File Changes for mspeir

v501_base to v502_preview (2026-07-20 to 2026-07-27) v502

• docs/browserSlideDecks.md
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
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    b120644088d912f130ada387e34067b40616edc0 Mon Jul 27 08:19:30 2026 -0700
    minor fixes based on CR, refs #37874
• docs/makefile
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    9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
    Move vendored reveal.js library out of docs/slideDecks into the source tree Per code review feedback on #37904, the reveal.js 5.1.0 files used by the training slide decks now live in their conventional homes rather than bundled under docs/slideDecks/reveal.js: - JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js), added to that makefile; MIT LICENSE kept alongside. - CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css), added to that makefile. - Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching the existing font-awesome pattern (auto-rsynced, no makefile edit). The white theme's @import and the five deck index.html files were updated to reference the assets by absolute /js, /style, and /fonts paths. refs #37904 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• docs/slideDecks/reveal.js/LICENSE
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
• docs/slideDecks/reveal.js/dist/reveal.css
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
• docs/slideDecks/reveal.js/dist/reveal.js
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
• docs/slideDecks/reveal.js/dist/theme/fonts/source-sans-pro/source-sans-pro-italic.eot
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
• docs/slideDecks/reveal.js/dist/theme/fonts/source-sans-pro/source-sans-pro-italic.ttf
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
• docs/slideDecks/reveal.js/dist/theme/fonts/source-sans-pro/source-sans-pro-italic.woff
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
• docs/slideDecks/reveal.js/dist/theme/fonts/source-sans-pro/source-sans-pro-regular.eot
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
• docs/slideDecks/reveal.js/dist/theme/fonts/source-sans-pro/source-sans-pro-regular.ttf
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
• docs/slideDecks/reveal.js/dist/theme/fonts/source-sans-pro/source-sans-pro-regular.woff
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
• docs/slideDecks/reveal.js/dist/theme/fonts/source-sans-pro/source-sans-pro-semibold.eot
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
• docs/slideDecks/reveal.js/dist/theme/fonts/source-sans-pro/source-sans-pro-semibold.ttf
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
• docs/slideDecks/reveal.js/dist/theme/fonts/source-sans-pro/source-sans-pro-semibold.woff
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
• docs/slideDecks/reveal.js/dist/theme/fonts/source-sans-pro/source-sans-pro-semibolditalic.eot
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
• docs/slideDecks/reveal.js/dist/theme/fonts/source-sans-pro/source-sans-pro-semibolditalic.ttf
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
• docs/slideDecks/reveal.js/dist/theme/fonts/source-sans-pro/source-sans-pro-semibolditalic.woff
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
• docs/slideDecks/reveal.js/dist/theme/fonts/source-sans-pro/source-sans-pro.css
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
• docs/slideDecks/reveal.js/dist/theme/white.css
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
• docs/slideDecks/reveal.js/plugin/notes/notes.js
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
• docs/slideDecks/tutorial1-basics/presentation/index.html
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
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    9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
    Move vendored reveal.js library out of docs/slideDecks into the source tree Per code review feedback on #37904, the reveal.js 5.1.0 files used by the training slide decks now live in their conventional homes rather than bundled under docs/slideDecks/reveal.js: - JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js), added to that makefile; MIT LICENSE kept alongside. - CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css), added to that makefile. - Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching the existing font-awesome pattern (auto-rsynced, no makefile edit). The white theme's @import and the five deck index.html files were updated to reference the assets by absolute /js, /style, and /fonts paths. refs #37904 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• docs/slideDecks/tutorial1-basics/tableOfContents/index.html
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
• docs/slideDecks/tutorial2-cancer/presentation/index.html
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
  • lines changed 4, context: html, text, full: html, text
    9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
    Move vendored reveal.js library out of docs/slideDecks into the source tree Per code review feedback on #37904, the reveal.js 5.1.0 files used by the training slide decks now live in their conventional homes rather than bundled under docs/slideDecks/reveal.js: - JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js), added to that makefile; MIT LICENSE kept alongside. - CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css), added to that makefile. - Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching the existing font-awesome pattern (auto-rsynced, no makefile edit). The white theme's @import and the five deck index.html files were updated to reference the assets by absolute /js, /style, and /fonts paths. refs #37904 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• docs/slideDecks/tutorial3-clinical/presentation/index.html
