Merge pull request #7 from UCLH-Foundry/jekyllify-docs

Jekyllify docs
SAFEHR-data · Dec 15, 2023 · 7438865 · 7438865
2 parents fc709e3 + aefdc42
commit 7438865
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diff --git a/_includes/project_card.html b/_includes/project_card.html
@@ -4,11 +4,10 @@
 			<h5>{{project.title}}</h5>
 
 			<small class="text-muted">
-				{%- if project.authors -%} {%- for author in project.authors -%} {%-
-				assign person = site.data.people[author] -%}
+				{%- if project.authors -%} {%- for author in project.authors -%}
 				<span itemprop="author" itemscope itemtype="http://schema.org/Person">
 					<span class="p-author h-card" itemprop="name"
-						>{{ person.name }}</span
+						>{{ author }}</span
 					></span
 				>
 				{%- if forloop.last == false -%}, {%- endif -%} {%- endfor -%} {%- endif

diff --git a/_layouts/project.html b/_layouts/project.html
@@ -19,9 +19,8 @@ <h1 class="post-title p-name" itemprop="name headline">{{ page.title | escape }}
       {%- endif -%}
       {%- if page.authors -%}
         • {% for author in page.authors %}
-            {% assign person = site.data.people[author] %}
           <span itemprop="author" itemscope itemtype="http://schema.org/Person">
-            <span class="p-author h-card" itemprop="name">{{ person.name }}</span></span>
+            <span class="p-author h-card" itemprop="name">{{ author }}</span></span>
             {%- if forloop.last == false %}, {% endif -%}
         {% endfor %}
       {%- endif -%}</p>

diff --git a/_projects/_project_template/01_extra.md b/_projects/_project_template/01_extra.md
@@ -0,0 +1 @@
+More content
diff --git a/_projects/_project_template/02_data.html b/_projects/_project_template/02_data.html
@@ -0,0 +1,5 @@
+<body>
+    <h1>Data</h1>
+    <p>Here's our synthetic data and code</p>
+    <iframe src="https://imgs.xkcd.com/comics/data_trap.png"></iframe>
+</body>
diff --git a/_projects/_project_template/authors.txt b/_projects/_project_template/authors.txt
@@ -0,0 +1,2 @@
+Alan Ahlberg
+Janet Ahlberg
diff --git a/_projects/_project_template/extra.html b/_projects/_project_template/extra.html
diff --git a/_projects/_project_template/index.md b/_projects/_project_template/index.md
@@ -1,24 +1 @@
----
-title: # project title
-tags: # space separated list
-layout: project
-# Add author data to _data/people and list here:
-authors:
-- author_1
-# Add additional tabs by linking to other sources
-tabs:
-  - { 
-    name: 'extra', # Two tabs cannot share the same name
-    type: 'html', # Optional: embed/html/markdown
-    source: 'extra.html', # filename or embed url
-    label: 'Extra tab' # Optional: label for tab, defaults to capitalised name
-    }
-  - { 
-    name: 'data', 
-    type: 'embed',
-    source: 'https://www.explainxkcd.com/wiki/images/d/d7/flawed_data.png',
-    label: 'Data and Code' # Optional: label for tab, defaults to capitalised name
-    }
----
-
 Write your project overview in markdown format here
diff --git a/_projects/cheese_therapy/_data.html b/_projects/cheese_therapy/_data.html
@@ -0,0 +1 @@
+<iframe src="https://widgets.figshare.com/articles/18692549/embed?show_title=1" width="568" height="351" allowfullscreen frameborder="0"></iframe>
diff --git a/_projects/cheese_therapy/authors.txt b/_projects/cheese_therapy/authors.txt
@@ -0,0 +1,2 @@
+Anne Onamus
+Professor Plum
diff --git a/_projects/example_project_d.md → _projects/cheese_therapy/index.md b/_projects/example_project_d.md → _projects/cheese_therapy/index.md
@@ -1,15 +1,16 @@
 ---
-title: Cheese therapy
-tags: cheese
 layout: project
+title: Cheese Therapy
 authors:
-- author_1
+- Anne Onamus
+- Professor Plum
 tabs:
-  - { 
-    name: 'appendix', 
-    type: 'embed', 
-    source: 'https://widgets.figshare.com/articles/18692549/embed?show_title=1'
-    }
+- {
+  name: laaitepn,
+  type: html,
+  source: _data.html,
+  label: Data
+  }
 ---
 
