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Fix Dead Links in MDAnalysis User Guide Documentation #393

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mhmohona opened this issue Oct 15, 2024 · 3 comments · May be fixed by #394
Open

Fix Dead Links in MDAnalysis User Guide Documentation #393

mhmohona opened this issue Oct 15, 2024 · 3 comments · May be fixed by #394

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@mhmohona
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mhmohona commented Oct 15, 2024 •
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I checked MDAnalysis User Guide - Stable Index and found several links that are either broken, lead to 404 errors, or are inaccessible. Below is a table summarizing the problematic links, including the pages where they are found and the anchor text associated with them.

# Error Anchor Text Linked From Broken Link
1 404 Not Found HOLE2 MDAKit Releases https://www.mdanalysis.org/hole2-mdakit/
2 404 Not Found @g2707 Releases https://github.com/g2707
3 404 Not Found align_structure Examples - README https://userguide.mdanalysis.org/examples/analysis/alignment_and_rms/aligning_structure_to_another.ipynb
4 404 Not Found align_trajectory_first Examples - README https://userguide.mdanalysis.org/examples/analysis/alignment_and_rms/aligning_trajectory_to_first_frame.ipynb
5 404 Not Found align_trajectory Examples - README https://userguide.mdanalysis.org/examples/analysis/alignment_and_rms/aligning_trajectory.ipynb
6 404 Not Found rmsf Examples - README https://userguide.mdanalysis.org/examples/analysis/alignment_and_rms/rmsf.ipynb
7 404 Not Found Pydagogue Contributing https://matthew-brett.github.com/pydagogue/
8 404 Not Found DataFrame RMSD Analysis https://pandas.pydata.org/pandas-docs/stable/getting_started/dsintro.html
9 -1 Not Found MMTF MMTF Format https://mmtf.rcsb.org/
10 -1 Not Found HOOMD-blue GSD Format http://codeblue.umich.edu/hoomd-blue/index.html
11 -1 Not Found XML XML Format http://codeblue.umich.edu/hoomd-blue/doc/page_xml_file_format.html
12 -1 Not Found GAMESS-UK GMS Format http://www.cfs.dl.ac.uk/
13 404 Not Found MOL2 MOL2 Format http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf
14 -1 Not Found FHI-aims IN Format https://aimsclub.fhi-berlin.mpg.de/
15 404 Not Found PQR PQR Format https://apbs-pdb2pqr.readthedocs.io/en/latest/formats/pqr.html
16 404 Not Found PDB2PQR PQR Format https://apbs-pdb2pqr.readthedocs.io/en/latest/pdb2pqr/index.html
17 404 Not Found APBS PQR Format https://apbs-pdb2pqr.readthedocs.io/en/latest/apbs/index.html
18 -1 Not Found CRD CRD Format https://www.charmmtutorial.org/index.php/CHARMM:The_Basics
19 404 Not Found PARM TOP Format https://ambermd.org/formats.html
20 -1 Not Found IBIsCO TRZ Format http://www.theo.chemie.tu-darmstadt.de/ibisco/IBISCO.html
21 -1 Not Found YASP TRZ Format http://www.theo.chemie.tu-darmstadt.de/group/services/yaspdoc/yaspdoc.html

I am ready to start working on fixing these issues, but I would appreciate some feedback or suggestions before proceeding. Also, if there are preferred sources to replace outdated links, please provide them.
@RMeli
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RMeli commented Oct 15, 2024

@mhmohona that is fantastic investigative work, thank you for doing this. I think it would be great to fix the broken links for sure. Tracking down the new links with Google is probably the best course of action; the old link should give you already quite a bit of information.

For example, Googling

hole2-mdakit

the first hit is the GitHub repository of mdahole2, while the second hit is already the link we want: https://mdakits.mdanalysis.org/mdahole2.html (i.e. a link to the official MDAnalysis MDAKit repository for the hole2 MDAKit).

@mhmohona mhmohona linked a pull request Oct 21, 2024 that will close this issue
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@mhmohona
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I wasn't able to fix the broken links in https://userguide.mdanalysis.org/stable/formats/format_reference.html because I couldn't find the correct links for row number 11 through 21.

@RMeli
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RMeli commented Oct 22, 2024

Hi @mhmohona, what have you tried in these cases? 11 through 21 seems to be linked to specific file formats of different software. Have you looked into the documentation of said software? The most likely cause of the link breakage is that the page about the file format has moved within the documentation of the software (or that the documentation of the software has moved all together).

@RMeli RMeli mentioned this issue Oct 22, 2024
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Fix broken links for User Guide mhmohona/MDAnalysis-UserGuide
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@RMeli @mhmohona