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| author | Erik Heeren <erik.heeren@epfl.ch> | 2022-12-14 19:00:26 +0100 |
|---|---|---|
| committer | GitHub <noreply@github.com> | 2022-12-14 12:00:26 -0600 |
| commit | 80e30222e1bc166ff40e50d50570c2a86b9918f8 (patch) | |
| tree | c58f6d919cc2a5d8fcec2334e2e88a8ee5a6b45e | |
| parent | 55356e9edb374bc2e547ed1706dace6c34042dd9 (diff) | |
| download | spack-80e30222e1bc166ff40e50d50570c2a86b9918f8.tar.gz spack-80e30222e1bc166ff40e50d50570c2a86b9918f8.tar.bz2 spack-80e30222e1bc166ff40e50d50570c2a86b9918f8.tar.xz spack-80e30222e1bc166ff40e50d50570c2a86b9918f8.zip | |
New neuroscience packages: py-bmtk, py-neurotools (#34464)
* Add py-bmtk and py-neurotools
* py-bmtk: version bump
* [@spackbot] updating style on behalf of heerener
* Maybe the copyright needs to be extended to 2022 for the check to pass
* Process review remarks
* Update var/spack/repos/builtin/packages/py-neurotools/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
3 files changed, 75 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/py-bmtk/package.py b/var/spack/repos/builtin/packages/py-bmtk/package.py new file mode 100644 index 0000000000..f3dc57b644 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-bmtk/package.py @@ -0,0 +1,28 @@ +# Copyright 2013-2022 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 PyBmtk(PythonPackage): + """The Brain Modeling Toolkit""" + + homepage = "https://github.com/AllenInstitute/bmtk" + pypi = "bmtk/bmtk-1.0.5.tar.gz" + + version("1.0.7", sha256="11e85098cf3c940a3d64718645f4a24ee13c8a47438ef5d28e054cb27ee01702") + version("1.0.5", sha256="e0cb47b334467a6d124cfb99bbc67cc88f39f0291f4c39929f50d153130642a4") + + depends_on("py-setuptools", type="build") + + depends_on("py-jsonschema", type=("build", "run")) + depends_on("py-pandas", type=("build", "run")) + depends_on("py-numpy", type=("build", "run")) + depends_on("py-six", type=("build", "run")) + depends_on("py-h5py", type=("build", "run")) + depends_on("py-matplotlib", type=("build", "run")) + depends_on("py-scipy", type=("build", "run")) + depends_on("py-scikit-image", type=("build", "run")) + depends_on("py-sympy", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/py-neurotools/neurotools-0.3.1.patch b/var/spack/repos/builtin/packages/py-neurotools/neurotools-0.3.1.patch new file mode 100644 index 0000000000..2f9d73ff19 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-neurotools/neurotools-0.3.1.patch @@ -0,0 +1,22 @@ +diff --git a/src/stgen.py b/src/stgen.py +index b818ea5..3cb45e6 100644 +--- a/src/stgen.py ++++ b/src/stgen.py +@@ -227,7 +227,7 @@ class StGen: + number = min(5+numpy.ceil(2*n),100) + + if number > 0: +- isi = self.rng.exponential(1.0/rate, number)*1000.0 ++ isi = self.rng.exponential(1.0/rate, int(number)) * 1000.0 + if number > 1: + spikes = numpy.add.accumulate(isi) + else: +@@ -301,7 +301,7 @@ class StGen: + number = min(5+numpy.ceil(2*n),100) + + if number > 0: +- isi = self.rng.gamma(a, b, number)*1000.0 ++ isi = self.rng.gamma(a, b, int(number))*1000.0 + if number > 1: + spikes = numpy.add.accumulate(isi) + else: diff --git a/var/spack/repos/builtin/packages/py-neurotools/package.py b/var/spack/repos/builtin/packages/py-neurotools/package.py new file mode 100644 index 0000000000..dc37019d6e --- /dev/null +++ b/var/spack/repos/builtin/packages/py-neurotools/package.py @@ -0,0 +1,25 @@ +# Copyright 2013-2022 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 PyNeurotools(PythonPackage): + """A collection of tools for representing and anlyzing neuroscientific + data.""" + + homepage = "http://neuralensemble.org/NeuroTools" + pypi = "neurotools/NeuroTools-0.3.1.tar.gz" + + version("0.3.1", sha256="a459420fc0e9ff6b59af28716ddb0c75d11a63b8db80a5f4844e0d7a90c2c653") + + depends_on("py-setuptools", type="build") + depends_on("py-scipy", type=("build", "run")) + depends_on("py-numpy", type=("build", "run")) + depends_on("py-matplotlib", type=("build", "run")) + depends_on("py-tables", type=("build", "run")) + depends_on("py-pyaml", type=("build", "run")) + + patch("neurotools-0.3.1.patch", when="@0.3.1") |