Add py netpyne, meautility, and lfpykit (#35262)

* py-netpyne: new package with dependencies

* py-netpyne, py-meautility, py-lfpykit: license update

* py-netpyne: review remarks

* py-netpyne: style

* py-netpyne: don't limit python version

3 files changed, 73 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/py-lfpykit/package.py b/var/spack/repos/builtin/packages/py-lfpykit/package.py
new file mode 100644
index 0000000000..f7397903c8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-lfpykit/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class PyLfpykit(PythonPackage):
+    """This Python module contain freestanding implementations of electrostatic forward models
+    incorporated in LFPy"""
+
+    homepage = "https://github.com/LFPy/LFPykit"
+    pypi = "lfpykit/LFPykit-0.5.tar.gz"
+
+    version("0.5", sha256="9a7ae80ad905bb8dd0eeab8517b43c3d5b4fff2b8766c9d5a36320a7a67bd545")
+
+    depends_on("py-setuptools", type="build")
+    depends_on("py-numpy@1.15.2:", type=("build", "run"))
+    depends_on("py-scipy", type=("build", "run"))
+    depends_on("py-meautility", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/py-meautility/package.py b/var/spack/repos/builtin/packages/py-meautility/package.py
new file mode 100644
index 0000000000..effc526f9d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-meautility/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class PyMeautility(PythonPackage):
+    """Python package for multi-electrode array (MEA) handling and stimulation."""
+
+    homepage = "https://github.com/alejoe91/MEAutility"
+    pypi = "meautility/MEAutility-1.5.1.tar.gz"
+
+    version("1.5.1", sha256="de12cc9c1772d3321e941af78e6bfb36cdcb5702a7b1272a852cc95f413bbfcb")
+
+    depends_on("py-setuptools", type="build")
+
+    depends_on("py-numpy", type=("build", "run"))
+    depends_on("py-pyyaml", type=("build", "run"))
+    depends_on("py-matplotlib", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/py-netpyne/package.py b/var/spack/repos/builtin/packages/py-netpyne/package.py
new file mode 100644
index 0000000000..3604320e7f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-netpyne/package.py
@@ -0,0 +1,31 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class PyNetpyne(PythonPackage):
+    """Netpyne: A python package to facilitate the development,
+    parallel simulation, optimization and analysis of multiscale
+    biological neuronal networks in NEURON."""
+
+    homepage = "http://www.netpyne.org/"
+    url = "https://github.com/suny-downstate-medical-center/netpyne/archive/refs/tags/v1.0.3.1.tar.gz"
+    git = "https://github.com/suny-downstate-medical-center/netpyne.git"
+
+    version("master", branch="master")
+    version("1.0.3.1", sha256="4f8492d58ff1dd7ec5ba6ed1f58f94548b8c1e4e9fd50b8a6d2e9f8eb400736d")
+
+    depends_on("py-setuptools", type="build")
+
+    depends_on("py-numpy", type=("build", "run"))
+    depends_on("py-scipy", type=("build", "run"))
+    depends_on("py-matplotlib@:3.5.1", type=("build", "run"))
+    depends_on("py-matplotlib-scalebar", type=("build", "run"))
+    depends_on("py-future", type=("build", "run"))
+    depends_on("py-pandas", type=("build", "run"))
+    depends_on("py-bokeh", type=("build", "run"))
+    depends_on("py-schema", type=("build", "run"))
+    depends_on("py-lfpykit", type=("build", "run"))