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docs: fix typo and malformed .NET link in Windows installation guide#266

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Tanush576:fix-windows-install-docs
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docs: fix typo and malformed .NET link in Windows installation guide#266
Tanush576 wants to merge 2 commits intoOpenMS:developfrom
Tanush576:fix-windows-install-docs

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@Tanush576 Tanush576 commented Mar 3, 2026

Describe the change

This PR fixes minor formatting and spelling errors in the Windows Installation "Known issues" section, addressing issue #265.

Changes made:

  • Corrected the typo "installion" to "installation".
  • Fixed the malformed markdown link for the Microsoft .NET 3.5 framework documentation and updated the URL to the current official Microsoft Learn page.

Fixes #265

Made with AI tools (Note: Used AI to assist with drafting the PR text and locating the updated Microsoft URL).

PR checklist

Summary by CodeRabbit

  • Documentation
    • Converted Windows top-level heading to an H1 and cleaned up surrounding spacing for readability.
    • Standardized installer prompts and wording (e.g., "Run anyway") and added a tip about installer behavior.
    • Normalized known-issues phrasing and quote spacing for error messages.
    • Updated external .NET guidance link to Microsoft Learn.
    • Fixed typos and improved overall formatting and line breaks.

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coderabbitai bot commented Mar 3, 2026

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📥 Commits

Reviewing files that changed from the base of the PR and between d907b05 and 32e3c57.

📒 Files selected for processing (1)
  • docs/about/installation/installation-on-windows.md
📝 Walkthrough

Walkthrough

This PR updates the Windows installation documentation: converts the top-level Windows heading to H1, fixes typos and punctuation (e.g., "installion" → "installation", "Run anyways" → "Run anyway"), normalizes Known Issues formatting, replaces a malformed .NET link with the Microsoft Learn page, and adds a Windows installer tip block.

Changes

Cohort / File(s) Summary
Windows Installation Documentation
docs/about/installation/installation-on-windows.md
Converted top-level heading to H1; corrected typos and punctuation; reworded defender/run prompts; added a tip block about installer behavior; normalized Known Issues wording and error-message quoting; replaced malformed .NET framework link with Microsoft Learn URL; general whitespace/formatting cleanup.

Poem

🐇 I hopped through docs with nimble paws,
Fixed a typo and mended flaws,
A .NET link now steers aright,
Headings gleam in proper light,
Happy installer—hop, rejoice!

🚥 Pre-merge checks | ✅ 5
✅ Passed checks (5 passed)
Check name Status Explanation
Description Check ✅ Passed Check skipped - CodeRabbit’s high-level summary is enabled.
Title check ✅ Passed The PR title directly and clearly summarizes the primary changes: fixing a typo and a malformed .NET link in the Windows installation documentation.
Linked Issues check ✅ Passed All coding requirements from issue #265 are met: typo 'installion' corrected to 'installation' and malformed .NET link fixed and updated to Microsoft Learn URL.
Out of Scope Changes check ✅ Passed The PR includes additional formatting improvements beyond the two core requirements, such as heading standardization and quote formatting adjustments, which are ancillary to the core fix.
Docstring Coverage ✅ Passed No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

✏️ Tip: You can configure your own custom pre-merge checks in the settings.

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Actionable comments posted: 3

🤖 Prompt for all review comments with AI agents
Verify each finding against the current code and only fix it if needed.

Inline comments:
In `@docs/about/installation/installation-on-windows.md`:
- Around line 26-27: Fix the malformed quoted error message by removing the
stray apostrophe after SP1 and ensuring proper surrounding quotes; locate the
string "The installation of the Microsoft .NET 3.5 SP1' package failed!" in the
documentation and change it to a cleanly quoted message such as "The
installation of the Microsoft .NET 3.5 SP1 package failed!" so punctuation and
quoting are correct.
- Line 55: Change the unhyphenated phrase "third party tools (ProteoWizard)" to
the compound adjective form "third-party tools (ProteoWizard)" in the sentence
beginning "Fix is to enable the .NET Framework 3.5 yourself..." so the prose
uses the correct hyphenation for the compound modifier.
- Line 12: Replace the informal phrase in the user-facing sentence that reads
Click on "More Info", and then "Run anyways". in
docs/about/installation/installation-on-windows.md by changing "Run anyways" to
the standard form "Run anyway" so the sentence becomes Click on "More Info", and
then "Run anyway". Ensure only that wording is updated and punctuation remains
unchanged.

ℹ️ Review info

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

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Reviewing files that changed from the base of the PR and between d412601 and 4e720f4.

📒 Files selected for processing (1)
  • docs/about/installation/installation-on-windows.md

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Actionable comments posted: 2

🤖 Prompt for all review comments with AI agents
Verify each finding against the current code and only fix it if needed.

