commit: 1a41a5294718de0da9a9e97f14d72440eeb588f8
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Fri Mar 8 16:43:01 2024 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Fri Mar 8 16:43:01 2024 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=1a41a529
dev-python/{numba*,llvmlite}: treeclean
llvmlite is *still* stuck on llvm:14
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
.../files/llvmlite-0.39.1-allow-py3.11.patch | 13 ---
.../llvmlite/files/llvmlite-0.39.1-llvm12.patch | 97 --------------------
dev-python/llvmlite/llvmlite-0.39.1.ebuild | 66 --------------
dev-python/llvmlite/llvmlite-0.40.1.ebuild | 63 -------------
dev-python/llvmlite/llvmlite-0.41.0.ebuild | 57 ------------
dev-python/llvmlite/metadata.xml | 18 ----
dev-python/numba-dpex/metadata.xml | 12 ---
dev-python/numba-dpex/numba-dpex-0.20.0_rc3.ebuild | 41 ---------
.../numba/files/numba-0.52.0-skip_tests.patch | 34 -------
.../numba/files/numba-0.56.4-allow-py3.11.patch | 13 ---
dev-python/numba/metadata.xml | 16 ----
dev-python/numba/numba-0.56.4.ebuild | 85 -----------------
dev-python/numba/numba-0.57.1.ebuild | 83 -----------------
dev-python/pynndescent/metadata.xml | 16 ----
dev-python/pynndescent/pynndescent-0.5.6.ebuild | 27 ------
dev-python/tridesclous/metadata.xml | 16 ----
dev-python/tridesclous/tridesclous-1.6.4.ebuild | 100 --------------------
dev-python/tridesclous/tridesclous-1.6.6.ebuild | 101 ---------------------
dev-python/umap-learn/metadata.xml | 15 ---
dev-python/umap-learn/umap-learn-0.5.2.ebuild | 25 -----
profiles/package.mask | 11 ---
21 files changed, 909 deletions(-)
diff --git a/dev-python/llvmlite/files/llvmlite-0.39.1-allow-py3.11.patch
b/dev-python/llvmlite/files/llvmlite-0.39.1-allow-py3.11.patch
deleted file mode 100644
index d35979ebc..000000000
--- a/dev-python/llvmlite/files/llvmlite-0.39.1-allow-py3.11.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff --git a/setup.py b/setup.py
-index 02b1604..a45c9b8 100644
---- a/setup.py
-+++ b/setup.py
-@@ -33,7 +33,7 @@ except ImportError:
-
-
- min_python_version = "3.7"
--max_python_version = "3.11" # exclusive
-+max_python_version = "3.12" # exclusive
-
-
- def _guard_py_ver():
diff --git a/dev-python/llvmlite/files/llvmlite-0.39.1-llvm12.patch
b/dev-python/llvmlite/files/llvmlite-0.39.1-llvm12.patch
deleted file mode 100644
index 17eb80e87..000000000
--- a/dev-python/llvmlite/files/llvmlite-0.39.1-llvm12.patch
+++ /dev/null
@@ -1,97 +0,0 @@
-From 1d928ebcd59b23b5050234a2bf71f9be7f5f6bd1 Mon Sep 17 00:00:00 2001
-From: Richard Barnes <[email protected]>
-Date: Wed, 1 Dec 2021 10:29:08 -0700
-Subject: [PATCH] Enable LLVM-12 and LLVM-13
-
----
- ffi/build.py | 5 ++---
- ffi/targets.cpp | 2 ++
- llvmlite/tests/test_binding.py | 19 ++++++++++++++++---
- 3 files changed, 20 insertions(+), 6 deletions(-)
-
-Index: llvmlite-0.39.0/ffi/build.py
-===================================================================
---- llvmlite-0.39.0.orig/ffi/build.py
-+++ llvmlite-0.39.0/ffi/build.py
-@@ -163,9 +163,8 @@ def main_posix(kind, library_ext):
- print(msg)
- print(warning + '\n')
- else:
--
-- if not out.startswith('11'):
-- msg = ("Building llvmlite requires LLVM 11.x.x, got "
-+ if not (out.startswith('11') or out.startswith('12') or
out.startswith('13')):
-+ msg = ("Building llvmlite requires LLVM 11-13.x.x, got "
- "{!r}. Be sure to set LLVM_CONFIG to the right executable "
- "path.\nRead the documentation at "
- "http://llvmlite.pydata.org/ for more information about "
-Index: llvmlite-0.39.0/ffi/targets.cpp
-===================================================================
---- llvmlite-0.39.0.orig/ffi/targets.cpp
-+++ llvmlite-0.39.0/ffi/targets.cpp
-@@ -204,7 +204,9 @@ LLVMPY_CreateTargetMachine(LLVMTargetRef
- rm = Reloc::DynamicNoPIC;
-
- TargetOptions opt;
-+#if LLVM_VERSION_MAJOR < 12
- opt.PrintMachineCode = PrintMC;
-+#endif
