BIBMS_2025

Update BIBMS strbio exercise for 2025-26

Author: mredrejo

docs/bims/_extensions/dragonstyle/share-post/_extension.yml

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+title: Share-post
+author: Charles Teague
+version: 0.1.1
+quarto-required: ">=1.3.0"
+contributes:
+  shortcodes:
+    - share-post.lua

docs/bims/_extensions/dragonstyle/share-post/share-post.lua

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+local kAfterBody = "after-body"
+local kInHeader = "in-header"
+local kBeforeBody = "before-body"
+
+local kUsePackages = "packages"
+
+local urlPattern = "(https?://[%w%$%-%_%.%+%!%*%'%(%)%:%%]+/)(.+)"
+
+-- TODO: Support alignment
+--  margin-left: auto; margin-right: auto; display: block;
+
+-- TODO: Place a link for non-html output
+
+local alignmentStyles = [[
+<style>
+.linkedin-post,
+.text-post-media,
+.pinterest-rendered,
+.twitter-tweet-rendered,
+.instagram-media, 
+.mastodon-embed {
+    display: block;
+    margin-left: auto !important;
+    margin-right: auto !important;
+}
+</style>
+]]
+
+local function parseUrl(url)
+    local baseUrl, urlPath = url:match(urlPattern)
+    return {
+        url = url,
+        base = baseUrl,
+        path = urlPath
+    }
+end
+
+
+local function makeBox(text, url, icon, color) 
+    return pandoc.Div(pandoc.List({
+        pandoc.RawInline('latex', '\\begin{centering}\\begin{tcolorbox}[hbox,\ncolframe=lightgray,\ncolback=white]\n'),
+        pandoc.RawInline('latex', '\\textcolor{' .. color .. '}{{\\Large {' .. icon .. '}}} %'),
+        pandoc.Link(pandoc.RawInline("latex", '\\raisebox{0.1 em}{' .. text .. '}'),url),
+        pandoc.RawInline('latex', '\n\\end{tcolorbox}\\end{centering}\n\\vspace{1em}')
+    }))
+end
+
+local boxPackages = {
+    "tcolorbox",
+    "fontawesome5"
+}
+
+local threads = {
+    canHandle = function(urlData)
+        return urlData.base:find("threads.net")
+    end,
+    handle = {
+        html = function(urlData)
+            local iframe = '<blockquote class="text-post-media" data-text-post-permalink="' .. urlData.url .. '" data-text-post-version="0"><a href="' .. urlData.url .. '"></a></blockquote>'
+            return {
+                block = pandoc.RawBlock("html", iframe),
+                [kAfterBody] = '<script async defer src="https://www.threads.net/embed.js"></script>',
+                [kInHeader] = alignmentStyles
+            }
+        end,
+        latex = function(urlData)
+            return {
+                block=makeBox("Click to view embedded Threads post.", urlData.url, "\\faShareSquare", "black"),
+                [kUsePackages] = boxPackages
+            }
+        end,
+        other = function(urlData)
+            return {
+                block=pandoc.Link("Click to view embedded Threads post.", urlData.url)
+            }
+        end
+    }
+}
+
+local instagram = {
+    canHandle = function(urlData)
+        return urlData.base:find("instagram.com") 
+    end,
+    handle = {
+        html = function(urlData)
+            local iframe = '<blockquote class="instagram-media" data-instgrm-version="7" ><a href="' .. urlData.url .. '"></a></blockquote>'
+            return {
+                block = pandoc.RawBlock("html", iframe),
+                [kAfterBody] = '<script async defer src="//platform.instagram.com/en_US/embeds.js"></script>'
+            }
+        end,
+        latex = function(urlData)
+            return {
+                block=makeBox("Click to view embedded Instagram post.", urlData.url, "\\faInstagram", "RubineRed"),
+                [kUsePackages] = boxPackages
+
+            }
+        end,
+        other = function(urlData)
+            return {
+                block=pandoc.Link("Click to view embedded Instagram post.", urlData.url)
+            }
+        end
+    }
+}
+
+local twitter = {
+    canHandle = function(urlData)
+        return urlData.base:find("twitter.com")
+    end,
+    handle = {
+        html = function(urlData)
+            local iframe = '<blockquote class="twitter-tweet" id="foobar123"><a href="' .. urlData.url .. '"></a></blockquote>'
+            return {
+                block = pandoc.RawBlock("html", iframe),
+                [kAfterBody] = '<script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>'
+            }
+        end,
+        latex = function(urlData)
+            return {
+                block=makeBox("Click to view embedded Twitter post.", urlData.url, "\\faTwitterSquare", "ProcessBlue"),
+                [kUsePackages] = boxPackages
+            }
+        end,
+        other = function(urlData)
+            return {
+                block=pandoc.Link("Click to view embedded Twitter post.", urlData.url)
+            }
+        end
+    }
+}
+
+local pinterest = {
+    canHandle = function(urlData)
+        return urlData.base:find("pinterest.com")
+    end,
+    handle = {
+        html = function(urlData)
+            local id = urlData.path:gsub("pin/", "")
+            if id:match("/$") then
+                id = id:sub(1, -2)
+            end
+            local iframe = '<iframe class="pinterest-rendered" src="https://assets.pinterest.com/ext/embed.html?id=' .. id .. '" height="316" width="345" frameborder="0" scrolling="no" style=""></iframe>'
+            return {