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
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    9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
    Move vendored reveal.js library out of docs/slideDecks into the source tree Per code review feedback on #37904, the reveal.js 5.1.0 files used by the training slide decks now live in their conventional homes rather than bundled under docs/slideDecks/reveal.js: - JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js), added to that makefile; MIT LICENSE kept alongside. - CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css), added to that makefile. - Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching the existing font-awesome pattern (auto-rsynced, no makefile edit). The white theme's @import and the five deck index.html files were updated to reference the assets by absolute /js, /style, and /fonts paths. refs #37904 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• docs/slideDecks/tutorial3-clinical/tableOfContents/index.html
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
• docs/slideDecks/tutorial4-clinical-cases/presentation/index.html
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
  • lines changed 4, context: html, text, full: html, text
    9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
    Move vendored reveal.js library out of docs/slideDecks into the source tree Per code review feedback on #37904, the reveal.js 5.1.0 files used by the training slide decks now live in their conventional homes rather than bundled under docs/slideDecks/reveal.js: - JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js), added to that makefile; MIT LICENSE kept alongside. - CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css), added to that makefile. - Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching the existing font-awesome pattern (auto-rsynced, no makefile edit). The white theme's @import and the five deck index.html files were updated to reference the assets by absolute /js, /style, and /fonts paths. refs #37904 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• docs/slideDecks/tutorial4-clinical-cases/tableOfContents/index.html
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
• docs/slideDecks/tutorial5-teaching/presentation/index.html
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
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    9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
    Move vendored reveal.js library out of docs/slideDecks into the source tree Per code review feedback on #37904, the reveal.js 5.1.0 files used by the training slide decks now live in their conventional homes rather than bundled under docs/slideDecks/reveal.js: - JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js), added to that makefile; MIT LICENSE kept alongside. - CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css), added to that makefile. - Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching the existing font-awesome pattern (auto-rsynced, no makefile edit). The white theme's @import and the five deck index.html files were updated to reference the assets by absolute /js, /style, and /fonts paths. refs #37904 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• docs/slideDecks/tutorial5-teaching/tableOfContents/index.html
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    b120644088d912f130ada387e34067b40616edc0 Mon Jul 27 08:19:30 2026 -0700
    minor fixes based on CR, refs #37874
• docs/tutorials/customTrackTutorial.md
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    dd6958bf3e8dfeb13dad8906a5c471293c471152 Wed Jul 22 07:56:17 2026 -0700
    Update Gateway, Table Browser, and Custom Track tutorials for the new assembly search box Replaced the old Clade/Genome/Assembly drop-down wording and screenshots with the current genome search box, re-recorded the step GIFs, and expanded the guided walkthroughs (Table Browser filter/intersection and output fields, Custom Track track line, Gateway GenArk/recent-genomes and species tree). refs #37355 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• docs/tutorials/gatewayTutorial.md
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    dd6958bf3e8dfeb13dad8906a5c471293c471152 Wed Jul 22 07:56:17 2026 -0700
    Update Gateway, Table Browser, and Custom Track tutorials for the new assembly search box Replaced the old Clade/Genome/Assembly drop-down wording and screenshots with the current genome search box, re-recorded the step GIFs, and expanded the guided walkthroughs (Table Browser filter/intersection and output fields, Custom Track track line, Gateway GenArk/recent-genomes and species tree). refs #37355 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• docs/tutorials/gb101.md
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    fc9499685c393b53e740badf03554c65e1a0db79 Wed Jul 22 10:14:35 2026 -0700
    Fix gb101 tutorial typo and expand the blue-bar menu list Correct the track visibility modes (dense, squish, pack, full) and add the Downloads and View menus to the Navigating the Menus section. refs #37355 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• docs/tutorials/tableBrowserTutorial.md
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    dd6958bf3e8dfeb13dad8906a5c471293c471152 Wed Jul 22 07:56:17 2026 -0700
    Update Gateway, Table Browser, and Custom Track tutorials for the new assembly search box Replaced the old Clade/Genome/Assembly drop-down wording and screenshots with the current genome search box, re-recorded the step GIFs, and expanded the guided walkthroughs (Table Browser filter/intersection and output fields, Custom Track track line, Gateway GenArk/recent-genomes and species tree). refs #37355 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/fonts/source-sans-pro/source-sans-pro-italic.eot
