first draft

.gitignore

@@ -2,5 +2,5 @@
 .Rhistory
 .RData
 .Ruserdata
-
 /.quarto/
+.httr-oauth

Blog.qmd

@@ -0,0 +1,11 @@
+---
+title: "Blog"
+listing:
+  contents: posts
+  type: default
+  sort: "date desc"
+  categories: true
+  feed: true
+---
+
+

Projects.qmd

@@ -0,0 +1,10 @@
+---
+title: "Projects"
+listing:
+  contents: projects
+  type: grid
+  categories: false
+---
+
+
+

Publications.qmd

@@ -0,0 +1,15 @@
+---
+title: "Publications"
+toc: true
+---
+
+### Articles
+
+- Quintero, Rodríguez‐Sánchez, Jordano (2022) [Reciprocity and interaction effectiveness in generalised mutualisms among free‐living species](https://doi.org/10.1111/ele.14141). *Ecology Letters* 26 (1): 132-146. [[PDF](https://onlinelibrary.wiley.com/doi/pdf/10.1111/ele.14141)]
+
+- Rodríguez-Sanchez, Pérez-Luque, Bartomeus, Varela (2016) [Ciencia reproducible: ¿qué, por qué, cómo?](https://doi.org/10.7818/ECOS.2016.25-2.11). *Ecosistemas* 25 (2): 83-92
+
+### Book chapters
+
+
+

_extensions/mcanouil/iconify/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 Mickaël Canouil
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

_extensions/mcanouil/iconify/_extension.yml

@@ -0,0 +1,7 @@
+title: Iconify support
+author: Mickaël Canouil
+version: 2.1.2
+quarto-required: ">=1.2.280"
+contributes:
+  shortcodes:
+    - iconify.lua

_extensions/mcanouil/iconify/iconify.lua

@@ -0,0 +1,156 @@
+--[[
+# MIT License
+#
+# Copyright (c) Mickaël Canouil
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+]]
+
+local function ensure_html_deps()
+  quarto.doc.add_html_dependency({
+    name = 'iconify',
+    version = '2.1.0',
+    scripts = {"iconify-icon.min.js"}
+  })
+end
+
+local function is_empty(s)
+  return s == nil or s == ''
+end
+
+local function is_valid_size(size)
+  if is_empty(size) then
+    return ''
+  end
+  local size_table = {
+    ["tiny"]         = "0.5em",
+    ["scriptsize"]   = "0.7em",
+    ["footnotesize"] = "0.8em",
+    ["small"]        = "0.9em",
+    ["normalsize"]   = "1em",
+    ["large"]        = "1.2em",
+    ["Large"]        = "1.5em",
+    ["LARGE"]        = "1.75em",
+    ["huge"]         = "2em",
+    ["Huge"]         = "2.5em",
+    ["1x"]           = "1em",
+    ["2x"]           = "2em",
+    ["3x"]           = "3em",
+    ["4x"]           = "4em",
+    ["5x"]           = "5em",
+    ["6x"]           = "6em",
+    ["7x"]           = "7em",
+    ["8x"]           = "8em",
+    ["9x"]           = "9em",
+    ["10x"]          = "10em",
+    ["2xs"]          = "0.625em",
+    ["xs"]           = "0.75em",
+    ["sm"]           = "0.875em",
+    ["lg"]           = "1.25em",
+    ["xl"]           = "1.5em",
+    ["2xl"]          = "2em"
+  }
+  for key, value in pairs(size_table) do
+    if key == size then
+      return 'font-size: ' .. value .. ';'
+    end
+  end
+  return 'font-size: ' .. size .. ';'
+end
+
+return {
+  ["iconify"] = function(args, kwargs)
+    -- detect html (excluding epub which won't handle fa)
+    if quarto.doc.is_format("html:js") then
+      ensure_html_deps()
+      local icon = pandoc.utils.stringify(args[1])
+      local set = "fluent-emoji"
+
+      if #args > 1 and string.find(pandoc.utils.stringify(args[2]), ":") then
+        quarto.log.warning(
+          'Use "set:icon" or "set icon" syntax, not both! ' ..
+          'Using "set:icon" syntax and discarding first argument!'
+        )
+        icon = pandoc.utils.stringify(args[2])
+      end
+
+      if string.find(icon, ":") then
+        set = string.sub(icon, 1, string.find(icon, ":") - 1)
+        icon = string.sub(icon, string.find(icon, ":") + 1)
+      elseif #args > 1 then
+        set = icon
+        icon = pandoc.utils.stringify(args[2])
+      end
+
+      local attributes = ' icon="' .. set .. ':' .. icon .. '"'
+      local default_label = 'Icon ' .. icon .. ' from ' .. set .. ' Iconify.design set.'
+
+      local size = is_valid_size(pandoc.utils.stringify(kwargs["size"]))
+      if not is_empty(size) then
+        attributes = attributes .. ' style="' .. size .. '"'
+      end
+
+      local aria_label = pandoc.utils.stringify(kwargs["label"])
+      if is_empty(aria_label) then
+        aria_label =  ' aria-label="' .. default_label .. '"'
+      else
+        aria_label =  ' aria-label="' .. aria_label .. '"'
+      end
+
+      local title = pandoc.utils.stringify(kwargs["title"])
+      if is_empty(title) then
+        title =  ' title="' .. default_label .. '"'
+      else
+        title =  ' title="' .. title .. '"'
+      end
+
+      attributes = attributes .. aria_label .. title
+
+      local width = pandoc.utils.stringify(kwargs["width"])
+      if not is_empty(width) and is_empty(size) then
+        attributes = attributes .. ' width="' .. width .. '"'
+      end
+      local height = pandoc.utils.stringify(kwargs["height"])
+      if not is_empty(height) and is_empty(size)  then
+        attributes = attributes .. ' height="' .. height .. '"'
+      end
+      local flip = pandoc.utils.stringify(kwargs["flip"])
+      if not is_empty(flip) then
+        attributes = attributes .. ' flip="' .. flip.. '"'
+      end
+      local rotate = pandoc.utils.stringify(kwargs["rotate"])
+      if not is_empty(rotate) then
+        attributes = attributes .. ' rotate="' .. rotate .. '"'
+      end
+
+      local inline = pandoc.utils.stringify(kwargs["inline"])
+      if is_empty(inline) or inline ~= "false" then
+        attributes = ' inline ' .. attributes
+      end
+
+
+      return pandoc.RawInline(
+        'html',
+        '<iconify-icon role="img"' .. attributes .. '></iconify-icon>'
+      )
+    else
+      return pandoc.Null()
+    end
+  end
+}

