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

Merge pull request #429 from OpenMS/dependabot/pip/docs/readthedocs-sphinx-search-0.3.2

Bump readthedocs-sphinx-search from 0.3.1 to 0.3.2 in /docs

6a0aab29763f4ca9cb90625b2671857595342114 authored 9 months ago by Samuel Wein <[email protected]>

Merge branch 'master' into dependabot/pip/docs/readthedocs-sphinx-search-0.3.2

1a4a84a337f4db62a8bd13a4c6467091ceb5d4cd authored 9 months ago by Samuel Wein <[email protected]>

Update plotting tutorials (#427)

* updated plotting tutorials

* increased plot resolution

*...

229a171523406f1895e3fac8573030fccd7e87ea authored 9 months ago by Matteo Pilz <[email protected]>

Bump readthedocs-sphinx-search from 0.3.1 to 0.3.2 in /docs

Bumps [readthedocs-sphinx-search](https://github.com/readthedocs/readthedocs-sphinx-search) from...

e7cb45ba0207442ed9922c48970d444e73e08058 authored 9 months ago by dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Spectramerger sprint (#426)

* Spectra Merging part has been added. How to list parameters is added in Parameter Handling sec...

27dfc2ad071fd16d27d57bbc631efda90b5e6b69 authored 9 months ago by KyowonJeong <[email protected]>

Bump tj-actions/changed-files from 35 to 41 in /.github/workflows (#428)

Bumps [tj-actions/changed-files](https://github.com/tj-actions/changed-files) from 35 to 41.
- ...

e40c469dbd7114193fca70a883fb45be810d55ae authored 9 months ago by dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

removed reference to isotopewavelet (#425)

bb095b81f273c80f035cba9b8ea6e63bbe75a0c2 authored 10 months ago by Timo Sachsenberg <[email protected]>

Update spectrum_normalization.rst (#424)

This commit enhances the 'Spectrum Normalization' section of the documentation. The changes incl...

5fc350318f8c54b62eb0f479caf01ec40de643b8 authored 11 months ago by Ayesha-Feroz <[email protected]>

Add files via upload

cae748a47938f4cf87967fc001874b78bb7f1b77 authored 11 months ago by Ayesha-Feroz <[email protected]>

Update build_from_source.rst

0a3ad66daeef4db1aac2586d73824cdcdb4534ff authored 11 months ago by Julianus Pfeuffer <[email protected]>

Update build_from_source.rst

7a092ec5d343a111718470fbc19b261ee8049991 authored 11 months ago by Timo Sachsenberg <[email protected]>

Update chemistry.rst

fix typo

ea2d0a9558be318f91c363cbe674984f7033eae2 authored 11 months ago by Samuel Wein <[email protected]>

Update quantitative_data.rst

Remove reference to outdated page

16607afc4ee38415cd98203b09cceb3baab4b94c authored 11 months ago by Samuel Wein <[email protected]>

Update charge_isotope_deconvolution.rst

Fix unescaped %

a852d88040b6ccadef9b5fbd698a0d3234cb9a4f authored 11 months ago by Samuel Wein <[email protected]>

Merge pull request #419 from axelwalter/adduct-detection-tutorial

Adduct detection tutorial

1d810aeeac69f36d3faac2a07ecdd6418debb5d7 authored 11 months ago by axelwalter <[email protected]>

add adduct detection tutorial

6e9bba53feec73eb07227416b0f68795819c0b1f authored 11 months ago by axelwalter <[email protected]>

choose binder instance able to run our notebooks

64016e743486c6986d52efc1b2140a49df6ec420 authored 12 months ago by Timo Sachsenberg <[email protected]>

Update build-push-notebooks.yaml

Doing this daily means that mybinder needs to rebuild the image every day. Commenting this out f...

