From 3e84a89fa417203df6dec5c85d927a961fa37ec5 Mon Sep 17 00:00:00 2001 From: Steven Roberts Date: Sat, 14 Sep 2024 13:30:24 -0700 Subject: [PATCH] handbook clean up --- docs/calendar.html | 152 +- docs/contact.html | 152 +- docs/courses.html | 296 ++- docs/dei.html | 296 ++- docs/index.html | 132 +- docs/index.xml | 355 ++-- docs/listings.json | 20 +- docs/notebooks.html | 419 +++- docs/notebooks.qmd | 19 - docs/people.html | 296 ++- docs/posts.html | 130 +- docs/posts.xml | 345 ++- docs/posts/aquamine/index.html | 152 +- docs/posts/cool-paper/index.html | 152 +- .../frontpage/ariana-hatchery/index.html | 421 +++- docs/posts/frontpage/sr320-enrich/index.html | 419 +++- .../posts/frontpage/sr320-handbook/index.html | 435 +++- docs/posts/grace-ac-WSN/index.html | 152 +- docs/posts/grace_L_WSN/index.html | 152 +- docs/posts/megan-rna/index.html | 441 +++- docs/posts/mytilus-genome/index.html | 152 +- docs/posts/ostrea/index.html | 152 +- docs/posts/sr320-DM/index.html | 419 +++- docs/posts/sr320-LGBTQ/index.html | 152 +- .../sr320-altsplice/index.html | 548 ++++- docs/posts/sr320-asi/index.html | 419 +++- docs/posts/sr320-cod/index.html | 419 +++- docs/posts/sr320-fhl/index.html | 152 +- docs/posts/sr320-george-paper/index.html | 152 +- .../{frontpage => }/sr320-lice/index.html | 467 +++- .../{frontpage => }/sr320-lsamp/index.html | 62 +- docs/posts/sr320-marineomics/index.html | 152 +- .../{frontpage => }/sr320-ostras/index.html | 467 +++- .../sr320-oyster_stage/index.html | 206 +- .../{frontpage => }/sr320-prep/index.html | 210 +- docs/posts/sr320-spencer-paper/index.html | 152 +- docs/publications.html | 541 ++++- .../articles/arredondo-espinoza2021.html | 152 +- .../articles/arredondo-espinoza2023.html | 152 +- docs/publications/articles/buckley2023.html | 152 +- docs/publications/articles/crandall2022.html | 152 +- docs/publications/articles/crandall2022b.html | 152 +- docs/publications/articles/dang2022.html | 152 +- docs/publications/articles/dimond2021.html | 152 +- docs/publications/articles/gallardo2021.html | 152 +- docs/publications/articles/gallardo2023.html | 152 +- docs/publications/articles/george2023.html | 152 +- docs/publications/articles/gurr2021.html | 152 +- docs/publications/articles/gurr2022.html | 152 +- docs/publications/articles/putnam2022.html | 152 +- docs/publications/articles/rajan2021.html | 152 +- .../articles/silliman-bogan2023.html | 152 +- docs/publications/articles/silliman2023.html | 152 +- docs/publications/articles/spencer2021.html | 152 +- docs/publications/articles/spencer2023.html | 152 +- .../articles/timmins-schiffman2021.html | 152 +- docs/publications/articles/trigg2021.html | 152 +- .../publications/articles/valenzuela2024.html | 416 +++- .../articles/venkataraman2022.html | 152 +- .../articles/venkataraman2024.html | 416 +++- docs/publications/notebooks/crandall2022.html | 152 +- docs/research.html | 490 ++++- docs/research/aquamine.html | 152 +- docs/research/art.html | 416 +++- docs/research/aust.html | 152 +- docs/research/ceabigr.html | 152 +- docs/research/cod.html | 152 +- docs/research/crabcod.html | 152 +- docs/research/e5.html | 152 +- docs/research/ffar.html | 152 +- docs/research/nprb.html | 152 +- docs/research/nrsp8.html | 152 +- docs/research/psmfc.html | 152 +- docs/research/safs.html | 152 +- docs/research/usda.html | 418 +++- docs/research/vernon.html | 152 +- docs/research/wsg-clam.html | 152 +- docs/research/wsg-ec.html | 152 +- docs/research/wsg-sc.html | 152 +- docs/search.json | 1881 +++++++++-------- docs/site_libs/quarto-html/light-border.css | 1 - .../site_libs/quarto-html/quarto-html.min.css | 5 - docs/site_libs/quarto-html/tabby.min.js | 418 ---- docs/sitemap.xml | 264 +-- docs/styles.css | 1 - posts/frontpage/sr320-handbook/index.qmd | 273 ++- .../{frontpage => }/sr320-altsplice/index.qmd | 11 +- posts/{frontpage => }/sr320-lice/index.qmd | 0 posts/{frontpage => }/sr320-lsamp/index.qmd | 0 posts/{frontpage => }/sr320-ostras/index.qmd | 0 .../sr320-oyster_stage/index.qmd | 0 posts/{frontpage => }/sr320-prep/index.qmd | 0 92 files changed, 17220 insertions(+), 3172 deletions(-) delete mode 100644 docs/notebooks.qmd rename docs/posts/{frontpage => }/sr320-altsplice/index.html (64%) rename docs/posts/{frontpage => }/sr320-lice/index.html (64%) rename docs/posts/{frontpage => }/sr320-lsamp/index.html (94%) rename docs/posts/{frontpage => }/sr320-ostras/index.html (65%) rename docs/posts/{frontpage => }/sr320-oyster_stage/index.html (83%) rename docs/posts/{frontpage => }/sr320-prep/index.html (83%) delete mode 100644 docs/site_libs/quarto-html/light-border.css delete mode 100644 docs/site_libs/quarto-html/quarto-html.min.css delete mode 100644 docs/site_libs/quarto-html/tabby.min.js delete mode 100644 docs/styles.css rename posts/{frontpage => }/sr320-altsplice/index.qmd (93%) rename posts/{frontpage => }/sr320-lice/index.qmd (100%) rename posts/{frontpage => }/sr320-lsamp/index.qmd (100%) rename posts/{frontpage => }/sr320-ostras/index.qmd (100%) rename posts/{frontpage => }/sr320-oyster_stage/index.qmd (100%) rename posts/{frontpage => }/sr320-prep/index.qmd (100%) diff --git a/docs/calendar.html b/docs/calendar.html index 517863d..2892b85 100644 --- a/docs/calendar.html +++ b/docs/calendar.html @@ -36,10 +36,12 @@ - + + - + + - @@ -219,6 +220,7 @@ + @@ -341,6 +343,150 @@

Calendar

} } toggleBodyColorPrimary(); + const disableStylesheet = (stylesheets) => { + for (let i=0; i < stylesheets.length; i++) { + const stylesheet = stylesheets[i]; + stylesheet.rel = 'prefetch'; + } + } + const enableStylesheet = (stylesheets) => { + for (let i=0; i < stylesheets.length; i++) { + const stylesheet = stylesheets[i]; + stylesheet.rel = 'stylesheet'; + } + } + const manageTransitions = (selector, allowTransitions) => { + const els = window.document.querySelectorAll(selector); + for (let i=0; i < els.length; i++) { + const el = els[i]; + if (allowTransitions) { + el.classList.remove('notransition'); + } else { + el.classList.add('notransition'); + } + } + } + const toggleGiscusIfUsed = (isAlternate, darkModeDefault) => { + const baseTheme = document.querySelector('#giscus-base-theme')?.value ?? 'light'; + const alternateTheme = document.querySelector('#giscus-alt-theme')?.value ?? 'dark'; + let newTheme = ''; + if(darkModeDefault) { + newTheme = isAlternate ? baseTheme : alternateTheme; + } else { + newTheme = isAlternate ? alternateTheme : baseTheme; + } + const changeGiscusTheme = () => { + // From: https://github.com/giscus/giscus/issues/336 + const sendMessage = (message) => { + const iframe = document.querySelector('iframe.giscus-frame'); + if (!iframe) return; + iframe.contentWindow.postMessage({ giscus: message }, 'https://giscus.app'); + } + sendMessage({ + setConfig: { + theme: newTheme + } + }); + } + const isGiscussLoaded = window.document.querySelector('iframe.giscus-frame') !== null; + if (isGiscussLoaded) { + changeGiscusTheme(); + } + } + const toggleColorMode = (alternate) => { + // Switch the stylesheets + const alternateStylesheets = window.document.querySelectorAll('link.quarto-color-scheme.quarto-color-alternate'); + manageTransitions('#quarto-margin-sidebar .nav-link', false); + if (alternate) { + enableStylesheet(alternateStylesheets); + for (const sheetNode of alternateStylesheets) { + if (sheetNode.id === "quarto-bootstrap") { + toggleBodyColorMode(sheetNode); + } + } + } else { + disableStylesheet(alternateStylesheets); + toggleBodyColorPrimary(); + } + manageTransitions('#quarto-margin-sidebar .nav-link', true); + // Switch the toggles + const toggles = window.document.querySelectorAll('.quarto-color-scheme-toggle'); + for (let i=0; i < toggles.length; i++) { + const toggle = toggles[i]; + if (toggle) { + if (alternate) { + toggle.classList.add("alternate"); + } else { + toggle.classList.remove("alternate"); + } + } + } + // Hack to workaround the fact that safari doesn't + // properly recolor the scrollbar when toggling (#1455) + if (navigator.userAgent.indexOf('Safari') > 0 && navigator.userAgent.indexOf('Chrome') == -1) { + manageTransitions("body", false); + window.scrollTo(0, 1); + setTimeout(() => { + window.scrollTo(0, 0); + manageTransitions("body", true); + }, 40); + } + } + const isFileUrl = () => { + return window.location.protocol === 'file:'; + } + const hasAlternateSentinel = () => { + let styleSentinel = getColorSchemeSentinel(); + if (styleSentinel !