+                block = pandoc.RawBlock("html", iframe),
+            }
+        end,
+        latex = function(urlData)
+            return {
+                block=makeBox("Click to view embedded Pinterest post.", urlData.url, "\\faPinterestSquare", "red"),
+                [kUsePackages] = boxPackages
+            }
+        end,
+        other = function(urlData)
+            return {
+                block=pandoc.Link("Click to view embedded Pinterest post.", urlData.url)
+            }
+        end
+    }
+}
+
+local linkedin = {
+    canHandle = function(urlData)
+        return urlData.base:find("linkedin.com")
+    end,
+    handle = {
+        html = function(urlData)
+            local pattern = "(%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d+)"
+            local id = urlData.path:match(pattern)
+            if (id) then
+                -- https://www.linkedin.com/posts/posit-software_quarto-quarto-14-activity-7156030921387778049-dHKD?utm_source=share&utm_medium=member_desktop
+                local iframe = '<iframe class="linkedin-post" src="https://www.linkedin.com/embed/feed/update/urn:li:activity:' .. id .. '" height="1062" width="504" frameborder="0" allowfullscreen="" title="Embedded post"></iframe>'
+                return {
+                    block = pandoc.RawBlock("html", iframe),
+                    [kAfterBody] = '<script src="' .. urlData.base .. 'embed.js" async="async"></script>',
+                    [kInHeader] = alignmentStyles
+                } 
+            else
+                return nil
+            end
+        end,
+        latex = function(urlData)
+            return {
+                block=makeBox("Click to view embedded LinkedIn post.", urlData.url, "\\faLinkedin", "RoyalBlue"),
+                [kUsePackages] = boxPackages
+            }
+        end,
+        other = function(urlData)
+            return {
+                block=pandoc.Link("Click to view embedded LinkedIn post.", urlData.url)
+            }
+        end
+    }
+}
+
+local mastodon = {
+    canHandle = function(urlData)
+        return urlData.path:find("@[%w._-]+/%d%d%d%d%d%d*")
+    end,
+    handle = {
+        html = function(urlData)
+            local iframe = '<iframe src="' .. urlData.url .. '/embed" class="mastodon-embed" style="max-width: 100%; border: 0;" width="400" allowfullscreen="allowfullscreen"></iframe>'
+            return {
+                block = pandoc.RawBlock("html", iframe),
+                [kAfterBody] = '<script src="' .. urlData.base .. 'embed.js" async="async"></script>',
+                [kInHeader] = alignmentStyles
+            }
+        end,
+        latex = function(urlData)
+            return {
+                block=makeBox("Click to view embedded Mastodon post.", urlData.url, "\\faMastodon", "Orchid"),
+                [kUsePackages] = boxPackages
+            }
+        end,
+        other = function(urlData)
+            return {
+                block=pandoc.Link("Click to view embedded Mastodon post.", urlData.url)
+            }
+        end
+    }
+}
+
+local handlers = {
+    threads,
+    instagram,
+    twitter,
+    pinterest,
+    linkedin,
+    mastodon
+}
+
+return {
+    ['share-post'] = function(args, kwargs, meta)
+        local result_block
+        local url = args[1]
+        -- html output
+        local urlData = parseUrl(url)
+        for i,handler in ipairs(handlers) do
+
+            if handler.canHandle(urlData) then 
+
+                local make_result = handler.handle.other
+                if quarto.doc.is_format("html") then
+                    make_result = handler.handle.html
+                elseif quarto.doc.is_format("pdf") then
+                    make_result = handler.handle.latex
+                end
+
+                -- return the raw html block
+                local result = make_result(urlData)
+                result_block = result.block
+                
+                -- inject dependencies
+                if result[kInHeader] ~= nil then
+                    quarto.doc.include_text(kInHeader, result[kInHeader])
+                end
+                if result[kBeforeBody] ~= nil then
+                    quarto.doc.include_text(kBeforeBody, result[kBeforeBody])
+                end
+                if result[kAfterBody] ~= nil then
+                    quarto.doc.include_text(kAfterBody, result[kAfterBody])
+                end
+                if result[kUsePackages] ~= nil then
+                    for _i,v in ipairs(result[kUsePackages]) do
+                        quarto.doc.use_latex_package(v)
+                    end
+                end
+            end
+        end
+        if result_block == nil then
+            quarto.log.warning("Unable to resolve post url " .. url .. "\nNo post was embedded.")
+        end
+        return result_block or {}
+    end
+}

docs/bims/_extensions/jmbuhr/molstar/_extension.yml

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+title: Molstar support
+author: Jannik Buhr
+version: 0.0.1
+contributes:
+  shortcodes:
+    - molstar.lua

docs/bims/_extensions/jmbuhr/molstar/assets/app-container.css

@@ -0,0 +1,10 @@
+div .molstar-app {
+  position: relative;
+  width: 100%;
+  padding-bottom: 56.25%;
+  margin-bottom: 1rem;
+}
+
+.msp-plugin .msp-layout-expanded {
+    z-index: 1;
+}