- opt.MCOptions.ABIName = ABIName;
-
- bool jit = JIT;
-Index: llvmlite-0.39.0/llvmlite/tests/test_binding.py
-===================================================================
---- llvmlite-0.39.0.orig/llvmlite/tests/test_binding.py
-+++ llvmlite-0.39.0/llvmlite/tests/test_binding.py
-@@ -18,6 +18,16 @@ from llvmlite.binding import ffi
- from llvmlite.tests import TestCase
-
-
-+def clean_string_whitespace(x: str) -> str:
-+ # Remove trailing whitespace from the end of each line
-+ x = re.sub(r"\s+$", "", x, flags=re.MULTILINE)
-+ # Remove intermediate blank lines
-+ x = re.sub(r"\n\s*\n", r"\n", x, flags=re.MULTILINE)
-+ # Remove extraneous whitespace from the beginning and end of the string
-+ x = x.strip()
-+ return x
-+
-+
- # arvm7l needs extra ABI symbols to link successfully
- if platform.machine() == 'armv7l':
- llvm.load_library_permanently('libgcc_s.so.1')
-@@ -555,7 +565,10 @@ class TestMisc(BaseTest):
- bd = ir.IRBuilder(fn.append_basic_block(name="<>!*''#"))
- bd.ret(ir.Constant(ir.IntType(32), 12345))
- asm = str(mod)
-- self.assertEqual(asm, asm_nonalphanum_blocklabel)
-+ self.assertEqual(
-+ clean_string_whitespace(asm),
-+ clean_string_whitespace(asm_nonalphanum_blocklabel)
-+ )
-
- def test_global_context(self):
- gcontext1 = llvm.context.get_global_context()
-@@ -640,7 +653,7 @@ class TestMisc(BaseTest):
- def test_version(self):
- major, minor, patch = llvm.llvm_version_info
- # one of these can be valid
-- valid = [(11,)]
-+ valid = [(11,), (12,), (13,)]
- self.assertIn((major,), valid)
- self.assertIn(patch, range(10))
-
-Index: llvmlite-0.39.0/ffi/passmanagers.cpp
-===================================================================
---- llvmlite-0.39.0.orig/ffi/passmanagers.cpp
-+++ llvmlite-0.39.0/ffi/passmanagers.cpp
-@@ -17,9 +17,6 @@
- #include "llvm-c/Transforms/IPO.h"
- #include "llvm-c/Transforms/Scalar.h"
- #include "llvm/IR/LegacyPassManager.h"
--#if LLVM_VERSION_MAJOR > 11
--#include "llvm/IR/RemarkStreamer.h"
--#endif
- #include "llvm/IR/LLVMRemarkStreamer.h"
- #include "llvm/Remarks/RemarkStreamer.h"
- #include "llvm/Transforms/IPO.h"
diff --git a/dev-python/llvmlite/llvmlite-0.39.1.ebuild
b/dev-python/llvmlite/llvmlite-0.39.1.ebuild
deleted file mode 100644
index 7302c93dd..000000000
--- a/dev-python/llvmlite/llvmlite-0.39.1.ebuild
+++ /dev/null
@@ -1,66 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{10..11} )
-DISTUTILS_USE_PEP517=setuptools
-inherit distutils-r1 llvm
-
-DESCRIPTION="Python wrapper around the llvm C++ library"
-HOMEPAGE="https://llvmlite.pydata.org/";
-SRC_URI="https://github.com/numba/llvmlite/archive/v${PV/_/}.tar.gz ->
${P/_/}.gh.tar.gz"
-S="${WORKDIR}/${P/_/}"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~arm ~arm64 ~x86"
-IUSE="examples"
-
-LLVM_MAX_SLOT=15
-
-RDEPEND="
- sys-devel/llvm:${LLVM_MAX_SLOT}
- sys-libs/zlib:0=
-"
-DEPEND="${RDEPEND}"
-
-PATCHES=(
- "${FILESDIR}/${P}-llvm12.patch"
- "${FILESDIR}/${P}-allow-py3.11.patch"
-)
-
-src_prepare() {
- sed -i -e '/max_python/s:3\.10:3.11:' setup.py || die
- distutils-r1_src_prepare
-}
-
-python_configure_all() {
- # upstream's build system is just horrible, and they ignored the PR
- # fixing it, so let's build the shared lib properly using implicit
- # make rules
-
- export LDLIBS=$(llvm-config --libs all)
- export CXXFLAGS="$(llvm-config --cxxflags) -fPIC ${CXXFLAGS}"
- export LDFLAGS="$(llvm-config --ldflags) ${LDFLAGS}"
-
- local files=( ffi/*.cpp )
- emake -f - <<EOF
-ffi/libllvmlite.so: ${files[*]/.cpp/.o}
- \$(CXX) -shared \$(CXXFLAGS) \$(LDFLAGS) -o \$@ \$^ \$(LDLIBS)
-EOF
-
- export LLVMLITE_SKIP_LLVM_VERSION_CHECK=1
-}
-
-python_test() {
- "${EPYTHON}" runtests.py -v || die "Tests failed under ${EPYTHON}"
-}
-
-python_install_all() {
- distutils-r1_python_install_all
- if use examples; then
- dodoc -r examples
- docompress -x /usr/share/doc/${PF}/examples
- fi
-}
diff --git a/dev-python/llvmlite/llvmlite-0.40.1.ebuild
