Restructure and Rearrange OpenMS RTD Documentation #112
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…yst extension to conf.py
trickyck
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axelwalter,
jpfeuffer,
tapaswenipathak and
timosachsenberg
trickyck
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axelwalter
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Jun 28, 2022
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Nice structure. Just an idea for the installation part and, as discussed in the meeting, the items in the developer section.
docs/index.rst
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| .. toctree:: | ||
| :maxdepth: 2 | ||
| :caption: Getting Started |
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Since we moved the build from source to the developer section, we could rename "Getting Started" to "Installation" and remove the redundancy from the items ("Installation on Windows" -- > "Windows").
docs/index.rst
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| additional-resources/write-and-label-github-issues.md | ||
| additional-resources/pull-request-checklist.md | ||
| develop-with-openms/cplusplus.md | ||
| develop-with-openms/python.md |
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As discussed I would be in favor of renaming "python" to "pyOpenMS". Of course the article needs to mention, that you can use pyOpenMS together with other python modules.
docs/index.rst
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| additional-resources/reporting-bugs-and-issues.md | ||
| additional-resources/write-and-label-github-issues.md | ||
| additional-resources/pull-request-checklist.md | ||
| develop-with-openms/cplusplus.md |
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Merge with "OpenMS core library" and call it "OpenMS C++ core library"?
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I'm not responsible for cc @axelwalter @enetz @jpfeuffer @KyowonJeong @poshul @OpenMS/doc-team. |
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@tapaswenipathak what do you mean? |
jpfeuffer
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There are some errors but we can fix them later.
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* Address review comments by @greengypsy Ref: #65. * add: exact syntax for adding admonition * add: soon to be deprecated important admonition for toppas * add: remaining toppview-introduction content Closes #76. * prettier: ui enhancements Fixes #66. Fixes #71. Closes #79. Fixes #81. * fixes: merge conflicts * Major fix of installation instructions * Fix * Fixes to tabbing * whitespace * [FIX] allow crosslinking in markdown * Update conda instructions for macOS * try different link syntax #93 * Try adding autosection #93 * Revert "Try adding autosection" This reverts commit e1f5b66. * Revert "try different link syntax" This reverts commit 940fbdf. * Revert "Update conda instructions for macOS" This reverts commit 4e7cf57. * Revert "[FIX] allow crosslinking in markdown" This reverts commit 0241aa2. * Revert "whitespace" This reverts commit 83540a0. * Revert "Fixes to tabbing" This reverts commit b46d112. * Revert "Fix" This reverts commit eaf3a63. * Revert "Major fix of installation instructions" This reverts commit ab7106e. * Documentation urls check (#114) * added action.yml * created workflows folder and added action.yml to workflows * moved workflows to .github * fixed pull request checklist deadlink * set max-depth to 2 * set max-depth to 7 and change link in toppas.md * edited action.yml and fixed links * added a config.json file for action.yml * corrected action.yml * made discussed changes to action.yml file * added quotation marks to main branch * added current branch to check if script works * removed rst extension * fixed indentation in action.yml * added current branch * added full file path to config.json * added current branch again * added base braanch as develop * base-branch * set base-branch to staging * remove current branch * Restructure and Rearrange OpenMS RTD Documentation (#112) * Add toppview tutorial (#119) * fixed xml code block in key concepts * added TOPPView tutorial * added additional topics to visualize-with-openms.md * rearranged files and added content * fixed image urls and fixed additional topics link in visualize-with-openms.md * edit image links so I can see them live * resize file-import-options.png * resize filtering options * add a sentence to getting started section in visualize with openms * added cross-linking description, added external links to toctree in index.rst * deleted unnecessary files as they are external links. changed toctree caption for core library and pyOpenMS * added knime and galaxy descriptions * added knime and galaxy descriptions * removed extra hash from url in openms-in-knime.md * fixed some alignment issues with the list and made major steps bold in knime description * fixed list in knime description * addressing issues raised * create build from source and delete sections from installation guides * restructured folders * remove redundant files and add proteomicslfq.md file to main suite * added a message on the developer tutorial saying it is under construction * removed TOPPAS tutorial and OMSSA references * add full stop * deleted some files, added a under constructed message for nextflow, and polished the galaxy section * minor correction in glossary. added image to how openms works * add link to KNIME tutorial * added note in how openms works, added construction message to core library page and added link to openms api reference * build custom knime plugin * change galaxy website link * change galaxy website link * added full stop and description to tutorials section (nextflow) * initialized structure of tutorial * testing first note * adding user tutorial to index * correct