Merge pull request #151 from AlexandrovLab/pdfwriter-fix

Pdfwriter fix
- closes AlexandrovLab/SigProfilerExtractor#262

Author: mdbarnesUCSD

.travis.yml

@@ -11,9 +11,8 @@ cache:
     - master
 
 before_install:
-  if ! [ -f ./src/GRCh37.tar.gz ]; then
-    wget ftp://alexandrovlab-ftp.ucsd.edu/pub/tools/SigProfilerMatrixGenerator/GRCh37.tar.gz -P ./src/;
-  fi
+  - pip install --upgrade pip setuptools packaging
+  - if ! [ -f ./src/GRCh37.tar.gz ]; then wget ftp://alexandrovlab-ftp.ucsd.edu/pub/tools/SigProfilerMatrixGenerator/GRCh37.tar.gz -P ./src/; fi
 
 install:
   - pip install .[tests]

CHANGELOG.md

@@ -6,6 +6,14 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 
 ## [Unreleased]
 
+## [0.1.9] - 2024-11-12
+
+### Changed
+- Replaced `PdfMerger` with `PdfWriter` due to deprecation in `pypdf >= 5.0.0`.
+
+### Fixed
+- Addressed deprecation issues with `PdfMerger`, ensuring compatibility with recent `pypdf` versions.
+
 ## [0.1.8] - 2024-08-20
 
 ### Added

SigProfilerAssignment/decompose_subroutines.py

@@ -23,7 +23,7 @@
 import pypdf
 import scipy
 
-from pypdf import PdfMerger
+from pypdf import PdfWriter, PdfReader
 import SigProfilerAssignment as spa
 from SigProfilerAssignment import single_sample as ss
 from scipy.spatial.distance import correlation as cor
@@ -410,7 +410,7 @@ def signature_decomposition(
     )
     # lognote.write("\n********** Starting Signature Decomposition **********\n\n")
     activity_percentages = []
-    merger = PdfMerger()
+    merger = PdfWriter()
 
     for i, j in zip(range(signatures.shape[1]), denovo_signature_names):
         # Only for context SBS96
@@ -606,7 +606,12 @@ def signature_decomposition(
                 exome=exome,
                 volume=volume,
             )
-            merger.append(byte_plot)
+
+            byte_plot.seek(0)
+            reader = PdfReader(byte_plot)
+            for page in reader.pages:
+                merger.add_page(page)
+
             with alive_bar(
                 1, ctrl_c=False, bar="blocks", title=f"Decompositon Plot:{denovo_name}"
             ) as bar:

SigProfilerAssignment/decomposition.py

@@ -24,7 +24,7 @@
 from sigProfilerPlotting import sigProfilerPlotting as sigPlot
 import sigProfilerPlotting
 import os, sys
-from pypdf import PdfMerger
+from pypdf import PdfWriter, PdfReader
 import fitz
 import time
 from pathlib import Path
@@ -93,7 +93,7 @@ def generate_sample_reconstruction(
     project = "test_run"
     mtype = "96"
 
-    final_pdf = PdfMerger()
+    final_pdf = PdfWriter()
     samples = samples_input.copy(deep=True)
     samples.reset_index(inplace=True)
     for sample_name in samples.columns[1:]:
@@ -133,7 +133,11 @@ def generate_sample_reconstruction(
             exome=execution_parameters["exome"],
             volume=get_storage_dir(execution_parameters["volume"]),
         )
-        final_pdf.append(result)
+
+        result.seek(0)
+        reader = PdfReader(result)
+        for page in reader.pages:
+            final_pdf.add_page(page)
 
     pdf_output_path = os.path.join(
         output_dir, "Reconstructed_Sample_Plots_" + str(mtype) + ".pdf"

setup.py

@@ -6,7 +6,7 @@
 if os.path.exists("dist"):
     shutil.rmtree("dist")
 
-VERSION = "0.1.8"
+VERSION = "0.1.9"
 
 
 def write_version_py(filename="SigProfilerAssignment/version.py"):
@@ -15,7 +15,7 @@ def write_version_py(filename="SigProfilerAssignment/version.py"):
 # THIS FILE IS GENERATED FROM SigProfilerAssignment SETUP.PY
 short_version = '%(version)s'
 version = '%(version)s'
-Update = 'v0.1.8: Add Dockerfile and remove uncessary dependencies'
+Update = 'v0.1.9: Replace PdfMerger with PdfReader and PdfWriter for pypdf 5.0.0'
 
