SigProfilerAssignment 0.1.7__tar.gz → 0.1.9__tar.gz

{SigProfilerAssignment-0.1.7/SigProfilerAssignment.egg-info → sigprofilerassignment-0.1.9}/PKG-INFO

@@ -1,14 +1,24 @@
 Metadata-Version: 2.1
 Name: SigProfilerAssignment
-Version: 0.1.7
+Version: 0.1.9
 Summary: Mutational signatures attribution and decomposition tool
 Home-page: https://github.com/AlexandrovLab/SigProfilerAssignment.git
 Author: Raviteja Vangara
 Author-email: rvangara@health.ucsd.edu
 License: UCSD
 Description-Content-Type: text/markdown
-Provides-Extra: tests
 License-File: LICENSE.txt
+Requires-Dist: scipy>=1.6.3
+Requires-Dist: numpy<2.0.0,>=1.21.2
+Requires-Dist: pandas<2.0.0,>=1.2.4
+Requires-Dist: SigProfilerMatrixGenerator>=1.2.28
+Requires-Dist: sigProfilerPlotting>=1.3.24
+Requires-Dist: reportlab>=3.5.42
+Requires-Dist: pypdf>=5.0.0
+Requires-Dist: alive_progress>=2.4.1
+Requires-Dist: PyMuPDF>=1.21.0
+Provides-Extra: tests
+Requires-Dist: pytest; extra == "tests"
 
 [![Docs](https://img.shields.io/badge/docs-latest-blue.svg)](https://osf.io/mz79v/wiki/home/) 
 [![License](https://img.shields.io/badge/License-BSD\%202--Clause-orange.svg)](https://opensource.org/licenses/BSD-2-Clause)

{SigProfilerAssignment-0.1.7 → sigprofilerassignment-0.1.9}/SigProfilerAssignment/decompose_subroutines.py

@@ -9,19 +9,12 @@ import string
 import numpy as np
 import os, sys
 
-# from matplot,pdblib.backends.backend_pdf import PdfPages
 import pandas as pd
 import matplotlib.pyplot as plt
 
 plt.switch_backend("agg")
 from matplotlib.backends.backend_pdf import PdfPages
 
-# from sklearn import metrics
-# import time
-# import multiprocessing
-# from multiprocessing import current_process
-# from functools import partial
-# from numpy import linalg as LA
 import sigProfilerPlotting as plot
 from SigProfilerAssignment.DecompositionPlots import PlotDecomposition as sp
 from sigProfilerPlotting import plotActivity as plot_ac
@@ -30,8 +23,7 @@ import string
 import pypdf
 import scipy
 
-# import SigProfilerAssignment as sspro
-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
@@ -418,7 +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
@@ -614,7 +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-0.1.7 → sigprofilerassignment-0.1.9}/SigProfilerAssignment/decomposition.py

@@ -6,13 +6,10 @@ Created on Sun May 19 12:21:06 2019
 @author: mishugeb
 """
 
-# from SigProfilerExtractor import subroutines as sub
-
 from cmath import cos
 import datetime
 import platform
 
-# from torch import sign
 from SigProfilerAssignment import decompose_subroutines as sub
 from SigProfilerAssignment.DecompositionPlots import PlotDecomposition as plot_decomp
 import SigProfilerAssignment
@@ -27,7 +24,7 @@ from SigProfilerMatrixGenerator.scripts import CNVMatrixGenerator as scna
 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
@@ -96,7 +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:]:
@@ -136,7 +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"

sigprofilerassignment-0.1.9/SigProfilerAssignment/version.py

@@ -0,0 +1,8 @@
+
+# THIS FILE IS GENERATED FROM SigProfilerAssignment SETUP.PY
+short_version = '0.1.9'
+version = '0.1.9'
+Update = 'v0.1.9: Replace PdfMerger with PdfReader and PdfWriter for pypdf 5.0.0'
+
+    
+    

{SigProfilerAssignment-0.1.7 → sigprofilerassignment-0.1.9/SigProfilerAssignment.egg-info}/PKG-INFO

