SigProfilerExtractor 1.1.25__tar.gz → 1.2.0__tar.gz

{SigProfilerExtractor-1.1.25/SigProfilerExtractor.egg-info → sigprofilerextractor-1.2.0}/PKG-INFO

@@ -1,13 +1,34 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: SigProfilerExtractor
-Version: 1.1.25
+Version: 1.2.0
 Summary: Extracts mutational signatures from mutational catalogues
 Home-page: https://github.com/AlexandrovLab/SigProfilerExtractor.git
 Author: S Mishu Ashiqul Islam
 Author-email: m0islam@ucsd.edu
 License: UCSD
+Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE.txt
+Requires-Dist: scipy>=1.6.3
+Requires-Dist: torch>=1.8.1
+Requires-Dist: numpy>=2.0.0
+Requires-Dist: pandas>=2.0.0
+Requires-Dist: nimfa>=1.1.0
+Requires-Dist: sigProfilerPlotting>=1.4.0
+Requires-Dist: SigProfilerMatrixGenerator>=1.3.0
+Requires-Dist: SigProfilerAssignment>=0.2.0
+Requires-Dist: statsmodels>=0.9.0
+Requires-Dist: scikit-learn>=0.24.2
+Requires-Dist: psutil>=5.6.1
+Dynamic: author
+Dynamic: author-email
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
 
 [![Docs](https://img.shields.io/badge/docs-latest-blue.svg)](https://osf.io/t6j7u/wiki/home/) 
 [![License](https://img.shields.io/badge/License-BSD\%202--Clause-orange.svg)](https://opensource.org/licenses/BSD-2-Clause)

{SigProfilerExtractor-1.1.25 → sigprofilerextractor-1.2.0}/SigProfilerExtractor/nmf_cpu.py

@@ -113,7 +113,7 @@ class NMF:
             H = np.zeros([self._V.shape[0], self._rank, self._V.shape[2]])
             nv = nndsvd.Nndsvd()
             for i in range(self._V.shape[0]):
-                vin = np.mat(self._V.cpu().numpy()[i])
+                vin = np.asmatrix(self._V.cpu().numpy()[i])
                 W[i, :, :], H[i, :, :] = nv.initialize(
                     vin, self._rank, options={"flag": 0}
                 )
@@ -123,7 +123,7 @@ class NMF:
             H = np.zeros([self._V.shape[0], self._rank, self._V.shape[2]])
             nv = nndsvd.Nndsvd()
             for i in range(self._V.shape[0]):
-                vin = np.mat(self._V.cpu().numpy()[i])
+                vin = np.asmatrix(self._V.cpu().numpy()[i])
                 W[i, :, :], H[i, :, :] = nv.initialize(
                     vin, self._rank, options={"flag": 1}
                 )
@@ -133,7 +133,7 @@ class NMF:
             H = np.zeros([self._V.shape[0], self._rank, self._V.shape[2]])
             nv = nndsvd.Nndsvd()
             for i in range(self._V.shape[0]):
-                vin = np.mat(self._V.cpu().numpy()[i])
+                vin = np.asmatrix(self._V.cpu().numpy()[i])
                 W[i, :, :], H[i, :, :] = nv.initialize(
                     vin, self._rank, options={"flag": 2}
                 )
@@ -142,7 +142,7 @@ class NMF:
             H = np.zeros([self._V.shape[0], self._rank, self._V.shape[2]])
             nv = nndsvd.Nndsvd()
             for i in range(self._V.shape[0]):
-                vin = np.mat(self._V.cpu().numpy()[i])
+                vin = np.asmatrix(self._V.cpu().numpy()[i])
                 w, h = nv.initialize(vin, self._rank, options={"flag": 2})
                 min_X = np.min(vin[vin > 0])
                 h[h <= min_X] = min_X

{SigProfilerExtractor-1.1.25 → sigprofilerextractor-1.2.0}/SigProfilerExtractor/nmf_gpu.py

@@ -100,7 +100,7 @@ class NMF:
             H = np.zeros([self._V.shape[0], self._rank, self._V.shape[2]])
             nv = nndsvd.Nndsvd()
             for i in range(self._V.shape[0]):
-                vin = np.mat(self._V.cpu().numpy()[i])
+                vin = np.asmatrix(self._V.cpu().numpy()[i])
                 W[i, :, :], H[i, :, :] = nv.initialize(
                     vin, self._rank, options={"flag": 0}
                 )
@@ -110,7 +110,7 @@ class NMF:
             H = np.zeros([self._V.shape[0], self._rank, self._V.shape[2]])
             nv = nndsvd.Nndsvd()
             for i in range(self._V.shape[0]):
-                vin = np.mat(self._V.cpu().numpy()[i])
+                vin = np.asmatrix(self._V.cpu().numpy()[i])
                 W[i, :, :], H[i, :, :] = nv.initialize(
                     vin, self._rank, options={"flag": 1}
                 )
@@ -120,7 +120,7 @@ class NMF:
             H = np.zeros([self._V.shape[0], self._rank, self._V.shape[2]])
             nv = nndsvd.Nndsvd()
             for i in range(self._V.shape[0]):
-                vin = np.mat(self._V.cpu().numpy()[i])
+                vin = np.asmatrix(self._V.cpu().numpy()[i])
                 W[i, :, :], H[i, :, :] = nv.initialize(
                     vin, self._rank, options={"flag": 2}
                 )
@@ -129,7 +129,7 @@ class NMF:
             H = np.zeros([self._V.shape[0], self._rank, self._V.shape[2]])
             nv = nndsvd.Nndsvd()
             for i in range(self._V.shape[0]):
-                vin = np.mat(self._V.cpu().numpy()[i])
+                vin = np.asmatrix(self._V.cpu().numpy()[i])
                 w, h = nv.initialize(vin, self._rank, options={"flag": 2})
                 min_X = np.min(vin[vin > 0])
                 h[h <= min_X] = min_X

