dev-python/fslpy: version bump 2.6.2 ahead of Gentoo Science

Package-Manager: Portage-2.3.78, Repoman-2.3.17
Signed-off-by: Horea Christian <chr@chymera.eu>

dev-python/fslpy/ChangeLog

@@ -1,3 +1,9 @@
+*fslpy-2.6.2 (04 Nov 2019)
+
+  04 Nov 2019;  <chymera@gentoo.org> +files/fslpy-2.6.2-exclude_tests.patch,
+  +fslpy-2.6.2.ebuild, -fslpy-1.11.1.ebuild, -fslpy-1.13.3.ebuild:
+  dev-python/fslpy: version bump 2.6.2 ahead of Gentoo Science
+
 *fslpy-1.11.1 (14 Oct 2018)
 
   14 Oct 2018; Horea Christian <h.chr@mail.ru> +fslpy-1.11.1.ebuild,

dev-python/fslpy/Manifest

@@ -1,2 +1 @@
-DIST fslpy-1.11.1.tar.gz 3444491 SHA256 033a1a4de6889d87e6db46a95173623272af84cce736d78244361e973de64a03 SHA512 b34640451a8bc94f7d0790095b343d2e93ead1145e5c31e2c7a831d5c08f3ae4e3f5120aa11f3dc2de734f69698d7102ce8caf80614759b15d1dd9047204aac8 WHIRLPOOL 174069b5826f3e8e5de57c8594cf68190ea808c2108e0c1f1a7f3e9451356774123ae2ea56cc4190eea95d0a72af346e4664343e4026fa274af53d729566e4c6
+DIST fslpy-2.6.2.tar.gz 4643661 SHA256 9363f02678e7e9cb815352129ab72b6af392b22958b00bb375c57c98600bcd7f SHA512 42c48ec362dc0830486d862171e22b1d9336285f6cf12fc4735909b26802c206aaa090b8a6a1cfbd2f55fc041723a39f7544800c6e10d4b9a4a7ad41b9e12d2e WHIRLPOOL d0eccb3f834880bf964a249bbea23f39a6420babaef1baa646c5c8880709e5b56ec9fe3e607770464701f99a72d785111b88fb38abc3fa41a48547be43db8394
-DIST fslpy-1.13.3.tar.gz 3448291 SHA256 b3f4bf9646ecd61841744368013e84c5a0d7ae87a67104b067bed2418bb9ca69 SHA512 473a054807fe8ff6da588f8bfc0cc0faaee02438014ceb18fccbcf1ac1ba6c69a5cb18a6b810a7a5c5bd7d1298369419c83aff99cb07c1629391192feba76581 WHIRLPOOL 02998aa35e0d0e9b6eb6f7dedbd6bf314db340e70b8a2d29adbab549d127a8b6c1f4d5aa3193cbcb9c5bad5ce21fe21fdb94abcb93d3632b989b59cf647def79

dev-python/fslpy/files/fslpy-2.6.2-exclude_tests.patch

@@ -0,0 +1,10 @@
+--- a/setup.py	2019-11-04 18:56:47.407791008 +0100
++++ b/setup.py	2019-11-04 20:00:24.844224851 +0100
+@@ -29,6 +29,6 @@
+ 
+ packages = find_packages(
+-    exclude=('doc', 'tests', 'dist', 'build', 'fslpy.egg-info'))
++    exclude=('doc', 'tests', 'tests.*', 'dist', 'build', 'fslpy.egg-info'))
+ 
+ # Figure out the current fslpy version, as defined in fsl/version.py. We
+ # don't want to import the fsl package,  as this may cause build problems.

