add notebook execution with hashing to build

.gitignore

@@ -1,4 +1,5 @@
-home
+# folders
+local
 references
 
 # OS, run, and IDE artifacts

build.py

@@ -1,13 +1,11 @@
 # %%
 import os
-# import re
 import pypandoc
-from create_page_index import update_page_index
-from create_navbar import generate_navbar_html
-# from bs4 import BeautifulSoup
+from scripts.create_page_index import update_page_index
+from scripts.create_navbar import generate_navbar_html
+from scripts.convert_notebooks import convert_notebooks_to_html
 
 
-# %% ######################################################################
 def compile_page_components():
     """Compile base html components for building webpage"""
 
@@ -26,11 +24,6 @@ def compile_page_components():
     return html_parts
 
 
-html_parts = compile_page_components()
-html_parts.keys()
-
-
-# %%
 def get_page_paths(path=None):
     """Get paths to all .md pages to be converted to html"""
 
@@ -50,10 +43,6 @@ def get_page_paths(path=None):
     return md_pages
 
 
-get_page_paths()
-
-
-# %%
 def generate_page_html(page_paths):
     html_parts = compile_page_components()
     order = [
@@ -66,6 +55,7 @@ def generate_page_html(page_paths):
 
     for page, path in page_paths.items():
         page_components = html_parts.copy()
+
         # get path only
         out_path = path.split(page)[0]
 
@@ -79,6 +69,7 @@ def generate_page_html(page_paths):
 
         # remove leading `##_` from page
         page = page.split("_", 1)[1]
+
         # change file extension for page
         page = page.split(".md")[0] + ".html"
 
@@ -108,7 +99,6 @@ def generate_page_html(page_paths):
             converted = pypandoc.convert_file(
                 path,
                 to='html',
-                # format='md',
                 extra_args=["--mathml"],
             )
         except Exception as ex:
@@ -119,12 +109,11 @@ def generate_page_html(page_paths):
                 converted = pypandoc.convert_file(
                     path,
                     to='html',
-                    # format='md',
+                    extra_args=["--mathml"],
                 )
             else:
                 raise ex
-        # format html for readability
-        # converted = BeautifulSoup(converted, 'html.parser').prettify()
+
         page_components['body'] = converted
 
         file_contents = ""
@@ -138,7 +127,13 @@ def generate_page_html(page_paths):
     return
 
 
+# %%
+content_path = os.path.join(os.getcwd(), "content")
+hash_path = os.path.join(os.getcwd(), "scripts", "notebook_hashes.json")
+
+_ = convert_notebooks_to_html(
+    input_folder=content_path,
+    hash_path=hash_path,
+)
 page_paths = get_page_paths()
 generate_page_html(page_paths)
-
-# %%

content/03_assumptions/primary_electric_currents.html

@@ -248,16 +248,17 @@ <h1 id="primary-electrical-currents">3.3 Primary Electrical
 horizontally-oriented oblique dendrites which do not have any vertical
 length component, do not contribute to the dipole signal, whereas for
 basal dendrites oriented at 45 degrees from the vertical axis, the
-scaling is <span class="math inline">$-\sqrt{2}/2$</span> (note the
-negative sign is because these dendrites are pointing downward). The
-contribution from all neighboring compartments within a neuron is
-integrated and then added to a value across the set of all pyramidal
-neurons. As a result of the multiplication between axial current and
-length, the model dipole output signal has the same units of measure as
-the experimental data (in units of nano-Ampere-meters) and we are then
-able to directly compare the two signals, as well as precisely tune
-model parameters to match characteristics of recorded signals (Okada,
-Wu, and Kyuhou 1997).</p>
+scaling is
+<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>−</mi><msqrt><mn>2</mn></msqrt><mi>/</mi><mn>2</mn></mrow><annotation encoding="application/x-tex">-\sqrt{2}/2</annotation></semantics></math>
+(note the negative sign is because these dendrites are pointing
+downward). The contribution from all neighboring compartments within a
+neuron is integrated and then added to a value across the set of all
+pyramidal neurons. As a result of the multiplication between axial
+current and length, the model dipole output signal has the same units of
+measure as the experimental data (in units of nano-Ampere-meters) and we
+are then able to directly compare the two signals, as well as precisely
+tune model parameters to match characteristics of recorded signals
+(Okada, Wu, and Kyuhou 1997).</p>
 <h2 id="tutorial-references">Tutorial References</h2>
 <p>Okada, Y. C., J. Wu, and S. Kyuhou. 1997. “Genesis of MEG Signals in
 a Mammalian CNS Structure.” Electroencephalography and Clinical

content/06_alpha_beta/api.html

@@ -235,8 +235,7 @@
     # Blake Caldwell <[email protected]>
     # Christopher Bailey <[email protected]>
 -->
-<!-- [[api_alpha_beta.ipynb]] -->
-<p>[[api_alpha_beta]]</p>
+<p>[[api_alpha_beta.ipynb]]</p>
     </div> <!-- close content wrapper -->
     </div> <!-- close content -->
 </div> <!-- close main -->