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Minor refinements in the links checking #808

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Merged
ypriverol merged 4 commits into from
Mar 9, 2026
Merged

Minor refinements in the links checking #808

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6d238e0
Minor changMinor changes es
ypriverol Mar 9, 2026
27589c3
Merge branch 'dev' of https://github.com/bigbio/proteomics-sample-met…
ypriverol Mar 9, 2026
7c0b421
Merge branch 'master' of https://github.com/bigbio/proteomics-sample-…
ypriverol Mar 9, 2026
3b4bb1b
Add PDF specification v1.1.0-dev
github-actions[bot] Mar 9, 2026
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4 changes: 4 additions & 0 deletions .lycheeignore
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Expand Up @@ -10,6 +10,10 @@ https://pubs.acs.org/
https://www.maxquant.org/
https://lessdrf.streamlit.app/

# Self-referential links to this repo (prone to 429 rate limits)
https://github.com/bigbio/proteomics-metadata-standard/blob/master/CHANGELOG.md
https://github.com/bigbio/proteomics-metadata-standard/blob/master/LICENSE

# URLs with AsciiDoc link syntax that may be misinterpreted
# Matches URLs ending with [text] or [text (incomplete bracket)
.*\[.*\]$
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12 changes: 6 additions & 6 deletions scripts/inject-headers.py
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Expand Up @@ -19,17 +19,17 @@

# Navigation header templates (use placeholder for version link)
HEADERS = {
'root': f'''<header class="doc-header"><div class="doc-header-brand"><a href="./index.html">SDRF-Proteomics</a></div><nav class="doc-header-nav"><a href="./index.html">Home</a><a href="./specification.html" class="nav-current">Specification</a><a href="./index.html#metadata-guidelines">Metadata Guidelines</a><a href="./index.html#templates">Templates</a><a href="./index.html#tools">Tools</a><a href="./sdrf-explorer.html">Explorer</a><a href="./sdrf-editor.html">Editor</a><a href="./sdrf-builder.html">Template Builder</a><a href="./index.html#contributors">Contributors</a>{VERSION_LINK_PLACEHOLDER}<a href="https://github.com/bigbio/proteomics-metadata-standard" target="_blank">GitHub</a></nav></header>''',
'root': f'''<header class="doc-header"><div class="doc-header-brand"><a href="./index.html">SDRF-Proteomics</a></div><nav class="doc-header-nav"><a href="./index.html">Home</a><a href="./specification.html" class="nav-current">Specification</a><a href="./index.html#metadata-guidelines">Metadata Guidelines</a><a href="./index.html#templates">Templates</a><a href="./sdrf-builder.html">Template Builder</a><a href="./index.html#tools">Tools</a><a href="./sdrf-explorer.html">Explorer</a><a href="./sdrf-editor.html">Editor</a><a href="./index.html#contributors">Contributors</a>{VERSION_LINK_PLACEHOLDER}<a href="https://github.com/bigbio/proteomics-metadata-standard" target="_blank">GitHub</a></nav></header>''',

'tools': f'''<header class="doc-header"><div class="doc-header-brand"><a href="./index.html">SDRF-Proteomics</a></div><nav class="doc-header-nav"><a href="./index.html">Home</a><a href="./specification.html">Specification</a><a href="./index.html#metadata-guidelines">Metadata Guidelines</a><a href="./index.html#templates">Templates</a><a href="./index.html#tools" class="nav-current">Tools</a><a href="./sdrf-explorer.html">Explorer</a><a href="./sdrf-editor.html">Editor</a><a href="./sdrf-builder.html">Template Builder</a><a href="./index.html#contributors">Contributors</a>{VERSION_LINK_PLACEHOLDER}<a href="https://github.com/bigbio/proteomics-metadata-standard" target="_blank">GitHub</a></nav></header>''',
'tools': f'''<header class="doc-header"><div class="doc-header-brand"><a href="./index.html">SDRF-Proteomics</a></div><nav class="doc-header-nav"><a href="./index.html">Home</a><a href="./specification.html">Specification</a><a href="./index.html#metadata-guidelines">Metadata Guidelines</a><a href="./index.html#templates">Templates</a><a href="./sdrf-builder.html">Template Builder</a><a href="./index.html#tools" class="nav-current">Tools</a><a href="./sdrf-explorer.html">Explorer</a><a href="./sdrf-editor.html">Editor</a><a href="./index.html#contributors">Contributors</a>{VERSION_LINK_PLACEHOLDER}<a href="https://github.com/bigbio/proteomics-metadata-standard" target="_blank">GitHub</a></nav></header>''',

