Merge pull request #108 from BlueBrain/bpo-update

Update replace_axon functions to be compatible with latest BPO

.github/workflows/build.yml

@@ -35,8 +35,8 @@ jobs:
 
       - name: Build a source tarball and wheel
         run: |
-            pip install wheel
-            python setup.py sdist bdist_wheel
+            pip install build
+            python -m build
 
       - name: Get and store tag from 'Bump version and push tag' step
         if: ${{ !startsWith(github.ref, 'refs/tags/') }}

.github/workflows/test.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
 
     steps:
     - uses: actions/checkout@v2

.pylintrc

@@ -8,6 +8,8 @@ max-line-length=100
 [DESIGN]
 # Maximum number of arguments for function / method
 max-args=8
+# Maximum number of positional arguments for function / method
+max-positional-arguments=8
 # Argument names that match this expression will be ignored. Default to name
 # with leading underscore
 ignored-argument-names=_.*

README.rst

@@ -260,7 +260,7 @@ Copyright (c) 2020-2024 Blue Brain Project/EPFL
 
 .. |license| image:: https://img.shields.io/badge/License-Apache_2.0-blue.svg
                 :target: https://github.com/BlueBrain/EModelRunner/blob/main/LICENSE.txt
-                :alt: Build Status
+                :alt: License
 
 .. |docs| image:: https://readthedocs.org/projects/emodelrunner/badge/?version=latest
                 :target: https://emodelrunner.readthedocs.io/en/latest/?badge=latest
@@ -284,3 +284,4 @@ Copyright (c) 2020-2024 Blue Brain Project/EPFL
 
 .. |zenodo| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.8116075.svg
                 :target: https://doi.org/10.5281/zenodo.8116075
+                :alt: Zenodo

emodelrunner/GUI_utils/plotshape.py

@@ -160,6 +160,7 @@ def get_morph_lines(
         - list: voltages previously plotted (mV)
         - bool: True to force the draw of figure, False to blit the figure
     """
+    # pylint: disable=too-many-positional-arguments
     # Adapted from the NEURON package (fct _do_plot in __init__):
     # https://www.neuron.yale.edu/neuron/
     # where this part of the code was itself adapted from

emodelrunner/create_cells.py

@@ -58,7 +58,7 @@ def create_cell(
     Returns:
         CellModelCustom: cell model
     """
-    # pylint: disable=too-many-arguments, too-many-locals
+    # pylint: disable=too-many-arguments, too-many-locals, too-many-positional-arguments
     # load mechanisms
     mechs = load_mechanisms(unopt_params_path)
 

emodelrunner/create_hoc_tools.py

@@ -544,7 +544,7 @@ def create_hoc(
     Returns:
         str: hoc script describing the cell model
     """
-    # pylint: disable=too-many-locals
+    # pylint: disable=too-many-locals, too-many-positional-arguments
     with open(template_path, "r", encoding="utf-8") as template_file:
         template = template_file.read()
         template = jinja2.Template(template)

emodelrunner/morphology/builder.py

@@ -56,12 +56,16 @@ def create_morphology(morph_args, package_type):
             morph_args.morph_path,
             do_replace_axon=morph_args.do_replace_axon,
             replace_axon_hoc=replace_axon_hoc,
+            axon_stub_length=60,
+            axon_nseg_frequency=15,
         )
     elif package_type == PackageType.thalamus:
         morph = ThalamusNrnFileMorphology(
             morph_args.morph_path,
             do_replace_axon=morph_args.do_replace_axon,
             replace_axon_hoc=replace_axon_hoc,
+            axon_stub_length=60,
+            axon_nseg_frequency=15,
         )
     else:
         raise ValueError(f"unsupported package type: {package_type}")

emodelrunner/morphology/morphology.py

@@ -38,6 +38,8 @@ class SSCXNrnFileMorphology(ephys.morphologies.NrnFileMorphology):
             'proc replace_axon(){ ... }
             If None,the default replace_axon is used
         do_set_nseg (bool): if True, it will use nseg_frequency
+        axon_stub_length (float): Length of replacement axon
+        axon_nseg_frequency (int): frequency of nseg, for axon
         nseg_frequency (float): frequency of nseg
         morph_modifiers (list): list of functions to modify the icell
             with (sim, icell) as arguments
@@ -46,17 +48,18 @@ class SSCXNrnFileMorphology(ephys.morphologies.NrnFileMorphology):
     """
 
     @staticmethod
-    def replace_axon(sim=None, icell=None):
+    def replace_axon(sim=None, icell=None, axon_stub_length=60, axon_nseg_frequency=15):
         """Replace axon.
 