b/dev-python/llvmlite/llvmlite-0.40.1.ebuild
deleted file mode 100644
index bacb0358b..000000000
--- a/dev-python/llvmlite/llvmlite-0.40.1.ebuild
+++ /dev/null
@@ -1,63 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{10..11} )
-DISTUTILS_USE_PEP517=setuptools
-inherit distutils-r1 llvm
-
-DESCRIPTION="Python wrapper around the llvm C++ library"
-HOMEPAGE="https://llvmlite.pydata.org/";
-SRC_URI="https://github.com/numba/llvmlite/archive/v${PV/_/}.tar.gz ->
${P/_/}.gh.tar.gz"
-S="${WORKDIR}/${P/_/}"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~arm ~arm64 ~x86"
-IUSE="examples"
-
-LLVM_MAX_SLOT=14
-
-RDEPEND="
- sys-devel/llvm:${LLVM_MAX_SLOT}
- sys-libs/zlib:0=
-"
-DEPEND="${RDEPEND}"
-
-PATCHES=()
-
-src_prepare() {
- sed -i -e '/max_python/s:3\.10:3.11:' setup.py || die
- distutils-r1_src_prepare
-}
-
-python_configure_all() {
- # upstream's build system is just horrible, and they ignored the PR
- # fixing it, so let's build the shared lib properly using implicit
- # make rules
-
- export LDLIBS=$(llvm-config --libs all)
- export CXXFLAGS="$(llvm-config --cxxflags) -fPIC ${CXXFLAGS}"
- export LDFLAGS="$(llvm-config --ldflags) ${LDFLAGS}"
-
- local files=( ffi/*.cpp )
- emake -f - <<EOF
-ffi/libllvmlite.so: ${files[*]/.cpp/.o}
- \$(CXX) -shared \$(CXXFLAGS) \$(LDFLAGS) -o \$@ \$^ \$(LDLIBS)
-EOF
-
- export LLVMLITE_SKIP_LLVM_VERSION_CHECK=1
-}
-
-python_test() {
- "${EPYTHON}" runtests.py -v || die "Tests failed under ${EPYTHON}"
-}
-
-python_install_all() {
- distutils-r1_python_install_all
- if use examples; then
- dodoc -r examples
- docompress -x /usr/share/doc/${PF}/examples
- fi
-}
diff --git a/dev-python/llvmlite/llvmlite-0.41.0.ebuild
b/dev-python/llvmlite/llvmlite-0.41.0.ebuild
deleted file mode 100644
index 595218e7c..000000000
--- a/dev-python/llvmlite/llvmlite-0.41.0.ebuild
+++ /dev/null
@@ -1,57 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{10..12} )
-DISTUTILS_USE_PEP517=setuptools
-DISTUTILS_EXT=1
-inherit distutils-r1 llvm
-
-DESCRIPTION="Python wrapper around the llvm C++ library"
-HOMEPAGE="https://llvmlite.pydata.org/";
-SRC_URI="https://github.com/numba/llvmlite/archive/v${PV/_/}.tar.gz ->
${P/_/}.gh.tar.gz"
-S="${WORKDIR}/${P/_/}"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~arm ~arm64 ~x86"
-IUSE="examples"
-
-LLVM_MAX_SLOT=14
-
-RDEPEND="
- sys-devel/llvm:${LLVM_MAX_SLOT}
- sys-libs/zlib:0=
-"
-DEPEND="${RDEPEND}"
-
-python_configure_all() {
- # upstream's build system is just horrible, and they ignored the PR
- # fixing it, so let's build the shared lib properly using implicit
- # make rules
-
- export LDLIBS=$(llvm-config --libs all)
- export CXXFLAGS="$(llvm-config --cxxflags) -fPIC ${CXXFLAGS}"
- export LDFLAGS="$(llvm-config --ldflags) ${LDFLAGS}"
-
- local files=( ffi/*.cpp )
- emake -f - <<EOF
-ffi/libllvmlite.so: ${files[*]/.cpp/.o}
- \$(CXX) -shared \$(CXXFLAGS) \$(LDFLAGS) -o \$@ \$^ \$(LDLIBS)
-EOF
-
- export LLVMLITE_SKIP_LLVM_VERSION_CHECK=1
-}
-
-python_test() {
- "${EPYTHON}" runtests.py -v || die "Tests failed under ${EPYTHON}"
-}
-
-python_install_all() {
- distutils-r1_python_install_all
- if use examples; then
- dodoc -r examples
- docompress -x /usr/share/doc/${PF}/examples
- fi
-}
diff --git a/dev-python/llvmlite/metadata.xml b/dev-python/llvmlite/metadata.xml
deleted file mode 100644
index 0983f7a41..000000000
--- a/dev-python/llvmlite/metadata.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd";>
-<pkgmetadata>
- <maintainer type="project">
- <email>[email protected]</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <longdescription>
- llvmlite uses the LLVM library for JIT (just-in-time) compilation of
- Python code into native machine instructions during runtime. Instead
- of exposing large parts of the LLVM C++ API for direct calls into the
- LLVM library, llvmlite follows a lightweight multi-layered approach.