@@ -1,14 +1,24 @@
 Metadata-Version: 2.1
 Name: SigProfilerAssignment
-Version: 0.1.7
+Version: 0.1.9
 Summary: Mutational signatures attribution and decomposition tool
 Home-page: https://github.com/AlexandrovLab/SigProfilerAssignment.git
 Author: Raviteja Vangara
 Author-email: rvangara@health.ucsd.edu
 License: UCSD
 Description-Content-Type: text/markdown
-Provides-Extra: tests
 License-File: LICENSE.txt
+Requires-Dist: scipy>=1.6.3
+Requires-Dist: numpy<2.0.0,>=1.21.2
+Requires-Dist: pandas<2.0.0,>=1.2.4
+Requires-Dist: SigProfilerMatrixGenerator>=1.2.28
+Requires-Dist: sigProfilerPlotting>=1.3.24
+Requires-Dist: reportlab>=3.5.42
+Requires-Dist: pypdf>=5.0.0
+Requires-Dist: alive_progress>=2.4.1
+Requires-Dist: PyMuPDF>=1.21.0
+Provides-Extra: tests
+Requires-Dist: pytest; extra == "tests"
 
 [![Docs](https://img.shields.io/badge/docs-latest-blue.svg)](https://osf.io/mz79v/wiki/home/) 
 [![License](https://img.shields.io/badge/License-BSD\%202--Clause-orange.svg)](https://opensource.org/licenses/BSD-2-Clause)

{SigProfilerAssignment-0.1.7 → sigprofilerassignment-0.1.9}/SigProfilerAssignment.egg-info/SOURCES.txt

@@ -30,6 +30,7 @@ SigProfilerAssignment/DecompositionPlots/ReferenceFiles/Accolade_fermante.png
 SigProfilerAssignment/DecompositionPlots/ReferenceFiles/CREDIT.md
 SigProfilerAssignment/DecompositionPlots/ReferenceFiles/Fonts/Arial Bold.ttf
 SigProfilerAssignment/controllers/cli_controller.py
+SigProfilerAssignment/data/.DS_Store
 SigProfilerAssignment/data/21_breast_WGS_substitutions.mat
 SigProfilerAssignment/data/CNV_features.tsv
 SigProfilerAssignment/data/CNV_signatures.txt

sigprofilerassignment-0.1.9/SigProfilerAssignment.egg-info/requires.txt

@@ -0,0 +1,12 @@
+scipy>=1.6.3
+numpy<2.0.0,>=1.21.2
+pandas<2.0.0,>=1.2.4
+SigProfilerMatrixGenerator>=1.2.28
+sigProfilerPlotting>=1.3.24
+reportlab>=3.5.42
+pypdf>=5.0.0
+alive_progress>=2.4.1
+PyMuPDF>=1.21.0
+
+[tests]
+pytest

{SigProfilerAssignment-0.1.7 → sigprofilerassignment-0.1.9}/setup.py

@@ -6,7 +6,7 @@ import os
 if os.path.exists("dist"):
     shutil.rmtree("dist")
 
-VERSION = "0.1.7"
+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 = 'v0.1.7: Update CLI, add pytest, and update pypdf dependency.'
+Update = 'v0.1.9: Replace PdfMerger with PdfReader and PdfWriter for pypdf 5.0.0'
 
     
     """
@@ -34,18 +34,14 @@ with open("README.md") as f:
 
 requirements = [
     "scipy>=1.6.3",
-    "numpy>=1.21.2",
+    "numpy>=1.21.2,<2.0.0",
     "pandas>=1.2.4,<2.0.0",
-    "SigProfilerMatrixGenerator>=1.2.17",
-    "sigProfilerPlotting>=1.3.23",
-    "statsmodels>=0.9.0",
-    "scikit-learn>=0.24.2",
-    "psutil>=5.6.1",
+    "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",
-    "pdf2image>=1.16.0",
-    "PyMuPDF>=1.21.0",
+    "PyMuPDF>=1.21.0",  # required for package "fitz"
 ]
 
 write_version_py()

SigProfilerAssignment-0.1.7/SigProfilerAssignment/version.py

@@ -1,8 +0,0 @@
-
-# THIS FILE IS GENERATED FROM SigProfilerAssignment SETUP.PY
-short_version = '0.1.7'
-version = '0.1.7'
-Update = 'v0.1.7: Update CLI, add pytest, and update pypdf dependency.'
-
-    
-    

SigProfilerAssignment-0.1.7/SigProfilerAssignment.egg-info/requires.txt

@@ -1,16 +0,0 @@
-scipy>=1.6.3
-numpy>=1.21.2
-pandas<2.0.0,>=1.2.4
-SigProfilerMatrixGenerator>=1.2.17
-sigProfilerPlotting>=1.3.23
-statsmodels>=0.9.0
-scikit-learn>=0.24.2
-psutil>=5.6.1
-reportlab>=3.5.42
-pypdf>=3.1.0
-alive_progress>=2.4.1
-pdf2image>=1.16.0
-PyMuPDF>=1.21.0
-
-[tests]
-pytest