_quarto.yml

@@ -1,19 +1,65 @@
 project:
   type: website
+  output-dir: docs
+
 
 website:
-  title: "academic-website-template-Quarto"
+  title: "My website"
+  description: "I am a scientist"
+  site-url: https://example.com
+  repo-url: "https://github.com/"
+  # favicon: logo.png
+  twitter-card: true
+  #   creator: "@handle"
+  #   site: "@handle"
+  open-graph: true
+  # google-analytics:
+  #   tracking-id: "UA-XXXXXXXX"
+  #   anonymize-ip: true
+  # cookie-consent: true
+
+
   navbar:
-    left:
+    right:
       - href: index.qmd
         text: Home
-      - about.qmd
+      - Projects.qmd
+      - Publications.qmd
+      - Blog.qmd
+
+      # - icon: twitter
+      #   href: https://twitter.com
+      - icon: mastodon
+        href: https://joinmastodon.org
+      - text: "{{< iconify fa6-brands bluesky title='BlueSky'>}}"
+        href: https://bsky.app
+      - text: "{{< iconify fa6-brands x-twitter title='Twitter'>}}"
+        href: https://x.com
+      - icon: github
+        href: https://github.com
+      - icon: linkedin
+        href: https://linkedin.com/
+      - text: "{{< iconify academicons google-scholar-square size=1.2em title='Scholar'>}}"
+        href: https://scholar.google.com
+      - text: "{{< iconify fa6-brands orcid size=1.2em title='ORCID' >}}"
+        href: https://orcid.org/
+      - icon: rss
+        href: index.xml
+
+  page-footer:
+    background: light
+    right: "Made with Quarto"
+  # back-to-top-navigation: true
+
 
 format:
   html:
-    theme: cosmo
+    theme: flatly
     css: styles.css
-    toc: true
+    toc: false
+
+execute:
+  freeze: auto  # re-render only when source changes