feat: create use_quarto_ext() & quarto-add cmd for using extensions

docs/_extensions/fnl/_extension.yml

@@ -0,0 +1,11 @@
+title: fnl
+author: Kelly Sovacool
+version: 0.1.3
+quarto-required: ">=1.5.0"
+contributes:
+  formats:
+    html:
+      theme:
+        dark: [darkly, fnl-dark.scss]
+        light: [flatly, fnl-light.scss]
+      toc: true

docs/_quarto.yml

@@ -46,7 +46,7 @@ website:
     background: black
     foreground: white
     left: |
-      [![](/img/fnl-logo-dark.png){height=70px}](https://frederick.cancer.gov/research/science-areas/bioinformatics-and-computational-science/advanced-biomedical-computational-science)
+      [![](/_extensions/fnl/fnl-logo-dark.png){height=70px}](https://frederick.cancer.gov/research/science-areas/bioinformatics-and-computational-science/advanced-biomedical-computational-science)
     center: |
       Created by the
       [CCR Collaborative Bioinformatics Resource](https://github.com/CCBR)
@@ -101,9 +101,4 @@ execute:
   eval: true
   echo: true
 
-format:
-  html:
-    theme:
-      dark: [darkly, themes/fnl-dark.scss]
-      light: [flatly, themes/fnl-light.scss]
-    toc: true
+format: fnl-html

src/ccbr_tools/__main__.py

@@ -13,6 +13,7 @@
     CustomClickGroup,
 )
 from .send_email import send_email_msg
+from .templates import use_quarto_ext
 
 
 all_commands = "All installed tools:\n" + "\n".join(
@@ -133,7 +134,24 @@ def send_email(to_address, text, subject, attach_html, from_addr, debug):
     send_email_msg(to_address, text, subject, attach_html, from_addr, debug)
 
 
+@click.command()
+@click.argument(
+    "ext_name",
+    type=str,
+    required=True,
+)
+def quarto_add(ext_name):
+    """
+    Add a quarto extension
+
+    Arguments:
+        ext_name    The name of the extension in ccbr_tools
+    """
+    use_quarto_ext(ext_name)
+
+
 cli.add_command(send_email)
+cli.add_command(quarto_add)
 cli.add_command(cite)
 cli.add_command(version)
 

src/ccbr_tools/templates/__init__.py

@@ -2,10 +2,14 @@
 Template files for CCBR Tools.
 
 Templates:
-    - `ccbr_tools.templates.submit_slurm.sh`
-"""
+    - `~ccbr_tools.templates.submit_slurm.sh`
 
+Quarto extensions
+    - `~ccbr_tools.templates._extensions.fnl`
+"""
 import importlib.resources
+import pathlib
+import shutil
 
 
 def read_template(template_name):
@@ -46,3 +50,22 @@ def use_template(template_name, output_filepath=None, **kwargs: str):
         output_filepath = template_name
     with open(output_filepath, "wt") as outfile:
         outfile.write(template_str.format(**kwargs))
+
+
+def use_quarto_ext(ext_name):
+    """
+    Use a Quarto extension
+
+    Args:
+        ext_name (str): The name of the extension in ccbr_tools
+
+    Examples:
+        >>> use_quarto_ext("fnl")
+    """
+    template_files = importlib.resources.files(__package__)
+    ext_dir = pathlib.Path("_extensions")
+    if not ext_dir.exists():
+        ext_dir.mkdir()
+    template_dir = template_files / "_extensions" / ext_name
+    shutil.copytree(template_dir, ext_dir / ext_name)
+    print(f"Copied {ext_name} to {ext_dir}")

src/ccbr_tools/templates/_extensions/fnl/__init__.py

@@ -0,0 +1,9 @@
+"""
+Quarto HTML format with FNL branding guidelines
+
+First run `ccbr_tools quarto-add fnl`, then add the following to your `_quarto.yml` file:
+
+```yaml
+format: fnl-html
+```
+"""

