuel Wein <[email protected]>

fix completely wrong section about fileconversion and replace with fileFilter demo. Add images

9f22c3e32b073c0d61349afcbb59056190626ebd authored 9 months ago by Samuel Wein <[email protected]>

PNG ify updated simple workflows

147f4981391bbfca4fb7834fb26f6564e9367c51 authored 9 months ago by Samuel Wein <[email protected]>

Update minimal workflow

58891e28e7d06f289ccdd670d32143e16eaa2d83 authored 9 months ago by Samuel Wein <[email protected]>

update name of input file node to File Importer

0252023c30e56e2dfa7a3a08e1da4a144765b4b7 authored 9 months ago by Samuel Wein <[email protected]>

remove ref to old KNIME, add description of where OpenMS thirdparty nodes are

f4862035d99b8d5785e3c8449712c0be71aab93c authored 9 months ago by Samuel Wein <[email protected]>

add instructions to install genericknimenodes

7036f6f4cbf932b5ba066023fa544473f2a8eac1 authored 9 months ago by Samuel Wein <[email protected]>

fixes to tutorial

da3615b51871e204c2b46555abfe7e3baf80de6b authored 9 months ago by Samuel Wein <[email protected]>

added hub.knime.com to lycheeignore, something about their security policy prevents lychee from loading.

23780f65d1e4fd0e0c2068098f8b49c65cd25b95 authored 9 months ago by Samuel Wein <[email protected]>

remove embedding of knime hub page that wasn't allowed by csp

0b898c496929e5559044de97b1a6d517cab10e14 authored 9 months ago by Samuel Wein <[email protected]>

remove unnecessary params to website

96bcb45c29b42bc61fe10be1ef38b3fe5a7f19fe authored 9 months ago by Samuel Wein <[email protected]>

fix broken external links

d8455b4c3bcca3ce5d476abb7a4a78ad9088ffa2 authored 9 months ago by Samuel Wein <[email protected]>

added figure to show how to switch back to classic knime interface and instructions on how to do so

bbabd13a47b91bde6048cb3b76b2151f85ee9c9d authored 9 months ago by Samuel Wein <[email protected]>

bump KNIME version

ea322ab680c364c289597d1eecc9d81338b27275 authored 9 months ago by Samuel Wein <[email protected]>

Update tutorial.md (#216)

* Update tutorial.md

Remove refs to OMSSA sin...

adb4f212efbdd1884a0e72313fd1a507f6073871 authored 12 months ago by Samuel Wein <[email protected]>

Update Knime versions and plugins

Update to KNIME 5

671efdeef6f894b7b0ec86dabf7af77fe83dc23c authored 12 months ago by Samuel Wein <[email protected]>

Increase Lychee timeout (#214)

Increase Lychee timeout

c7cc5a1596c83a71bbacf8a92dffc11693427f06 authored 12 months ago by Samuel Wein <[email protected]>

Update downloads.md (#188)

* Update downloads.md

* cleaned up

* removed releases section

* fix broken link

* fi...

2b851d896846ff02238765ff96c49b142a330472 authored 12 months ago by Samuel Wein <[email protected]>

Add some glossary terms (#213)

* fix some links and expand glossary

99a6ab58ed142f0c5bacbf6aacc1ee63308aee29 authored about 1 year ago by Chris Bielow <[email protected]>

Relink Developer Quickstart Guide (#212)

* relink developer quickstart guide

92940becfb087db5a8d56a4014b3b3840b26e9e1 authored about 1 year ago by Matteo Pilz <[email protected]>

Docs toppas (#210)

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

* linking to TOP...

de5e6d1d2248755dade26a24bb1d283e6aa50206 authored about 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...

d88c71b7530a53231cbcd303954f1046c3bce74c authored about 1 year ago by Chris Bielow <[email protected]>

Fix broken links (#209)

* fix broken links

* circumvent wrong SSL certificate

* get rid of h...

2f132d7335dcfdcc4d26fe10022e4729050935ba authored about 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...

32b0c8c3c45475c70710e6a0d8e8800f2158e753 authored about 1 year ago by Chris Bielow <[email protected]>

Update openms-user-tutorial.md (#204)

* Update openms-user-tutorial.md

I have reviewed the tutorial and identified a few minor gram...

