Minor edits

Author: jorgensd

LICENSE

@@ -1,4 +1,4 @@
-Copyright 2022 Simula Reaseach Laboratory
+Copyright 2022 Simula Research Laboratory
 
 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:
 

code/pre_processing.py

@@ -1,17 +1,26 @@
 """
-Script for converting gmsh files to dolfin format
+Script for converting GMSH files to Dolfin format
 using cardiac geometries
 
 https://computationalphysiology.github.io/cardiac_geometries/
 
+SPDX-License-Identifier:    MIT
 """
 import typing
 from pathlib import Path
-
+import logging
 import cardiac_geometries
 import config
 from cardiac_geometries.geometry import Geometry
 from cardiac_geometries.geometry import H5Path
+import sys
+
+# We set default log level to be info
+logger = logging.Logger("Preprocessing", level=logging.INFO)
+logger.addHandler(logging.StreamHandler(sys.stdout))
+# Mute FFC and UFL errors at this stage
+logging.getLogger('FFC').setLevel(logging.WARNING)
+logging.getLogger('UFL').setLevel(logging.WARNING)
 
 schema = {
     "mesh": H5Path(
@@ -35,10 +44,15 @@ def convert_mesh(
     msh_file: typing.Union[Path, str],
     outfile: typing.Union[Path, str],
 ) -> None:
+    """
+    Convert an .msh file to DOLFIN h5 format
 
-    print("Converting 'msh' file to dolfin xdmf format")
+    Args:
+        msh_file (typing.Union[Path, str]): Path to input mesh (.msh extension)
+        outfile (typing.Union[Path, str]): Path to outfile (.h5 extension)
+    """
     geometry = cardiac_geometries.gmsh2dolfin(msh_file, unlink=True)
-
+    logger.info(f"Converting {msh_file}")
     geo = Geometry(
         mesh=geometry.mesh,
         markers=geometry.markers,
@@ -47,10 +61,16 @@ def convert_mesh(
     )
 
     geo.save(outfile)
-    print(f"Saved to {outfile}")
+    logger.info(f"Saved to {outfile}")
 
 
 def main() -> int:
+    """
+    Convert meshes from `../data/mesh/heart0*.msh` to `../data/heart_0*.h5`
+
+    Returns:
+        int: 0 if code runs as expected
+    """
     for heart_nr in [1, 2]:
         msh_file = config.get_msh_path(heart_nr=heart_nr)
         outfile = config.get_h5_path(heart_nr=heart_nr)

docs/docker.md

@@ -1,4 +1,4 @@
-## Running in Docker
+# Running in Docker
 
 We have created a docker image containing all the dependencies as well as the source code in the repository. To get the most recent version of the docker image, make sure to pull the latest image first
 ```bash

docs/refs.bib

@@ -6,12 +6,14 @@ @article{bayer2012novel
   number={10},
   pages={2243--2254},
   year={2012},
-  publisher={Springer}
+  publisher={Springer},
+  doi={10.1007/s10439-012-0593-5}
 }
 
 @misc{martinez2019repository,
   title={Repository for modelling acute myocardial ischemia: simulation scripts and torso-heart mesh},
   author={Martinez-Navarro, Hector and Rodriguez, Blanca and Bueno-Orovio, Alfonso and Minchole, Ana},
   year={2019},
-  publisher={University of Oxford}
+  publisher={University of Oxford},
+  doi={10.5287/bodleian:9RxJPo9po}
 }