src/ccbr_tools/templates/_extensions/fnl/_extension.yml

@@ -0,0 +1,11 @@
+title: fnl
+author: Kelly Sovacool
+version: 0.1.3
+quarto-required: ">=1.5.0"
+contributes:
+  formats:
+    html:
+      theme:
+        dark: [darkly, fnl-dark.scss]
+        light: [flatly, fnl-light.scss]
+      toc: true

src/ccbr_tools/templates/_extensions/fnl/fnl-dark.scss

@@ -0,0 +1,45 @@
+/*-- scss:defaults --*/
+
+// colors
+// https://nih.sharepoint.com/:b:/r/sites/NCI-Fred/Communications/Shared%20Documents/Branding%20guidelines%20LIVE.pdf?csf=1&web=1&e=e9PrVO
+
+// primary
+$black: #000000;
+$white: #ffffff;
+$lime: #7cc349;
+$teal: #296b7f;
+
+//secondary
+$teal-light: #4e9db5;
+$teal-dark: #19424e;
+$almost-black: #03191f;
+$lime-light: #b1ee85;
+$lime-dark: #528230;
+$orange: #ecba4c;
+
+// set colors
+$primary: $teal;
+$secondary: $lime;
+
+$body-bg: $almost-black;
+$body-color: $white;
+$link-color: $lime;
+
+$navbar-bg: $teal-dark;
+$navbar-hl: $lime-light;
+
+$footer-bg: $black;
+$footer-fg: $white;
+$footer-hl: $lime-light;
+
+$sidebar-hl: $lime-light;
+
+$code-block-bg-alpha: -0.8;
+$code-bg-alpha: -0.8;
+$code-alpha: 0.9;
+$code-bg: $teal-dark;
+$code-color: $orange;
+
+// font
+$font-family-sans-serif: "Roboto", sans-serif;
+$font-family-monospace: "Roboto Mono", monospace;

src/ccbr_tools/templates/_extensions/fnl/fnl-light.scss

@@ -0,0 +1,32 @@
+/*-- scss:defaults --*/
+
+// colors
+// https://nih.sharepoint.com/:b:/r/sites/NCI-Fred/Communications/Shared%20Documents/Branding%20guidelines%20LIVE.pdf?csf=1&web=1&e=e9PrVO
+
+// primary
+$black: #000000;
+$white: #ffffff;
+$lime: #7cc349;
+$teal: #296b7f;
+
+//secondary
+$teal-light: #4e9db5;
+$teal-dark: #19424e;
+$almost-black: #03191f;
+$lime-light: #b1ee85;
+$lime-dark: #528230;
+$orange: #ecba4c;
+
+// set colors
+$primary: $teal-dark;
+$secondary: $lime;
+$link-color: $teal;
+
+$footer-bg: black;
+$footer-fg: white;
+
+$code-color: $lime-dark;
+
+// font
+$font-family-sans-serif: "Roboto", sans-serif;
+$font-family-monospace: "Roboto Mono", monospace;

tests/test_templates.py

@@ -3,7 +3,7 @@
 import pytest
 import tempfile
 
-from ccbr_tools.templates import read_template, use_template
+from ccbr_tools.templates import read_template, use_template, use_quarto_ext
 
 
 def test_read_template():
@@ -65,3 +65,17 @@ def test_use_template_blanks():
                 output_filepath=out_filepath,
             )
             assert str(exc_info.value) == "KeyError: 'MODULES'"
+
+
+def test_use_quarto_ext():
+    with tempfile.TemporaryDirectory() as tmp_dir:
+        current_wd = os.getcwd()
+        tmp_wd = pathlib.Path(current_wd) / tmp_dir
+        os.chdir(tmp_wd)
+        use_quarto_ext("fnl")
+        assertions = [
+            pathlib.Path("_extensions/fnl").is_dir(),
+            pathlib.Path("_extensions/fnl/_extension.yml").is_file(),
+        ]
+        os.chdir(current_wd)
+    assert all(assertions)