'guidelines': f'''<header class="doc-header"><div class="doc-header-brand"><a href="../index.html">SDRF-Proteomics</a></div><nav class="doc-header-nav"><a href="../index.html">Home</a><a href="../specification.html">Specification</a><a href="../index.html#metadata-guidelines" class="nav-current">Metadata Guidelines</a><a href="../index.html#templates">Templates</a><a href="../index.html#tools">Tools</a><a href="../sdrf-explorer.html">Explorer</a><a href="../sdrf-editor.html">Editor</a><a href="../sdrf-builder.html">Template Builder</a><a href="../index.html#contributors">Contributors</a>{VERSION_LINK_PLACEHOLDER}<a href="https://github.com/bigbio/proteomics-metadata-standard" target="_blank">GitHub</a></nav></header>''',
'guidelines': f'''<header class="doc-header"><div class="doc-header-brand"><a href="../index.html">SDRF-Proteomics</a></div><nav class="doc-header-nav"><a href="../index.html">Home</a><a href="../specification.html">Specification</a><a href="../index.html#metadata-guidelines" class="nav-current">Metadata Guidelines</a><a href="../index.html#templates">Templates</a><a href="../sdrf-builder.html">Template Builder</a><a href="../index.html#tools">Tools</a><a href="../sdrf-explorer.html">Explorer</a><a href="../sdrf-editor.html">Editor</a><a href="../index.html#contributors">Contributors</a>{VERSION_LINK_PLACEHOLDER}<a href="https://github.com/bigbio/proteomics-metadata-standard" target="_blank">GitHub</a></nav></header>''',

'templates': f'''<header class="doc-header"><div class="doc-header-brand"><a href="../index.html">SDRF-Proteomics</a></div><nav class="doc-header-nav"><a href="../index.html">Home</a><a href="../specification.html">Specification</a><a href="../index.html#metadata-guidelines">Metadata Guidelines</a><a href="../index.html#templates" class="nav-current">Templates</a><a href="../index.html#tools">Tools</a><a href="../sdrf-explorer.html">Explorer</a><a href="../sdrf-editor.html">Editor</a><a href="../sdrf-builder.html">Template Builder</a><a href="../index.html#contributors">Contributors</a>{VERSION_LINK_PLACEHOLDER}<a href="https://github.com/bigbio/proteomics-metadata-standard" target="_blank">GitHub</a></nav></header>''',
'templates': f'''<header class="doc-header"><div class="doc-header-brand"><a href="../index.html">SDRF-Proteomics</a></div><nav class="doc-header-nav"><a href="../index.html">Home</a><a href="../specification.html">Specification</a><a href="../index.html#metadata-guidelines">Metadata Guidelines</a><a href="../index.html#templates" class="nav-current">Templates</a><a href="../sdrf-builder.html">Template Builder</a><a href="../index.html#tools">Tools</a><a href="../sdrf-explorer.html">Explorer</a><a href="../sdrf-editor.html">Editor</a><a href="../index.html#contributors">Contributors</a>{VERSION_LINK_PLACEHOLDER}<a href="https://github.com/bigbio/proteomics-metadata-standard" target="_blank">GitHub</a></nav></header>''',

'sample_guidelines': f'''<header class="doc-header"><div class="doc-header-brand"><a href="./index.html">SDRF-Proteomics</a></div><nav class="doc-header-nav"><a href="./index.html">Home</a><a href="./specification.html">Specification</a><a href="./index.html#metadata-guidelines" class="nav-current">Metadata Guidelines</a><a href="./index.html#templates">Templates</a><a href="./index.html#tools">Tools</a><a href="./sdrf-explorer.html">Explorer</a><a href="./sdrf-editor.html">Editor</a><a href="./sdrf-builder.html">Template Builder</a><a href="./index.html#contributors">Contributors</a>{VERSION_LINK_PLACEHOLDER}<a href="https://github.com/bigbio/proteomics-metadata-standard" target="_blank">GitHub</a></nav></header>''',
'sample_guidelines': f'''<header class="doc-header"><div class="doc-header-brand"><a href="./index.html">SDRF-Proteomics</a></div><nav class="doc-header-nav"><a href="./index.html">Home</a><a href="./specification.html">Specification</a><a href="./index.html#metadata-guidelines" class="nav-current">Metadata Guidelines</a><a href="./index.html#templates">Templates</a><a href="./sdrf-builder.html">Template Builder</a><a href="./index.html#tools">Tools</a><a href="./sdrf-explorer.html">Explorer</a><a href="./sdrf-editor.html">Editor</a><a href="./index.html#contributors">Contributors</a>{VERSION_LINK_PLACEHOLDER}<a href="https://github.com/bigbio/proteomics-metadata-standard" target="_blank">GitHub</a></nav></header>''',

