From 6419dea811ebf89c8c730639a7eedf7c8b15228d Mon Sep 17 00:00:00 2001
From: Martin Schobben <martin.schobben@geo.tuwien.ac.at>
Date: Mon, 25 Nov 2024 15:27:49 +0100
Subject: [PATCH] fix reference format

---
 src/eo_datascience/clean_nb.py | 28 +++++++++++++++-------------
 1 file changed, 15 insertions(+), 13 deletions(-)

diff --git a/src/eo_datascience/clean_nb.py b/src/eo_datascience/clean_nb.py
index a62f4ad..5ac348c 100644
--- a/src/eo_datascience/clean_nb.py
+++ b/src/eo_datascience/clean_nb.py
@@ -38,18 +38,20 @@ def clean_up_frontmatter(dir="./notebooks", save=True):
             return nb
 
 
-def convert_bibliography(nb_path="./notebooks/references.ipynb", save=True):
-    nb = nbformat.read(nb_path, as_version=4)
-    nb.cells[0].source = """# References
+def convert_bibliography(nb_path=Path("./notebooks/references.ipynb"), save=True):
+    
+    if nb_path.exists():
+        nb = nbformat.read(nb_path, as_version=4)
+        nb.cells[0].source = """# References
 
-```{bibliography}
-```
-"""
-    # Save the notebook
-    if save:
-        nbformat.write(nb, nb_path)
-    else:
-        return nb
+    ```{bibliography}
+    ```
+    """
+        # Save the notebook
+        if save:
+            nbformat.write(nb, nb_path)
+        else:
+            return nb
 
 
 def convert_callout_notes(dir="./notebooks", save=True):
@@ -106,14 +108,14 @@ def convert_refs(dir="./notebooks", save=True):
 def quarto_ref_figure_replace(quarto):
     bibs = re.findall(r"(?<=\(\@)[^\)]+", quarto)
     for i in bibs:
-        quarto = re.sub(r"\(\@" + i + "\)", r"", quarto)
+        quarto = re.sub(r"\(\@" + i + r"\)", "", quarto)
     return quarto
 
 
 def quarto_ref_person_replace(quarto):
     bibs = re.findall(r"(?<=\[\@)[^\]]+", quarto)
     for i in bibs:
-        quarto = re.sub(r"\[\@" + i + "\]", r"{cite:p}`" + i + "`", quarto)
+        quarto = re.sub(r"\[\@" + i + r"\]", r"{cite:p}`" + i + "`", quarto)
     return quarto