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    9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
    Move vendored reveal.js library out of docs/slideDecks into the source tree Per code review feedback on #37904, the reveal.js 5.1.0 files used by the training slide decks now live in their conventional homes rather than bundled under docs/slideDecks/reveal.js: - JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js), added to that makefile; MIT LICENSE kept alongside. - CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css), added to that makefile. - Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching the existing font-awesome pattern (auto-rsynced, no makefile edit). The white theme's @import and the five deck index.html files were updated to reference the assets by absolute /js, /style, and /fonts paths. refs #37904 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/fonts/source-sans-pro/source-sans-pro-italic.ttf
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    9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
    Move vendored reveal.js library out of docs/slideDecks into the source tree Per code review feedback on #37904, the reveal.js 5.1.0 files used by the training slide decks now live in their conventional homes rather than bundled under docs/slideDecks/reveal.js: - JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js), added to that makefile; MIT LICENSE kept alongside. - CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css), added to that makefile. - Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching the existing font-awesome pattern (auto-rsynced, no makefile edit). The white theme's @import and the five deck index.html files were updated to reference the assets by absolute /js, /style, and /fonts paths. refs #37904 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/fonts/source-sans-pro/source-sans-pro-italic.woff
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    9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
    Move vendored reveal.js library out of docs/slideDecks into the source tree Per code review feedback on #37904, the reveal.js 5.1.0 files used by the training slide decks now live in their conventional homes rather than bundled under docs/slideDecks/reveal.js: - JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js), added to that makefile; MIT LICENSE kept alongside. - CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css), added to that makefile. - Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching the existing font-awesome pattern (auto-rsynced, no makefile edit). The white theme's @import and the five deck index.html files were updated to reference the assets by absolute /js, /style, and /fonts paths. refs #37904 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/fonts/source-sans-pro/source-sans-pro-regular.eot
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    9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
    Move vendored reveal.js library out of docs/slideDecks into the source tree Per code review feedback on #37904, the reveal.js 5.1.0 files used by the training slide decks now live in their conventional homes rather than bundled under docs/slideDecks/reveal.js: - JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js), added to that makefile; MIT LICENSE kept alongside. - CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css), added to that makefile. - Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching the existing font-awesome pattern (auto-rsynced, no makefile edit). The white theme's @import and the five deck index.html files were updated to reference the assets by absolute /js, /style, and /fonts paths. refs #37904 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/fonts/source-sans-pro/source-sans-pro-regular.ttf
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    9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
    Move vendored reveal.js library out of docs/slideDecks into the source tree Per code review feedback on #37904, the reveal.js 5.1.0 files used by the training slide decks now live in their conventional homes rather than bundled under docs/slideDecks/reveal.js: - JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js), added to that makefile; MIT LICENSE kept alongside. - CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css), added to that makefile. - Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching the existing font-awesome pattern (auto-rsynced, no makefile edit). The white theme's @import and the five deck index.html files were updated to reference the assets by absolute /js, /style, and /fonts paths. refs #37904 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/fonts/source-sans-pro/source-sans-pro-regular.woff
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    9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
    Move vendored reveal.js library out of docs/slideDecks into the source tree Per code review feedback on #37904, the reveal.js 5.1.0 files used by the training slide decks now live in their conventional homes rather than bundled under docs/slideDecks/reveal.js: - JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js), added to that makefile; MIT LICENSE kept alongside. - CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css), added to that makefile. - Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching the existing font-awesome pattern (auto-rsynced, no makefile edit). The white theme's @import and the five deck index.html files were updated to reference the assets by absolute /js, /style, and /fonts paths. refs #37904 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/fonts/source-sans-pro/source-sans-pro-semibold.eot