mistake in file path in index.rst * added images and a footnote * added more content including fig 5 * try to render R code * try to render R code * added knime-setup images, adding references * fix references * fix references2 * fix references3 * fix references4 * add metabo image folder and added task admonition * fix render of fig 9 * trying to fix task admonition rendering * added html admonitions to conf.py myst-enable-extensions. Structured task admonition * tried to add tip inside task admonition * fix rendering of bold text and title for tip admonition inside task admonition * trying to make title in admonition more visible * added labelfree images * added a number of images to the labelfree folder and added more content to user-tutorial * fixed url to image 12 and caption for table 1 * add handout-clean.css * removed purple background from task admonition * added matrix image. adding mathjax to render log equation * edited log equation * use amsmath instead of mathjax * add math directive to equation * added more content up to chapter 4 protein inference * up to statistical validation of protein inference results 4.2 * changed rconsole to r for codeblocks * trying cross-referencing * added numref to conf.py and trying out link in openms-tutorial * added numref to conf.py and trying out link in openms-tutorial * trying to get linking to figures working 1 * trying to get linking to figures working 1 * trying to get linking to figures working 2 * trying to get linking to figures working 3 * trying to get linking to figures working 4 * added more content to user tutorial * up to 6.3 of user tutorial * fixed some links and rendering of tables. Also tried to link footnote to external website * added references as footnotes * test using VS code editor * up to spectral library search * up to OpenSWATH chapter 7 * up to OpenSWATH chapter 7 * changing the custom css of the question admonition * fixing color of svg question in question admonition * edited custom css and up to 8 OpenSWATH for Metabolomics * up to quality control * added quality control and faqs * added links in references * added metababolomics preprocessing tutorial * added workflow tutorial to index.rst * added link to empty idXML file to untargeted metabolomics preprocessing file * made changes to tutorials.md * changed task admonition icon * add url prefix and brackets to variable in custom.css * added quotation marks around url for image * trying to render icon by using direct path to svg * adjust size of task admonition image and change color to match left border * made a few corrections according to comments to openms-user-tutorial * trying substitution with variables * substitution trial 2 * substitution trial 3 * adding paths * substitution trial 4 * added important tag to path icons * adjusted css for path rendering and changed substitution 6 * substitution trial 1 * changed more paths * removed linkify fuzzylinks * major fixes * revert comment * changed the path of some images so that the would render. Styling paths with folder * more fixes * cleaning up warnings * deleted files not used and added file to index.rst * added css * glossary editsand edits to custom.css * modified css and orphaned ini file editor and swath wizard files * changed orphan flags * tried something else for the orphan directive to work * tried something else for the orphan directive to work * removing warnings * removing warnings * added paths through user tutorial * trying to fix admonition rendering * formatting admonition with explanation * formatting admonition with explanation 2 * formatting admonition with explanation 3 * formatting admonition with explanation 4 * formatting admonition with explanation 4 * removed unicode from python block * wrap text after codeblock in admonition in p tags * adding variables * adding variables * fixed spelling error of the * adding path variables 1 * adding path variables 2 * adding path variables 2 * adding path variables 3 * adding path variables 4 * checking if paths work within admonitions * checking if paths work within admonitions * trying paths and substitutions again * trying paths and substitutions again * trying paths and substitutions again * trying paths and substitutions again * added searchtools.js * added sphinx search extension and removed searchtools.js * fixed paths but removed sub within paths * fixed a couple of minor errors. one where the p title didn't include admonition and a missing backtick * fix path * added link to contact us on line 2816 * clean up errors * cleanup warnings * cleaning up more warnings and removed problematic admonition * add sub to paths * fixing all references of 2.7 and adding variable subs * fixing all references of 2.7 and adding variable subs * added a link to KNIME doc about creating GKNs * Fixes all warnings, better path styling, fixes tables and other styles * fixed broken links * fix more broken links * fixed a couple more links * added a couple of links to citations * added .lycheeignore file * moved lycheeignore to root of repository * use regexes in lychee ignore file * added one extra link * edited one link in installation guide linux * updated lycheeignore to include publication links * updated lycheeignore to include publication links Co-authored-by: Tapasweni Pathak <tapaswenipathak@gmail.com> Co-authored-by: Julianus Pfeuffer <pfeuffer@informatik.uni-tuebingen.de> Co-authored-by: Timo Sachsenberg <timo.sachsenberg@uni-tuebingen.de> Co-authored-by: Julianus Pfeuffer <jpfeuffer@fu-berlin.de>
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Describe the change
I have restructured the documentation according to Julianus's document (closes #59).
I have also sorted the glossary (closes #63) and added a definition for FASTA format.
The branch can be viewed here.
New structure:
PR checklist
CHANGELOG.mdis updated.