Merge pull request #244 from LebedevV/master

minor

dev-python/abTEM/abTEM-1.0.5.ebuild

@@ -35,6 +35,7 @@ RDEPEND="
 	dev-python/distributed[${PYTHON_USEDEP}]
 	dev-python/dask-labextension[${PYTHON_USEDEP}]
 	dev-python/pyFFTW[${PYTHON_USEDEP}]
+	dev-python/tabulate[${PYTHON_USEDEP}]
 "
 
 DEPEND="${RDEPEND}

dev-python/cupy/cupy-12.2.0-r1.ebuild

@@ -36,7 +36,8 @@ DEPEND="
 		>=sci-libs/hipFFT-${ROCM_VERSION}[${ROCM_USEDEP}]
 		>=sci-libs/hipRAND-${ROCM_VERSION}[${ROCM_USEDEP}]
 		>=sci-libs/rocThrust-${ROCM_VERSION}[${ROCM_USEDEP}]
-		>=sci-libs/hipSPARSE-${ROCM_VERSION}[${ROCM_USEDEP}] )"
+		>=sci-libs/hipSPARSE-${ROCM_VERSION}[${ROCM_USEDEP}] )
+		"
 RDEPEND=">=dev-python/fastrlock-0.8.1
 	${DEPEND}"
 

dev-python/cupy/cupy-13.1.0.ebuild

@@ -35,8 +35,8 @@ DEPEND="
 		>=sci-libs/hipFFT-${ROCM_VERSION}[${ROCM_USEDEP}]
 		>=sci-libs/hipRAND-${ROCM_VERSION}[${ROCM_USEDEP}]
 		>=sci-libs/rocThrust-${ROCM_VERSION}[${ROCM_USEDEP}]
-		>=sci-libs/hipSPARSE-${ROCM_VERSION}[${ROCM_USEDEP}] )"
-#	<dev-python/cython-3[${PYTHON_USEDEP}]
+		>=sci-libs/hipSPARSE-${ROCM_VERSION}[${ROCM_USEDEP}] )
+		<dev-python/cython-3[${PYTHON_USEDEP}]"
 RDEPEND=">=dev-python/fastrlock-0.8.1
 	${DEPEND}"
 

dev-python/cupy/cupy-13.2.0.ebuild

@@ -35,8 +35,9 @@ DEPEND="
 		>=sci-libs/hipFFT-${ROCM_VERSION}[${ROCM_USEDEP}]
 		>=sci-libs/hipRAND-${ROCM_VERSION}[${ROCM_USEDEP}]
 		>=sci-libs/rocThrust-${ROCM_VERSION}[${ROCM_USEDEP}]
-		>=sci-libs/hipSPARSE-${ROCM_VERSION}[${ROCM_USEDEP}] )"
-#	<dev-python/cython-3[${PYTHON_USEDEP}]
+		>=sci-libs/hipSPARSE-${ROCM_VERSION}[${ROCM_USEDEP}] )
+		<dev-python/cython-3[${PYTHON_USEDEP}]"
+#
 RDEPEND=">=dev-python/fastrlock-0.8.1
 	${DEPEND}"
 

dev-python/cython/Manifest

@@ -0,0 +1 @@
+DIST cython-0.29.37.1.gh.tar.gz 2115631 BLAKE2B b81e527ee1da7d16d074102378b531e4b0c161a3d66e47df46b624b02464cbd5c3d08d0e32f8175d56807ed8c6603108b85953db9f51892cfdf8952b4d287399 SHA512 6038499f13914b8a1957eee4d04e0499f448c89c3d519320e5218bf518aacb7d345f3c48614839222eaee016edf549b719520500b0088d28163635a74d35f3c6