{SigProfilerExtractor-1.1.25 → sigprofilerextractor-1.2.0}/SigProfilerExtractor/subroutines.py

@@ -203,8 +203,8 @@ def normalize_samples(
         bootstrapGenomes = np.array(bootstrapGenomes)
         indices = np.where(totalMutations > normalization_cutoff)[0]
         norm_genome = (
-            bootstrapGenomes[:, list(indices)]
-            / totalMutations[list(indices)][:, np.newaxis].T
+            np.array(bootstrapGenomes)[:, list(indices)]
+            / np.array(totalMutations)[list(indices)][:, np.newaxis].T
             * normalization_cutoff
         )
         bootstrapGenomes[:, list(indices)] = norm_genome
@@ -214,8 +214,8 @@ def normalize_samples(
         rows = bootstrapGenomes.shape[0]
         indices = np.where(totalMutations > (rows * 100))[0]
         norm_genome = (
-            bootstrapGenomes[:, list(indices)]
-            / totalMutations[list(indices)][:, np.newaxis].T
+            np.array(bootstrapGenomes)[:, list(indices)]
+            / np.array(totalMutations)[list(indices)][:, np.newaxis].T
             * (rows * 100)
         )
         bootstrapGenomes[:, list(indices)] = norm_genome
@@ -231,8 +231,8 @@ def normalize_samples(
             rows = bootstrapGenomes.shape[0]
             indices = np.where(totalMutations > int(norm))[0]
             norm_genome = (
-                bootstrapGenomes[:, list(indices)]
-                / totalMutations[list(indices)][:, np.newaxis].T
+                np.array(bootstrapGenomes)[:, list(indices)]
+                / np.array(totalMutations)[list(indices)][:, np.newaxis].T
                 * (int(norm))
             )
             bootstrapGenomes[:, list(indices)] = norm_genome
@@ -465,7 +465,7 @@ def pnmf(
         for i in range(len(W)):
             _W = np.array(W[i])
             _H = np.array(H[i])
-            total = _W.sum(axis=0)[np.newaxis]
+            total = _W.sum(axis=0, keepdims=True)#[np.newaxis]
             _W = _W / total
             _H = _H * total.T
             _H = denormalize_samples(_H, totalMutations)
@@ -508,7 +508,7 @@ def pnmf(
 
         W = np.array(W)
         H = np.array(H)
-        total = W.sum(axis=0)[np.newaxis]
+        total = W.sum(axis=0, keepdims=True) #[np.newaxis]
         W = W / total
         H = H * total.T
 
@@ -913,14 +913,17 @@ def reclustering(
 
     count = 0
     labels = []
-    clusters = pd.DataFrame()
+    clusters_list = []  # Use a list to collect DataFrames
+
     for cluster_id in range(processes3D.shape[0]):
         cluster_vectors = pd.DataFrame(processes3D[cluster_id, :, :])
-        clusters = clusters.append(cluster_vectors.T)
+        clusters_list.append(cluster_vectors.T)  # Collect DataFrames into a list
         for k in range(cluster_vectors.shape[1]):
             labels.append(count)
         count = count + 1
 
+    # Concatenate all DataFrames at once
+    clusters = pd.concat(clusters_list, ignore_index=True)
     try:
         if dist == "cosine":
             SilhouetteCoefficients = metrics.silhouette_samples(
@@ -1109,7 +1112,7 @@ def probabilities(W, H, index, allsigids, allcolnames):
 
     result = 0
     for i in range(H.shape[1]):  # here H.shape is the number of sample
-        M = genomes[:, i][np.newaxis]
+        M = np.array(genomes)[:, i][np.newaxis]
         probs = W * H[:, i] / M.T
         probs = pd.DataFrame(probs)
         probs.columns = sigs

sigprofilerextractor-1.2.0/SigProfilerExtractor/version.py

@@ -0,0 +1,7 @@
+
+# THIS FILE IS GENERATED FROM SIGPROFILEREXTRACTOR SETUP.PY
+short_version = '1.2.0'
+version = '1.2.0'
+Update = 'Upgrade v1.2.0: Require Pandas and Numpy >= 2.0.0 and Python >= 3.9'
+    
+    