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    9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
    Move vendored reveal.js library out of docs/slideDecks into the source tree Per code review feedback on #37904, the reveal.js 5.1.0 files used by the training slide decks now live in their conventional homes rather than bundled under docs/slideDecks/reveal.js: - JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js), added to that makefile; MIT LICENSE kept alongside. - CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css), added to that makefile. - Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching the existing font-awesome pattern (auto-rsynced, no makefile edit). The white theme's @import and the five deck index.html files were updated to reference the assets by absolute /js, /style, and /fonts paths. refs #37904 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/fonts/source-sans-pro/source-sans-pro-semibold.ttf
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    9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
    Move vendored reveal.js library out of docs/slideDecks into the source tree Per code review feedback on #37904, the reveal.js 5.1.0 files used by the training slide decks now live in their conventional homes rather than bundled under docs/slideDecks/reveal.js: - JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js), added to that makefile; MIT LICENSE kept alongside. - CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css), added to that makefile. - Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching the existing font-awesome pattern (auto-rsynced, no makefile edit). The white theme's @import and the five deck index.html files were updated to reference the assets by absolute /js, /style, and /fonts paths. refs #37904 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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    9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
    Move vendored reveal.js library out of docs/slideDecks into the source tree Per code review feedback on #37904, the reveal.js 5.1.0 files used by the training slide decks now live in their conventional homes rather than bundled under docs/slideDecks/reveal.js: - JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js), added to that makefile; MIT LICENSE kept alongside. - CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css), added to that makefile. - Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching the existing font-awesome pattern (auto-rsynced, no makefile edit). The white theme's @import and the five deck index.html files were updated to reference the assets by absolute /js, /style, and /fonts paths. refs #37904 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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    9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
    Move vendored reveal.js library out of docs/slideDecks into the source tree Per code review feedback on #37904, the reveal.js 5.1.0 files used by the training slide decks now live in their conventional homes rather than bundled under docs/slideDecks/reveal.js: - JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js), added to that makefile; MIT LICENSE kept alongside. - CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css), added to that makefile. - Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching the existing font-awesome pattern (auto-rsynced, no makefile edit). The white theme's @import and the five deck index.html files were updated to reference the assets by absolute /js, /style, and /fonts paths. refs #37904 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/fonts/source-sans-pro/source-sans-pro-semibolditalic.ttf
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    9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
    Move vendored reveal.js library out of docs/slideDecks into the source tree Per code review feedback on #37904, the reveal.js 5.1.0 files used by the training slide decks now live in their conventional homes rather than bundled under docs/slideDecks/reveal.js: - JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js), added to that makefile; MIT LICENSE kept alongside. - CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css), added to that makefile. - Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching the existing font-awesome pattern (auto-rsynced, no makefile edit). The white theme's @import and the five deck index.html files were updated to reference the assets by absolute /js, /style, and /fonts paths. refs #37904 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/fonts/source-sans-pro/source-sans-pro-semibolditalic.woff
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    9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
    Move vendored reveal.js library out of docs/slideDecks into the source tree Per code review feedback on #37904, the reveal.js 5.1.0 files used by the training slide decks now live in their conventional homes rather than bundled under docs/slideDecks/reveal.js: - JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js), added to that makefile; MIT LICENSE kept alongside. - CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css), added to that makefile. - Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching the existing font-awesome pattern (auto-rsynced, no makefile edit). The white theme's @import and the five deck index.html files were updated to reference the assets by absolute /js, /style, and /fonts paths. refs #37904 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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    9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