 Stinking bishop manchego cheese triangles. Monterey jack when the cheese comes out everybody's happy goat cream cheese roquefort gouda cheese triangles cheeseburger. Melted cheese lancashire airedale macaroni cheese mozzarella babybel stilton port-salut. Camembert de normandie ricotta cheese triangles who moved my cheese mascarpone manchego roquefort cheese slices. Lancashire.

diff --git a/_projects/fainting_goats/_03_data.html b/_projects/fainting_goats/_03_data.html
@@ -0,0 +1 @@
+<iframe src="https://widgets.figshare.com/articles/17025359/embed?show_title=1" width="568" height="351" allowfullscreen frameborder="0"></iframe>
diff --git a/_projects/fainting_goats/authors.txt b/_projects/fainting_goats/authors.txt
@@ -0,0 +1,2 @@
+Professor Plum
+Doctor Foster
diff --git a/_projects/example_project_c.md → _projects/fainting_goats/index.md b/_projects/example_project_c.md → _projects/fainting_goats/index.md
@@ -1,15 +1,16 @@
 ---
-title: Fainting goats
-tags: goats fainting
 layout: project
+title: Fainting Goats
 authors:
-- author_1
-- author_3
+- Professor Plum
+- Doctor Foster
 tabs:
-  - { 
-    name: 'data', 
-    type: 'embed', 
-    source: 'https://widgets.figshare.com/articles/17025359/embed?show_title=1'}
+- {
+  name: qlcxqfnn,
+  type: html,
+  source: _03_data.html,
+  label: 03 Data
+  }
 ---
 
 The myotonic goat or Tennessee fainting goat is an American breed of goat. It is characterised by myotonia congenita, a hereditary condition that may cause it to stiffen or fall over when excited or startled. It may also be known as the fainting goat, falling goat, stiff-legged goat or nervous goat, or as the Tennessee wooden-leg goat. Four goats of this type were brought to Tennessee in the 1880s.