2c839282d7e8cb79eb3adae9f515fd78d25f0a23 authored about 1 year ago by Ayesha-Feroz <[email protected]>

remove utils. some minor cleanups (#206)

2bcda50d8ba98fa3905979095583b25925fcd511 authored about 1 year ago by Timo Sachsenberg <[email protected]>

new release cycle

d9544b592d082729da98abe15f8eeac076e2c772 authored about 1 year ago by Julianus Pfeuffer <[email protected]>

update PR default text (#202)

* Update PULL_REQUEST_TEMPLATE.md

* Update CONTRIBUTING.md

073626c4313eccb00b20cebd4c326561204c9c6d authored over 1 year ago by Chris Bielow <[email protected]>

update contributors (#199)

616a552bfc1d3e372036e20b5cfe9aaa20dde4e3 authored over 1 year ago by Chris Bielow <[email protected]>

add gmc.js to conf.py

e44c06cd22ea0f402e4085ed5c712854b775b4d2 authored over 1 year ago by Julianus Pfeuffer <[email protected]>

nextflow (#200)

* nextflow

* added gmc script

* no end transition

f3882a2724a83698dcfd032d9135a59b1bd4f3ca authored over 1 year ago by Julianus Pfeuffer <[email protected]>

Large restructure of docs (#198)

* Huge restructure of the docs

* More restructure

* fix piwik script

* delete old insta...

db3e774f4c231cac1d87b2119a26eec3afb8bf19 authored over 1 year ago by Julianus Pfeuffer <[email protected]>

update to version 3.0.0

89221bf3650814f9a652810c9b0d8848a9160e20 authored over 1 year ago by Chris Bielow <[email protected]>

Piwik scripts added (#181)

* piwik scripts added

* include js the correct way

---------

Co-authored-by: Julianus P...

b66d4c5267404975cc9ba3fb9330ff7667258f2d authored over 1 year ago by Rahul Agrawal <[email protected]>

Re-organize quick start guide locations (#195)

* Re-organize quick start guide locations

Both user and contributors quick start guides were ...

9845341586c2416c5b5ec42c155c6ff19fae6835 authored over 1 year ago by axelwalter <[email protected]>

fix keyboard shortcut (#191)

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

c2af13b2d8d0b90b69d7d7337a6f75ab46a148ee authored over 1 year ago by Chris Bielow <[email protected]>

update user guide (#192)

* update user guide

* Update openms-user-tutorial.md

*...

41a3252cc80764bf06aba582f36ab8cc80fe5e98 authored over 1 year ago by Julianus Pfeuffer <[email protected]>

show how to correctly reference stuff (#152)

* show how to correctly reference stuff.

* old webserver

18d02aa1afa7f3f924cbe2541b63b3e8759a0e23 authored over 1 year ago by Julianus Pfeuffer <[email protected]>

Update installation-on-gnu-linux.md

e0e7ef2b37f954bc3f44d99f2af675ee71f06ffd authored over 1 year ago by Julianus Pfeuffer <[email protected]>

Update installation-on-macos.md

1a28dea07f5651e3e405b79027913adfc1ca66c9 authored over 1 year ago by Julianus Pfeuffer <[email protected]>

Update openms-user-tutorial.md

1091190c9e1d320ae0941976d3cf18ebec2ad2f1 authored over 1 year ago by Julianus Pfeuffer <[email protected]>

New background (#179)

* added css including video image

* added extended background

* added equation for time of...

ba85a32b6b0ab2adb69b738ee6df1775dbe74266 authored over 1 year ago by greengypsy <[email protected]>

Update main.yml

e23a8f2411ff53d3f7f546b8c8dfa7aa0097941e authored over 1 year ago by Samuel Wein <[email protected]>

explicitly state python version

d6d0c6fa991f2ed1dda7e931127902af13a45928 authored over 1 year ago by Samuel Wein <[email protected]>

bump setup-python version

254feb45ab1c62ad687328a0313ba27de1fbbcfc authored over 1 year ago by Samuel Wein <[email protected]>

Do not use deprecated method (#180)

do not use deprecated method

c62e0e34917ec99b70fd0d6cabfcde279cb42ec7 authored almost 2 years ago by Julianus Pfeuffer <[email protected]>

Update main.yml

ad360e516a95c33d0dc6b22316148fd7e8daca9e authored almost 2 years ago by Timo Sachsenberg <[email protected]>

Update requirements.txt

991a2e527d7d017ae5c50ab5e08b2671a1e799a8 authored almost 2 years ago by Timo Sachsenberg <[email protected]>

Update requirements.txt

5c71687d9ae52062c5a334147d7a5a43be776839 authored almost 2 years ago by Timo Sachsenberg <[email protected]>

Update .readthedocs.yaml

755ed8ed7f308c59bc42a0dc1970d6ef5416af94 authored almost 2 years ago by Timo Sachsenberg <[email protected]>

Update openms-user-tutorial.md

8d53108f080f6b3b54a0a35f2d0275d798d3a5bd authored almost 2 years ago by Julianus Pfeuffer <[email protected]>

Better Installation instructions (#169)

* Major fix of installation instructions

* Fix

* use new tab syntax

* fix links

* fi...

b03e3c8822d7801dea8c238115237156c9b6c213 authored about 2 years ago by Julianus Pfeuffer <[email protected]>

Update installation-on-macos.md (#171)

* Update installation-on-macos.md

* restored images

* Update installation-on-macos.md

656c5cbb1cffb8bad9515b63fc4b8dd322a2934d authored about 2 years ago by Julianus Pfeuffer <[email protected]>

Modify background (#170)

* modified content of background and added one image of peak map

* added link to openms commu...