    Move vendored reveal.js library out of docs/slideDecks into the source tree Per code review feedback on #37904, the reveal.js 5.1.0 files used by the training slide decks now live in their conventional homes rather than bundled under docs/slideDecks/reveal.js: - JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js), added to that makefile; MIT LICENSE kept alongside. - CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css), added to that makefile. - Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching the existing font-awesome pattern (auto-rsynced, no makefile edit). The white theme's @import and the five deck index.html files were updated to reference the assets by absolute /js, /style, and /fonts paths. refs #37904 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/images/assemblySelection.gif
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    dd6958bf3e8dfeb13dad8906a5c471293c471152 Wed Jul 22 07:56:17 2026 -0700
    Update Gateway, Table Browser, and Custom Track tutorials for the new assembly search box Replaced the old Clade/Genome/Assembly drop-down wording and screenshots with the current genome search box, re-recorded the step GIFs, and expanded the guided walkthroughs (Table Browser filter/intersection and output fields, Custom Track track line, Gateway GenArk/recent-genomes and species tree). refs #37355 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/images/defineRegions.gif
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    dd6958bf3e8dfeb13dad8906a5c471293c471152 Wed Jul 22 07:56:17 2026 -0700
    Update Gateway, Table Browser, and Custom Track tutorials for the new assembly search box Replaced the old Clade/Genome/Assembly drop-down wording and screenshots with the current genome search box, re-recorded the step GIFs, and expanded the guided walkthroughs (Table Browser filter/intersection and output fields, Custom Track track line, Gateway GenArk/recent-genomes and species tree). refs #37355 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/images/downloadData.gif
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    dd6958bf3e8dfeb13dad8906a5c471293c471152 Wed Jul 22 07:56:17 2026 -0700
    Update Gateway, Table Browser, and Custom Track tutorials for the new assembly search box Replaced the old Clade/Genome/Assembly drop-down wording and screenshots with the current genome search box, re-recorded the step GIFs, and expanded the guided walkthroughs (Table Browser filter/intersection and output fields, Custom Track track line, Gateway GenArk/recent-genomes and species tree). refs #37355 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/images/tableBrowserAnnotated.png
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    dd6958bf3e8dfeb13dad8906a5c471293c471152 Wed Jul 22 07:56:17 2026 -0700
    Update Gateway, Table Browser, and Custom Track tutorials for the new assembly search box Replaced the old Clade/Genome/Assembly drop-down wording and screenshots with the current genome search box, re-recorded the step GIFs, and expanded the guided walkthroughs (Table Browser filter/intersection and output fields, Custom Track track line, Gateway GenArk/recent-genomes and species tree). refs #37355 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/images/tableSelection.gif
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    dd6958bf3e8dfeb13dad8906a5c471293c471152 Wed Jul 22 07:56:17 2026 -0700
    Update Gateway, Table Browser, and Custom Track tutorials for the new assembly search box Replaced the old Clade/Genome/Assembly drop-down wording and screenshots with the current genome search box, re-recorded the step GIFs, and expanded the guided walkthroughs (Table Browser filter/intersection and output fields, Custom Track track line, Gateway GenArk/recent-genomes and species tree). refs #37355 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/images/trackSelection.gif
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    dd6958bf3e8dfeb13dad8906a5c471293c471152 Wed Jul 22 07:56:17 2026 -0700
    Update Gateway, Table Browser, and Custom Track tutorials for the new assembly search box Replaced the old Clade/Genome/Assembly drop-down wording and screenshots with the current genome search box, re-recorded the step GIFs, and expanded the guided walkthroughs (Table Browser filter/intersection and output fields, Custom Track track line, Gateway GenArk/recent-genomes and species tree). refs #37355 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/images/tutorialImages/gif/hgCustomStep1.gif
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    dd6958bf3e8dfeb13dad8906a5c471293c471152 Wed Jul 22 07:56:17 2026 -0700
    Update Gateway, Table Browser, and Custom Track tutorials for the new assembly search box Replaced the old Clade/Genome/Assembly drop-down wording and screenshots with the current genome search box, re-recorded the step GIFs, and expanded the guided walkthroughs (Table Browser filter/intersection and output fields, Custom Track track line, Gateway GenArk/recent-genomes and species tree). refs #37355 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/images/tutorialImages/gif/hgCustomStep4.gif
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    dd6958bf3e8dfeb13dad8906a5c471293c471152 Wed Jul 22 07:56:17 2026 -0700
    Update Gateway, Table Browser, and Custom Track tutorials for the new assembly search box Replaced the old Clade/Genome/Assembly drop-down wording and screenshots with the current genome search box, re-recorded the step GIFs, and expanded the guided walkthroughs (Table Browser filter/intersection and output fields, Custom Track track line, Gateway GenArk/recent-genomes and species tree). refs #37355 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/images/tutorialImages/hgCustomAnnotated_pt1.png