Inline comments:
In `@docs/about/installation/installation-on-windows.md`:
- Line 29: The document uses inconsistent casing for ProteoWizard: change the
phrase "Third Party - Proteowizard" to "Third Party - ProteoWizard" (match the
usage on Line 55) so the product name is consistently capitalized; search for
occurrences of "Proteowizard" in this file and update them to "ProteoWizard" to
standardize casing.
- Line 55: The sentence "Fix is to enable the .NET Framework 3.5 yourself
through Control Panel..." that documents Known issue 4 is not indented and
renders outside the numbered item; update the Markdown so that this sentence is
a continuation of list item "4." by indenting that line by four spaces (or one
tab) so it is nested under the "4." list item (edit the paragraph containing the
.NET Framework 3.5 guidance in the Known issue 4 block).

ℹ️ Review info

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 4e720f4 and d907b05.

📒 Files selected for processing (1)
  • docs/about/installation/installation-on-windows.md


You must download and install it manually in order for Proteowizard to work.
This should only happen if installion is done by selecting the "Third Party - Proteowizard" components. The reason is
This should only happen if installation is done by selecting the "Third Party - Proteowizard" components. The reason is
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⚠️ Potential issue | 🟡 Minor

Use consistent product casing for ProteoWizard.

Line 29 says "Third Party - Proteowizard" while Line 55 uses ProteoWizard. Please standardize casing to avoid confusion.

🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed.

In `@docs/about/installation/installation-on-windows.md` at line 29, The document
uses inconsistent casing for ProteoWizard: change the phrase "Third Party -
Proteowizard" to "Third Party - ProteoWizard" (match the usage on Line 55) so
the product name is consistently capitalized; search for occurrences of
"Proteowizard" in this file and update them to "ProteoWizard" to standardize
casing.

that `.net3.5` does not get properly installed during the process.

Fix is to enable the .NET Framework 3.5 yourself through Control Panel. See this [Microsoft help page](https://docs.microsoft.com/en-us/dotnet/framework/install/dotnet-35-windows).aspx#ControlPanel) for detailed information. Even if this step fails, this does not affect the functionality of OpenMS, except for the executability of included third party tools (ProteoWizard).
Fix is to enable the .NET Framework 3.5 yourself through Control Panel. See this [Microsoft help page](https://learn.microsoft.com/en-us/dotnet/framework/install/dotnet-35-windows) for detailed information. Even if this step fails, this does not affect the functionality of OpenMS, except for the executability of included third-party tools (ProteoWizard).
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⚠️ Potential issue | 🟡 Minor

Fix list-item continuation formatting for Known issue 4.

Line 55 should be indented as part of list item 4.; currently it can render as a separate paragraph outside the numbered item.

Suggested edit
-Fix is to enable the .NET Framework 3.5 yourself through Control Panel. See this [Microsoft help page](https://learn.microsoft.com/en-us/dotnet/framework/install/dotnet-35-windows) for detailed information. Even if this step fails, this does not affect the functionality of OpenMS, except for the executability of included third-party tools (ProteoWizard).
+   Fix is to enable the .NET Framework 3.5 yourself through Control Panel. See this [Microsoft help page](https://learn.microsoft.com/en-us/dotnet/framework/install/dotnet-35-windows) for detailed information. Even if this step fails, this does not affect the functionality of OpenMS, except for the executability of included third-party tools (ProteoWizard).
📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
Fix is to enable the .NET Framework 3.5 yourself through Control Panel. See this [Microsoft help page](https://learn.microsoft.com/en-us/dotnet/framework/install/dotnet-35-windows) for detailed information. Even if this step fails, this does not affect the functionality of OpenMS, except for the executability of included third-party tools (ProteoWizard).
Fix is to enable the .NET Framework 3.5 yourself through Control Panel. See this [Microsoft help page](https://learn.microsoft.com/en-us/dotnet/framework/install/dotnet-35-windows) for detailed information. Even if this step fails, this does not affect the functionality of OpenMS, except for the executability of included third-party tools (ProteoWizard).
🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed.

In `@docs/about/installation/installation-on-windows.md` at line 55, The sentence
"Fix is to enable the .NET Framework 3.5 yourself through Control Panel..." that
documents Known issue 4 is not indented and renders outside the numbered item;
update the Markdown so that this sentence is a continuation of list item "4." by
indenting that line by four spaces (or one tab) so it is nested under the "4."
list item (edit the paragraph containing the .NET Framework 3.5 guidance in the
Known issue 4 block).

@Tanush576 Tanush576 force-pushed the fix-windows-install-docs branch from d907b05 to 32e3c57 Compare March 3, 2026 21:03
@Tanush576
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Hi maintainers! Just a quick update: I have accepted and merged all of the coderabbitai bot's suggestions for grammar and punctuation into this PR.
I also wanted to give a heads-up regarding the build-sphinx CI check failure. I checked the logs, and it looks like the lychee link checker is throwing network errors (502/503) on a few external links in unrelated files (specifically in msstats.html and webapps.html).
My changes are strictly isolated to the typography and link fixes in the Windows Installation guide, so this PR should be fully ready for review whenever you have a moment. Thanks!

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Docs: Typo and malformed link in Windows Installation Known Issues

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