{lib}[foss/2023a] MorphoSONIC v1.0-20240110, PySONIC v1.0-20250519

easybuild/easyconfigs/m/MorphoSONIC/MorphoSONIC-1.0-20240110-foss-2023a.eb

@@ -0,0 +1,61 @@
+easyblock = 'PythonBundle'
+
+name = 'MorphoSONIC'
+version = '1.0-20240110'
+local_commit = '64a0a23'
+
+homepage = 'https://github.com/tjjlemaire/MorphoSONIC'
+description = """
+MorphoSONIC is a Python+NEURON implementation of spatially extended representations of the multi-Scale Optimized
+Neuronal Intramembrane Cavitation (SONIC) model. It enables the simulation of the distributed electrical
+response of morphologically realistic neuron representations to acoustic stimuli, as predicted by the intramembrane
+cavitation hypothesis. The details of the MorphoSONIC framework and of its application to study ultrasound
+neuromodulation in peripheral nerve fibers are described in.
+"""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('NEURON', '8.2.6'),
+    ('Seaborn', '0.13.2'),
+    ('PySONIC', '1.0-20250519'),
+]
+
+exts_list = [
+    ('MarkdownPP', '1.5.1', {
+        'modulename': '%(name)s',
+        'checksums': ['a70babf819a6cf7f1035400ffa5763799fa67f2efcb5e701a59fc5ff79dd9696'],
+    }),
+    ('watchdog', '6.0.0', {
+        'checksums': ['9ddf7c82fda3ae8e24decda1338ede66e1c99883db93711d8fb941eaa2d8c282'],
+    }),
+    (name, version, {
+        'patches': ['%(name)s-%(version)s_fix-setup.py.patch'],
+        'source_urls': ['https://github.com/tjjlemaire/MorphoSONIC/archive/'],
+        'sources': [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}],
+        'preinstallopts': "sed -i '/neuron/d' requirements.txt && ",
+        'modulename': name,
+        'checksums': [
+            {'MorphoSONIC-1.0-20240110.tar.gz': 'd264f0af5471bfccac09b7eb1ffa340bcb70192e2c73ff37ae58bfee2c9ddfef'},
+            {'MorphoSONIC-1.0-20240110_fix-setup.py.patch':
+             '240c74a5ca911b9dcdf8a321ddc914c5295510c8a55c8fe19f460e7417a5449d'},
+        ],
+    }),
+]
+
+# generate libs from mod files by neuron's nrnivmodl
+postinstallcmds = [f'cd %(installdir)s/lib/python%(pyshortver)s/site-packages/{name}/nmodl  && nrnivmodl']
+
+sanity_check_commands = [
+    "python -c 'from MorphoSONIC.core import ExtracellularCurrent'",
+    "python -c 'from MorphoSONIC.parsers import IextraFiberParser'",
+    "python -c 'from MorphoSONIC.models import Node'",
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': [f'lib/python%(pyshortver)s/site-packages/{name}/nmodl'],
+}
+
+moduleclass = 'lib'

easybuild/easyconfigs/m/MorphoSONIC/MorphoSONIC-1.0-20240110_fix-setup.py.patch

@@ -0,0 +1,30 @@
+There are 2 fixes in setup.py:
+1. use setuptools find_packages()
+2. copy either /nmodl dir to installdirs
+Author: Pavel Tomanek (Inuits)
+--- setup.py.orig	2025-06-12 16:51:55.114977170 +0200
++++ setup.py	2025-06-12 16:24:32.966212906 +0200
+@@ -6,7 +6,7 @@
+ # @Last Modified time: 2023-03-16 13:22:53
+
+ import os
+-from setuptools import setup
++from setuptools import setup, find_packages
+
+ readme_file = 'README.md'
+ requirements_file = 'requirements.txt'
+@@ -61,8 +61,12 @@
+     author='Théo Lemaire',
+     author_email='[email protected]',
+     license='MIT',
+-    packages=['MorphoSONIC'],
++    packages=find_packages(),
+     scripts=getFiles('scripts') + getFiles('tests') + getFiles('examples'),
+     install_requires=get_requirements(),
+-    zip_safe=False
++    zip_safe=False,
++    include_package_data=True,
++    package_data={
++        'MorphoSONIC': ['nmodl/*', 'nmodl/x86_64/.libs/*'],
++    },
+ )