4bc75aa6485de06868035c460783db35efa497c3 authored 12 months ago by Samuel Wein <[email protected]>

Update requirements.txt

Use release pyOpenMS package

c004193c9b7286eb51432bd717eb856885032247 authored 12 months ago by Samuel Wein <[email protected]>

Merge pull request #410 from OpenMS/poshul-patch-2

Update ms_data.rst

b44adfe31d1b1682019ac372de29b91ecac9708b authored about 1 year ago by Samuel Wein <[email protected]>

Update ms_data.rst

Fix broken link in ms_data

67dc5d88b77700401d578ad4401c20c1a677c007 authored about 1 year ago by Samuel Wein <[email protected]>

Update README.md

8c63f0224b4ffbcf75692060eb4c269fb89f921c authored about 1 year ago by Julianus Pfeuffer <[email protected]>

Update test-notebooks.yml

7a1dd1e58d7babc939a4de3d3d09773093cdeb61 authored about 1 year ago by Julianus Pfeuffer <[email protected]>

??? triggeR???

65345925cd3a7a8fda2ff0ae503e1c11337d561b authored about 1 year ago by Julianus Pfeuffer <[email protected]>

Update test-notebooks.yml

23c6e2b3a6d44aa78dc72c4dee31fa63805dd47c authored about 1 year ago by Julianus Pfeuffer <[email protected]>

Update test-notebooks.yml

8e3abc098a31d24c3ce8848f8d3f3c2a2ef3456c authored about 1 year ago by Julianus Pfeuffer <[email protected]>

automatically add dev tag based on branch (RTD-only)

0c624d085763b930333dd9cad93cceabda3daab7 authored about 1 year ago by Julianus Pfeuffer <[email protected]>

Update docs/source/conf.py

0d5e4f3244e70bb41e310090f6a65e9b480ba126 authored about 1 year ago by Julianus Pfeuffer <[email protected]>

Update docs/source/user_guide/logging.rst

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

15accd0523d85992bddae8b6b27c23bc8683b2d2 authored about 1 year ago by Julianus Pfeuffer <[email protected]>

import

076fb11a6e89b9b19c227bc7384a54a3048ee8fe authored about 1 year ago by Julianus Pfeuffer <[email protected]>

add page on logging

96c765e55d9a600ebfebcd2353026e36fa5f1cd3 authored about 1 year ago by Julianus Pfeuffer <[email protected]>

Update supported versions of python

04c8016d6dd22cf38b71ce6374b22bf445100f26 authored about 1 year ago by Radu Suciu <[email protected]>

now increase version

155f6c47b12c476ff5319d0cfd83939571fc6ca3 authored about 1 year ago by Julianus Pfeuffer <[email protected]>

.

360bef7000e3e89b0233297b55586a322275a1ab authored about 1 year ago by Julianus Pfeuffer <[email protected]>

new release cycle

df91acb9e33d7af8fd781164eae1875953ef9ecb authored about 1 year ago by Julianus Pfeuffer <[email protected]>

Update installation.rst

577aca40cec7eba1158127e3d42bdd8e1464a7f6 authored over 1 year ago by Arslan-Siraj <[email protected]>

add new-binderIntegration.gif (#403)

1f51abceff30ffa58561685d3f437dcabc91a54b authored over 1 year ago by Arslan-Siraj <[email protected]>

Update installation.rst for pyopenms (#401)

simple edit to correct pyopenms nightly intto pyopenms

6326886bd21539ae4dd76690cc7eb172aaf6cd47 authored over 1 year ago by KyowonJeong <[email protected]>

added glossary references

db7568a1470118d6a74c268a4078477c8f358397 authored over 1 year ago by matteopilz <[email protected]>

comments

3aa80124318922e2004f567b6ddbb1032352ba56 authored over 1 year ago by Julianus Pfeuffer <[email protected]>

small change to py domain pandoc filter

178b2412e56f372d3a1200201bc47de4ca54d46a authored over 1 year ago by Julianus Pfeuffer <[email protected]>