- </longdescription>
- <upstream>
- <remote-id type="pypi">llvmlite</remote-id>
- <remote-id type="github">numba/llvmlite</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/dev-python/numba-dpex/metadata.xml
b/dev-python/numba-dpex/metadata.xml
deleted file mode 100644
index c98aa52a0..000000000
--- a/dev-python/numba-dpex/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";>
-<pkgmetadata>
- <maintainer type="project">
- <email>[email protected]</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <upstream>
- <remote-id type="github">IntelPython/numba-dpex</remote-id>
- <remote-id type="pypi">numba-dpex</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/dev-python/numba-dpex/numba-dpex-0.20.0_rc3.ebuild
b/dev-python/numba-dpex/numba-dpex-0.20.0_rc3.ebuild
deleted file mode 100644
index a3b63bf1f..000000000
--- a/dev-python/numba-dpex/numba-dpex-0.20.0_rc3.ebuild
+++ /dev/null
@@ -1,41 +0,0 @@
-# Copyright 2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_10 )
-DISTUTILS_USE_PEP517=setuptools
-inherit distutils-r1
-
-DESCRIPTION="Data Parallel Extension for Numba"
-HOMEPAGE="https://github.com/IntelPython/numba-dpex";
-SRC_URI="https://github.com/IntelPython/numba-dpex/archive/refs/tags/${PV//_rc/dev}.tar.gz
-> ${P}.gh.tar.gz"
-S="${WORKDIR}/${PN}-${PV//_rc/dev}"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64"
-
-BDEPEND="
- dev-python/cython[${PYTHON_USEDEP}]
- sys-devel/DPC++
-"
-
-RDEPEND="
- dev-python/dpctl[${PYTHON_USEDEP}]
- dev-python/dpnp[${PYTHON_USEDEP}]
- dev-python/numba[${PYTHON_USEDEP}]
- dev-python/packaging[${PYTHON_USEDEP}]
-"
-DEPEND="${RDEPEND}"
-
-distutils_enable_tests pytest
-
-python_prepare_all() {
- # DPC++ compiler required for full functionality
- export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang"
- export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++"
- export DPCPPROOT="${ESYSROOT}/usr/lib/llvm/intel"
-
- distutils-r1_python_prepare_all
-}
diff --git a/dev-python/numba/files/numba-0.52.0-skip_tests.patch
b/dev-python/numba/files/numba-0.52.0-skip_tests.patch
deleted file mode 100644
index f31af4bfb..000000000
--- a/dev-python/numba/files/numba-0.52.0-skip_tests.patch
+++ /dev/null
@@ -1,34 +0,0 @@
-Index: numba-0.52.0/numba/tests/test_jitclasses.py
-===================================================================
---- numba-0.52.0.orig/numba/tests/test_jitclasses.py
-+++ numba-0.52.0/numba/tests/test_jitclasses.py
-@@ -929,6 +929,7 @@ class TestJitClass(TestCase, MemoryLeakM
- self.assertEqual(t[2:2:1], 2)
- self.assertEqual(t[6:6:1], 3)
-
-+ @unittest.skip("Gentoo has not reverted the LLVM 'truncate longlabel'
patch")
- def test_jitclass_longlabel_not_truncated(self):
- # See issue #3872, llvm 7 introduced a max label length of 1024 chars
- # Numba ships patched llvm 7.1 (ppc64le) and patched llvm 8 to undo
this
-Index: numba-0.52.0/numba/tests/test_record_dtype.py
-===================================================================
---- numba-0.52.0.orig/numba/tests/test_record_dtype.py
-+++ numba-0.52.0/numba/tests/test_record_dtype.py
-@@ -796,7 +796,7 @@ class TestRecordDtype(unittest.TestCase)
- # len(transformed) is generally 10, but could be longer if a large
- # number of typecodes are in use. Checking <20 should provide enough
- # tolerance.
-- self.assertLess(len(transformed), 20)
-+ self.assertLessEqual(len(transformed), 20)
-
- struct_arr = types.Array(rec, 1, 'C')
- transformed = mangle_type(struct_arr)
-@@ -804,7 +804,7 @@ class TestRecordDtype(unittest.TestCase)
- self.assertNotIn('first', transformed)
- self.assertNotIn('second', transformed)
- # Length is usually 50 - 5 chars tolerance as above.
-- self.assertLess(len(transformed), 50)
-+ self.assertLessEqual(len(transformed), 50)
-
- def test_record_two_arrays(self):
- """
diff --git a/dev-python/numba/files/numba-0.56.4-allow-py3.11.patch
b/dev-python/numba/files/numba-0.56.4-allow-py3.11.patch
deleted file mode 100644
index 07c1b5d88..000000000
--- a/dev-python/numba/files/numba-0.56.4-allow-py3.11.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff --git a/setup.py b/setup.py
-index 68feca4..1d254ec 100644
---- a/setup.py
-+++ b/setup.py
-@@ -20,7 +20,7 @@ except ImportError:
-
-
- min_python_version = "3.7"
--max_python_version = "3.11" # exclusive
-+max_python_version = "3.12" # exclusive
- min_numpy_build_version = "1.11"
- min_numpy_run_version = "1.18"
- max_numpy_run_version = "1.24"
diff --git a/dev-python/numba/metadata.xml b/dev-python/numba/metadata.xml
deleted file mode 100644
index 63bc398e0..000000000
--- a/dev-python/numba/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";>
-<pkgmetadata>
- <maintainer type="person">
- <email>[email protected]</email>
- <name>Aisha Tammy</name>
- </maintainer>
- <maintainer type="project">
- <email>[email protected]</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <upstream>
- <remote-id type="github">numba/numba</remote-id>
- <remote-id type="pypi">numba</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/dev-python/numba/numba-0.56.4.ebuild
b/dev-python/numba/numba-0.56.4.ebuild
deleted file mode 100644
index 3fcfd4a94..000000000
--- a/dev-python/numba/numba-0.56.4.ebuild
+++ /dev/null
@@ -1,85 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-# py3.11 fails to compile:
-# error: ‘CFrame’ does not name a type; did you mean ‘_frame’?