96fa2d8fd708d716c6812a117f04f00f00d8ecbe authored about 2 years ago by greengypsy <[email protected]>

Change number of cards per row for smaller screens. (#168)

bd70e0b860a2bca72414932911d74da293138181 authored about 2 years ago by Julianus Pfeuffer <[email protected]>

FIX invalid file names.. (#166)

* FIX invalid file names..

* wow.. fix everything

59915fefc130eaa0c263e67c1108cc18ad8b6586 authored about 2 years ago by Julianus Pfeuffer <[email protected]>

Add logos and cards as initially discussed (#163)

d40a17f3e4c3bc0cc3555ec2c29913a579d78638 authored about 2 years ago by Julianus Pfeuffer <[email protected]>

replaced abibuilder.informatik with abibuilder.cs (#165)

deb59ab22d42766210b92293a2856ccce3790e61 authored about 2 years ago by greengypsy <[email protected]>

modified entry points title and content and modified image (#162)

* modified entry points title and content and modified image

* added entry points page to index

576196bc029a1bb07b575aa75f70175c57b89d94 authored about 2 years ago by greengypsy <[email protected]>

Merge tutorials (#160)

* move metabolomics tutorial inside openms user tutorial

* move metabolomics tutorial inside ...

f70c324527cb53475eddfce1eb2d4bf369e4c34d authored about 2 years ago by greengypsy <[email protected]>

Add "user tutorial plus develop" to "develop" (#157)

* Address review comments by @greengypsy

Ref: https://github.com/OpenMS/OpenMS-docs/pull/65.
...

a09072794980c100edbced47611291ff2daf621c authored about 2 years ago by greengypsy <[email protected]>

try newer python (#158)

bf8b14421121b920ccc78ce60e1319f317f3f4d8 authored about 2 years ago by Julianus Pfeuffer <[email protected]>

Sphinx extension for paths (#150)

* add variables

* Update conf.py

Co-authored-by: Timo Sachsenberg <timo.sachsenberg@uni-tu...

dcb0002ae0753e75731c9bd44ca7abf8d5d3d526 authored about 2 years ago by Julianus Pfeuffer <[email protected]>

add and correctly style hoverref (#154)

* correctly style hoverref

* spelling of css var. now the hover underline is dark grey.

6db28398ba928d790ca77b8664f23443fdcb5d22 authored about 2 years ago by Julianus Pfeuffer <[email protected]>

add variables (#135)

* add variables

* Update conf.py

Co-authored-by: Timo Sachsenberg <timo.sachsenberg@uni-tu...

c36fac31d7e40a953fad3eee18b99b0025f1216c authored about 2 years ago by Julianus Pfeuffer <[email protected]>

tabs errors' on ReadTheDocs epub format support (#147)

* tabs error

ref: https://github.com/OpenMS/OpenMS-docs/pull/146

* Fix css not found

* ...

1f4f6b292b6b0ad5d11ccb1b4b22e823320ed122 authored about 2 years ago by Tapasweni Pathak <[email protected]>

Update CI build params to keep going (#151)

* Update CI build params to keep going

* use make mode

1c6bd49fd44f71245643b1fa9cb8379048285be1 authored about 2 years ago by Julianus Pfeuffer <[email protected]>

CI (#148)

* CI

* remove comment

* add link checking of the final html

* comment

7a176aadfbd4d346565d21253af22f93294e1a16 authored about 2 years ago by Julianus Pfeuffer <[email protected]>

fix rtd build failure (#146)

if triggered build from a new branch rtd build errors. could be because
it builds all files not...

859d45c3f129f32dc80708f09a1af9ba24fc5604 authored about 2 years ago by Tapasweni Pathak <[email protected]>

Merge pull request #144 from tapaswenipathak/main-branch

Add latest/main ready docs

00279c0f459933eb8337e62457be6734bbe99b0e authored about 2 years ago by Timo Sachsenberg <[email protected]>

Add latest/main ready docs

Adds offline documentation support, default page, instructions to build
locally and a few introd...

013a249e9752028fb14942de291815a8840e822d authored about 2 years ago by Tapasweni Pathak <[email protected]>

Converting the masses. (#105)

* Converting the masses.

