Use correct admonitions #36

trickyck · 2022-05-25T10:54:15Z

Describe the change

Made one spelling correct. The other changes relate to adding the agreed upon admonition syntax.
Closes #26.

PR checklist

I have added description of the change I'm proposing in the OpenMS Documentation.
I have read and followed OpenMS Documentation Contributing guidelines.
I have attached a screenshot of the relevant area after this change.
CHANGELOG.md is updated.
I have added my name in CONTRIBUTING.md.

tapaswenipathak · 2022-05-25T11:37:43Z

docs/installations/installation-on-macos.md

   Since macOS Catalina (maybe also Mojave) notarized apps and executables are mandatory.

-   > **_NOTE:_** Although there is a lot of effort in signing and notarizing everything, it seems like openms software
+   ```{note}


let's make this:

important.

tapaswenipathak · 2022-05-25T11:38:02Z

docs/installations/installation-on-windows.md

   installation. When asked for an admin authentication, please enter the credentials.

-> **_NOTE:_** The windows binary version works with most versions of windows from Win7 to Win10 (older versions might
+```{note}


tapaswenipathak · 2022-05-25T11:40:28Z

docs/tutorials/TOPP/feature-detection.md

 Spectrometry Data Using the Isotope Wavelet" (2007).

-Please note that this algorithm features no "modelling stage", since the structure of the isotopic pattern is explicitly
+```{note}


tapaswenipathak · 2022-05-25T11:40:54Z

docs/tutorials/TOPP/feature-grouping.md

 ![TOPP labelfree quant](../../images/tutorials/topp/TOPP_labelfree_quant.png)

-> **_NOTE:_** This algorithm assumes that the retention time axes of all input maps are very similar. To correct for
+```{note}


tapaswenipathak · 2022-05-25T11:41:22Z

docs/tutorials/TOPP/general-introduction.md

 files are the recommended way to store all settings of such a pipeline in a single place.

-Note that the issue of finding suitable parameters for the tools is not addressed here. For problems during the
+```{note}


tapaswenipathak · 2022-05-25T11:44:33Z

docs/tutorials/TOPPAS/examples.md

 intermediate results.

-> **_NOTE:_** The intensities and retention times are slightly different between the runs. To correct for retention
+```{note}


tapaswenipathak

(this. should. work. nice.)

@jpfeuffer

* Changed format to backticks for code and bold for tools and UI elements (#33) * made changes to several files * formatted text with backticks and bold * add internal link within the page to quality-control.md * removed backticks from Qt and related software * Fixes: review comments by @greengypsy (#34) * Fixes: review comments by @greengypsy * review fixes and add a few links to tutorials * Added keyboard syntax plus other minor changes (#35) * added keyboard syntax plus other minor changes such as adding full stops to sentences * added spaces between symbols as discussed Co-authored-by: Tapasweni Pathak <tapaswenipathak@gmail.com> * Use correct admonitions (#36) * added one note to installation on gnu linux md file * added one note to installation on gnu linux md file * added admonitions to noted text * changed admonition types as discussed in review * Add downloads page * Add introduction of a few concepts (#39) * Add introduction of a few concepts Fixes #14. * Fixes: review comments by @greengypsy * Fixes: review comments by @jpfeuffer * Update docs/introduction.md Co-authored-by: Julianus Pfeuffer <pfeuffer@informatik.uni-tuebingen.de> * Update docs/introduction.md Co-authored-by: Julianus Pfeuffer <pfeuffer@informatik.uni-tuebingen.de> * Update docs/introduction.md Co-authored-by: Julianus Pfeuffer <pfeuffer@informatik.uni-tuebingen.de> * Update docs/introduction.md Co-authored-by: Julianus Pfeuffer <pfeuffer@informatik.uni-tuebingen.de> * delete: redundant note Co-authored-by: Julianus Pfeuffer <pfeuffer@informatik.uni-tuebingen.de> * More docs (#40) * created About.rst * linked Developer FAQ to external website * linked Developer FAQ to external website * linked Developer FAQ to external website * fix links in About.rst * Update About.rst * Update About.rst * Update About.rst * changed About.rst to about.rst * Rename About.rst to about.rst * added known-issues.rst * fix bullet point in known-rst * add code to known-issues.rst * add code to known-issues.rst * fix code to known-issues.rst * added VS output to known-issues.rst * added VS output to known-issues.rst * added VS output to known-issues.rst * added VS output to known-issues.rst * added VS output to known-issues.rst * added more text to known-issues.rst * tried adding console code to known-issues.rst * completed copying content for known-issues.rst * added topp-faq.rst and docutils.conf * changed contents title