dev-python/cython/cython-0.29.37.1.ebuild

@@ -0,0 +1,94 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_EXT=1
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_TESTED=( python3_{10..11} )
+# 3.12 not tested yet for https://github.com/cython/cython/issues/5285.
+PYTHON_COMPAT=( "${PYTHON_TESTED[@]}" python3_12 pypy3 )
+PYTHON_REQ_USE="threads(+)"
+
+inherit distutils-r1 multiprocessing toolchain-funcs elisp-common
+
+DESCRIPTION="A Python to C compiler"
+HOMEPAGE="
+	https://cython.org/
+	https://github.com/cython/cython/
+	https://pypi.org/project/Cython/
+"
+SRC_URI="
+	https://github.com/cython/cython/archive/${PV}.tar.gz
+		-> ${P}.gh.tar.gz
+"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~alpha ~amd64 ~arm ~arm64 ~hppa ~ia64 ~loong ~m68k ~mips ~ppc ~ppc64 ~riscv ~s390 sparc ~x86 ~amd64-linux ~x86-linux ~arm64-macos ~ppc-macos ~x64-macos ~x64-solaris"
+IUSE="emacs test"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+	emacs? ( >=app-editors/emacs-23.1:* )
+"
+BDEPEND="
+	${RDEPEND}
+	test? (
+		$(python_gen_cond_dep '
+			dev-python/numpy[${PYTHON_USEDEP}]
+		' "${PYTHON_TESTED[@]}")
+	)
+"
+
+PATCHES=(
+	"${FILESDIR}/${PN}-0.29.22-spawn-multiprocessing.patch"
+	"${FILESDIR}/${PN}-0.29.23-test_exceptions-py310.patch"
+	"${FILESDIR}/${PN}-0.29.23-pythran-parallel-install.patch"
+)
+
+SITEFILE=50cython-gentoo.el
+
+distutils_enable_sphinx docs
+
+python_compile() {
+	# Python gets confused when it is in sys.path before build.
+	local -x PYTHONPATH=
+
+	distutils-r1_python_compile
+}
+
+python_compile_all() {
+	use emacs && elisp-compile Tools/cython-mode.el
+}
+
+python_test() {
+	if ! has "${EPYTHON/./_}" "${PYTHON_TESTED[@]}"; then
+		einfo "Skipping tests on ${EPYTHON} (xfail)"
+		return
+	fi
+
+	tc-export CC
+	# https://github.com/cython/cython/issues/1911
+	local -x CFLAGS="${CFLAGS} -fno-strict-overflow"
+	"${PYTHON}" runtests.py -vv -j "$(makeopts_jobs)" --work-dir "${BUILD_DIR}"/tests ||
+		die "Tests fail with ${EPYTHON}"
+}
+
+python_install_all() {
+	local DOCS=( CHANGES.rst README.rst ToDo.txt USAGE.txt )
+	distutils-r1_python_install_all
+
+	if use emacs; then
+		elisp-install ${PN} Tools/cython-mode.*
+		elisp-site-file-install "${FILESDIR}/${SITEFILE}"
+	fi
+}
+
+pkg_postinst() {
+	use emacs && elisp-site-regen
+}
+
+pkg_postrm() {
+	use emacs && elisp-site-regen
+}

dev-python/cython/files/cython-0.29.22-spawn-multiprocessing.patch

@@ -0,0 +1,27 @@
+Needed to prevent a loop while calling cythonize on macOS - or any platform
+defaulting to the 'spawn' method, as Python 3.8 does on Darwin.
+
+https://github.com/cython/cython/pull/3263
+
+[Rebased on 0.29.22]
+
+From 15ae78bb74a856836dd64828326f4f0812d36520 Mon Sep 17 00:00:00 2001
+From: Marcel Bargull <marcel.bargull@udo.edu>
+Date: Fri, 6 Dec 2019 18:21:19 +0100
+Subject: [PATCH] Disable parallel cythonization for "spawn" start method.
+
+---
+--- a/Cython/Build/Dependencies.py
++++ b/Cython/Build/Dependencies.py
+@@ -1071,6 +1071,11 @@ def cythonize(module_list, exclude=None, nthreads=0, aliases=None, quiet=False,
+
+     if N <= 1:
+         nthreads = 0
++    if nthreads:
++        import multiprocessing
++        if multiprocessing.get_start_method() == 'spawn':
++            print('Disabling parallel cythonization for "spawn" process start method.')
++            nthreads = 0
+     if nthreads:
+         # Requires multiprocessing (or Python >= 2.6)
+         try:

dev-python/cython/files/cython-0.29.23-pythran-parallel-install.patch

@@ -0,0 +1,20 @@
+An empty directory in site-packages is a valid Python module, unfortunately, because
+of namespaces. If installing packages in parallel, the pythran module might "exist"
+but be empty (hence no __version__ attribute). Catch AttributeError to avoid a narrow
+race.
+
+See https://bugs.gentoo.org/902713.
+
+This might still be a Portage issue if there's a substantial delay between creating
+the directory and installing the remaining files though.
+--- a/Cython/Compiler/Pythran.py
++++ b/Cython/Compiler/Pythran.py
+@@ -10,7 +10,7 @@ try:
+     import pythran
+     pythran_is_pre_0_9 = tuple(map(int, pythran.__version__.split('.')[0:2])) < (0, 9)
+     pythran_is_pre_0_9_6 = tuple(map(int, pythran.__version__.split('.')[0:3])) < (0, 9, 6)
+-except ImportError:
++except (AttributeError, ImportError):
+     pythran = None
+     pythran_is_pre_0_9 = True
+     pythran_is_pre_0_9_6 = True