* Update docs/introduction.md

Co-authored-by: Tapasweni Pathak <t...

f825580cf075a80e6b12807ce31a39d6ca934e00 authored about 2 years ago by Leron T <[email protected]>

PRs to develop (#137)

d039875437570050498cc64d64197e08f4e1e9ab authored about 2 years ago by Tapasweni Pathak <[email protected]>

Further corrected documents placed within 120 chars, Ref 73. (#110)

* more introduction.md edits

* introduction.md complete

* Fixed Additional Resources, Doc ...

958a2ae15a3ae23cc1b351242f5449373419cb69 authored over 2 years ago by Julian PG Riches <[email protected]>

Lines within 120 characters for several documents. Ref 73. (#108)

* more introduction.md edits

* introduction.md complete

* Fixed Additional Resources, Doc ...

b36e02355cdc7f9063e2355cd48150f7e81db03b authored over 2 years ago by Julian PG Riches <[email protected]>

Create codeql-analysis.yml

b8641b6a395fc2ec8aa4136da3214b63537b1843 authored over 2 years ago by Timo Sachsenberg <[email protected]>

https://openms.readthedocs.io/en/develop

609cdb6959644308eccd3c867cfcbaa6808fc960 authored over 2 years ago by Tapasweni Pathak <[email protected]>

admonition indent

f17bfdaa3e668ba4d8da2aecadb3c0b1c40c3867 authored over 2 years ago by Tapasweni Pathak <[email protected]>

Address review comments by @matchy233, @pranavich18, and @axelwalter. (#84)

* Address review comments by @matchy233, @pranavich18, and @axelwalter.

Ref https://github.co...

fde80240e8fcbae2bb69d1bb534d1df37dc79d66 authored over 2 years ago by Tapasweni Pathak <[email protected]>

a few fixes here and there for staging to main merge (#87)

* Address review comments by @greengypsy

Ref: https://github.com/OpenMS/OpenMS-docs/pull/65.
...

61abe5ac1917f84fd2aeda8a4da1dc7ed900f4c9 authored over 2 years ago by Tapasweni Pathak <[email protected]>

add: remaining toppview-introduction content

Closes https://github.com/OpenMS/OpenMS-docs/issues/76.

dccf2841504c3745c6fe32ef41a9f37d7afd2a37 authored over 2 years ago by Tapasweni Pathak <[email protected]>

fix: grammatical errors docs/guides/user-guides/user-quickstart-guide.md

Co-authored-by: Eugen Netz <[email protected]>

c690e51b77c5f38dc93ccb83c31b03609eac8077 authored over 2 years ago by Tapasweni Pathak <[email protected]>

fix: grammatical errors docs/installations/installation-on-gnu-linux.md

Co-authored-by: Eugen Netz <[email protected]>

3bbb4b447e4d1754b1fae05034a2a29dd191ddf1 authored over 2 years ago by Tapasweni Pathak <[email protected]>

fix: grammatical errors docs/installations/installation-on-gnu-linux.md

Co-authored-by: Eugen Netz <[email protected]>

30f7541f4350f32d1157cae3169e5db122dfda83 authored over 2 years ago by Tapasweni Pathak <[email protected]>

Address review comments by @enetz and @jpfeuffer (#83)

Ref https://github.com/OpenMS/OpenMS-docs/pull/65.

a6c592bcf71d5e6c2b43d1d62fa7fedbdf712f7a authored over 2 years ago by Tapasweni Pathak <[email protected]>

Address review comments by @timosachsenberg (#78)

Ref: https://github.com/OpenMS/OpenMS-docs/pull/65.

f3a6dc8fe8c7e2e6b9f44b5ab121d6bcaf82ed86 authored over 2 years ago by Tapasweni Pathak <[email protected]>

Address review comments by @greengypsy (#77)

Ref: https://github.com/OpenMS/OpenMS-docs/pull/65.

5493c1eadc19ed1fec4b22c21b9085bdf633bca2 authored over 2 years ago by Tapasweni Pathak <[email protected]>

Address review comments by @erik-whiting (#82)

Ref https://github.com/OpenMS/OpenMS-docs/pull/65.

6ea8049f85f248d124e4dde10257943234a627fc authored over 2 years ago by Tapasweni Pathak <[email protected]>

fixup: use :term: in .rst!

d4bbf8ecd240ec58d1cc067f3aa2b0286565e2c1 authored over 2 years ago by Tapasweni Pathak <[email protected]>

fixes: improvements: touchup and cleanup (#64)

5097262ddaffdd3f8f62f0922920eb1f886e1651 authored over 2 years ago by Tapasweni Pathak <[email protected]>