-PYTHON_COMPAT=( python3_{10..11} )
-DISTUTILS_USE_PEP517=setuptools
-inherit optfeature multiprocessing distutils-r1
-
-DESCRIPTION="NumPy aware dynamic Python compiler using LLVM"
-HOMEPAGE="https://numba.pydata.org/
- https://github.com/numba";
-SRC_URI="https://github.com/numba/numba/archive/${PV}.tar.gz -> ${P}.gh.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~arm ~arm64 ~x86"
-IUSE="openmp threads"
-
-RDEPEND="
- >=dev-python/llvmlite-0.39.0[${PYTHON_USEDEP}]
- <=dev-python/llvmlite-0.40.0
- >=dev-python/numpy-1.18.0[${PYTHON_USEDEP}]
- <dev-python/numpy-1.24[${PYTHON_USEDEP}]
- threads? ( >=dev-cpp/tbb-2021.1 <dev-cpp/tbb-2021.6 )
-"
-BDEPEND="
- dev-python/pip[${PYTHON_USEDEP}]
- dev-python/versioneer[${PYTHON_USEDEP}]
-"
-
-distutils_enable_tests unittest
-distutils_enable_sphinx docs/source dev-python/numpydoc
dev-python/sphinx-rtd-theme
-
-PATCHES=(
- "${FILESDIR}/${PN}-0.52.0-skip_tests.patch"
- "${FILESDIR}/${PN}-0.56.4-allow-py3.11.patch"
-)
-
-pkg_setup() {
- if ! use openmp; then
- export NUMBA_DISABLE_OPENMP=1 || die
- else
- unset NUMBA_DISABLE_OPENMP || die
- fi
- if ! use threads; then
- export NUMBA_DISABLE_TBB=1 || die
- else
- unset NUMBA_DISABLE_TBB || die
- export TBBROOT="${EPREFIX}/usr" || die
- fi
-}
-
-python_prepare_all() {
- # This conf.py only works in a git repo
- if use doc; then
- git init -q || die
- git config user.email "[email protected]" || die
- git config user.name "Larry the Cow" || die
- git add . || die
- git commit -m "init" || die
- fi
- distutils-r1_python_prepare_all
-}
-
-python_compile() {
- # FIXME: parallel python building fails. See Portage bug #614464 and
- # gentoo/sci issue #1080.
- export MAKEOPTS=-j1 || die
- distutils-r1_python_compile
-}
-
-#
https://numba.pydata.org/numba-doc/latest/developer/contributing.html?highlight=test#running-tests
-python_test() {
- ${EPYTHON} setup.py build_ext --inplace || die \
- "${EPYTHON} failed to build_ext"
- ${EPYTHON} runtests.py -m $(makeopts_jobs) || die \
- "${EPYTHON} failed unittests"
-}
-
-pkg_postinst() {
- optfeature "compile cuda code" dev-util/nvidia-cuda-sdk
-}
diff --git a/dev-python/numba/numba-0.57.1.ebuild
b/dev-python/numba/numba-0.57.1.ebuild
deleted file mode 100644
index 814dc36f9..000000000
--- a/dev-python/numba/numba-0.57.1.ebuild
+++ /dev/null
@@ -1,83 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{10..11} )
-DISTUTILS_USE_PEP517=setuptools
-DISTUTILS_EXT=1
-inherit optfeature multiprocessing distutils-r1
-
-DESCRIPTION="NumPy aware dynamic Python compiler using LLVM"
-HOMEPAGE="https://numba.pydata.org/
- https://github.com/numba";
-SRC_URI="https://github.com/numba/numba/archive/${PV}.tar.gz -> ${P}.gh.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~arm ~arm64 ~x86"
-IUSE="openmp threads"
-
-RDEPEND="
- >=dev-python/llvmlite-0.40.0[${PYTHON_USEDEP}]
- <=dev-python/llvmlite-0.41.0
- >=dev-python/numpy-1.18.0[${PYTHON_USEDEP}]
- <dev-python/numpy-1.25[${PYTHON_USEDEP}]
- threads? ( >=dev-cpp/tbb-2021.6 )
-"
-BDEPEND="
- dev-python/pip[${PYTHON_USEDEP}]
- dev-python/versioneer[${PYTHON_USEDEP}]
-"
-
-distutils_enable_tests unittest
-distutils_enable_sphinx docs/source dev-python/numpydoc
dev-python/sphinx-rtd-theme
-
-PATCHES=(
- "${FILESDIR}/${PN}-0.52.0-skip_tests.patch"
-)
-
-pkg_setup() {
- if ! use openmp; then
- export NUMBA_DISABLE_OPENMP=1 || die
- else
- unset NUMBA_DISABLE_OPENMP || die
- fi
- if ! use threads; then
- export NUMBA_DISABLE_TBB=1 || die
- else
- unset NUMBA_DISABLE_TBB || die
- export TBBROOT="${EPREFIX}/usr" || die
- fi
-}
-
-python_prepare_all() {
- # This conf.py only works in a git repo
- if use doc; then
- git init -q || die
- git config user.email "[email protected]" || die
- git config user.name "Larry the Cow" || die
- git add . || die
- git commit -m "init" || die
- fi
- distutils-r1_python_prepare_all
-}
-
-python_compile() {
- # FIXME: parallel python building fails. See Portage bug #614464 and
- # gentoo/sci issue #1080.