         Args:
             sim (bluepyopt.ephys.NrnSimulator): neuron simulator
             icell (neuron cell): cell instantiation in simulator
+            axon_stub_length (float): Length of replacement axon
+            axon_nseg_frequency (int): frequency of nseg, for axon
         """
-        L_target = 60  # length of stub axon
-        nseg0 = 5  # number of segments for each of the two axon sections
+        L_target = axon_stub_length  # length of stub axon
 
-        nseg_total = nseg0 * 2
+        nseg_total = 2 + 4 * int(L_target / 2.0 / axon_nseg_frequency)  # -> 10
         chunkSize = L_target / nseg_total
 
         diams = []
@@ -133,6 +136,8 @@ class ThalamusNrnFileMorphology(ephys.morphologies.NrnFileMorphology):
             'proc replace_axon(){ ... }
             If None,the default replace_axon is used
         do_set_nseg (bool): if True, it will use nseg_frequency
+        axon_stub_length (float): Length of replacement axon
+        axon_nseg_frequency (int): frequency of nseg, for axon
         nseg_frequency (float): frequency of nseg
         morph_modifiers (list): list of functions to modify the icell
             with (sim, icell) as arguments
@@ -141,17 +146,19 @@ class ThalamusNrnFileMorphology(ephys.morphologies.NrnFileMorphology):
     """
 
     @staticmethod
-    def replace_axon(sim=None, icell=None):
+    def replace_axon(sim=None, icell=None, axon_stub_length=60, axon_nseg_frequency=15):
         """Replace axon.
 
         Args:
             sim (bluepyopt.ephys.NrnSimulator): neuron simulator
             icell (neuron cell): cell instantiation in simulator
+            axon_stub_length (float): Length of replacement axon
+            axon_nseg_frequency (int): frequency of nseg, for axon
         """
-        L_target = 60  # length of stub axon
-        nseg0 = 5  # number of segments for each of the two axon sections
+        # pylint: disable=too-many-locals
+        L_target = axon_stub_length  # length of stub axon
 
-        nseg_total = nseg0 * 2
+        nseg_total = 2 + 4 * int(L_target / 2.0 / axon_nseg_frequency)  # -> 10
         chunkSize = L_target / nseg_total
 
         diams = []

emodelrunner/protocols/create_protocols.py

@@ -415,7 +415,7 @@ def define_pairsim_protocols(
     Returns:
         synplas_protocols.SweepProtocolPairSim: pair simulation synapse plasticity protocols
     """
-    # pylint: disable=too-many-arguments, too-many-locals
+    # pylint: disable=too-many-arguments, too-many-locals, too-many-positional-arguments
     # locations
     soma_loc = ephys.locations.NrnSeclistCompLocation(
         name="soma", seclist_name="somatic", sec_index=0, comp_x=0.5

emodelrunner/protocols/sscx_protocols.py

@@ -79,7 +79,7 @@ def __init__(
             pre_protocols (bluepyopt.ephys.protocols.Protocol): protocols to run
                 before the 'other protocols'
         """
-        # pylint: disable=too-many-arguments
+        # pylint: disable=too-many-arguments, too-many-positional-arguments
         super().__init__(name=name)
 
         self.rmp_protocol = rmp_protocol
@@ -697,7 +697,7 @@ def search_spike_threshold(
         Returns:
             float: threshold current amplitude (nA)
         """
-        # pylint: disable=undefined-loop-variable, too-many-arguments
+        # pylint: disable=undefined-loop-variable, too-many-arguments, too-many-positional-arguments
         step_currents = np.linspace(lower_bound, upper_bound, num=self.short_steps)
 
         if len(step_currents) == 0:

emodelrunner/protocols/thalamus_protocols.py

@@ -59,7 +59,7 @@ def __init__(
         pre_protocols=None,
     ):
         """Constructor."""
-        # pylint: disable=too-many-arguments
+        # pylint: disable=too-many-arguments, too-many-positional-arguments
         super().__init__(name=name)
 