dev-python/cython/files/cython-0.29.23-test_exceptions-py310.patch

@@ -0,0 +1,14 @@
+--- a/tests/run/test_exceptions.pyx
++++ b/tests/run/test_exceptions.pyx
+@@ -188,7 +188,10 @@
+
+         # should not apply to subclasses, see issue #31161
+         s = '''if True:\nprint "No indent"'''
+-        ckmsg(s, "expected an indented block", IndentationError)
++        if sys.version_info >= (3, 10):
++            ckmsg(s, "expected an indented block after 'if' statement on line 1", IndentationError)
++        else:
++            ckmsg(s, "expected an indented block", IndentationError)
+
+         s = '''if True:\n        print()\n\texec "mixed tabs and spaces"'''
+         ckmsg(s, "inconsistent use of tabs and spaces in indentation", TabError)

dev-python/cython/metadata.xml

@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<longdescription lang="en">
+		Cython is a language that makes writing C extensions for the Python
+		language as easy as Python itself. It's based on Pyrex, but supports
+		more cutting edge functionality and optimizations.
+	</longdescription>
+	<upstream>
+		<remote-id type="pypi">Cython</remote-id>
+		<remote-id type="github">cython/cython</remote-id>
+	</upstream>
+</pkgmetadata>

dev-python/diffpy_structure/diffpy_structure-3.0.1.ebuild

@@ -2,48 +2,23 @@
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
-
+MYPN="${PN/_/.}"
+MYP="${MYPN}-${PV}"
 PYTHON_COMPAT=( python3_{9..12} )
 
-inherit distutils-r1 flag-o-matic
-
-MYPN="${PN/diffpy_structure/diffpy.structure}"
-MYP="${MYPN}-${PV}"
+inherit distutils-r1 flag-o-matic pypi
 
 DESCRIPTION="Crystal structure container and parsers for structure formats"
 HOMEPAGE="https://github.com/diffpy/diffpy.structure"
-SRC_URI="mirror://pypi/${MYP:0:1}/${MYPN}/${MYP}.tar.gz"
+SRC_URI="$(pypi_sdist_url --no-normalize "${MYPN}" "${PV}")"
+S=${WORKDIR}/${MYP}
+
 
 LICENSE="BSD"
 SLOT="0"
 KEYWORDS="~amd64"
-IUSE="doc python"
 
 RDEPEND="
 	>=dev-python/numpy-1.5.1[${PYTHON_USEDEP}]
 	dev-python/setuptools[${PYTHON_USEDEP}]
 "
-
-DEPEND="${RDEPEND}
-	doc? ( dev-util/gtk-doc )
-"
-
-REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
-
-S="${WORKDIR}/${MYP}"
-
-python_compile() {
-	distutils-r1_python_compile
-}
-
-python_compile_all() {
-	use doc && setup.py build
-}
-
-python_test() {
-	setup.py test
-}
-
-python_install_all() {
-	distutils-r1_python_install_all
-}

dev-python/diffpy_structure/diffpy_structure-3.1.0.ebuild

@@ -2,48 +2,23 @@
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
-
+MYPN="${PN/_/.}"
+MYP="${MYPN}-${PV}"
 PYTHON_COMPAT=( python3_{9..12} )
 
-inherit distutils-r1 flag-o-matic
-
-MYPN="${PN/diffpy_structure/diffpy.structure}"
-MYP="${MYPN}-${PV}"
+inherit distutils-r1 flag-o-matic pypi
 
 DESCRIPTION="Crystal structure container and parsers for structure formats"
 HOMEPAGE="https://github.com/diffpy/diffpy.structure"
-SRC_URI="mirror://pypi/${MYP:0:1}/${MYPN}/${MYP}.tar.gz"
+SRC_URI="$(pypi_sdist_url --no-normalize "${MYPN}" "${PV}")"
+S=${WORKDIR}/${MYP}
+
 
 LICENSE="BSD"
 SLOT="0"
 KEYWORDS="~amd64"
-IUSE="doc python"
 
 RDEPEND="
 	>=dev-python/numpy-1.5.1[${PYTHON_USEDEP}]
 	dev-python/setuptools[${PYTHON_USEDEP}]
 "
-
-DEPEND="${RDEPEND}
-	doc? ( dev-util/gtk-doc )
-"
-
-REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
-
-S="${WORKDIR}/${MYP}"
-
-python_compile() {
-	distutils-r1_python_compile
-}
-
-python_compile_all() {
-	use doc && setup.py build
-}
-
-python_test() {
-	setup.py test
-}
-
-python_install_all() {
-	distutils-r1_python_install_all
-}

dev-python/hyperspy/hyperspy-1.7.3.ebuild

@@ -19,6 +19,7 @@ KEYWORDS="~amd64 ~x86"
 IUSE="python doc +learning +gui-jupyter speed +gui-traitsui mrcz test"
 
