bluecellulab 2.3.4__py3-none-any.whl → 2.3.6__py3-none-any.whl

bluecellulab/cell/ballstick/__init__.py

@@ -1,11 +1,11 @@
 """A simple ball and stick model."""
 
-import pkg_resources
+import importlib_resources as resources
 from bluecellulab.cell import Cell
 
 
 def create_ball_stick() -> Cell:
     """Creates a ball and stick model by using package's hoc and asc."""
-    hoc = pkg_resources.resource_filename("bluecellulab", "cell/ballstick/emodel.hoc")
-    morphology = pkg_resources.resource_filename("bluecellulab", "cell/ballstick/morphology.asc")
+    hoc = resources.files("bluecellulab") / "cell/ballstick/emodel.hoc"
+    morphology = resources.files("bluecellulab") / "cell/ballstick/morphology.asc"
     return Cell(template_path=hoc, morphology_path=morphology)

bluecellulab/importer.py

@@ -13,15 +13,15 @@
 # limitations under the License.
 """Main importer of bluecellulab."""
 
+import importlib_resources as resources
 import logging
 import os
 from types import ModuleType
-import pkg_resources
 
 import neuron
 
 from bluecellulab.exceptions import BluecellulabError
-from bluecellulab.utils import run_once
+from bluecellulab.utils import CaptureOutput, run_once
 
 
 logger = logging.getLogger(__name__)
@@ -62,8 +62,10 @@ def import_neurodamus(neuron: ModuleType) -> None:
     ]
 
     for hoc_file in hoc_files:
-        hoc_file_path = pkg_resources.resource_filename("bluecellulab", f"hoc/{hoc_file}")
-        neuron.h.load_file(hoc_file_path)
+        hoc_file_path = str(resources.files("bluecellulab") / f"hoc/{hoc_file}")
+        with CaptureOutput() as stdoud:
+            neuron.h.load_file(hoc_file_path)
+            logger.debug(f"Loaded {hoc_file}. stdout from the hoc: {stdoud}")
 
 
 def print_header(neuron: ModuleType, mod_lib_path: str) -> None:

bluecellulab/tools.py

@@ -15,14 +15,12 @@
 
 
 from __future__ import annotations
-import io
 import json
 import math
 import multiprocessing
 import multiprocessing.pool
 import os
 from pathlib import Path
-import sys
 from typing import Any, Optional, Tuple
 import logging
 
@@ -32,6 +30,7 @@ import numpy as np
 import bluecellulab
 from bluecellulab.circuit.circuit_access import EmodelProperties
 from bluecellulab.exceptions import UnsteadyCellError
+from bluecellulab.utils import CaptureOutput
 
 logger = logging.getLogger(__name__)
 
@@ -652,21 +651,9 @@ class NumpyEncoder(json.JSONEncoder):
         return json.JSONEncoder.default(self, obj)
 
 
-class get_stdout(list):
-    def __enter__(self):
-        self.orig_stdout = sys.stdout
-        sys.stdout = self.stringio = io.StringIO()
-        return self
-
-    def __exit__(self, *args):
-        self.extend(self.stringio.getvalue().splitlines())
-        del self.stringio
-        sys.stdout = self.orig_stdout
-
-
 def check_empty_topology() -> bool:
     """Return true if NEURON simulator topology command is empty."""
-    with get_stdout() as stdout:
+    with CaptureOutput() as stdout:
         neuron.h.topology()
 
     return stdout == ['', '']

bluecellulab/utils.py

@@ -1,4 +1,6 @@
 """Utility functions."""
+import contextlib
+import io
 
 
 def run_once(func):
@@ -9,3 +11,15 @@ def run_once(func):
             return func(*args, **kwargs)
     wrapper.has_run = False
     return wrapper
+
+
+class CaptureOutput(list):
+    def __enter__(self):
+        self._stringio = io.StringIO()
+        self._redirect_stdout = contextlib.redirect_stdout(self._stringio)
+        self._redirect_stdout.__enter__()
+        return self
+
+    def __exit__(self, exc_type, exc_val, exc_tb):
+        self._redirect_stdout.__exit__(exc_type, exc_val, exc_tb)
+        self.extend(self._stringio.getvalue().splitlines())