diff --git a/...ts/example_project_b/_quarto_example.html → ...jects/mega_project_1/_quarto_example.html b/...ts/example_project_b/_quarto_example.html → ...jects/mega_project_1/_quarto_example.html
diff --git a/_projects/mega_project_1/authors.txt b/_projects/mega_project_1/authors.txt
@@ -0,0 +1,2 @@
+Anne Onamus
+Sue Donnymous
diff --git a/_projects/example_project_b/index.md → _projects/mega_project_1/index.md b/_projects/example_project_b/index.md → _projects/mega_project_1/index.md
diff --git a/..._files/figure-html/fig-polar-output-1.png → ..._files/figure-html/fig-polar-output-1.png b/..._files/figure-html/fig-polar-output-1.png → ..._files/figure-html/fig-polar-output-1.png
diff --git a/..._files/libs/bootstrap/bootstrap-icons.css → ..._files/libs/bootstrap/bootstrap-icons.css b/..._files/libs/bootstrap/bootstrap-icons.css → ..._files/libs/bootstrap/bootstrap-icons.css
diff --git a/...files/libs/bootstrap/bootstrap-icons.woff → ...files/libs/bootstrap/bootstrap-icons.woff b/...files/libs/bootstrap/bootstrap-icons.woff → ...files/libs/bootstrap/bootstrap-icons.woff
diff --git a/...to_files/libs/bootstrap/bootstrap.min.css → ...to_files/libs/bootstrap/bootstrap.min.css b/...to_files/libs/bootstrap/bootstrap.min.css → ...to_files/libs/bootstrap/bootstrap.min.css
diff --git a/...rto_files/libs/bootstrap/bootstrap.min.js → ...rto_files/libs/bootstrap/bootstrap.min.js b/...rto_files/libs/bootstrap/bootstrap.min.js → ...rto_files/libs/bootstrap/bootstrap.min.js
diff --git a/...rto_files/libs/clipboard/clipboard.min.js → ...rto_files/libs/clipboard/clipboard.min.js b/...rto_files/libs/clipboard/clipboard.min.js → ...rto_files/libs/clipboard/clipboard.min.js
diff --git a/...arto_files/libs/quarto-html/anchor.min.js → ...arto_files/libs/quarto-html/anchor.min.js b/...arto_files/libs/quarto-html/anchor.min.js → ...arto_files/libs/quarto-html/anchor.min.js
diff --git a/...arto_files/libs/quarto-html/popper.min.js → ...arto_files/libs/quarto-html/popper.min.js b/...arto_files/libs/quarto-html/popper.min.js → ...arto_files/libs/quarto-html/popper.min.js
diff --git a/...uarto-html/quarto-syntax-highlighting.css → ...uarto-html/quarto-syntax-highlighting.css b/...uarto-html/quarto-syntax-highlighting.css → ...uarto-html/quarto-syntax-highlighting.css
diff --git a/...b/quarto_files/libs/quarto-html/quarto.js → ...1/quarto_files/libs/quarto-html/quarto.js b/...b/quarto_files/libs/quarto-html/quarto.js → ...1/quarto_files/libs/quarto-html/quarto.js
diff --git a/...b/quarto_files/libs/quarto-html/tippy.css → ...1/quarto_files/libs/quarto-html/tippy.css b/...b/quarto_files/libs/quarto-html/tippy.css → ...1/quarto_files/libs/quarto-html/tippy.css
diff --git a/...o_files/libs/quarto-html/tippy.umd.min.js → ...o_files/libs/quarto-html/tippy.umd.min.js b/...o_files/libs/quarto-html/tippy.umd.min.js → ...o_files/libs/quarto-html/tippy.umd.min.js
diff --git a/_projects/example_project_a/_analysis.md → _projects/scurvy_time/_analysis.md b/_projects/example_project_a/_analysis.md → _projects/scurvy_time/_analysis.md
diff --git a/_projects/example_project_a/_data.html → _projects/scurvy_time/_data.html b/_projects/example_project_a/_data.html → _projects/scurvy_time/_data.html
diff --git a/_projects/example_project_a/_gdpr.md → _projects/scurvy_time/_gdpr.md b/_projects/example_project_a/_gdpr.md → _projects/scurvy_time/_gdpr.md
diff --git a/_projects/example_project_a/authors.txt → _projects/scurvy_time/authors.txt b/_projects/example_project_a/authors.txt → _projects/scurvy_time/authors.txt
@@ -1,2 +1,2 @@
 Test Testerson
-Trial Runterton
+Trial Runner
diff --git a/_projects/example_project_a/index.md → _projects/scurvy_time/index.md b/_projects/example_project_a/index.md → _projects/scurvy_time/index.md
@@ -1,24 +1,24 @@
 ---
 layout: project
-title: Example Project A
+title: Scurvy Time
 authors:
 - Test Testerson
-- Trial Runterton
+- Trial Runner
 tabs:
 - {
-  name: roozwhna,
+  name: vphbybwh,
   type: md,
-  source: _gdpr.md,
-  label: Gdpr
+  source: _analysis.md,
+  label: Analysis
   }
 - {
-  name: ucqrttey,
+  name: npuufhpv,
   type: md,
-  source: _analysis.md,
-  label: Analysis
+  source: _gdpr.md,
+  label: Gdpr
   }
 - {
-  name: ndflidwz,
+  name: kqfokysy,
   type: html,
   source: _data.html,
   label: Data