     
     """
@@ -39,7 +39,7 @@ def write_version_py(filename="SigProfilerAssignment/version.py"):
     "SigProfilerMatrixGenerator>=1.2.28",
     "sigProfilerPlotting>=1.3.24",
     "reportlab>=3.5.42",
-    "pypdf>=3.1.0",
+    "pypdf>=5.0.0",
     "alive_progress>=2.4.1",
     "PyMuPDF>=1.21.0",  # required for package "fitz"
 ]

test.py

@@ -8,7 +8,7 @@
 import SigProfilerAssignment as spa
 from SigProfilerAssignment import Analyzer as Analyze
 from SigProfilerAssignment.DecompositionPlots import PlotDecomposition as sp
-from pypdf import PdfMerger
+from pypdf import PdfWriter, PdfReader
 import numpy as np
 import pandas as pd
 import time
@@ -282,7 +282,7 @@ def denovo_fit_vcf_test():
 def gen_SBS96():
     np.random.seed(1234567)
     s = time.time()
-    merger = PdfMerger()
+    merger = PdfWriter()
     file1 = "SigProfilerAssignment/DecompositionPlots/ExampleSample/De_Novo_Solution_Signatures_SBS96.txt"
     file2 = "SigProfilerAssignment/DecompositionPlots/ExampleSample/Decomposed_Solution_Signatures_SBS96.txt"
     denovo_mtx = pd.read_csv(file1, sep="\t")
@@ -309,7 +309,10 @@ def gen_SBS96():
         project,
         mtype,
     )
-    merger.append(result)
+    result.seek(0)
+    reader = PdfReader(result)
+    for page in reader.pages:
+        merger.add_page(page)
 
     for ind in range(5, 0, -1):
         basis_names = basis_names[:ind]
@@ -329,7 +332,10 @@ def gen_SBS96():
             project,
             mtype,
         )
-        merger.append(result)
+        result.seek(0)
+        reader = PdfReader(result)
+        for page in reader.pages:
+            merger.add_page(page)
 
     merger.write(os.path.join(output_path, "Result_Decomposition_Plots_SBS96.pdf"))
     return time.time() - s
@@ -338,7 +344,7 @@ def gen_SBS96():
 def gen_SBS1536():
     np.random.seed(1234567)
     s = time.time()
-    merger = PdfMerger()
+    merger = PdfWriter()
     file1 = "SigProfilerAssignment/DecompositionPlots/ExampleSample/De_Novo_Solution_Signatures_SBS1536.txt"
     file2 = "SigProfilerAssignment/DecompositionPlots/ExampleSample/Decomposed_Solution_Signatures_SBS1536.txt"
     denovo_mtx = pd.read_csv(file1, sep="\t")
@@ -366,7 +372,10 @@ def gen_SBS1536():
         mtype,
     )
     # sp.run_PlotDecomposition(denovo_mtx, basis_names, weights, output_path, project, mtype, True, statistics, "COSMICv3-GRCh37", "This is where a custom message would go.")
-    merger.append(result)
+    result.seek(0)
+    reader = PdfReader(result)
+    for page in reader.pages:
+        merger.add_page(page)
 
     for ind in range(5, 0, -1):
         basis_names = basis_names[:ind]
@@ -386,7 +395,10 @@ def gen_SBS1536():
             project,
             mtype,
         )
-        merger.append(result)
+        result.seek(0)
+        reader = PdfReader(result)
+        for page in reader.pages:
+            merger.add_page(page)
 
     merger.write(os.path.join(output_path, "Result_Decomposition_Plots_SBS1536.pdf"))
     return time.time() - s
@@ -395,7 +407,7 @@ def gen_SBS1536():
 def gen_SBS288():
     np.random.seed(1234567)
     s = time.time()
-    merger = PdfMerger()
+    merger = PdfWriter()
     file1 = "SigProfilerAssignment/DecompositionPlots/ExampleSample/De_Novo_Solution_Signatures_SBS288.txt"
     file2 = "SigProfilerAssignment/DecompositionPlots/ExampleSample/COSMIC_SBS288_Signatures.txt"
     denovo_mtx = pd.read_csv(file1, sep="\t")
@@ -422,7 +434,10 @@ def gen_SBS288():
         project,
         mtype,
     )
-    merger.append(result)
+    result.seek(0)
+    reader = PdfReader(result)
+    for page in reader.pages:
+        merger.add_page(page)
 
     for ind in range(5, 0, -1):
         basis_names = basis_names[:ind]
@@ -442,7 +457,10 @@ def gen_SBS288():
             project,
             mtype,
         )
-        merger.append(result)
+        result.seek(0)
+        reader = PdfReader(result)
+        for page in reader.pages:
+            merger.add_page(page)
 
     merger.write(os.path.join(output_path, "Result_Decomposition_Plots_SBS288.pdf"))
     return time.time() - s
@@ -451,7 +469,7 @@ def gen_SBS288():
 def gen_ID83():
     np.random.seed(1234567)
     s = time.time()
-    merger = PdfMerger()
+    merger = PdfWriter()
     file1 = "SigProfilerAssignment/DecompositionPlots/ExampleSample/De_Novo_Solution_Signatures_INDEL.txt"
     file2 = "SigProfilerAssignment/DecompositionPlots/ExampleSample/COSMIC_ID83_Signatures.txt"
     denovo_mtx = pd.read_csv(file1, sep="\t")
@@ -478,7 +496,10 @@ def gen_ID83():
         project,
         mtype,
     )
-    merger.append(result)
+    result.seek(0)
+    reader = PdfReader(result)
+    for page in reader.pages:
+        merger.add_page(page)
 