== null) { + return styleSentinel === "alternate"; + } else { + return false; + } + } + const setStyleSentinel = (alternate) => { + const value = alternate ? "alternate" : "default"; + if (!isFileUrl()) { + window.localStorage.setItem("quarto-color-scheme", value); + } else { + localAlternateSentinel = value; + } + } + const getColorSchemeSentinel = () => { + if (!isFileUrl()) { + const storageValue = window.localStorage.getItem("quarto-color-scheme"); + return storageValue != null ? storageValue : localAlternateSentinel; + } else { + return localAlternateSentinel; + } + } + const darkModeDefault = false; + let localAlternateSentinel = darkModeDefault ? 'alternate' : 'default'; + // Dark / light mode switch + window.quartoToggleColorScheme = () => { + // Read the current dark / light value + let toAlternate = !hasAlternateSentinel(); + toggleColorMode(toAlternate); + setStyleSentinel(toAlternate); + toggleGiscusIfUsed(toAlternate, darkModeDefault); + }; + // Ensure there is a toggle, if there isn't float one in the top right + if (window.document.querySelector('.quarto-color-scheme-toggle') === null) { + const a = window.document.createElement('a'); + a.classList.add('top-right'); + a.classList.add('quarto-color-scheme-toggle'); + a.href = ""; + a.onclick = function() { try { window.quartoToggleColorScheme(); } catch {} return false; }; + const i = window.document.createElement("i"); + i.classList.add('bi'); + a.appendChild(i); + window.document.body.appendChild(a); + } + // Switch to dark mode if need be + if (hasAlternateSentinel()) { + toggleColorMode(true); + } else { + toggleColorMode(false); + } const icon = ""; const anchorJS = new window.AnchorJS(); anchorJS.options = { diff --git a/docs/contact.html b/docs/contact.html index 47cf539..576e765 100644 --- a/docs/contact.html +++ b/docs/contact.html @@ -36,10 +36,12 @@ - + + - + + - @@ -219,6 +220,7 @@ + @@ -362,6 +364,150 @@

Contact Us

} } toggleBodyColorPrimary(); + const disableStylesheet = (stylesheets) => { + for (let i=0; i < stylesheets.length; i++) { + const stylesheet = stylesheets[i]; + stylesheet.rel = 'prefetch'; + } + } + const enableStylesheet = (stylesheets) => { + for (let i=0; i < stylesheets.length; i++) { + const stylesheet = stylesheets[i]; + stylesheet.rel = 'stylesheet'; + } + } + const manageTransitions = (selector, allowTransitions) => { + const els = window.document.querySelectorAll(selector); + for (let i=0; i < els.length; i++) { + const el = els[i]; + if (allowTransitions) { + el.classList.remove('notransition'); + } else { + el.classList.add('notransition'); + } + } + } + const toggleGiscusIfUsed = (isAlternate, darkModeDefault) => { + const baseTheme = document.querySelector('#giscus-base-theme')?.value ?? 'light'; + const alternateTheme = document.querySelector('#giscus-alt-theme')?.value ?? 'dark'; + let newTheme = ''; + if(darkModeDefault) { + newTheme = isAlternate ? baseTheme : alternateTheme; + } else { + newTheme = isAlternate ? alternateTheme : baseTheme; + } + const changeGiscusTheme = () => { + // From: https://github.com/giscus/giscus/issues/336 + const sendMessage = (message) => { + const iframe = document.querySelector('iframe.giscus-frame'); + if (!iframe) return; + iframe.contentWindow.postMessage({ giscus: message }, 'https://giscus.app'); + } + sendMessage({ + setConfig: { + theme: newTheme + } + }); + } + const isGiscussLoaded = window.document.querySelector('iframe.giscus-frame') !