         self.rmp_protocol = rmp_protocol
@@ -426,7 +426,7 @@ def binsearch_holdi(
         depth=1,
     ):
         """Do binary search to find holding current."""
-        # pylint: disable=too-many-arguments
+        # pylint: disable=too-many-arguments, too-many-positional-arguments
         middle_bound = upper_bound - abs(upper_bound - lower_bound) / 2
 
         if depth > max_depth:
@@ -739,7 +739,7 @@ def binsearch_spike_threshold(
 
         Assumption is that lower_bound has no spike, upper_bound has.
         """
-        # pylint: disable=too-many-arguments
+        # pylint: disable=too-many-arguments, too-many-positional-arguments
         if depth > max_depth or abs(upper_bound - lower_bound) < precision:
             return upper_bound
         middle_bound = upper_bound - abs(upper_bound - lower_bound) / 2

emodelrunner/synapses/glusynapse.py

@@ -65,7 +65,7 @@ def __init__(
             number (int/None): force synapse to fire N times when using NetStim
             noise (int/None): force synapse to have given noise when using NetStim
         """
-        # pylint: disable=too-many-arguments
+        # pylint: disable=too-many-arguments, too-many-positional-arguments
         self.seed = seed
         self.rng_settings_mode = rng_settings_mode
         self.section = section

emodelrunner/synapses/mechanism.py

@@ -73,7 +73,7 @@ def __init__(
             syn_setup_params (dict): contains extra parameters to setup synapses
                 when using GluSynapseCustom
         """
-        # pylint: disable=too-many-arguments
+        # pylint: disable=too-many-arguments, too-many-positional-arguments
         super().__init__(name, comment)
         self.synapses_data = synapses_data
         self.synconf_dict = synconf_dict

emodelrunner/synapses/minis.py

@@ -34,7 +34,7 @@ def __init__(
         spont_minis_rate=None,
     ):
         """Constructor."""
-        # pylint: disable=too-many-arguments
+        # pylint: disable=too-many-arguments, too-many-positional-arguments
         super().__init__()
         self.gid = gid
         if stop is None:

emodelrunner/synapses/synapse.py

@@ -128,7 +128,7 @@ def __init__(
             number (int/None): force synapse to fire N times when using NetStim
             noise (int/None): force synapse to have given noise when using NetStim
         """
-        # pylint: disable=too-many-arguments
+        # pylint: disable=too-many-arguments, too-many-positional-arguments
         self.seed = seed
         self.rng_settings_mode = rng_settings_mode
         self.section = section

pyproject.toml

@@ -0,0 +1,58 @@
+[build-system]
+requires = ["setuptools >= 64", "setuptools_scm"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "EModelRunner"
+authors = [
+    {name = "Blue Brain Project, EPFL"},
+]
+description="Runs cells from Blue Brain Project cell packages, such as sscx, synapse plasticity, etc."
+readme = "README.rst"
+license = {file = "LICENSE.txt"}
+requires-python = ">= 3.8"
+dynamic = ["version"]
+dependencies = [
+    "numpy",
+    "efel>=4.2,<6",
+    "bluepyopt>=1.14.15",
+    "neurom>=3.1.0",
+    "h5py",
+    "matplotlib",
+    "schema",
+    "Pebble>=4.3.10",
+    "tqdm>=4.65.0",
+]
+classifiers=[
+    "Development Status :: 5 - Stable",
+    "Intended Audience :: Education",
+    "Intended Audience :: Science/Research",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+
+[project.optional-dependencies]
+docs = ["sphinx", "sphinx-bluebrain-theme"]
+
+[project.urls]
+Homepage = "https://github.com/BlueBrain/EModelRunner"
+Source = "https://github.com/BlueBrain/EModelRunner"
+Repository = "https://github.com/BlueBrain/EModelRunner.git"
+Tracker = "https://github.com/BlueBrain/EModelRunner/issues"
+Documentation = "https://emodelrunner.readthedocs.io/en/latest"
+
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools.packages.find]
+exclude = ["tests",]
+
+[tool.setuptools_scm]
+version_scheme = "python-simplified-semver"
+local_scheme = "no-local-version"