{SigProfilerExtractor-1.1.25 → sigprofilerextractor-1.2.0/SigProfilerExtractor.egg-info}/PKG-INFO

@@ -1,13 +1,34 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: SigProfilerExtractor
-Version: 1.1.25
+Version: 1.2.0
 Summary: Extracts mutational signatures from mutational catalogues
 Home-page: https://github.com/AlexandrovLab/SigProfilerExtractor.git
 Author: S Mishu Ashiqul Islam
 Author-email: m0islam@ucsd.edu
 License: UCSD
+Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE.txt
+Requires-Dist: scipy>=1.6.3
+Requires-Dist: torch>=1.8.1
+Requires-Dist: numpy>=2.0.0
+Requires-Dist: pandas>=2.0.0
+Requires-Dist: nimfa>=1.1.0
+Requires-Dist: sigProfilerPlotting>=1.4.0
+Requires-Dist: SigProfilerMatrixGenerator>=1.3.0
+Requires-Dist: SigProfilerAssignment>=0.2.0
+Requires-Dist: statsmodels>=0.9.0
+Requires-Dist: scikit-learn>=0.24.2
+Requires-Dist: psutil>=5.6.1
+Dynamic: author
+Dynamic: author-email
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
 
 [![Docs](https://img.shields.io/badge/docs-latest-blue.svg)](https://osf.io/t6j7u/wiki/home/) 
 [![License](https://img.shields.io/badge/License-BSD\%202--Clause-orange.svg)](https://opensource.org/licenses/BSD-2-Clause)

sigprofilerextractor-1.2.0/SigProfilerExtractor.egg-info/requires.txt

@@ -0,0 +1,11 @@
+scipy>=1.6.3
+torch>=1.8.1
+numpy>=2.0.0
+pandas>=2.0.0
+nimfa>=1.1.0
+sigProfilerPlotting>=1.4.0
+SigProfilerMatrixGenerator>=1.3.0
+SigProfilerAssignment>=0.2.0
+statsmodels>=0.9.0
+scikit-learn>=0.24.2
+psutil>=5.6.1

{SigProfilerExtractor-1.1.25 → sigprofilerextractor-1.2.0}/setup.py

@@ -8,7 +8,7 @@ import subprocess
 if os.path.exists("dist"):
     shutil.rmtree("dist")
 
-VERSION = "1.1.25"
+VERSION = "1.2.0"
 
 
 with open("README.md") as f:
@@ -21,7 +21,7 @@ def write_version_py(filename="SigProfilerExtractor/version.py"):
 # THIS FILE IS GENERATED FROM SIGPROFILEREXTRACTOR SETUP.PY
 short_version = '%(version)s'
 version = '%(version)s'
-Update = 'Upgrade v1.1.25: Add CLI support, README formatting udpate, and CI/CD badge fix.'
+Update = 'Upgrade v1.2.0: Require Pandas and Numpy >= 2.0.0 and Python >= 3.9'
     
     """
     fh = open(filename, "w")
@@ -37,12 +37,12 @@ Update = 'Upgrade v1.1.25: Add CLI support, README formatting udpate, and CI/CD
 requirements = [
     "scipy>=1.6.3",
     "torch>=1.8.1",
-    "numpy>=1.21.2",
-    "pandas>=1.2.4",
+    "numpy>=2.0.0",
+    "pandas>=2.0.0",
     "nimfa>=1.1.0",
-    "SigProfilerMatrixGenerator>=1.2.25",
-    "sigProfilerPlotting>=1.3.22",
-    "SigProfilerAssignment>=0.1.4",
+    "sigProfilerPlotting>=1.4.0",
+    "SigProfilerMatrixGenerator>=1.3.0",
+    "SigProfilerAssignment>=0.2.0",
     "statsmodels>=0.9.0",
     "scikit-learn>=0.24.2",
     "psutil>=5.6.1",
@@ -104,6 +104,7 @@ setup(
     packages=["SigProfilerExtractor"],
     install_requires=requirements,
     include_package_data=True,
+    python_requires=">=3.9",
     entry_points={
         "console_scripts": [
             "SigProfilerExtractor=SigProfilerExtractor.sigprofilerextractor_cli:main_function",

SigProfilerExtractor-1.1.25/SigProfilerExtractor/version.py

@@ -1,7 +0,0 @@
-
-# THIS FILE IS GENERATED FROM SIGPROFILEREXTRACTOR SETUP.PY
-short_version = '1.1.25'
-version = '1.1.25'
-Update = 'Upgrade v1.1.25: Add CLI support, README formatting udpate, and CI/CD badge fix.'
-    
-    

SigProfilerExtractor-1.1.25/SigProfilerExtractor.egg-info/requires.txt

@@ -1,11 +0,0 @@
-scipy>=1.6.3
-torch>=1.8.1
-numpy>=1.21.2
-pandas>=1.2.4
-nimfa>=1.1.0
-SigProfilerMatrixGenerator>=1.2.25
-sigProfilerPlotting>=1.3.22
-SigProfilerAssignment>=0.1.4
-statsmodels>=0.9.0
-scikit-learn>=0.24.2
-psutil>=5.6.1