'templates_guide': f'''<header class="doc-header"><div class="doc-header-brand"><a href="./index.html">SDRF-Proteomics</a></div><nav class="doc-header-nav"><a href="./index.html">Home</a><a href="./specification.html">Specification</a><a href="./index.html#metadata-guidelines">Metadata Guidelines</a><a href="./index.html#templates" class="nav-current">Templates</a><a href="./index.html#tools">Tools</a><a href="./sdrf-explorer.html">Explorer</a><a href="./sdrf-editor.html">Editor</a><a href="./sdrf-builder.html">Template Builder</a><a href="./index.html#contributors">Contributors</a>{VERSION_LINK_PLACEHOLDER}<a href="https://github.com/bigbio/proteomics-metadata-standard" target="_blank">GitHub</a></nav></header>'''
'templates_guide': f'''<header class="doc-header"><div class="doc-header-brand"><a href="./index.html">SDRF-Proteomics</a></div><nav class="doc-header-nav"><a href="./index.html">Home</a><a href="./specification.html">Specification</a><a href="./index.html#metadata-guidelines">Metadata Guidelines</a><a href="./index.html#templates" class="nav-current">Templates</a><a href="./sdrf-builder.html">Template Builder</a><a href="./index.html#tools">Tools</a><a href="./sdrf-explorer.html">Explorer</a><a href="./sdrf-editor.html">Editor</a><a href="./index.html#contributors">Contributors</a>{VERSION_LINK_PLACEHOLDER}<a href="https://github.com/bigbio/proteomics-metadata-standard" target="_blank">GitHub</a></nav></header>'''
}


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3 changes: 1 addition & 2 deletions site/index.html
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Expand Up @@ -17,12 +17,11 @@
<a href="./specification.html">Specification</a>
<a href="#metadata-guidelines">Metadata Guidelines</a>
<a href="#templates">Templates</a>
<a href="./sdrf-builder.html">Template Builder</a>
<a href="#tools">Tools</a>
<a href="./sdrf-explorer.html">Explorer</a>
<a href="./sdrf-editor.html">Editor</a>
<a href="./sdrf-builder.html">Template Builder</a>
<a href="#contributors">Contributors</a>
<a href="/dev/" class="version-link">Dev Version</a>
<a href="https://github.com/bigbio/proteomics-metadata-standard" target="_blank">GitHub</a>
<div class="nav-search">
<input type="text" id="search-input" placeholder="Search..." disabled>
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2 changes: 1 addition & 1 deletion site/quickstart.html
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Expand Up @@ -104,10 +104,10 @@
<a href="./index.html">Home</a>
<a href="./specification.html">Specification</a>
<a href="./index.html#templates">Templates</a>
<a href="./sdrf-builder.html">Template Builder</a>
<a href="./index.html#tools">Tools</a>
<a href="./sdrf-explorer.html">Explorer</a>
<a href="./sdrf-editor.html">Editor</a>
<a href="./sdrf-builder.html">Template Builder</a>
<a href="./quickstart.html" class="nav-current">Quick Start</a>
<a href="/dev/" class="version-link">Dev Version</a>
<a href="https://github.com/bigbio/proteomics-metadata-standard" target="_blank">GitHub</a>
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2 changes: 1 addition & 1 deletion site/sdrf-builder.html
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Expand Up @@ -13,10 +13,10 @@
<a href="./index.html">Home</a>
<a href="./specification.html">Specification</a>
<a href="./index.html#templates">Templates</a>
<a href="./sdrf-builder.html" class="nav-current">Template Builder</a>
<a href="./index.html#tools">Tools</a>
<a href="./sdrf-explorer.html">Explorer</a>
<a href="./sdrf-editor.html">Editor</a>
<a href="./sdrf-builder.html" class="nav-current">Template Builder</a>
<a href="/dev/" class="version-link">Dev Version</a>
<a href="https://github.com/bigbio/proteomics-metadata-standard" target="_blank">GitHub</a>
</nav>
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