Merge pull request #76 from SynBioDex/75-pdf_reader

Fix #75

.github/workflows/python-app.yml

@@ -26,7 +26,11 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
     - name: Setup Graphviz
-      uses: ts-graphviz/setup-graphviz@v1
+      uses: ts-graphviz/[email protected]
+      with:
+        # Skip to run brew update command on macOS.
+        # See https://github.com/ts-graphviz/setup-graphviz/issues/457
+        macos-skip-brew-update: 'true' # defalt false
     - name: Install Python dependencies
       shell: bash
       run: |

sbol_factory/uml_factory.py

@@ -2,7 +2,12 @@
 
 import sbol3 as sbol
 import pylatex
-from PyPDF2 import PdfFileReader
+import PyPDF2
+if PyPDF2.__version__.split('.')[0] < '3':
+   from PyPDF2 import PdfFileReader
+else:
+   # PdfFileReader is deprecated and was removed in PyPDF2 3.0.0. Use PdfReader instead.
+   from PyPDF2 import PdfReader as PdfFileReader
 
 import os
 import graphviz
@@ -61,7 +66,12 @@ def generate(self, output_path):
             outfile += '.pdf'
             width = 470  # default \textwidth of LaTeX document
             with open(os.path.join(output_path, outfile), 'rb') as pdf:
-                width = PdfFileReader(pdf).getPage(0).mediaBox[2]
+                if PyPDF2.__version__.split('.')[0] < '3':
+                    # reader.getPage(pageNumber) is deprecated and was removed in PyPDF2 3.0.0. Use reader.pages[page_number] instead.
+                    width = PdfFileReader(pdf).getPage(0).mediaBox[2]
+                else:
+                    width = PdfFileReader(pdf).pages[0].mediabox[2]
+
             self._generate(class_uri, self.write_class_definition, 0, class_name, output_path, width)
 
         fname_tex = f'{self.prefix}DataModel'

setup.py

@@ -6,7 +6,7 @@
 
 setup(name='sbol_factory',
       description='Ontology-driven data modeling',
-      version='1.1',
+      version='1.1.1.post1',
       install_requires=[
             'sbol3>=1.0b12',  # Note: implicitly includes rdflib
             'sparqlwrapper>=1.8.5',