{bluecellulab-2.3.4.dist-info → bluecellulab-2.3.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bluecellulab
-Version: 2.3.4
+Version: 2.3.6
 Summary: The Pythonic Blue Brain simulator access
 Home-page: https://github.com/BlueBrain/BlueCelluLab
 Author: Blue Brain Project, EPFL

{bluecellulab-2.3.4.dist-info → bluecellulab-2.3.6.dist-info}/RECORD

@@ -3,16 +3,16 @@ bluecellulab/connection.py,sha256=volV2YKtmqAF7MOEJar5ldF1ARAo7k2vF9MB1NXybUY,46
 bluecellulab/dendrogram.py,sha256=w0vvv0Q169DolTX1j9dAZIvHIl4H258gAjQ1xQaNiGk,6427
 bluecellulab/exceptions.py,sha256=KIxF7s_7gPVJ07TiQ-Z1D8de7ylV74gNMhzl0339CVM,2379
 bluecellulab/graph.py,sha256=ODiQy4xjRVxtNITXeXpYnqHas0wR7gZ_aXuDAF7jMq4,3419
-bluecellulab/importer.py,sha256=Sf8_aWqBCp98WfNkLMhNSp4UdurEneFF5leNYRlXjAw,2852
+bluecellulab/importer.py,sha256=l5nvD0y41-AheqoDNBGAX5qFTCG6_UFlLmqyFbUo77E,2998
 bluecellulab/neuron_interpreter.py,sha256=hXig_u3T6JmEHbkV8ZblEZtX0kY80ate4VpRtANNFrM,2185
 bluecellulab/plotwindow.py,sha256=UVHzml-BB83m5Qr-YGkjR9kB-vSW8mM0Owh2j95yIaU,2721
 bluecellulab/psection.py,sha256=EgAS8IS9DcYv2xOkNISgfg_CfRc0nDfRFjvgQhyi9eY,6328
 bluecellulab/psegment.py,sha256=rBryDYHC_uDK9itfXXrFZ0DL9F6WgRICL0j5EHN56QM,3125
 bluecellulab/rngsettings.py,sha256=SLvkgM8K26Z-zTTN__CnFl_KjIJNuF4n_jzviyei5P4,3986
 bluecellulab/ssim.py,sha256=_MyUObeKIHhuT4cbB1uSD7izpZZHNRACiPlO9R1TNa8,33552
-bluecellulab/tools.py,sha256=s4NTE0DzK8z8oAy1BF1C2f19nBx-qBPuArz7e7hUTnw,24231
+bluecellulab/tools.py,sha256=z8jU4XO5tWMHwxr2IRo5BG0wnGCfCZPsEKz9L6gkwfc,23943
 bluecellulab/type_aliases.py,sha256=EMrunY-pIgZrsmetpAM8lA7tr0TFEzFoU5SX9sBuiOk,312
-bluecellulab/utils.py,sha256=GKZkRYI2LY08tsIkG95MGn7EfmV4pBrIAqfRQCW14fs,300
+bluecellulab/utils.py,sha256=xF-qXb1uCH6_EmchSH6aQxhFI4P8SD08z-t_AZz3lF0,736
 bluecellulab/cell/__init__.py,sha256=Sbc0QOsJ8E7tSwf3q7fsXuE_SevBN6ZmoCVyyU5zfII,208
 bluecellulab/cell/cell_dict.py,sha256=PVmZsjhZ9jp3HC-8QmdFqp-crAcVMSVeLWujcOPLlpo,1346
 bluecellulab/cell/core.py,sha256=UtPjq_SYX8wOehQe7GqkbPxDWG1vIIJQ5-e3T_g29YU,31480
@@ -24,7 +24,7 @@ bluecellulab/cell/serialized_sections.py,sha256=UQUecO07ChRZ7xHuDp-QAQRUpUiIwROz
