Change utf8 encoding

Author: IvanHCenalmor

.tools/python_tools/create_docker_info.py

@@ -3,7 +3,7 @@
 import sys
 
 def add_docker_extra(filename_path):
-    f = open(filename_path, "a")
+    f = open(filename_path, "a", encoding='utf8')
 
     f.write('\n')
 
@@ -14,7 +14,7 @@ def create_docker_arguments(filename_path, ubuntu_version, cuda_version, cudnn_v
                             sections_to_remove, notebook_name, gpu_flag, python_version
                             ):
 
-    f = open(filename_path, "w")
+    f = open(filename_path, "w", encoding='utf8')
     f.write('The arguments that have been used to build the Docker image are:\n')
     f.write(f'\tUBUNTU_VERSION="{ubuntu_version}"\n')
     f.write(f'\tCUDA_VERSION="{cuda_version}"\n')

.tools/python_tools/list_of_notebooks.py

@@ -11,7 +11,7 @@
 urlretrieve(zcdl4m_url, 'Home.md')
 
 # Load all the text data from ZCDL4M wiki into memory
-home = open('Home.md', 'r')
+home = open('Home.md', 'r', encoding='utf8')
 fileString = home.readlines()
 print(f"Number of lines to process {len(fileString)}. ")
 
@@ -29,7 +29,7 @@
         notebooks_task = fileString[l:k] # save the entire table
         del notebooks_task[1] # Remove the table delimiter from markdown
         # Write a text file that will be loaded as a pandas dataframe
-        with open(save_dir, 'w') as f:
+        with open(save_dir, 'w', encoding='utf8') as f:
             for line in notebooks_task:
                 f.write(line)
         # load the notebooks information as a pandas dataframe
@@ -80,7 +80,7 @@
 for ref, ref_url in Dict.items():
     notebooks = notebooks.replace(f"[{ref}]", f"({ref_url})")
 # Store the text as a markdown
-with open(save_dir, 'w') as f:
+with open(save_dir, 'w', encoding='utf8') as f:
     f.write(notebooks)
 print(f"Notebook markdown stored at {save_dir}")
 

notebooks/Bespoke_notebooks/bioimageio-pytorch/configuration.yaml

@@ -1,5 +1,5 @@
 authors:
-- "Estibaliz G\xF3mez-de-Mariscal"
+- "Estibaliz Gómez-de-Mariscal"
 - Constantin Pape
 - Mariana Ferreira
 - BioImage Model Zoo team
@@ -9,9 +9,9 @@ badges:
   url: https://colab.research.google.com/github/HenriquesLab/DL4MicEverywhere/blob/main/notebooks/Bespoke_notebooks/bioimageio-pytorch/load_bioimageio_pytorch.ipynb
 cite:
 - doi: https://doi.org/10.1101/2022.06.07.495102
-  text: "Wei Ouyang, Fynn Beuttenmueller, Estibaliz G\xF3mez-de-Mariscal, Constantin Pape, et al., BioImage Model Zoo: A Community-Driven Resource for Accessible Deep Learning in BioImage Analysis, bioRxiv 2022"
+  text: "Wei Ouyang, Fynn Beuttenmueller, Estibaliz Gómez-de-Mariscal, Constantin Pape, et al., BioImage Model Zoo: A Community-Driven Resource for Accessible Deep Learning in BioImage Analysis, bioRxiv 2022"
 - doi: https://doi.org/10.1101/2023.11.19.567606
-  text: "Iv\xE1n Hidalgo-Cenalmor, Joanna W. Pylv\xE4n\xE4inen, Mariana G Ferreira, et al., DL4MicEverywhere: Deep learning for microscopy made flexible, shareable, and reproducible, bioRxiv 2023"
+  text: "Iván Hidalgo-Cenalmor, Joanna W. Pylvänäinen, Mariana G Ferreira, et al., DL4MicEverywhere: Deep learning for microscopy made flexible, shareable, and reproducible, bioRxiv 2023"
 config:
   dl4miceverywhere:
     cuda_version: 11.2.2