intermediate save

Code/Lof/_extension.yml

@@ -0,0 +1,8 @@
+title: Lof
+author: Shafayet Khan Shafee
+version: 1.0.0
+quarto-required: ">=1.2.0"
+contributes:
+  shortcodes:
+    - lof.lua
+

Code/Lof/lof.lua

@@ -0,0 +1,91 @@
+--[[
+MIT License
+
+Copyright (c) 2023 Shafayet Khan Shafee
+
+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.
+]]--
+
+
+return {
+  ['lof'] = function(args, kwargs, meta) 
+    
+    -- args and kwargs    
+    local file_path = str(args[1])
+    local extension = "." .. file_path:match("[^.]+$")
+    local dname = optional(str(kwargs["dname"]), "file")
+    local dfilename = dname .. extension
+    local btn_label = " " .. optional(str(kwargs["label"]), "Download") .. " "
+    local btn_type = optional(str(kwargs["type"]), "default")
+    local icon = optional(str(kwargs["icon"]), "download")
+    local class = " " .. optional(str(kwargs["class"]), "")
+    local rand = "dnldts" .. str(math.random(1, 65000))
+    local id = optional(str(kwargs["id"]), rand)
+    -- reading files
+    local fh = io.open(file_path, "rb")
+    if not fh then
+        io.stderr:write("Cannot open file " .. 
+          file_path .. 
+          " | Javed Skipping adding buttons\n")
+        return pandoc.Null()
+    else
+      local contents = fh:read("*all")
+      fh:close()
+      
+      -- creating dataURI object
+      local b64_encoded = b64.encode(contents)
+      local mimetype = puremagic.via_path(file_path)
+      local data_uri = 'data:' .. mimetype .. ";base64," .. b64_encoded
+      
+      -- js code taken from
+      -- https://github.com/fmmattioni/downloadthis/blob/master/R/utils.R#L59
+      local js = [[fetch('%s').then(res => res.blob()).then(blob => {
+      const downloadURL = window.URL.createObjectURL(blob);
+      const a = document.createElement('a');
+      document.body.appendChild(a);
+      a.href = downloadURL;
+      a.download = '%s'; a.click();
+      window.URL.revokeObjectURL(downloadURL);
+      document.body.removeChild(a);
+        });]]
+      
+      local clicked = js:format(data_uri, dfilename)
+      
+      -- creating button
+      local button = 
+          "<button class=\"btn btn-" .. btn_type .. " downloadthis " .. 
+          class .. "\"" ..
+          " id=\"" .. id .. "\"" ..
+          "><i class=\"bi bi-" .. icon .. "\"" .. "></i>" ..
+          btn_label .. 
+          "</button>"
+      if quarto.doc.is_format("html:js") and quarto.doc.has_bootstrap()
+      then
+        ensureHtmlDeps()
+        return pandoc.RawInline('html',
+        "<a href=\"#" .. id .. "\"" ..
+        " onclick=\"" .. clicked .. "\">" .. button .. "</a>"
+        )
+      else
+        return pandoc.Null()
+      end
+    end
+  end
+}
+

Data/1_Writing/1_Task/1_Introduction.qmd

@@ -11,10 +11,13 @@ subsection [-@sec-subsec_1_1_1_Principles] and in-depth explanations about \gls{
 chapter [-@sec-chap_2_Methodlogy]. \newline 
 
 However, for a short and broad introduction to \gls{cnmc} the workflow depicted in figure @fig-fig_1_CNMC_Workflow shall be highlighted. 
+
+
 The input it receives is data of a dynamical system or space state vectors for a range of model parameter values. The two main important outcomes are some accuracy measurements and the predicted trajectory for each desired model parameter value.
 Any inexperienced user may only have a look at the predicted trajectories to 
 quickly decide visually whether the prediction matches the trained data. Since \gls{cnmc} is written in a modular manner, meaning it can be regarded as 
 a black-box function, it can easily be integrated into other existing codes or 
 workflows. \newline
 
-![Broad overview: Workflow of \gls{cnmc}](../../3_Figs_Pyth/1_Task/1_CNMc_1.svg){#fig-fig_1_CNMC_Workflow}
+![Broad overview: Workflow of \gls{cnmc}](../../3_Figs_Pyth/1_Task/1_CNMc_1.svg){#fig-fig_1_CNMC_Workflow}
+

Data/1_Writing/2_Task/0_Methodlogy.qmd

@@ -3,6 +3,7 @@ In this chapter, the entire pipeline for designing the proposed
 \gls{cnmc} is elaborated. For this purpose, the ideas behind 
 the individual processes are explained. 
 Results from the step tracking onwards will be presented in chapter [-@sec-ch_3].
+
 Having said that, \gls{cnmc} consists of multiple main process steps or stages. 
 First, a broad overview of the \gls{cnmc}'s workflow shall be given.
 Followed by a detailed explanation for each major operational step. The 
@@ -52,7 +53,7 @@ ODE solution can take a few minutes. Applying \gls{cnmc} on latter dynamical
 systems results in solving their \gls{ode}s for multiple different model parameter values. Thus, deploying the parallelization can be advised in the latter mentioned time-consuming \gls{ode}s.\newline 
 
 By far the most time-intensive part of the improved \gls{cnmc} is the clustering step. The main computation for this step is done with
-{Scikit-learn} [@scikit-learn]. It is heavily parallelized and the 
+*Scikit-learn* [@scikit-learn]. It is heavily parallelized and the 
 computation time can be reduced drastically when multiple threads are available.
 Other than that, *NumPy* and *SciPy* are well-optimized libraries and 
 are assumed to benefit from powerful computers. In summary, it shall be stated that a powerful machine is for sure advised when multiple dynamical 