Merge pull request #399 from matteopilz/ipynb_links

Convert References to html Links for ipynb

8c1f16113f36b5de98001fef2f39ea75f984d07f authored over 1 year ago by Matteo Pilz <[email protected]>

updated function docstring

1156fede57e33cae5ca38d6a1077ad16174e1d28 authored over 1 year ago by matteopilz <[email protected]>

Merge remote-tracking branch 'origin/ipynb_links' into ipynb_links

36dbc2cfb9889b461787363fed1c3a7fb50ecfc7 authored over 1 year ago by matteopilz <[email protected]>

differentiate between main & submodule

86b7dcee3fc8cc7e14a42586fa10364d9bc5b4b2 authored over 1 year ago by matteopilz <[email protected]>

Merge branch 'OpenMS:master' into ipynb_links

6e46f419c272cfd845f37267befd551cf521fab9 authored over 1 year ago by Matteo Pilz <[email protected]>

Added reference links conversion & changed simple-example & advanced-example links in wrapping workflows

5192fb0913e838cdfcfdabf35d80c51eaf8e7193 authored over 1 year ago by matteopilz <[email protected]>

Update scoring_spectra_hyperscore.rst (#394)

* Update scoring_spectra_hyperscore.rst

* Update s...

4d0b9a5339b8f810b8a9cd3071ec8878af86a2dc authored over 1 year ago by Timo Sachsenberg <[email protected]>

Merge pull request #390 from OpenMS/modified_peptide_generator_doc

Update peptides_proteins.rst

fd4ceca023c637b433a29d56a5003938dacfdf08 authored over 1 year ago by Timo Sachsenberg <[email protected]>

Update peptides_proteins.rst

441aee0c6ce12d7106b14cfd06959ee1c5e4ce5c authored over 1 year ago by Ayesha-Feroz <[email protected]>

Merge pull request #396 from OpenMS/explicit_importing

Explicitly import pyOpenMS in the example python codes

1dba25c76a379b37be431c7b1767892bcbf891ac authored over 1 year ago by Timo Sachsenberg <[email protected]>

broken link fixed

15c0e44b9cc977c5c6dee93f376abcb1c811ab45 authored over 1 year ago by JeeH-K <[email protected]>

adding missing oms

6b5e9854cde08a7e2d9c3d2cfa87db32846f79b3 authored over 1 year ago by JeeH-K <[email protected]>

Update docs/source/user_guide/reading_raw_ms_data.rst

ddcc8f4c86e974d01f00f6eb1f922c7eb4289dca authored over 1 year ago by Timo Sachsenberg <[email protected]>

Update docs/source/user_guide/algorithms.rst

Co-authored-by: Julianus Pfeuffer <[email protected]>

ede975dd62d485f2bad37fd2b11f3ac278c6b5aa authored over 1 year ago by Timo Sachsenberg <[email protected]>

Apply suggestions from code review

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

45e51e564a7e13952c5ffcaaf4010eb5298df296 authored over 1 year ago by Timo Sachsenberg <[email protected]>

Explicitly import pyOpenMS in the example python codes

de7a87ebcf1a419cc9dd45b7f825b2b19730572a authored over 1 year ago by JeeH-K <[email protected]>

Update chemistry.rst

Bug fixed in all amino acid modification example.

96ce56be9e9434d0641cd6f56202bbc792b9cea9 authored over 1 year ago by KyowonJeong <[email protected]>

Update chemistry.rst

Added the part in which all amino acid modifications are stored and retrieved with UniMod accession

944a7040505f326748e56a9caa379fe98c1703f7 authored over 1 year ago by KyowonJeong <[email protected]>

added back changes removed in the revert

as basis for fixing the remaining issues

9a8ec167dbd4d94eecedb029fc3dd66e9f28f343 authored over 1 year ago by Timo Sachsenberg <[email protected]>

Revert "Update peptides_proteins.rst" (#392)

837bd75af0c0c2ce20e6adcd3fdb8205487ea1fc authored over 1 year ago by Julianus Pfeuffer <[email protected]>