== null; + if (isGiscussLoaded) { + changeGiscusTheme(); + } + } + const toggleColorMode = (alternate) => { + // Switch the stylesheets + const alternateStylesheets = window.document.querySelectorAll('link.quarto-color-scheme.quarto-color-alternate'); + manageTransitions('#quarto-margin-sidebar .nav-link', false); + if (alternate) { + enableStylesheet(alternateStylesheets); + for (const sheetNode of alternateStylesheets) { + if (sheetNode.id === "quarto-bootstrap") { + toggleBodyColorMode(sheetNode); + } + } + } else { + disableStylesheet(alternateStylesheets); + toggleBodyColorPrimary(); + } + manageTransitions('#quarto-margin-sidebar .nav-link', true); + // Switch the toggles + const toggles = window.document.querySelectorAll('.quarto-color-scheme-toggle'); + for (let i=0; i < toggles.length; i++) { + const toggle = toggles[i]; + if (toggle) { + if (alternate) { + toggle.classList.add("alternate"); + } else { + toggle.classList.remove("alternate"); + } + } + } + // Hack to workaround the fact that safari doesn't + // properly recolor the scrollbar when toggling (#1455) + if (navigator.userAgent.indexOf('Safari') > 0 && navigator.userAgent.indexOf('Chrome') == -1) { + manageTransitions("body", false); + window.scrollTo(0, 1); + setTimeout(() => { + window.scrollTo(0, 0); + manageTransitions("body", true); + }, 40); + } + } + const isFileUrl = () => { + return window.location.protocol === 'file:'; + } + const hasAlternateSentinel = () => { + let styleSentinel = getColorSchemeSentinel(); + if (styleSentinel !== null) { + return styleSentinel === "alternate"; + } else { + return false; + } + } + const setStyleSentinel = (alternate) => { + const value = alternate ? "alternate" : "default"; + if (!isFileUrl()) { + window.localStorage.setItem("quarto-color-scheme", value); + } else { + localAlternateSentinel = value; + } + } + const getColorSchemeSentinel = () => { + if (!isFileUrl()) { + const storageValue = window.localStorage.getItem("quarto-color-scheme"); + return storageValue != null ? storageValue : localAlternateSentinel; + } else { + return localAlternateSentinel; + } + } + const darkModeDefault = false; + let localAlternateSentinel = darkModeDefault ? 'alternate' : 'default'; + // Dark / light mode switch + window.quartoToggleColorScheme = () => { + // Read the current dark / light value + let toAlternate = !hasAlternateSentinel(); + toggleColorMode(toAlternate); + setStyleSentinel(toAlternate); + toggleGiscusIfUsed(toAlternate, darkModeDefault); + }; + // Ensure there is a toggle, if there isn't float one in the top right + if (window.document.querySelector('.quarto-color-scheme-toggle') === null) { + const a = window.document.createElement('a'); + a.classList.add('top-right'); + a.classList.add('quarto-color-scheme-toggle'); + a.href = ""; + a.onclick = function() { try { window.quartoToggleColorScheme(); } catch {} return false; }; + const i = window.document.createElement("i"); + i.classList.add('bi'); + a.appendChild(i); + window.document.body.appendChild(a); + } + // Switch to dark mode if need be + if (hasAlternateSentinel()) { + toggleColorMode(true); + } else { + toggleColorMode(false); + } const icon = ""; const anchorJS = new window.AnchorJS(); anchorJS.options = { diff --git a/docs/courses.html b/docs/courses.html index a36804f..cab4c94 100644 --- a/docs/courses.html +++ b/docs/courses.html @@ -2,7 +2,7 @@ - + @@ -48,7 +48,13 @@ "collapse-after": 3, "panel-placement": "end", "type": "overlay", - "limit": 20, + "limit": 50, + "keyboard-shortcut": [ + "f", + "/", + "s" + ], + "show-item-context": false, "language": { "search-no-results-text": "No results", "search-matching-documents-text": "matching documents", @@ -57,6 +63,7 @@ "search-more-match-text": "more match in this document", "search-more-matches-text": "more matches in this document", "search-clear-button-title": "Clear", + "search-text-placeholder": "", "search-detached-cancel-button-title": "Cancel", "search-submit-button-title": "Submit", "search-label": "Search" @@ -78,10 +85,10 @@
-
-