- export MAKEOPTS=-j1 || die
- distutils-r1_python_compile
-}
-
-#
https://numba.pydata.org/numba-doc/latest/developer/contributing.html?highlight=test#running-tests
-python_test() {
- ${EPYTHON} setup.py build_ext --inplace || die \
- "${EPYTHON} failed to build_ext"
- ${EPYTHON} runtests.py -m $(makeopts_jobs) || die \
- "${EPYTHON} failed unittests"
-}
-
-pkg_postinst() {
- optfeature "compile cuda code" dev-util/nvidia-cuda-sdk
-}
diff --git a/dev-python/pynndescent/metadata.xml
b/dev-python/pynndescent/metadata.xml
deleted file mode 100644
index 7930c1730..000000000
--- a/dev-python/pynndescent/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";>
-<pkgmetadata>
- <maintainer type="person">
- <email>[email protected]</email>
- <name>Aisha Tammy</name>
- </maintainer>
- <maintainer type="project">
- <email>[email protected]</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <upstream>
- <remote-id type="github">lmcinnes/pynndescent</remote-id>
- <remote-id type="pypi">pynndescent</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/dev-python/pynndescent/pynndescent-0.5.6.ebuild
b/dev-python/pynndescent/pynndescent-0.5.6.ebuild
deleted file mode 100644
index 770630cac..000000000
--- a/dev-python/pynndescent/pynndescent-0.5.6.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_10 )
-
-inherit distutils-r1 pypi
-
-DESCRIPTION="nearest neighbor descent for approximate nearest neighbors"
-HOMEPAGE="https://github.com/lmcinnes/pynndescent";
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- dev-python/joblib[${PYTHON_USEDEP}]
- >=dev-python/numba-0.51.2[${PYTHON_USEDEP}]
- >=dev-python/numpy-1.17[${PYTHON_USEDEP}]
- >=dev-python/llvmlite-0.34[${PYTHON_USEDEP}]
- >=dev-python/scipy-1.0[${PYTHON_USEDEP}]
- >=sci-libs/scikit-learn-0.18.0[${PYTHON_USEDEP}]
-"
-DEPEND="${RDEPEND}"
-
-distutils_enable_tests pytest
diff --git a/dev-python/tridesclous/metadata.xml
b/dev-python/tridesclous/metadata.xml
deleted file mode 100644
index 819340cd1..000000000
--- a/dev-python/tridesclous/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";>
-<pkgmetadata>
- <maintainer type="person">
- <email>[email protected]</email>
- <name>Horea Christian</name>
- </maintainer>
- <maintainer type="project">
- <email>[email protected]</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <upstream>
- <remote-id type="github">tridesclous/tridesclous</remote-id>
- <remote-id type="pypi">tridesclous</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/dev-python/tridesclous/tridesclous-1.6.4.ebuild
b/dev-python/tridesclous/tridesclous-1.6.4.ebuild
deleted file mode 100644
index 131156160..000000000
--- a/dev-python/tridesclous/tridesclous-1.6.4.ebuild
+++ /dev/null
@@ -1,100 +0,0 @@
-# Copyright 2021-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{10..11} )
-DISTUTILS_USE_PEP517=setuptools
-inherit distutils-r1 pypi
-
-DESCRIPTION="offline/online spike sorting"
-HOMEPAGE="https://github.com/tridesclous/tridesclous";
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="gui test"
-
-RDEPEND="
- <dev-python/numpy-1.24.0[${PYTHON_USEDEP}]
- dev-python/cython[${PYTHON_USEDEP}]
- dev-python/hdbscan[${PYTHON_USEDEP}]
- dev-python/loky[${PYTHON_USEDEP}]
- dev-python/matplotlib[${PYTHON_USEDEP}]
- dev-python/neo[${PYTHON_USEDEP}]
- dev-python/numba
- dev-python/openpyxl[${PYTHON_USEDEP}]
- dev-python/pandas[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- dev-python/seaborn[${PYTHON_USEDEP}]
- dev-python/tqdm[${PYTHON_USEDEP}]
- sci-libs/scikit-learn[${PYTHON_USEDEP}]
- gui? (
- dev-python/PyQt5[${PYTHON_USEDEP}]
- )
-"
-
-distutils_enable_tests pytest
-
-# Network sandboxing, this is sadly more than half the test suite :(
-EPYTEST_DESELECT=(
- tridesclous/tests/test_cleancluster.py::test_auto_split
- tridesclous/tests/test_cleancluster.py::test_trash_not_aligned
- tridesclous/tests/test_cleancluster.py::test_auto_merge
- tridesclous/tests/test_cleancluster.py::test_trash_low_extremum
- tridesclous/tests/test_cleancluster.py::test_trash_small_cluster
- tridesclous/tests/test_cluster.py::test_sawchaincut
- tridesclous/tests/test_cluster.py::test_pruningshears
- tridesclous/tests/test_decomposition.py::test_all_decomposition
- tridesclous/tests/test_export.py::test_export
- tridesclous/tests/test_export.py::test_export_catalogue_spikes
