Merge pull request #33 from AlexandrovLab/py3_12

Py3 12

Author: mdbarnesUCSD

.travis.yml

@@ -1,11 +1,11 @@
-dist: xenial
+dist: focal
 language: python
 
 python:
-  - '3.8'
+  - '3.9'
+  - '3.12'
 
 install:
-  - pip install --force-reinstall "setuptools<60.0"
   - pip install .
 
 script: python3 test.py

CHANGELOG.md

@@ -6,6 +6,12 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 
 ## [Unreleased]
 
+## [1.2.0] - 2024-02-24
+
+### Changed
+- Updated dependencies: Now requires **Pandas >= 2.0.0**, **NumPy >= 2.0.0**, and **Python >= 3.9**.
+- Dropped support for **Python 3.8**
+
 ## [1.1.3] - 2024-10-31
 
 ### Added

SigProfilerClusters/hotspot.py

@@ -479,14 +479,14 @@ def first_run(
             bin_std_dev_cum.append(cumulativeBackground[l][i])
 
         bin_std_dev.sort()
-        std_dev.append(stdev(bin_std_dev))
+        std_dev.append(stdev([int(x) for x in bin_std_dev]))
         mean_counts.append(mean(bin_std_dev))
         avg_bin_counts.append(int(round(median(bin_std_dev), 0)))
         upper_CI.append(bin_std_dev[CI - 1])
         lower_CI.append(bin_std_dev[-CI])
 
         bin_std_dev_cum.sort()
-        std_dev_cum.append(stdev(bin_std_dev_cum))
+        std_dev_cum.append(stdev([int(x) for x in bin_std_dev_cum]))
         mean_counts_cum.append(median(bin_std_dev_cum))
 
     y2, binEdges2 = np.histogram(distances_orig, bins=bin1)

SigProfilerClusters/version.py

@@ -1,6 +1,7 @@
 
 # THIS FILE IS GENERATED FROM SIGPROFILECLUSTERS SETUP.PY
-short_version = '1.1.3'
-version = '1.1.3'
+short_version = '1.2.0'
+version = '1.2.0'
+Update = 'v1.2.0: Require Pandas and Numpy >= 2.0.0 and Python >= 3.9'
 
 

setup.py

@@ -17,7 +17,7 @@ def readme():
     # 	return(f.read())
 
 
-VERSION = "1.1.3"
+VERSION = "1.2.0"
 
 
 def write_version_py(filename="SigProfilerClusters/version.py"):
@@ -26,6 +26,7 @@ def write_version_py(filename="SigProfilerClusters/version.py"):
 # THIS FILE IS GENERATED FROM SIGPROFILECLUSTERS SETUP.PY
 short_version = '%(version)s'
 version = '%(version)s'
+Update = 'v1.2.0: Require Pandas and Numpy >= 2.0.0 and Python >= 3.9'
 	
 	"""
     fh = open(filename, "w")
@@ -51,17 +52,17 @@ def write_version_py(filename="SigProfilerClusters/version.py"):
     author_email="ebergstr@eng.ucsd.edu",
     license="UCSD",
     packages=find_packages(),  # ['SigProfilerMatrixGenerator'],
-    python_requires=">=3.8",
+    python_requires=">=3.9",
     install_requires=[
         "matplotlib>=3.5",
-        "sigProfilerPlotting>=1.3.18",
-        "SigProfilerMatrixGenerator>=1.2.19",
-        "SigProfilerSimulator>=1.1.5",
+        "sigProfilerPlotting>=1.4.0",
+        "SigProfilerMatrixGenerator>=1.3.0",
+        "SigProfilerSimulator>=1.2.0",
         "statsmodels>=0.9.0",
         "scipy>=1.1.0",
-        "pandas>=0.23.4",
-        "numpy>= 1.17.3",
-        "SigProfilerExtractor>=1.0.17",
+        "pandas>=2.0.0",
+        "numpy>=2.0.0",
+        "SigProfilerExtractor>=1.2.0",
         "seaborn>=0.13.0",
     ],
     include_package_data=True,