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New documentation page - #1131

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Cajac102 merged 40 commits into
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new-docs
Aug 14, 2026
Merged

New documentation page#1131
Cajac102 merged 40 commits into
mainfrom
new-docs

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@Cajac102

@Cajac102 Cajac102 commented Aug 5, 2026

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  • layout more intuitive
  • Your first submission tab
  • updated a few outdated points

Might look like a lot, but most of the file changes are just updated paths.

Cajac102 added 13 commits July 17, 2026 13:53
@Cajac102
overhaul the documentation completely
ecc97f9
@Cajac102
overhaul completely pt 2
b17a790
@Cajac102
add first submission button to homepage
1484730
@Cajac102
update description for DOM module
292ae39
@Cajac102
small qol
800f901
@Cajac102
small qol
83c317b
@Cajac102
entrapment no longer alpha
262035e
@Cajac102
fix column names in custom for plasma
563fd3b
@Cajac102
proforma is nonnegotiable for custom
1415a0e
@Cajac102
update first submission page
af9818d
@Cajac102
Fix stale documentation links after the docs restructuring
9ebf4c5 
doc_url fields, parse_settings_custom.toml upload_info links, and webinterface
help-text links still pointed at docs/available-modules/, which was deleted when
the docs were restructured into docs/modules/dda|dia/*.md. Update every link to
the new paths, remapping anchors that no longer resolve (#custom-format is now a
collapsible dropdown with no HTML id, so it points at #tool-specific-setup
instead). Regenerate module_grid_generated.rst so the homepage grid picks up the
corrected doc_url values.
@Cajac102
Repair generate_input_tables.py for the new docs/modules layout
24173a4 
The script still pointed at the deleted docs/available-modules/active-modules/
directory and searched for table markers that no longer exist, so it would have
crashed CI the next time a PR touched an io_parse_settings TOML (the check only
runs conditionally on that). Point it at docs/modules/, add the AIF and
entrapment modules it never covered, and derive entrapment's extra "Parsed FDR
column" from each tool's [mapper]. Regenerating surfaced real pre-existing drift
independent of this fix: AIF's table was missing a FragPipe row and called
MaxQuant "MaxDIA", and entrapment's table was missing its plain FragPipe tool.
Also fix the CI workflow's now-dead git diff path for this check.
@Cajac102
Merge branch 'main' into new-docs
103970e 
Brings in main's finished entrapment feature work (custom format support,
modification support, Spectronaut, PEAKS protein-FDR fix, funding logos) on top
of new-docs's documentation restructuring.

Conflict resolution:
- docs/available-modules/{active,archived}-modules/*.md: kept deleted (superseded
  by docs/modules/dda|dia/*.md). Ported main's real content changes into the new
  pages: a PEAKS sample-naming-correction note (ZenoTOF, diaPASEF, Astral, AIF),
  and the entrapment page's beta-stage promotion, updated modification-support
  behavior, corrected dataset description, Spectronaut/Custom-format
  instructions, and dropped the FragPipe dropdown (not in main's finished tool
  registry) in favor of a short "not supported" note.
- webinterface/pages/pages_variables/Entrapment/Entrapment_DIA_ion_Astral_variables.py:
  took main's beta_warning=True (a deliberate stage promotion, vs. this
  session's earlier alpha_warning=False fix which only addressed the alpha flag).
- docs/module_grid_generated.rst: regenerated from source after resolving the
  above, rather than hand-merging the auto-generated content.
- proteobench/io/parsing/io_parse_settings/parse_settings_files.toml: kept
  main's entrapment tool list (DIA-NN, AlphaDIA, Custom, Spectronaut) rather
  than new-docs's independent FragPipe/FragPipe(DIA-NN quant) additions, per
  main being the authoritative finished state for this module. The two FragPipe
  TOML configs remain on disk, unregistered.

Also fixed a stale readthedocs link in the (re-added) entrapment Custom format
TOML that main's own history still had, and re-ran generate_input_tables.py so
every module's input-files table reflects the merged registry.
@rodvrees

rodvrees commented Aug 5, 2026

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@copilot resolve the merge conflicts in this pull request

rodvrees
rodvrees reviewed Aug 5, 2026
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Comment thread docs/about/faq.md
Copilot AI requested a review from rodvrees August 5, 2026 12:51
mlocardpaulet
mlocardpaulet reviewed Aug 13, 2026
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Comment thread docs/about/index.md
mlocardpaulet
mlocardpaulet reviewed Aug 13, 2026
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Comment thread docs/contributing/index.md
mlocardpaulet
mlocardpaulet reviewed Aug 13, 2026
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Comment thread docs/contributing/index.md
@mlocardpaulet

mlocardpaulet commented Aug 13, 2026

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Thanks a lot Caro, this looks great.
Unfortunately, I did not manage to generate the new docs locally (must be my fault), so I could not test the links between pages and the new design...
Two main comments:

  1. I really want to keep the text in the current page https://proteobench.readthedocs.io/en/stable/general-information/0-about/ as is. A lot of very long discussions and a lot of effort has be made to reach an agreement on this text, I don't want it to drift to something different with time. This is important.
  2. why are there 3 different documents "generic_text", "generic_test_dia" and "generic_text_denovo"?
    We can discuss this whenever.

mlocardpaulet
mlocardpaulet reviewed Aug 14, 2026
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Comment thread docs/your-first-submission/index.md
mlocardpaulet
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mlocardpaulet
mlocardpaulet reviewed Aug 14, 2026
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mlocardpaulet
mlocardpaulet reviewed Aug 14, 2026
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mlocardpaulet reviewed Aug 14, 2026
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I love it.
Just a few things:

  • I said it in the comments, and I feel very strongly about it: we must keep the "about" page as was written with everyone in the first ProteoBench meetings. I don't want any time-dilution/drift of the important concepts agreed upon together (and with some intense discussions sometimes ;))
  • I like "benchmark module(s)", I saw that you removed the "benchmark" in most places. It is OK... But I would keep "benchmark module" in titles, and for example in the left-hand side menu. Then of course we can have in the drop down "DIA modules" and "DDA modules". It is clearly explained in the glossary too. So I like it.
  • I didn't check all modules, but we removed the PXDs of the raw date? I think it would be nice to have it somewhere even if it is not prominent.
  • in the documentation of the DIA entrapment, there is a nice visible warning because it is beta. I like it. But I don't see anything in other beta modules, and I don't see an alpha warning banner for the alpha modules.

Cajac102 and others added 17 commits August 14, 2026 08:55
@Cajac102 @mlocardpaulet
Update docs/about/faq.md
922cd2a 
Co-authored-by: Marie Locard-Paulet <8386272+mlocardpaulet@users.noreply.github.com>
@Cajac102 @mlocardpaulet
Update docs/about/faq.md
8dcac82 
Co-authored-by: Marie Locard-Paulet <8386272+mlocardpaulet@users.noreply.github.com>
@Cajac102 @mlocardpaulet
Update docs/about/faq.md
a6ead0c 
Co-authored-by: Marie Locard-Paulet <8386272+mlocardpaulet@users.noreply.github.com>
@Cajac102 @mlocardpaulet
Update docs/about/faq.md
00651d5 
Co-authored-by: Marie Locard-Paulet <8386272+mlocardpaulet@users.noreply.github.com>
@Cajac102 @mlocardpaulet
Update docs/about/faq.md
876ae83 
Co-authored-by: Marie Locard-Paulet <8386272+mlocardpaulet@users.noreply.github.com>
@Cajac102 @mlocardpaulet
Update docs/about/faq.md
b471fb8 
Co-authored-by: Marie Locard-Paulet <8386272+mlocardpaulet@users.noreply.github.com>
@Cajac102 @mlocardpaulet
Update docs/about/faq.md
8421d32 
Co-authored-by: Marie Locard-Paulet <8386272+mlocardpaulet@users.noreply.github.com>
@Cajac102 @mlocardpaulet
Update docs/about/faq.md
1a8ff38 
Co-authored-by: Marie Locard-Paulet <8386272+mlocardpaulet@users.noreply.github.com>
@Cajac102 @mlocardpaulet
Update docs/about/faq.md
d0c3c45 
Co-authored-by: Marie Locard-Paulet <8386272+mlocardpaulet@users.noreply.github.com>
@Cajac102 @mlocardpaulet
Update docs/about/faq.md
79e22b2 
Co-authored-by: Marie Locard-Paulet <8386272+mlocardpaulet@users.noreply.github.com>
@Cajac102 @mlocardpaulet
Update docs/about/faq.md
db05392 
Co-authored-by: Marie Locard-Paulet <8386272+mlocardpaulet@users.noreply.github.com>
@Cajac102 @mlocardpaulet
Update docs/your-first-submission/index.md
b2305ea 
Co-authored-by: Marie Locard-Paulet <8386272+mlocardpaulet@users.noreply.github.com>
@SamvPy
Somehow the % makes this line invisible otherwise
080b0f0
@Cajac102 @mlocardpaulet
Update docs/your-first-submission/index.md
56d190d 
Co-authored-by: Marie Locard-Paulet <8386272+mlocardpaulet@users.noreply.github.com>
@Cajac102
small updates to documentation
d5fa5aa
@Cajac102
Merge branch 'new-docs' of https://github.com/Proteobench/ProteoBench …
0c8fc1c 
…into new-docs
@Cajac102
make cards for joining community section
619dc69
@Cajac102
Cajac102 requested a review from SamvPy August 14, 2026 08:40
@Cajac102
Cajac102 merged commit 8edf308 into main Aug 14, 2026
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@Cajac102
Cajac102 deleted the new-docs branch August 14, 2026 08:42
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Add info on ProteoRunners to docs

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@Cajac102 @rodvrees @mlocardpaulet @SamvPy