- tridesclous/tests/test_jobtools.py::test_run_parallel_signalprocessor
- tridesclous/tests/test_matplotlibplot.py::test_plot_probe_geometry
- tridesclous/tests/test_matplotlibplot.py::test_plot_signals
-
tridesclous/tests/test_matplotlibplot.py::test_plot_waveforms_with_geometry
- tridesclous/tests/test_matplotlibplot.py::test_plot_waveforms
- tridesclous/tests/test_matplotlibplot.py::test_plot_features_scatter_2d
- tridesclous/tests/test_metrics.py::test_all_metrics
- tridesclous/tests/test_metrics.py::test_cluster_ratio
- tridesclous/tests/test_peeler.py::test_peeler_geometry
- tridesclous/tests/test_peeler.py::test_peeler_geometry_cl
- tridesclous/tests/test_peeler.py::test_peeler_empty_catalogue
- tridesclous/tests/test_peeler.py::test_peeler_several_chunksize
-
tridesclous/tests/test_peeler.py::test_peeler_with_and_without_preprocessor
- tridesclous/tests/test_peeler.py::test_export_spikes
- tridesclous/tests/test_report.py::test_summary_catalogue_clusters
- tridesclous/tests/test_report.py::test_summary_noise
- tridesclous/tests/test_report.py::test_summary_after_peeler_clusters
- tridesclous/tests/test_report.py::test_generate_report
- tridesclous/tests/test_autoparams.py::test_get_auto_params
-
tridesclous/tests/test_catalogueconstructor.py::test_catalogue_constructor
- tridesclous/tests/test_catalogueconstructor.py::test_make_catalogue
- tridesclous/tests/test_catalogueconstructor.py::test_ratio_amplitude
-
tridesclous/tests/test_catalogueconstructor.py::test_create_savepoint_catalogue_constructor
-
tridesclous/tests/test_catalogueconstructor.py::test_feature_with_lda_selection
- tridesclous/tests/test_cataloguetools.py::test_apply_all_catalogue_steps
- tridesclous/tests/test_dataio.py::test_DataIO
- tridesclous/tests/test_dataio.py::test_DataIO_probes
- tridesclous/tests/test_datasets.py::test_download_dataset
- tridesclous/tests/test_datasets.py::test_get_dataset
- tridesclous/tests/test_datasource.py::test_RawDataSource
- tridesclous/tests/test_datasource.py::test_NeoRawIOAggregator
-
tridesclous/tests/test_peakdetector.py::test_compare_offline_online_engines
- tridesclous/tests/test_peakdetector.py::test_detect_geometrical_peaks
- tridesclous/tests/test_peakdetector.py::test_peak_sign_symetry
-
tridesclous/tests/test_signalpreprocessor.py::test_compare_offline_online_engines
- tridesclous/tests/test_signalpreprocessor.py::test_auto_pad_width
- tridesclous/tests/test_tools.py::test_fix_prb_file_py2
-)
-
-python_test() {
- local EPYTEST_IGNORE=(
- tridesclous/online/tests/*
- )
- if use !gui ; then
- local EPYTEST_IGNORE+=(
- tridesclous/gui/*
- )
- fi
- epytest
-}
diff --git a/dev-python/tridesclous/tridesclous-1.6.6.ebuild
b/dev-python/tridesclous/tridesclous-1.6.6.ebuild
deleted file mode 100644
index fb401397f..000000000
--- a/dev-python/tridesclous/tridesclous-1.6.6.ebuild
+++ /dev/null
@@ -1,101 +0,0 @@
-# Copyright 2021-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{10..11} )
-DISTUTILS_USE_PEP517=setuptools
-inherit distutils-r1
-
-DESCRIPTION="offline/online spike sorting"
-HOMEPAGE="https://github.com/tridesclous/tridesclous";
-SRC_URI="https://github.com/tridesclous/tridesclous/archive/refs/tags/${PV}.tar.gz
-> ${P}.gh.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="gui test"
-
-RDEPEND="
- <dev-python/numpy-1.24.0[${PYTHON_USEDEP}]
- dev-python/cython[${PYTHON_USEDEP}]
- dev-python/hdbscan[${PYTHON_USEDEP}]
- dev-python/loky[${PYTHON_USEDEP}]
- dev-python/matplotlib[${PYTHON_USEDEP}]
- dev-python/neo[${PYTHON_USEDEP}]
- dev-python/numba
- dev-python/openpyxl[${PYTHON_USEDEP}]
- dev-python/pandas[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- dev-python/seaborn[${PYTHON_USEDEP}]
- dev-python/tqdm[${PYTHON_USEDEP}]
- sci-libs/scikit-learn[${PYTHON_USEDEP}]
- gui? (
- dev-python/PyQt5[${PYTHON_USEDEP}]
- )
-"
-
-distutils_enable_tests pytest
-
-# Network sandboxing, this is sadly more than half the test suite :(
-EPYTEST_DESELECT=(
- tridesclous/tests/test_cleancluster.py::test_auto_split
- tridesclous/tests/test_cleancluster.py::test_trash_not_aligned
- tridesclous/tests/test_cleancluster.py::test_auto_merge
- tridesclous/tests/test_cleancluster.py::test_trash_low_extremum
- tridesclous/tests/test_cleancluster.py::test_trash_small_cluster
- tridesclous/tests/test_cluster.py::test_sawchaincut