Merge pull request #391 from OpenMS/Ayesha-Feroz-patch-2

Update peptides_proteins.rst

c4b520d65e47207c58fba401f15b13fb8da52c65 authored over 1 year ago by Ayesha-Feroz <[email protected]>

Update docs/source/user_guide/peptides_proteins.rst

7f42d4e0f015792bc6698e071c684cc5a67317b1 authored over 1 year ago by Julianus Pfeuffer <[email protected]>

Update docs/source/user_guide/peptides_proteins.rst

ee29a8df97fe2974a6f6fc108f623bd6dee51be8 authored over 1 year ago by Julianus Pfeuffer <[email protected]>

Apply suggestions from code linting

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

32154f956e93a72e5b06c32722796b88454e723b authored over 1 year ago by Julianus Pfeuffer <[email protected]>

Update peptides_proteins.rst

db4eaaeff749a246c728ab25104053307f545d66 authored over 1 year ago by Ayesha-Feroz <[email protected]>

Update peptides_proteins.rst

39748b802d8d71bf6a052071b380afc3f99e107f authored over 1 year ago by Timo Sachsenberg <[email protected]>

Merge pull request #389 from matteopilz/docs_request_template

Update documentation issue or request template

a149d5004f7e527b4dc724b69d004d942d6f448f authored over 1 year ago by Matteo Pilz <[email protected]>

documentation issue or request template

967cf6cb758c44a1a3f4c1d8140c933007d49b5a authored over 1 year ago by matteopilz <[email protected]>

Update postBuild to use or new nightly pyopenms name scheme (#386)

* Update postBuild to use or new nightly pyopenms name scheme

* Update requirements.txt

b238a663f957cb37c24b77662113c97a7d784c39 authored over 1 year ago by Timo Sachsenberg <[email protected]>

fix nb generation

d5bb33b4607b012796984523570a965b89ecdd6f authored over 1 year ago by Julianus Pfeuffer <[email protected]>

Update generate_ipynb.sh

d43c75c318d3f0a891f3ddc29953105d36c24b7d authored over 1 year ago by Julianus Pfeuffer <[email protected]>

modify icon bar (#385)

b489b4b159fd1c20a7de8764d1b2f56a720cd1d6 authored over 1 year ago by Julianus Pfeuffer <[email protected]>

text for userguide subpage and uncollapse toc (#384)

68e14452a66562fcc33fb179d7df1a5288eafb93 authored over 1 year ago by Julianus Pfeuffer <[email protected]>

fix some filepaths after pydata restructure

d949356c4a403dc823beb4df914df0d0c0d366d2 authored over 1 year ago by Julianus Pfeuffer <[email protected]>

Update admonitionfilter.py

8fe4c51b72274d5f0123b2dc2d8652a9bd1a8f3d authored over 1 year ago by Julianus Pfeuffer <[email protected]>

Try pandoc 3.x for generating ipynbs (#381)

* Try pandoc 3.x for generating ipynbs

* also update test-pr.yaml

* generate notebooks rec...

a583c73b0dad03f7e651a0bea92a0f140c9006fe authored over 1 year ago by Julianus Pfeuffer <[email protected]>

[FEATURE] First try with pydata theme (#354)

* [FEATURE] First try with pydata theme

* Update requirements.txt

* stash

* fix untrack...

4628e0b3573a80805c1fdd48c482a07ac666f5c8 authored over 1 year ago by Julianus Pfeuffer <[email protected]>

Fix some code blocks (#380)

* Fix some code blocks

* fix corner case of nested codeblock

4e49d49ff17b5d56d10f419f94139c0805977a5b authored over 1 year ago by Julianus Pfeuffer <[email protected]>

Update requirements.txt (#379)

19d3537f3f33996eb159fe4a51a011b4c33e1f19 authored over 1 year ago by Julianus Pfeuffer <[email protected]>

