dcnum 0.16.7__tar.gz → 0.16.8__tar.gz

{dcnum-0.16.7 → dcnum-0.16.8}/CHANGELOG

@@ -1,3 +1,7 @@
+0.16.8
+ - fix: correctly set number of workers for CPUSegmenter
+ - enh: update list of environment variables that should be set to
+   disable multithreading in subprocesses
 0.16.7
  - fix: if the writer dequeue fills up, stall the feature extractor
  - enh: optimize DequeWriterThread loop

{dcnum-0.16.7 → dcnum-0.16.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dcnum
-Version: 0.16.7
+Version: 0.16.8
 Summary: numerics toolbox for imaging deformability cytometry
 Author: Maximilian Schlögel, Paul Müller
 Maintainer-email: Paul Müller <dev@craban.de>

{dcnum-0.16.7 → dcnum-0.16.8}/src/dcnum/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.16.7'
-__version_tuple__ = version_tuple = (0, 16, 7)
+__version__ = version = '0.16.8'
+__version_tuple__ = version_tuple = (0, 16, 8)

{dcnum-0.16.7 → dcnum-0.16.8}/src/dcnum/feat/event_extractor_manager_thread.py

@@ -99,7 +99,7 @@ class EventExtractorManagerThread(threading.Thread):
             if ldq > 100:
                 stallsec = ldq / 100
                 self.logger.warning(
-                    f"Stalling {stallsec:.1f}s for slow writer.")
+                    f"Stalling {stallsec:.1f}s for slow writer")
                 time.sleep(stallsec)
 
             cur_slot = 0

{dcnum-0.16.7 → dcnum-0.16.8}/src/dcnum/logic/ctrl.py

@@ -124,21 +124,23 @@ class DCNumJobRunner(threading.Thread):
         self.logger = logging.getLogger(f"dcnum.Runner-{self.pphash[:2]}")
 
         # Sanity checks
-        for os_env in [
-            "OMP_NUM_THREADS",
-            "MKL_NUM_THREADS",
-            "NUMEXPR_NUM_THREADS",
-                "NUMBA_NUM_THREADS"]:
+        for os_env in ["MKL_NUM_THREADS", "NUMBA_NUM_THREADS",
+                       "NUMEXPR_NUM_THREADS", "NUMPY_NUM_THREADS",
+                       "OPENBLAS_NUM_THREADS", "OMP_NUM_THREADS",
+                       "VECLIB_MAXIMUM_THREADS"]:
             # You should disable multithreading for all major tools that
             # use dcnum.logic. We don't want multithreading, because dcnum
             # uses linear code and relies on multiprocessing for
             # parallelization. This has to be done before importing numpy
             # or any other library affected. In your scripts, you can use:
             #
-            #    os.environ.setdefault("OMP_NUM_THREADS", "1")
             #    os.environ.setdefault("MKL_NUM_THREADS", "1")
-            #    os.environ.setdefault("NUMEXPR_NUM_THREADS", "1")
             #    os.environ.setdefault("NUMBA_NUM_THREADS", "1")
+            #    os.environ.setdefault("NUMEXPR_NUM_THREADS", "1")
+            #    os.environ.setdefault("NUMPY_NUM_THREADS", "1")
+            #    os.environ.setdefault("OPENBLAS_NUM_THREADS", "1")
+            #    os.environ.setdefault("OMP_NUM_THREADS", "1")
+            #    os.environ.setdefault("VECLIB_MAXIMUM_THREADS", "1")
             #
             val_act = os.environ.get(os_env)
             if val_act != "1":
@@ -515,7 +517,7 @@ class DCNumJobRunner(threading.Thread):
             num_segmenters = 1
         num_extractors = max(1, num_extractors)
         num_segmenters = max(1, num_segmenters)
-        self.job["segmenter_kwargs"]["num_workers"] = num_segmenters
+        self.job.kwargs["segmenter_kwargs"]["num_workers"] = num_segmenters
 
         slot_chunks = mp_spawn.Array("i", num_slots)
         slot_states = mp_spawn.Array("u", num_slots)

{dcnum-0.16.7 → dcnum-0.16.8}/src/dcnum.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dcnum
-Version: 0.16.7
+Version: 0.16.8
 Summary: numerics toolbox for imaging deformability cytometry
 Author: Maximilian Schlögel, Paul Müller
 Maintainer-email: Paul Müller <dev@craban.de>