in topp-faq.rst * inline cpp class in topp-faq.rst * FileInfo is not a cpp class its a tool * adding console code * adding console code * adding console code * add monospace text to topp-faq.rst * fixed code blocks * created about contact for-developers for-users reporting-bugs-issues rst files * created developer-faq.rst * developer-faq changes * developer-faq changes * developer-faq changes * developer-faq changes * testing * developer-faq * developer-faq * developer-faq * developer-faq * developer-faq * developer-faq * developer-faq * minor change * renamed folder to lower case * made small changes to files and created 3 empty .md files * added pyopenmswrapping classes link * removed about.rst and added about.md * added contact.md * created for-developers.md * modified for-developers.md * created building-openms.md * just checking links in contact.md * added contributor quickstart guide, users quick start guide and reporting bugs and issues md files * added linkstobs to flag dead links * fixed some links and deleted for-developers.md * modified about.md, deleted building-openms.md, created build-openms-from-source.md, developer-faq.md * modified quickstart guide contributors, developer faq, reporting bugs, and user quick start guide * added coding convents and write and label github issues md files, edited several others * added Notes to developer-faq.md plus other minor edits * added contributor-faq * added coding-convetions.md * added contributor-faq.md * updated pull request checklist md file * updated write-and-label-github-issues * made changes suggested in the review * updated folder structure as suggested in review * added installations folder with build-openms-from-source.md as discussed * created openms-git-workflow.md and click-fork.png under new directories additional-resources and images * minor changes * fix spacing issues * fix alignment issues * Add a few more from #4 * Fixes: review comments by @jpfeuffer Co-authored-by: greengypsy <ckumar073@gmail.com> Co-authored-by: greengypsy <31978630+greengypsy@users.noreply.github.com> * Add lexers to project (#47) * modified conf.py and requirements.txt to include pygments code * added lexers to code in several files * Add conda installation instructions and a few reorderings (#38) Fixes #15. Fixes #16. * Add wiki and a few more docs (#48) * Add: Adding your own tool to the TOPP suite * Add: writing and shipping external code using openms * Add: Compiling with self built compilers and non default standard libraries * Add: wiki: Build your own OpenMS KNIME package * Add: wiki: OpenMS-2.0-kernel-whitepaper * Add: wiki: Developer Guidelines for adding new dependent libraries * Add: Glossary 🎉 (#49) * Production ready[1]: Touchup and cleanup (#51) * Add: build-openms-from-source in sidebar menu * let's make everything work on staging-openms, too * reduce: sidebar menu under introduction * reduce: sidebar menu list * Add: a few sections in sidebar menu of topp tut * Add tabs for installations using installers Fixes #17. * minor fixes + cleanup * add Discord invite link * Update docs/tutorials/TOPP/quality-control.md Co-authored-by: Julianus Pfeuffer <pfeuffer@informatik.uni-tuebingen.de> Co-authored-by: Julianus Pfeuffer <pfeuffer@informatik.uni-tuebingen.de> * Spell out RC * Production ready[2]: Touchup and cleanup (#58) * fix: follow Sentence case for h2 or less * fix: glossary terms in introduction page * add tabs: ux * fix: follow Title Case and reword * add: description plus file name * fix: dropdown menu sidebar toppas tut * add: +reword .github templates * add: more glossary * fix: include faq * add: glossary more Co-authored-by: greengypsy <31978630+greengypsy@users.noreply.github.com> Co-authored-by: Julianus Pfeuffer <pfeuffer@informatik.uni-tuebingen.de> Co-authored-by: greengypsy <ckumar073@gmail.com>

trickyck added 3 commits May 25, 2022 19:54

added one noteto installation on gnu linux md file

2df5118

added one noteto installation on gnu linux md file

9eb7a53

added admonitions to noted text

830f7b7

trickyck requested a review from tapaswenipathak May 25, 2022 10:54

tapaswenipathak reviewed May 25, 2022

View reviewed changes

changed admonition types as discussed in review

d21697e

tapaswenipathak approved these changes May 25, 2022

View reviewed changes

trickyck merged commit 55f743c into OpenMS:staging May 25, 2022

Use correct admonitions #36

Use correct admonitions #36

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trickyck commented May 25, 2022 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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trickyck commented May 25, 2022 •

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