Merge pull request #378 from axelwalter/master

Update export to pandas dataframes file - solves warnings during notebook generation

af55784bb2d2cc8e13eb214eeae25c90d3597ef7 authored over 1 year ago by axelwalter <[email protected]>

Update export_pandas_dataframe.rst

- escape | character not to be interpreted as reference

d6de64cac90ec91d00504ebd192ffba8f45f0e29 authored over 1 year ago by axelwalter <[email protected]>

Update export_pandas_dataframe.rst

- edit link to installation
- remove Python Class references

279cf3d224229f3ec9ba026bb84c286be6393a6a authored over 1 year ago by axelwalter <[email protected]>

Update background.rst

012faa655f1377953475814327b52d005f4e844c authored over 1 year ago by Timo Sachsenberg <[email protected]>

Merge pull request #376 from OpenMS/Ayesha-Feroz-patch-1

Update wrapping_workflows_new_classes.rst

3e684a2f8eb3329cc79cd224b2e5e846d02ea766 authored over 1 year ago by Timo Sachsenberg <[email protected]>

Update wrapping_workflows_new_classes.rst

c37de858c0819803daa48db80cb83ec5c1a8cfb1 authored over 1 year ago by Ayesha-Feroz <[email protected]>

Update wrapping_workflows_new_classes.rst

4bcae8d72e71ae70a01941fc42be7c9dd44bce82 authored over 1 year ago by Julianus Pfeuffer <[email protected]>

Update wrapping_workflows_new_classes.rst

e50211fb67e361aa1968c6c02c47b59bc6af13e3 authored over 1 year ago by Julianus Pfeuffer <[email protected]>

Update wrapping_workflows_new_classes.rst

ac2f31db39325c5b364873618313723dc16329a2 authored over 1 year ago by Timo Sachsenberg <[email protected]>

Update background.rst

14a8638c35265e53749a80d12bb37226713e92be authored over 1 year ago by Timo Sachsenberg <[email protected]>

fix many glossary terms (#331)

* Update .github/workflows/flakeheaven.yml

* added packages

* fix many glossary terms

*...

0068b5c0d20fd00bb8f811542bc907e0911a3dad authored over 1 year ago by Julianus Pfeuffer <[email protected]>

[FIX] fix the code! (#357)

* [FIX] fix the code!

* Apply suggestions from code review

Co-authored-by: github-actions[...

4d9551d80716bbccc49c5c61d1ffef134b1d5f4b authored over 1 year ago by Julianus Pfeuffer <[email protected]>

Update test-pr.yaml

ffd5eaf8000512b2dd8cf5579c2ce8c2cfbf72ad authored over 1 year ago by Samuel Wein <[email protected]>

Merge pull request #356 from JeeH-K/fix_missing_plt

adding "import matplotlib" in example codes

58bd40c718163b0f555ba82f39bf8fa63a2ba06e authored over 1 year ago by JihyungKim <[email protected]>

Merge branch 'master' into fix_missing_plt

c2d373f2f37f193df66ba2a3f77ff05f5e1e3114 authored over 1 year ago by JihyungKim <[email protected]>

adding "import matplotlib"

6267d79e16e0b64226585e0df134561be33d5295 authored over 1 year ago by JeeH-K <[email protected]>

Merge pull request #344 from JeeH-K/master

Expanding theoretical spectrum generation tutorial

09112e4870986f99103e28fa10f8699d924c5c70 authored over 1 year ago by JihyungKim <[email protected]>

Merge branch 'master' into master

0cf43235d9ad39f2e2d9c7b1e7ab4cc002437096 authored over 1 year ago by JihyungKim <[email protected]>

Merge pull request #348 from OpenMS/poshul_fix

re-added requirements processing

540f021852cab407efb86ae800a8a6628ccc9af3 authored over 1 year ago by Samuel Wein <[email protected]>

fix

56e69fa366ae90f71a23f4846ed900acc3cee3e7 authored over 1 year ago by Julianus Pfeuffer <[email protected]>