diff --git a/_utils/jekyllify.py b/_utils/jekyllify.py
@@ -74,10 +74,36 @@ def get_project_dirs(name:str=None)->list[Path]:
         else:
             raise FileNotFoundError(f"No directory named {name} found under {PROJECTS_DIR}")
     else:
-        return [path for path in PROJECTS_DIR.iterdir() if path.is_dir()]
+        return [
+            path for path in PROJECTS_DIR.iterdir() 
+            if 
+              path.is_dir() 
+            and 
+              path.stem[0] != "_"
+            ]
 
 def get_random_string(len:int) -> str:
     return ''.join(random.choice(ascii_lowercase) for i in range(len))
+
+def get_tab_source_files(dir:Path) -> list[Path]:
+    source_files = list(dir.glob("*.md")) + list(dir.glob("*.html"))
+    # Remove index.md or index.html
+    for index in [dir/"index.md", dir/"index.html"]:
+        if index in source_files:
+            source_files.remove(index)
+    return source_files
+
+def generate_label_from_filename(stem:str) -> str:
+    """Given a filename stem (e.g. 03_code-and_data) convert this to a label by:
+    
+    1. replacing any - or _ characters with spaces
+    2. removing any digits at the start of the filename
+    3. removing any whitespace remaining at the start or end of the name
+    4. converting the name to title case"""
+    label = stem.replace("_"," ").replace("-"," ")
+    label = re.sub("^[\d]*","",label)
+    label = label.strip()
+    return label.title()
 
 def generate_title_yaml(dir:Path) -> str:
     """Title can come from title.txt, or the project folder name will be used.
@@ -107,24 +133,31 @@ def generate_tabs_yaml(dir:Path) -> str:
     index.html) and return a yaml block style list of tabs referencing those files.
     Attributes type, source, and label are generated from the file name, and name is
     a randomly generated string."""
-    extra_files = list(dir.glob("*.md")) + list(dir.glob("*.html"))
-    # Remove index.md or index.html as that's already accounted for
-    for index in [dir/"index.md", dir/"index.html"]:
-        if index in extra_files:
-            extra_files.remove(index)
+    source_files = get_tab_source_files(dir)
     tabs = "tabs:\n"
-    for file in extra_files:
+    for file in source_files:
         tabs += "- {\n"
         tabs += f"  name: {get_random_string(8)},\n"  # Used as html element id
         tabs += f"  type: {file.suffix[1:]},\n"  # Remove the dot from suffix
         tabs += f"  source: {file.name},\n"
-        tabs += f"  label: {file.stem.replace('_',' ').replace('-',' ').strip().title()}\n"
+        tabs += f"  label: {generate_label_from_filename(file.stem)}\n"
         tabs += "  }\n"
     return tabs
 
+def prepend_underscores_to_tab_sources(dir:Path)-> None:
+    """For each file in the directory with a .html or .md suffix, rename and prepend
+    with an underscore character (except for index.md)"""
+    source_files = get_tab_source_files(dir)
+    for file in source_files:
+        if not file.stem[0] == "_":
+            file.rename(file.with_stem("_"+file.stem))
+
 def jekyllify(dir:Path)->None:
-    """Given a project directory, generate yaml front matter and prepend to index.md"""
-    print(f"Adding front matter to {dir}")
+    """Given a project directory, add underscores to any .md or .html files other than 
+    index.md to ensure they do not get processed by Jekyll, then generate yaml front 
+    matter and prepend to index.md."""
+    print(f"Jekyllifying {dir}")
+    prepend_underscores_to_tab_sources(dir)
     front_matter = "---\n"
     front_matter += "layout: project\n"  # layout is always project
     front_matter += generate_title_yaml(dir)
@@ -135,7 +168,7 @@ def jekyllify(dir:Path)->None:
         content = f.read()
         f.seek(0,0)
         f.write(front_matter + content)
-
+    
 if __name__=="__main__":
     print("Jekyllify script running...")
     args = argument_parser.parse_args()
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		<iframe src="https://widgets.figshare.com/articles/18692549/embed?show_title=1" width="568" height="351" allowfullscreen frameborder="0"></iframe>