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    dd6958bf3e8dfeb13dad8906a5c471293c471152 Wed Jul 22 07:56:17 2026 -0700
    Update Gateway, Table Browser, and Custom Track tutorials for the new assembly search box Replaced the old Clade/Genome/Assembly drop-down wording and screenshots with the current genome search box, re-recorded the step GIFs, and expanded the guided walkthroughs (Table Browser filter/intersection and output fields, Custom Track track line, Gateway GenArk/recent-genomes and species tree). refs #37355 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/style/makefile
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    9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
    Move vendored reveal.js library out of docs/slideDecks into the source tree Per code review feedback on #37904, the reveal.js 5.1.0 files used by the training slide decks now live in their conventional homes rather than bundled under docs/slideDecks/reveal.js: - JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js), added to that makefile; MIT LICENSE kept alongside. - CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css), added to that makefile. - Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching the existing font-awesome pattern (auto-rsynced, no makefile edit). The white theme's @import and the five deck index.html files were updated to reference the assets by absolute /js, /style, and /fonts paths. refs #37904 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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    9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
    Move vendored reveal.js library out of docs/slideDecks into the source tree Per code review feedback on #37904, the reveal.js 5.1.0 files used by the training slide decks now live in their conventional homes rather than bundled under docs/slideDecks/reveal.js: - JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js), added to that makefile; MIT LICENSE kept alongside. - CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css), added to that makefile. - Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching the existing font-awesome pattern (auto-rsynced, no makefile edit). The white theme's @import and the five deck index.html files were updated to reference the assets by absolute /js, /style, and /fonts paths. refs #37904 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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    9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
    Move vendored reveal.js library out of docs/slideDecks into the source tree Per code review feedback on #37904, the reveal.js 5.1.0 files used by the training slide decks now live in their conventional homes rather than bundled under docs/slideDecks/reveal.js: - JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js), added to that makefile; MIT LICENSE kept alongside. - CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css), added to that makefile. - Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching the existing font-awesome pattern (auto-rsynced, no makefile edit). The white theme's @import and the five deck index.html files were updated to reference the assets by absolute /js, /style, and /fonts paths. refs #37904 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/js/external/makefile
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    9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
    Move vendored reveal.js library out of docs/slideDecks into the source tree Per code review feedback on #37904, the reveal.js 5.1.0 files used by the training slide decks now live in their conventional homes rather than bundled under docs/slideDecks/reveal.js: - JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js), added to that makefile; MIT LICENSE kept alongside. - CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css), added to that makefile. - Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching the existing font-awesome pattern (auto-rsynced, no makefile edit). The white theme's @import and the five deck index.html files were updated to reference the assets by absolute /js, /style, and /fonts paths. refs #37904 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/js/external/reveal-5.1.0.LICENSE
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    9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
    Move vendored reveal.js library out of docs/slideDecks into the source tree Per code review feedback on #37904, the reveal.js 5.1.0 files used by the training slide decks now live in their conventional homes rather than bundled under docs/slideDecks/reveal.js: - JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js), added to that makefile; MIT LICENSE kept alongside. - CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css), added to that makefile. - Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching the existing font-awesome pattern (auto-rsynced, no makefile edit). The white theme's @import and the five deck index.html files were updated to reference the assets by absolute /js, /style, and /fonts paths. refs #37904 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/js/external/reveal-5.1.0.js
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    9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