easybuild/easyconfigs/p/PySONIC/PySONIC-1.0-20250519-foss-2023a.eb

@@ -0,0 +1,64 @@
+easyblock = 'PythonBundle'
+
+name = 'PySONIC'
+version = '1.0-20250519'
+local_commit = '10ed530'
+
+homepage = 'https://github.com/tjjlemaire/PySONIC'
+description = """
+Python implementation of the NICE & SONIC models, allowing for rapid
+simulations of ultrasound-evoked membrane dynamics in various point-neuron models.
+"""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('matplotlib', '3.7.2'),
+    ('tqdm', '4.66.1'),
+    ('multiprocess', '0.70.15'),
+    ('openpyxl', '3.1.2'),
+    ('JupyterLab', '4.0.5'),
+]
+
+exts_list = [
+    ('boltons', '23.0.0', {
+        'checksums': ['8c50a71829525835ca3c849c7ed2511610c972b4dddfcd41a4a5447222beb4b0'],
+    }),
+    ('colorlog', '6.9.0', {
+        'checksums': ['bfba54a1b93b94f54e1f4fe48395725a3d92fd2a4af702f6bd70946bdc0c6ac2'],
+    }),
+    (name, version, {
+        'patches': ['%(name)s-%(version)s_fix-setup.py.patch'],
+        'modulename': name,
+        # you need to have git-lfs installed or git-lfs module loaded to get full version of sources -
+        #  there are only templates in /lookups dir, if the sources are downloaded from GitHub
+        'sources': [{
+            'filename': f'%(name)s-%(version)s-{local_commit}.tar.xz',
+            'git_config': {
+                'url': 'https://github.com/tjjlemaire',
+                'repo_name': name,
+                'commit': local_commit,
+            },
+        }],
+        'checksums': [
+            {'PySONIC-1.0-20250519-10ed530.tar.xz':
+             '025d900480dd59bb7bc509e9fdfeb8a72ce4cec560713aff536d03e908b1d84c'},
+            {'PySONIC-1.0-20250519_fix-setup.py.patch':
+             '317e7e3c30df726d8aea206d1b373c1d9c9499c2877d86609dfb466844d3be6d'},
+        ],
+    }),
+]
+
+sanity_check_commands = [
+    "python -c 'from PySONIC.core import NeuronalBilayerSonophore, AcousticDrive'",
+    "python -c 'from PySONIC.neurons import getPointNeuron'",
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': [f'lib/python%(pyshortver)s/site-packages/{name}/lookups'],
+}
+
+moduleclass = 'lib'

easybuild/easyconfigs/p/PySONIC/PySONIC-1.0-20250519_fix-setup.py.patch

@@ -0,0 +1,26 @@
+Fix setup.py to add either lookups dir to installdir
+Author: Pavel Tomanek (Inuits)
+--- setup.py.orig	2025-06-18 16:34:19.958477374 +0200
++++ setup.py	2025-06-18 16:36:22.079482402 +0200
+@@ -6,7 +6,7 @@
+ # @Last Modified time: 2023-05-18 09:06:45
+
+ import os
+-from setuptools import setup
++from setuptools import setup, find_packages
+
+ readme_file = 'README.md'
+ requirements_file = 'requirements.txt'
+@@ -56,7 +56,11 @@
+     author='Theo Lemaire',
+     author_email='[email protected]',
+     license='MIT',
+-    packages=['PySONIC'],
++    packages=find_packages(),
++    include_package_data=True,
++    package_data={
++        'PySONIC': ['lookups/*'],
++    },
+     scripts=getFiles('scripts') + getFiles('tests'),
+     install_requires=get_requirements(),
+     zip_safe=False