added materials to documentation

.github/workflows/doxygen.yml

@@ -15,10 +15,10 @@ jobs:
         run: sudo apt install sqlite3 libsqlite3-dev python3-pip
 
       - name: Install Python packages
-        run: sudo pip3 install pandas
+        run: sudo pip3 install pandas tabulate
 
       - name: Generate Materials HTML
-        run: sudo mkdir ./docs/html && sudo python3 ./docs/gen_materials_page.py
+        run: sudo python3 ./docs/additional_docs/gen_materials_page.py
 
       - name: Doxygen Action
         uses: mattnotmitt/[email protected]

docs/Doxyfile

@@ -773,7 +773,7 @@ FILE_VERSION_FILTER    =
 # DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE
 # tag is left empty.
 
-LAYOUT_FILE            = ./docs/layout.xml
+LAYOUT_FILE            =
 
 # The CITE_BIB_FILES tag can be used to specify one or more bib files containing
 # the reference definitions. This must be a list of .bib files. The .bib
@@ -865,7 +865,8 @@ WARN_LOGFILE           =
 # Note: If this tag is empty the current directory is searched.
 
 INPUT                  = ./include \
-                         ./README.md
+                         ./README.md \
+                         ./docs/additional_docs
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses

docs/additional_docs/gen_materials_page.py

@@ -0,0 +1,28 @@
+import sqlite3
+import pandas as pd
+import os
+
+# Change working directory to the directory of this file
+os.chdir(os.path.dirname(os.path.abspath(__file__)))
+
+db_path = '../../data/data_sources/EPDL/EPDL.db'
+conn = sqlite3.connect(db_path)
+c = conn.cursor()
+
+# Export Materials table to pandas dataframe
+df = pd.read_sql_query("SELECT * FROM Materials", conn)
+
+# Add units to density column name
+df.rename(columns={'Density': 'Density (g/cm3)'}, inplace=True)
+
+# Export df to markdown
+df.to_markdown('Materials.md', index=False)
+
+header = "# Materials Available For Simulation"
+
+# Add header to markdown file
+with open('Materials.md', 'r+') as f:
+    content = f.read()
+    f.seek(0, 0)
+    f.write(header + '\n' + content)
+