bluecellulab 2.3.4__tar.gz → 2.3.6__tar.gz

{bluecellulab-2.3.4 → bluecellulab-2.3.6}/PKG-INFO

@@ -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 → bluecellulab-2.3.6}/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-2.3.4 → bluecellulab-2.3.6}/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-2.3.4 → bluecellulab-2.3.6}/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-2.3.6/bluecellulab/utils.py

@@ -0,0 +1,25 @@
+"""Utility functions."""
+import contextlib
+import io
+
+
+def run_once(func):
+    """A decorator to ensure a function is only called once."""
+    def wrapper(*args, **kwargs):
+        if not wrapper.has_run:
+            wrapper.has_run = True
+            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 → bluecellulab-2.3.6}/bluecellulab.egg-info/PKG-INFO

@@ -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 → bluecellulab-2.3.6}/tests/test_importer.py

@@ -1,5 +1,6 @@
 import logging
 import os
+from pathlib import Path
 import pytest
 from types import ModuleType
 from unittest.mock import MagicMock, patch
@@ -51,16 +52,16 @@ def test_import_mod_lib_no_env_with_folder():
 
 
 @patch.object(
-    importer.pkg_resources,
-    "resource_filename",
-    return_value="/fake/path/to/hoc_file.hoc",
+    importer.resources,
+    "files",
+    return_value=Path("/fake/path/"),
 )
-def test_import_neurodamus(mocked_pkg_resources):
+def test_import_neurodamus(mocked_resources):
     mock_neuron = MagicMock()
     importer.import_neurodamus(mock_neuron)
     assert mock_neuron.h.load_file.called
     # Check that it was called with the expected arguments
-    mock_neuron.h.load_file.assert_any_call("/fake/path/to/hoc_file.hoc")
+    mock_neuron.h.load_file.assert_any_call("/fake/path/hoc/Cell.hoc")
 
 
 def test_print_header(caplog):

{bluecellulab-2.3.4 → bluecellulab-2.3.6}/tests/test_tools.py

@@ -7,8 +7,9 @@ import numpy as np
 import pytest
 
 import bluecellulab
+from bluecellulab.cell.ballstick import create_ball_stick
 from bluecellulab.circuit.circuit_access import EmodelProperties
-from bluecellulab.tools import NumpyEncoder, Singleton, template_accepts_cvode
+from bluecellulab.tools import NumpyEncoder, Singleton, template_accepts_cvode, check_empty_topology
 
 script_dir = Path(__file__).parent
 
@@ -229,3 +230,10 @@ class TestOnSonataCircuit:
         )
         assert i_hold == pytest.approx(-0.03160848349)
         assert v_control == pytest.approx(v_hold)
+
+
+def test_check_empty_topology():
+    """Unit test for the check_empty_topology function."""
+    assert check_empty_topology() is True
+    cell = create_ball_stick()
+    assert check_empty_topology() is False

{bluecellulab-2.3.4 → bluecellulab-2.3.6}/tests/test_utils.py

@@ -1,4 +1,4 @@
-from bluecellulab.utils import run_once
+from bluecellulab.utils import CaptureOutput, run_once
 
 
 # Decorated function for testing
@@ -24,3 +24,20 @@ def test_run_once_execution():
     assert counter[0] == 1
 
     assert increment_counter(counter) is None
+
+
+def test_capture_output():
+    with CaptureOutput() as output:
+        print("Hello, World!")
+        print("This is a test.")
+
+    assert len(output) == 2
+    assert "Hello, World!" in output
+    assert "This is a test." in output
+
+
+def test_no_output():
+    with CaptureOutput() as output:
+        pass  # No output
+
+    assert len(output) == 0

bluecellulab-2.3.4/bluecellulab/utils.py

@@ -1,11 +0,0 @@
-"""Utility functions."""
-
-
-def run_once(func):
-    """A decorator to ensure a function is only called once."""
-    def wrapper(*args, **kwargs):
-        if not wrapper.has_run:
-            wrapper.has_run = True
-            return func(*args, **kwargs)
-    wrapper.has_run = False
-    return wrapper