Web_Code/CSS/css_0.css

@@ -29,29 +29,3 @@
 .modebar-btn--logo{
     visibility: hidden;
 }
-
-
-/* <div id="loader_Initial" class="cl_Loader"> 
-</div>  */
-
-/* when the main page is opened, it might take some time to load everything - for that a loader shall be made visibe.  */
-/* .cl_Loader {
-    border: 16px solid #f3f3f3;
-    border-radius: 50%;
-    border-top: 16px solid #3498db;
-    width: 120px;
-    height: 120px;
-    animation: spin 2s linear infinite;
-    position: absolute;
-    top: 50%;
-    left: 50%;
-    margin-top: -60px;
-    margin-left: -60px;
-  }
- 
-
-@keyframes spin {
-    0% { transform: rotate(0deg); }
-    100% { transform: rotate(360deg); }
-  }
-    */

_quarto.yml

@@ -13,15 +13,19 @@ project:
 
 filters:
   # see: https://dialoa.github.io/first-line-indent/
-  - first-line-indent
+  # - first-line-indent
 
   # see: https://github.com/quarto-ext/lightbox :MIT 
+  # destroys the figure cross referecning, because it removes the fig id
   - lightbox
 
   # https://github.com/schochastics/quarto-social-share :MIT
   # - social-share
 
   - Code/Gls/gls_Main.lua
+  # - Code/Lof/lof.lua
+  # - Lof
+  # - toc_lof
 
 # see: https://github.com/quarto-ext/lightbox 
 lightbox: 
@@ -42,18 +46,19 @@ lightbox:
 
 # see: https://quarto.org/docs/reference/formats/html.html#table-of-contents
 toc-depth: 4
-toc-location: right
+toc-location: right 
+
 
 # number-sections: false
 number-depth: 4
 
 crossref:
   # see: https://quarto.org/docs/authoring/cross-references.html#options
-  fig-prefix: ""     # (default is "Figure")
-  eq-prefix: ""     # (default is "Equation")
-  tbl-prefix: ""    # (default is "Table")
-  sec-prefix: ""    # default is Chapter
-  title-delim: —     # (default is ":")
+  fig-prefix: ""      # (default is "Figure")
+  eq-prefix: ""       # (default is "Equation")
+  tbl-prefix: ""      # (default is "Table")
+  sec-prefix: ""      # default is Chapter
+  title-delim: —      # (default is ":")
 
 
 # ============================================================================ #
@@ -117,12 +122,10 @@ cluster-based network modeling"
         - Data/1_Writing/0_Deco/1_Erkl.qmd
 
         # add pdfs intro and tasks
-        - Data/1_Writing/0_Deco/4_Mast.pdf
+        - Data/1_Writing/0_Deco/2_0_Task_Def.qmd
 
         - Data/1_Writing/0_Deco/2_1_Abstract.qmd
 
-        - Data/1_Writing/0_Deco/2_0_Task_Def.qmd
-
         # toc, list figures, list tables
 
         - Data/1_Writing/0_Deco/3_Used_Abbrev.qmd
@@ -211,6 +214,10 @@ format:
     # see: https://dialoa.github.io/first-line-indent/
     indent: false
     keep-tex: true
+    number-sections: true
+    lof: true
+    lot: true
+    toc: true 
 
 # make the table captions appear at the bottom
 tbl-cap-location: bottom

toc_lof/.gitignore

@@ -0,0 +1,4 @@
+*.html
+*.pdf
+*_files/
+/.luarc.json

toc_lof/README.md

@@ -0,0 +1,23 @@
+# Toc_lof Extension For Quarto
+
+_TODO_: Add a short description of your extension.
+
+## Installing
+
+_TODO_: Replace the `<github-organization>` with your GitHub organization.
+
+```bash
+quarto add <github-organization>/toc_lof
+```
+
+This will install the extension under the `_extensions` subdirectory.
+If you're using version control, you will want to check in this directory.
+
+## Using
+
+_TODO_: Describe how to use your extension.
+
+## Example
+
+Here is the source code for a minimal example: [example.qmd](example.qmd).
+

toc_lof/example.qmd

@@ -0,0 +1,11 @@
+---
+title: "Toc_lof Example"
+filters:
+  - toc_lof
+---
+
+## Heading
+
+This filter adds formatting to heading text.
+
+

trials.qmd

@@ -1,45 +1,14 @@
-# Trials
-
+# Trials {.unnumbered}
+asdasd
 Thissince \gls{cnmc} 
+Hello thre
 
-<!-- load lotti js code -->
-<script src="https://unpkg.com/@dotlottie/[email protected]/dist/dotlottie-player.js"></script>
-
-<dotlottie-player autoplay controls loop mode="normal" style="width: 320px"> </dotlottie-player>
-
-<script>
-
-  // when th full page is laoded --> slows down quite  abite
-  window.addEventListener("load", function() {
-    // when the tornada plotly plot is shown let the riksha disappear
-      const player = document.querySelector('dotlottie-player');
-    player.load('./Data/7_Animation/Riksha.lottie');
-});
-
-  // this without addEventListener is much faster
-  // const player = document.querySelector('dotlottie-player');
-  // player.load('./Data/7_Animation/Riksha.lottie');
-</script
-
-
-
-<div>
-  <h1>Hello, World!</h1>
-  <p>This is my first HTML code.</p>
-</div>
-
-<div>
-  <h1>Hello, World!</h1>
-  <script>
-    document.write("This text is generated by JavaScript!");
-  </script>
-</div>
-
-
-<div>
-  <h1>Final header</h1>
-  <p>This is my first HTML code.</p>
-</div>
-
+## ANd some more
+asdad
+asd
+ad
+asf
+as
 
-                 
+{{< lof image.png >}}
+{{< downloadthis image.png >}}