     for ind in range(5, 0, -1):
         basis_names = basis_names[:ind]
@@ -498,7 +519,10 @@ def gen_ID83():
             project,
             mtype,
         )
-        merger.append(result)
+        result.seek(0)
+        reader = PdfReader(result)
+        for page in reader.pages:
+            merger.add_page(page)
 
     merger.write(os.path.join(output_path, "Result_Decomposition_Plots_ID83.pdf"))
     return time.time() - s
@@ -507,7 +531,7 @@ def gen_ID83():
 def gen_DBS78():
     np.random.seed(1234567)
     s = time.time()
-    merger = PdfMerger()
+    merger = PdfWriter()
     file1 = "SigProfilerAssignment/DecompositionPlots/ExampleSample/De_Novo_Solution_Signatures_DINUC.txt"
     file2 = "SigProfilerAssignment/DecompositionPlots/ExampleSample/COSMIC_DBS78_Signatures.txt"
     denovo_mtx = pd.read_csv(file1, sep="\t")
@@ -534,7 +558,10 @@ def gen_DBS78():
         project,
         mtype,
     )
-    merger.append(result)
+    result.seek(0)
+    reader = PdfReader(result)
+    for page in reader.pages:
+        merger.add_page(page)
 
     for ind in range(5, 0, -1):
         basis_names = basis_names[:ind]
@@ -554,7 +581,10 @@ def gen_DBS78():
             project,
             mtype,
         )
-        merger.append(result)
+        result.seek(0)
+        reader = PdfReader(result)
+        for page in reader.pages:
+            merger.add_page(page)
 
     merger.write(os.path.join(output_path, "Result_Decomposition_Plots_DBS78.pdf"))
     return time.time() - s
@@ -563,7 +593,7 @@ def gen_DBS78():
 def gen_CNV48():
     np.random.seed(1234567)
     s = time.time()
-    merger = PdfMerger()
+    merger = PdfWriter()
     file1 = "SigProfilerAssignment/DecompositionPlots/ExampleSample/CNV48_De-Novo_Signatures.txt"
     file2 = "SigProfilerAssignment/DecompositionPlots/ExampleSample/COSMIC_CNV48_Signatures.txt"
     denovo_mtx = pd.read_csv(file1, sep="\t")
@@ -592,7 +622,10 @@ def gen_CNV48():
         mtype,
     )
     # sp.run_PlotDecomposition(denovo_mtx, basis_names, weights, output_path, project, mtype, True, statistics, "COSMICv3-GRCh37", "This is where a custom message would go.")
-    merger.append(result)
+    result.seek(0)
+    reader = PdfReader(result)
+    for page in reader.pages:
+        merger.add_page(page)
 
     for ind in range(5, 0, -1):
         basis_names = basis_names[:ind]
@@ -612,7 +645,10 @@ def gen_CNV48():
             project,
             mtype,
         )
-        merger.append(result)
+        result.seek(0)
+        reader = PdfReader(result)
+        for page in reader.pages:
+            merger.add_page(page)
 
     merger.write(os.path.join(output_path, "Result_Decomposition_Plots_CNV48.pdf"))
     return time.time() - s
@@ -621,7 +657,7 @@ def gen_CNV48():
 def gen_SV32():
     np.random.seed(1234567)
     s = time.time()
-    merger = PdfMerger()
+    merger = PdfWriter()
     file1 = "SigProfilerAssignment/DecompositionPlots/ExampleSample/SV32_De-Novo_Signatures.txt"
     file2 = "SigProfilerAssignment/DecompositionPlots/ExampleSample/COSMIC_SV32_Signatures.txt"
     denovo_mtx = pd.read_csv(file1, sep="\t")
@@ -649,7 +685,10 @@ def gen_SV32():
         mtype,
     )
     # sp.run_PlotDecomposition(denovo_mtx, basis_names, weights, output_path, project, mtype, True, statistics, "COSMICv3-GRCh37", "This is where a custom message would go.")
-    merger.append(result)
+    result.seek(0)
+    reader = PdfReader(result)
+    for page in reader.pages:
+        merger.add_page(page)
 
     for ind in range(5, 0, -1):
         basis_names = basis_names[:ind]
@@ -669,7 +708,10 @@ def gen_SV32():
             project,
             mtype,
         )
-        merger.append(result)
+        result.seek(0)
+        reader = PdfReader(result)
+        for page in reader.pages:
+            merger.add_page(page)
 
     merger.write(os.path.join(output_path, "Result_Decomposition_Plots_SV32.pdf"))
     return time.time() - s