Merge pull request #129 from FelixMoelder/feat/replace_pypdf2_by_pypdf

replace PyPDF2 by pypdf

Author: mdbarnesUCSD

SigProfilerAssignment/DecompositionPlots/PlotDecomposition_CNV48.py

@@ -11,7 +11,7 @@
 from reportlab.pdfbase.ttfonts import TTFont
 from reportlab.pdfbase import pdfmetrics
 import SigProfilerAssignment as spa_path
-from PyPDF2 import PdfWriter, PdfReader
+from pypdf import PdfWriter, PdfReader
 
 # imports for saving plots to memory
 import io

SigProfilerAssignment/DecompositionPlots/PlotDecomposition_DBS78.py

@@ -11,7 +11,7 @@
 from reportlab.pdfbase.ttfonts import TTFont
 from reportlab.pdfbase import pdfmetrics
 import SigProfilerAssignment as spa_path
-from PyPDF2 import PdfWriter, PdfReader
+from pypdf import PdfWriter, PdfReader
 
 # imports for saving plots to memory
 import io

SigProfilerAssignment/DecompositionPlots/PlotDecomposition_ID83.py

@@ -11,7 +11,7 @@
 from reportlab.pdfbase.ttfonts import TTFont
 from reportlab.pdfbase import pdfmetrics
 import SigProfilerAssignment as spa_path
-from PyPDF2 import PdfWriter, PdfReader
+from pypdf import PdfWriter, PdfReader
 
 # imports for saving plots to memory
 import io

SigProfilerAssignment/DecompositionPlots/PlotDecomposition_SBS1536.py

@@ -11,7 +11,7 @@
 from reportlab.pdfbase.ttfonts import TTFont
 from reportlab.pdfbase import pdfmetrics
 import SigProfilerAssignment as spa_path
-from PyPDF2 import PdfWriter, PdfReader
+from pypdf import PdfWriter, PdfReader
 
 # imports for saving plots to memory
 import io

SigProfilerAssignment/DecompositionPlots/PlotDecomposition_SBS288.py

@@ -11,7 +11,7 @@
 from reportlab.pdfbase.ttfonts import TTFont
 from reportlab.pdfbase import pdfmetrics
 import SigProfilerAssignment as spa_path
-from PyPDF2 import PdfWriter, PdfReader
+from pypdf import PdfWriter, PdfReader
 
 # imports for saving plots to memory
 import io

SigProfilerAssignment/DecompositionPlots/PlotDecomposition_SBS96.py

@@ -11,7 +11,7 @@
 from reportlab.pdfbase.ttfonts import TTFont
 from reportlab.pdfbase import pdfmetrics
 import SigProfilerAssignment as spa_path
-from PyPDF2 import PdfWriter, PdfReader
+from pypdf import PdfWriter, PdfReader
 
 # imports for saving plots to memory
 import io

SigProfilerAssignment/DecompositionPlots/PlotDecomposition_SV32.py

@@ -11,7 +11,7 @@
 from reportlab.pdfbase.ttfonts import TTFont
 from reportlab.pdfbase import pdfmetrics
 import SigProfilerAssignment as spa_path
-from PyPDF2 import PdfWriter, PdfReader
+from pypdf import PdfWriter, PdfReader
 
 # imports for saving plots to memory
 import io

SigProfilerAssignment/decompose_subroutines.py

@@ -27,11 +27,11 @@
 from sigProfilerPlotting import plotActivity as plot_ac
 from sigProfilerPlotting import tmbplot as tmb
 import string
-import PyPDF2
+import pypdf
 import scipy
 
 # import SigProfilerAssignment as sspro
-from PyPDF2 import PdfMerger
+from pypdf import PdfMerger
 import SigProfilerAssignment as spa
 from SigProfilerAssignment import single_sample as ss
 from scipy.spatial.distance import correlation as cor
@@ -1776,10 +1776,10 @@ def merge_pdf(input_folder, output_file):
             pdf2merge.append(filename)
 
     pdf2merge.sort()
-    pdfWriter = PyPDF2.PdfFileWriter()
+    pdfWriter = pypdf.PdfFileWriter()
     for filename in pdf2merge:
         pdfFileObj = open(input_folder + "/" + filename, "rb")
-        pdfReader = PyPDF2.PdfFileReader(pdfFileObj)
+        pdfReader = pypdf.PdfFileReader(pdfFileObj)
         for pageNum in range(pdfReader.numPages):
             pageObj = pdfReader.getPage(pageNum)
             pdfWriter.addPage(pageObj)

SigProfilerAssignment/decomposition.py

@@ -27,7 +27,7 @@
 from sigProfilerPlotting import sigProfilerPlotting as sigPlot
 import sigProfilerPlotting
 import os, sys
-from PyPDF2 import PdfMerger
+from pypdf import PdfMerger
 import fitz
 import time
 from pathlib import Path

requirements.txt

@@ -8,5 +8,5 @@ statsmodels
 scikit-learn
 psutil
 reportlab
-PyPDF2
+pypdf
 alive_progress

setup.py

@@ -42,7 +42,7 @@ def write_version_py(filename="SigProfilerAssignment/version.py"):
     "scikit-learn>=0.24.2",
     "psutil>=5.6.1",
     "reportlab>=3.5.42",
-    "PyPDF2>=3.0.0",
+    "pypdf>=3.1.0",
     "alive_progress>=2.4.1",
     "pdf2image>=1.16.0",
     "PyMuPDF>=1.21.0",

test.py

@@ -8,7 +8,7 @@
 import SigProfilerAssignment as spa
 from SigProfilerAssignment import Analyzer as Analyze
 from SigProfilerAssignment.DecompositionPlots import PlotDecomposition as sp
-from PyPDF2 import PdfMerger
+from pypdf import PdfMerger
 import numpy as np
 import pandas as pd
 import time