 RDEPEND="
+	=dev-python/pillow-9.5.0[${PYTHON_USEDEP}]
 	>=dev-python/numpy-1.17.1[${PYTHON_USEDEP}]
 	>=dev-python/scipy-1.1[${PYTHON_USEDEP}]
 	dev-python/natsort[${PYTHON_USEDEP}]
@@ -38,7 +39,7 @@ RDEPEND="
 	dev-python/statsmodels[${PYTHON_USEDEP}]
 	dev-python/numexpr[${PYTHON_USEDEP}]
 	dev-python/sparse[${PYTHON_USEDEP}]
-	dev-python/imageio[${PYTHON_USEDEP}]
+	=dev-python/imageio-2.27.0[${PYTHON_USEDEP}]
 	dev-python/pyyaml[${PYTHON_USEDEP}]
 	dev-python/zarr[${PYTHON_USEDEP}]
 	dev-python/prettytable[${PYTHON_USEDEP}]
@@ -47,6 +48,8 @@ RDEPEND="
 	doc? ( >=app-misc/sphinx-1.7 dev-python/sphinx_rtd_theme )
 	learning? ( dev-python/scikit-learn[${PYTHON_USEDEP}] )
 	speed? ( dev-python/numba[${PYTHON_USEDEP}] dev-python/cython[${PYTHON_USEDEP}] )
+	!dev-python/rosettasciio[${PYTHON_USEDEP}]
+	!dev-python/exspy[${PYTHON_USEDEP}]
 "
 	##
 	##mrcz? ( >=dev-python/blosc-1.5 >=dev-python/mrcz-0.3.6 )
@@ -63,8 +66,8 @@ DEPEND="${RDEPEND}
 "
 
 PDEPEND="
-	gui-jupyter? ( >=dev-python/hyperspy-gui-ipywidgets-1.1.0 )
-	gui-traitsui? ( >=dev-python/hyperspy-gui-traitsui-1.1.0 )
+	gui-jupyter? ( <=dev-python/hyperspy-gui-ipywidgets-2.0.0 )
+	gui-traitsui? ( <=dev-python/hyperspy-gui-traitsui-2.0.0 )
 "
 
 REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"

dev-python/zarr/Manifest

@@ -1,2 +1,3 @@
 DIST zarr-2.13.3.tar.gz 3577628 BLAKE2B a46324937b5d6e9227a19c5fb7a979664a8d7f352dd7a33800705433be02fb368397758c4b023b7e8f1bce4660ff1601e7371f99dbb1c73549e3aa1885580be0 SHA512 fe914b7f94b6ac3703621a79f1b809c68abf9f03c0a682bdb8eb10a1fc428ad6a1fdc5f6a899d311277fccafc0cc88ee01216df34c854d7664954a4577d1262c
 DIST zarr-2.16.1.tar.gz 3597771 BLAKE2B 459f8022b3a4e3298b0f9650738713f6c13bb474ae50005b9387fefc87360f6358e4899037b26b9893d87298b14606d7b29bc1539fc8fa1479a08b30f2c8323b SHA512 e3b7c234c6376bea535d47304d83ee5b4d8b4bfc6952dde5e0bf1276833c1f427c98a7af0867f351e0139404d3729024b591a1f9b2242e219846a994e0762ee5
+DIST zarr-2.18.2.tar.gz 3603055 BLAKE2B bf6dd3a9e23f9e6cbb73acabbd07b3ec61b88518c882c207bd7f05da21ae29204ee2f43f797e597fd50063b6054967cb9f631233d59c36bd80a542b80670403d SHA512 57a2fe78d8dc5794b38e89fd4cc7ca9edf17dc767880cf58efa4266771b4e1e4035ed80301081f4057f9a47f0e6387a45853e6f5bc9dcd54f54d4d50872b7791

dev-python/zarr/zarr-2.13.3.ebuild

@@ -20,6 +20,7 @@ IUSE="doc python"
 RDEPEND="
 	dev-python/numpy[${PYTHON_USEDEP}]
 	dev-python/numcodecs[${PYTHON_USEDEP}]
+	dev-python/asciitree[${PYTHON_USEDEP}]
 "
 #asciitree==0.3.3
 #fasteners==0.18

dev-python/zarr/zarr-2.16.1.ebuild

@@ -20,9 +20,10 @@ IUSE="doc python"
 RDEPEND="
 	dev-python/numpy[${PYTHON_USEDEP}]
 	dev-python/numcodecs[${PYTHON_USEDEP}]
+	dev-python/asciitree[${PYTHON_USEDEP}]
+	dev-python/fasteners[${PYTHON_USEDEP}]
 "
-#asciitree==0.3.3
-#fasteners==0.18
+
 #numcodecs==0.10.2
 #msgpack-python==0.5.6
 #setuptools-scm==7.0.5