dev-python/fslpy/fslpy-1.11.1.ebuild

@@ -1,52 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python2_7 python3_{5,6} )
-
-inherit distutils-r1 virtualx
-
-DESCRIPTION="The new FSL image viewer, released with FSL 5.0.10"
-HOMEPAGE="https://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/tree/master"
-SRC_URI="https://github.com/pauldmccarthy/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="test"
-
-DEPEND="
-	test? ( dev-python/pytest[${PYTHON_USEDEP}] )
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	"
-RDEPEND="
-	dev-python/deprecation[${PYTHON_USEDEP}]
-	=dev-python/numpy-1*[${PYTHON_USEDEP}]
-	=dev-python/six-1*[${PYTHON_USEDEP}]
-	dev-python/trimesh[${PYTHON_USEDEP}]
-	dev-python/wxpython[${PYTHON_USEDEP}]
-	sci-libs/Rtree[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]
-	=sci-libs/nibabel-2*[${PYTHON_USEDEP}]
-	"
-
-# Tests fail on Gentoo with mysterious `Fatal Python error: deallocating None`
-# https://github.com/pauldmccarthy/fslpy/issues/3
-RESTRICT="test"
-
-python_prepare_all() {
-	if use test; then
-		# Reported upstream
-		# https://github.com/pauldmccarthy/fslpy/issues/3
-		#sed -i -e \
-		#	"/def test_loadVestLutFile():/i@pytest.mark.xfail(reason='Known to fail on Gentoo')" \
-		#	tests/test_vest.py || die
-		rm tests/test_vest.py
-	fi
-	distutils-r1_python_prepare_all
-}
-
-python_test() {
-	virtx pytest -m "not (dicomtest or fsltest)" --verbose || die
-}

dev-python/fslpy/fslpy-2.6.2.ebuild

@@ -1,14 +1,14 @@
-# Copyright 1999-2018 Gentoo Authors
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
 
-PYTHON_COMPAT=( python2_7 python3_{5,6} )
+PYTHON_COMPAT=( python3_{5,6} )
 
 inherit distutils-r1 virtualx
 
-DESCRIPTION="The new FSL image viewer, released with FSL 5.0.10"
+DESCRIPTION="The FSL Python Library"
-HOMEPAGE="https://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/tree/master"
+HOMEPAGE="https://git.fmrib.ox.ac.uk/fsl/fslpy"
 SRC_URI="https://github.com/pauldmccarthy/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz"
 
 LICENSE="BSD"
@@ -17,18 +17,23 @@ KEYWORDS="~amd64 ~x86"
 IUSE="test"
 
 DEPEND="
-	test? ( dev-python/pytest[${PYTHON_USEDEP}] )
+	test? (
+		dev-python/pytest[${PYTHON_USEDEP}]
+		dev-python/pytest-cov[${PYTHON_USEDEP}]
+	)
 	dev-python/setuptools[${PYTHON_USEDEP}]
 	"
 RDEPEND="
 	dev-python/deprecation[${PYTHON_USEDEP}]
+	dev-python/h5py[${PYTHON_USEDEP}]
+	dev-python/indexed_gzip[${PYTHON_USEDEP}]
 	=dev-python/numpy-1*[${PYTHON_USEDEP}]
 	=dev-python/six-1*[${PYTHON_USEDEP}]
 	dev-python/trimesh[${PYTHON_USEDEP}]
-	dev-python/wxpython[${PYTHON_USEDEP}]
+	=dev-python/wxpython-4*[${PYTHON_USEDEP}]
-	sci-libs/Rtree[${PYTHON_USEDEP}]
+	=sci-libs/Rtree-0.8.3*[${PYTHON_USEDEP}]
 	sci-libs/scipy[${PYTHON_USEDEP}]
-	=sci-libs/nibabel-2*[${PYTHON_USEDEP}]
+	>=sci-libs/nibabel-2.3.1[${PYTHON_USEDEP}]
 	"
 
 # Tests fail on Gentoo with mysterious `Fatal Python error: deallocating None`
@@ -47,6 +52,8 @@ RDEPEND="
 #	distutils-r1_python_prepare_all
 #}
 
+PATCHES=( "${FILESDIR}/${P}-exclude_tests.patch" )
+
 python_test() {
 	virtx pytest -m "not (dicomtest or fsltest)" --verbose || die
 }