 bluecellulab/cell/sonata_proxy.py,sha256=dLT9mLlGVpXxj2O2lXN0g7Sq4BwroPLVdPikR2yNMv4,1529
 bluecellulab/cell/stimuli_generator.py,sha256=cJwjNwsQeEBHLjuJIFv6VBSqd9IpmbR7CuSMyotCiWc,6320
 bluecellulab/cell/template.py,sha256=EGZDS7Lb7kScwh0LqKl7BcvA6r5UdNx1_HiYo7ALbPs,8015
-bluecellulab/cell/ballstick/__init__.py,sha256=vywMSPAeTuCcK_E9gD8UX2XD1KfKbfCVFOFnFSgznzg,450
+bluecellulab/cell/ballstick/__init__.py,sha256=v1Z8tHFfbpWShxOBdShCUaE0utoz-7rZumuNBQtNOFI,439
 bluecellulab/cell/ballstick/emodel.hoc,sha256=7WcuepK-wB9bASRvNdCwO9Woc9-SpBCFqBqCXKgjsV8,1517
 bluecellulab/cell/ballstick/morphology.asc,sha256=EO0VIRilJAwpiDP2hIevwusfvYptNYhvsu1f5GgbSQo,190
 bluecellulab/circuit/__init__.py,sha256=Khpa13nzNvDlDS2JduyoFTukEduEkWCc5ML_JwGpmZs,361
@@ -57,9 +57,9 @@ bluecellulab/stimulus/factory.py,sha256=AOby3Sp2g8BJsRccz3afazfCyysyWIgLtcliWlye
 bluecellulab/synapse/__init__.py,sha256=RW8XoAMXOvK7OG1nHl_q8jSEKLj9ZN4oWf2nY9HAwuk,192
 bluecellulab/synapse/synapse_factory.py,sha256=ZBRpjvIRyHc4hBfBvtLukLf7E2PjHhzwqGt9O4MBOTk,6862
 bluecellulab/synapse/synapse_types.py,sha256=wWVBfvPYF6g3dSoaXsjJ6QI929yWYrTh_OmauS5Y-Uk,17027
-bluecellulab-2.3.4.dist-info/AUTHORS.txt,sha256=EDs3H-2HXBojbma10psixk3C2rFiOCTIREi2ZAbXYNQ,179
-bluecellulab-2.3.4.dist-info/LICENSE,sha256=xOouu1gC1GGklDxkITlaVl60I9Ab860O-nZsFbWydvU,11749
-bluecellulab-2.3.4.dist-info/METADATA,sha256=yHhr0rLAtPPkvKwp24sE3r0SjokOe5A9re-yT5aY7BA,6907
-bluecellulab-2.3.4.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
-bluecellulab-2.3.4.dist-info/top_level.txt,sha256=VSyEP8w9l3pXdRkyP_goeMwiNA8KWwitfAqUkveJkdQ,13
-bluecellulab-2.3.4.dist-info/RECORD,,
+bluecellulab-2.3.6.dist-info/AUTHORS.txt,sha256=EDs3H-2HXBojbma10psixk3C2rFiOCTIREi2ZAbXYNQ,179
+bluecellulab-2.3.6.dist-info/LICENSE,sha256=xOouu1gC1GGklDxkITlaVl60I9Ab860O-nZsFbWydvU,11749
+bluecellulab-2.3.6.dist-info/METADATA,sha256=sceGz_1cnk0708w26E4YdIx8t1APJltWN45xjmBakD8,6907
+bluecellulab-2.3.6.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
+bluecellulab-2.3.6.dist-info/top_level.txt,sha256=VSyEP8w9l3pXdRkyP_goeMwiNA8KWwitfAqUkveJkdQ,13
+bluecellulab-2.3.6.dist-info/RECORD,,