Merge pull request #183 from AlexandrovLab/parallel-update

v1.0.1:  Refine CPU parameter logic to pass directly instead of via d…

Author: mdbarnesUCSD

CHANGELOG.md

@@ -6,6 +6,14 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 
 ## [Unreleased]
 
+## [1.0.1] - 2025-10-20
+
+### Fixed
+- Refactored the handling of the `cpu` parameter. The logic has been updated to pass the CPU count directly via the function's parameters, instead of through an internal `devopts` dictionary, to reduce complexity and improve code clarity.
+
+### Added
+- Added the `cpu` parameter to the metadata output log.
+
 ## [1.0.0] - 2025-10-07
 
 ### Added

SigProfilerAssignment/decomposition.py

@@ -177,6 +177,8 @@ def record_parameters(sysdata, execution_parameters, start_time):
         sysdata.write("\tsamples: {}\n".format(execution_parameters["samples"]))
     else:
         sysdata.write("\tsamples: {}\n".format(type(execution_parameters["samples"])))
+
+    sysdata.write("\tcpu: {}\n".format(execution_parameters["cpu"]))
     if execution_parameters["volume"] is not None:
         sysdata.write("\tvolume: {}\n".format(execution_parameters["volume"]))
     sysdata.write(
@@ -498,6 +500,7 @@ def spa_analyze(
         "export_probabilities": export_probabilities,
         "make_plots": make_plots,
         "volume": volume,
+        "cpu": cpu,
     }
 
     if make_metadata:
@@ -686,7 +689,7 @@ def spa_analyze(
                 denovo_refit_option=denovo_refit_option,
                 exome=exome,
                 volume=volume,
-                cpu=-1,
+                cpu=cpu,
             )
 
         else:
@@ -695,7 +698,6 @@ def spa_analyze(
             signature_stats = devopts["signature_stats"]
             sequence = devopts["sequence"]
             processSTE = devopts["processSTE"]
-            cpu_extractor = devopts["cpu"]
 
             exposureAvg = sub.make_final_solution(
                 processAvg,
@@ -727,7 +729,7 @@ def spa_analyze(
                 denovo_refit_option=denovo_refit_option,
                 exome=exome,
                 volume=volume,
-                cpu=cpu_extractor,
+                cpu=cpu,
             )
 
         if make_metadata:

setup.py

@@ -6,7 +6,7 @@
 if os.path.exists("dist"):
     shutil.rmtree("dist")
 
-VERSION = "1.0.0"
+VERSION = "1.0.1"
 
 
 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 = 'v1.0.0:  Parallel version for SigProfilerAssignment'
+Update = 'v1.0.1:  Refine CPU parameter logic to pass directly instead of via devopts'
 
     """
     fh = open(filename, "w")