dev-python/spikeextractors: new package (DANDI ephys stack)

Package-Manager: Portage-3.0.28, Repoman-3.0.3
Signed-off-by: Horea Christian <chr@chymera.eu>

dev-python/spikeextractors/ChangeLog

@@ -0,0 +1,6 @@
+*spikeextractors-0.9.7 (14 Oct 2021)
+
+  14 Oct 2021;  <chymera@gentoo.org> +.spikeinterface-0.10.0.ebuild.swp,
+  +files/spikeextractors-0.9.7-no-test-install.patch, +metadata.xml,
+  +spikeextractors-0.9.7.ebuild:
+  dev-python/spikeextractors: new package (DANDI ephys stack)

dev-python/spikeextractors/Manifest

@@ -0,0 +1 @@
+DIST spikeextractors-0.9.7.tar.gz 132128 SHA256 5f5d0edb842773648b64258c193a52e56de574e3f451e5a247810db0f8143cc8 SHA512 b4b3ba2d20779d453e85a0fc4964f1ecbe414d629d42202e57ec1191a839e87a22fb3b17702feffd5837554d400883061bb299bbc957bd5752227aac9847a4d7 WHIRLPOOL 0057949ad0a5cd84c5317d2d1bfec22748e05eea387747a9472e81d837a7e23fff759b924ed5469c588556702461d897a8f298d3e581130c075f274ca28b3530

dev-python/spikeextractors/files/spikeextractors-0.9.7-no-test-install.patch

@@ -0,0 +1,11 @@
+--- a/setup.py	2021-10-13 15:04:56.840925521 -0400
++++ b/setup.py	2021-10-14 16:15:24.934360987 -0400
+@@ -21,7 +21,7 @@
+     url="https://github.com/SpikeInterface/spikeextractors",
+     long_description=long_description,
+     long_description_content_type="text/markdown",
+-    packages=setuptools.find_packages(),
++    packages=setuptools.find_packages(exclude=["tests"]),
+     package_data={},
+     include_package_data=True,
+     install_requires=[

dev-python/spikeextractors/metadata.xml

@@ -0,0 +1,15 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">SpikeInterface/spikeextractors</remote-id>
+	</upstream>
+</pkgmetadata>

dev-python/spikeextractors/spikeextractors-0.9.7.ebuild

@@ -0,0 +1,61 @@
+# Copyright 2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..9} )
+# dev-python/hdf5storage is holding 3.10 back
+inherit distutils-r1
+
+DESCRIPTION="Extract, convert, and interface with extracellular data, now in spikeinterfaces"
+HOMEPAGE="https://github.com/SpikeInterface/spikeextractors"
+SRC_URI="https://github.com/SpikeInterface/spikeextractors/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+# dev-python/hdf5storage, datalad, and neo hold back ~x86
+IUSE="test"
+RESTRICT="!test? ( test )"
+
+DEPEND=""
+RDEPEND="
+	dev-python/h5py[${PYTHON_USEDEP}]
+	dev-python/hdf5storage[${PYTHON_USEDEP}]
+	dev-python/joblib[${PYTHON_USEDEP}]
+	dev-python/loky[${PYTHON_USEDEP}]
+	dev-python/lxml[${PYTHON_USEDEP}]
+	dev-python/matplotlib[${PYTHON_USEDEP}]
+	dev-python/neo[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/pandas[${PYTHON_USEDEP}]
+	dev-python/pynwb[${PYTHON_USEDEP}]
+	dev-python/pyyaml[${PYTHON_USEDEP}]
+	dev-python/scipy[${PYTHON_USEDEP}]
+	dev-python/tqdm[${PYTHON_USEDEP}]
+	dev-vcs/datalad
+"
+# also needs
+# pyintan
+# pyopenephys
+# nixio
+# shybird
+# mtscomp
+# exdir
+# sonpy
+# pyyaml and shybird might not really be needed
+BDEPEND=""
+
+PATCHES=(
+	"${FILESDIR}/${PN}-0.9.7-no-test-install.patch"
+)
+
+distutils_enable_tests pytest
+
+src_install() {
+	pwd
+	ls -lah
+	rm -rf tests/ || die "Could not remove tests directory incorrectly selected by package for install."
+	ls -lah
+	distutils-r1_src_install
+}