Merge pull request #174 from AustralianCancerDataNetwork/docs-fix

Small formatting fixes

Author: pchlap

CITATION.cff

@@ -61,6 +61,7 @@ preferred-citation:
   date-published: "2024-12-14"
   doi: 10.1016/j.softx.2024.102010
   journal: SoftwareX
+  issn: 2352-7110
   publisher:
     name: Elsevier
   title: "PyDicer: An open-source python library for conversion and analysis of radiotherapy DICOM data"

README.md

@@ -41,7 +41,7 @@ PyDicer will place converted and intermediate files into a specific directory st
 - `[working]/[dataset_name]`: Clean datasets prepared using the Dataset Preparation Module will be stored in a directory with their name and will symbolically link to converted in the `[working]/data` directory
 
 ![PyDicer Working Directory structure](assets/pydicer-working-directory-structure.png)
-*PyDicer working directory structure ([Chlap, P. et al. SoftwareX](https://doi.org/10.1016/j.softx.2024.102010))*
+PyDicer working directory structure. Ref. [Chlap, P. et al. SoftwareX](https://doi.org/10.1016/j.softx.2024.102010)
 
 ## Pipeline
 
@@ -91,7 +91,7 @@ pydicer.run_pipeline()
 
 If you make use of PyDicer within your research work, please consider citing our SoftwareX paper:
 
-**Chlap P, Al Mouiee D, Finnegan RN, et al. PyDicer: An open-source python library for conversion and analysis of radiotherapy DICOM data. *SoftwareX*. 2025;[29:102010. doi:10.1016/j.softx.2024.102010](https://doi.org/10.1016/j.softx.2024.102010)**
+Chlap P, Al Mouiee D, Finnegan RN, et al. PyDicer: An open-source python library for conversion and analysis of radiotherapy DICOM data. *SoftwareX*. 2025;29:102010. [doi:10.1016/j.softx.2024.102010](https://doi.org/10.1016/j.softx.2024.102010)
 
 ## Contributing
 

docs/conf.py

@@ -93,3 +93,7 @@ def setup(app):
 shutil.copy("../examples/ObjectGeneration.ipynb", "_examples/ObjectGeneration.ipynb")
 shutil.copy("../examples/AutoSegmentation.ipynb", "_examples/AutoSegmentation.ipynb")
 shutil.copy("../examples/nnUNet.ipynb", "_examples/nnUNet.ipynb")
+
+shutil.rmtree("site/assets", ignore_errors=True)
+os.makedirs("site", exist_ok=True)
+shutil.copytree("../assets", "site/assets")