    Move vendored reveal.js library out of docs/slideDecks into the source tree Per code review feedback on #37904, the reveal.js 5.1.0 files used by the training slide decks now live in their conventional homes rather than bundled under docs/slideDecks/reveal.js: - JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js), added to that makefile; MIT LICENSE kept alongside. - CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css), added to that makefile. - Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching the existing font-awesome pattern (auto-rsynced, no makefile edit). The white theme's @import and the five deck index.html files were updated to reference the assets by absolute /js, /style, and /fonts paths. refs #37904 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/js/external/reveal-notes-5.1.0.js
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    9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
    Move vendored reveal.js library out of docs/slideDecks into the source tree Per code review feedback on #37904, the reveal.js 5.1.0 files used by the training slide decks now live in their conventional homes rather than bundled under docs/slideDecks/reveal.js: - JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js), added to that makefile; MIT LICENSE kept alongside. - CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css), added to that makefile. - Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching the existing font-awesome pattern (auto-rsynced, no makefile edit). The white theme's @import and the five deck index.html files were updated to reference the assets by absolute /js, /style, and /fonts paths. refs #37904 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/doc/hg38/singleCellSignalsPeaks.txt
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    38d5c1e91f3a867c589da441f549c9d46bc9b9f4 Mon Jul 20 14:05:31 2026 -0700
    Add singleCellSignalsPeaks track to hg38 Native faceted composite built from the per-cell-type signal (bigWig) and peak (bigBed/bigNarrowPeak) tracks of the UCSC Cell Browser single-cell ATAC datasets, re-parented under one track in the regulation group. 936 subtracks across 9 datasets. Data files live in /hive/data/genomes/hg38/bed/singleCellSignalsPeaks and are served via a /gbdb/hg38/bbi symlink; the .ra is regenerated from the Cell Browser hub build by makeDb/scripts/singleCellSignalsPeaks/makeSingleCellSignalsPeaksRa.py. refs #37820 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/singleCellSignalsPeaks/makeSingleCellSignalsPeaksRa.py
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    38d5c1e91f3a867c589da441f549c9d46bc9b9f4 Mon Jul 20 14:05:31 2026 -0700
    Add singleCellSignalsPeaks track to hg38 Native faceted composite built from the per-cell-type signal (bigWig) and peak (bigBed/bigNarrowPeak) tracks of the UCSC Cell Browser single-cell ATAC datasets, re-parented under one track in the regulation group. 936 subtracks across 9 datasets. Data files live in /hive/data/genomes/hg38/bed/singleCellSignalsPeaks and are served via a /gbdb/hg38/bbi symlink; the .ra is regenerated from the Cell Browser hub build by makeDb/scripts/singleCellSignalsPeaks/makeSingleCellSignalsPeaksRa.py. refs #37820 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/singleCellSignalsPeaks.html
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    38d5c1e91f3a867c589da441f549c9d46bc9b9f4 Mon Jul 20 14:05:31 2026 -0700
    Add singleCellSignalsPeaks track to hg38 Native faceted composite built from the per-cell-type signal (bigWig) and peak (bigBed/bigNarrowPeak) tracks of the UCSC Cell Browser single-cell ATAC datasets, re-parented under one track in the regulation group. 936 subtracks across 9 datasets. Data files live in /hive/data/genomes/hg38/bed/singleCellSignalsPeaks and are served via a /gbdb/hg38/bbi symlink; the .ra is regenerated from the Cell Browser hub build by makeDb/scripts/singleCellSignalsPeaks/makeSingleCellSignalsPeaksRa.py. refs #37820 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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    037672a61d01d3109e8b20dff4d9142f3c8a8c66 Mon Jul 20 16:28:24 2026 -0700
    singleCellSignalsPeaks.html: reword two dataset descriptions Recast two dangling participial phrases ("...describing about 1.2 million elements", "...defining 359,022 elements") as plain clauses. refs #37820 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/singleCellSignalsPeaks.ra
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    38d5c1e91f3a867c589da441f549c9d46bc9b9f4 Mon Jul 20 14:05:31 2026 -0700
    Add singleCellSignalsPeaks track to hg38 Native faceted composite built from the per-cell-type signal (bigWig) and peak (bigBed/bigNarrowPeak) tracks of the UCSC Cell Browser single-cell ATAC datasets, re-parented under one track in the regulation group. 936 subtracks across 9 datasets. Data files live in /hive/data/genomes/hg38/bed/singleCellSignalsPeaks and are served via a /gbdb/hg38/bbi symlink; the .ra is regenerated from the Cell Browser hub build by makeDb/scripts/singleCellSignalsPeaks/makeSingleCellSignalsPeaksRa.py. refs #37820 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    38d5c1e91f3a867c589da441f549c9d46bc9b9f4 Mon Jul 20 14:05:31 2026 -0700
    Add singleCellSignalsPeaks track to hg38 Native faceted composite built from the per-cell-type signal (bigWig) and peak (bigBed/bigNarrowPeak) tracks of the UCSC Cell Browser single-cell ATAC datasets, re-parented under one track in the regulation group. 936 subtracks across 9 datasets. Data files live in /hive/data/genomes/hg38/bed/singleCellSignalsPeaks and are served via a /gbdb/hg38/bbi symlink; the .ra is regenerated from the Cell Browser hub build by makeDb/scripts/singleCellSignalsPeaks/makeSingleCellSignalsPeaksRa.py. refs #37820 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/utils/otto/otto.crontab
  • lines changed 5, context: html, text, full: html, text
    57bd4d13fdfcbf7c479087eb6151a4cf2f956cbb Mon Jul 27 09:17:50 2026 -0700
    otto cron: keep cbAnnotServer gunicorn alive, refs #37492