- tridesclous/tests/test_cluster.py::test_pruningshears
- tridesclous/tests/test_decomposition.py::test_all_decomposition
- tridesclous/tests/test_export.py::test_export
- tridesclous/tests/test_export.py::test_export_catalogue_spikes
- tridesclous/tests/test_jobtools.py::test_run_parallel_signalprocessor
- tridesclous/tests/test_matplotlibplot.py::test_plot_probe_geometry
- tridesclous/tests/test_matplotlibplot.py::test_plot_signals
-
tridesclous/tests/test_matplotlibplot.py::test_plot_waveforms_with_geometry
- tridesclous/tests/test_matplotlibplot.py::test_plot_waveforms
- tridesclous/tests/test_matplotlibplot.py::test_plot_features_scatter_2d
- tridesclous/tests/test_metrics.py::test_all_metrics
- tridesclous/tests/test_metrics.py::test_cluster_ratio
- tridesclous/tests/test_peeler.py::test_peeler_geometry
- tridesclous/tests/test_peeler.py::test_peeler_geometry_cl
- tridesclous/tests/test_peeler.py::test_peeler_empty_catalogue
- tridesclous/tests/test_peeler.py::test_peeler_several_chunksize
-
tridesclous/tests/test_peeler.py::test_peeler_with_and_without_preprocessor
- tridesclous/tests/test_peeler.py::test_export_spikes
- tridesclous/tests/test_report.py::test_summary_catalogue_clusters
- tridesclous/tests/test_report.py::test_summary_noise
- tridesclous/tests/test_report.py::test_summary_after_peeler_clusters
- tridesclous/tests/test_report.py::test_generate_report
- tridesclous/tests/test_autoparams.py::test_get_auto_params
-
tridesclous/tests/test_catalogueconstructor.py::test_catalogue_constructor
- tridesclous/tests/test_catalogueconstructor.py::test_make_catalogue
- tridesclous/tests/test_catalogueconstructor.py::test_ratio_amplitude
-
tridesclous/tests/test_catalogueconstructor.py::test_create_savepoint_catalogue_constructor
-
tridesclous/tests/test_catalogueconstructor.py::test_feature_with_lda_selection
- tridesclous/tests/test_cataloguetools.py::test_apply_all_catalogue_steps
- tridesclous/tests/test_dataio.py::test_DataIO
- tridesclous/tests/test_dataio.py::test_DataIO_probes
- tridesclous/tests/test_datasets.py::test_download_dataset
- tridesclous/tests/test_datasets.py::test_get_dataset
- tridesclous/tests/test_datasource.py::test_RawDataSource
- tridesclous/tests/test_datasource.py::test_NeoRawIOAggregator
-
tridesclous/tests/test_peakdetector.py::test_compare_offline_online_engines
- tridesclous/tests/test_peakdetector.py::test_detect_geometrical_peaks
- tridesclous/tests/test_peakdetector.py::test_peak_sign_symetry
-
tridesclous/tests/test_signalpreprocessor.py::test_compare_offline_online_engines
- tridesclous/tests/test_signalpreprocessor.py::test_auto_pad_width
- tridesclous/tests/test_tools.py::test_fix_prb_file_py2
-)
-
-python_test() {
- local EPYTEST_IGNORE=(
- tridesclous/online/tests/*
- )
- if use !gui ; then
- local EPYTEST_IGNORE+=(
- tridesclous/gui/*
- )
- fi
- epytest
-}
diff --git a/dev-python/umap-learn/metadata.xml
b/dev-python/umap-learn/metadata.xml
deleted file mode 100644
index 36f603448..000000000
--- a/dev-python/umap-learn/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";>
-<pkgmetadata>
- <maintainer type="person">
- <email>[email protected]</email>
- <name>Aisha Tammy</name>
- </maintainer>
- <maintainer type="project">
- <email>[email protected]</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <upstream>
- <remote-id type="pypi">umap-learn</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/dev-python/umap-learn/umap-learn-0.5.2.ebuild
b/dev-python/umap-learn/umap-learn-0.5.2.ebuild
deleted file mode 100644
index ea2769294..000000000
--- a/dev-python/umap-learn/umap-learn-0.5.2.ebuild
+++ /dev/null
@@ -1,25 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_10 )
-PYPI_NO_NORMALIZE=1
-inherit distutils-r1 pypi
-
-DESCRIPTION="Uniform Manifold Approximation and Projection"
-HOMEPAGE="https://umap-learn.readthedocs.io/";
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- >=dev-python/numba-0.49[${PYTHON_USEDEP}]
- >=dev-python/numpy-1.17[${PYTHON_USEDEP}]
- >=dev-python/pynndescent-0.5[${PYTHON_USEDEP}]
- >=dev-python/scipy-1.0[${PYTHON_USEDEP}]
- dev-python/tqdm[${PYTHON_USEDEP}]
- >=sci-libs/scikit-learn-0.22[${PYTHON_USEDEP}]
-"
-DEPEND="${RDEPEND}"
diff --git a/profiles/package.mask b/profiles/package.mask
index 527c834e4..9f3b8e7f5 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,17 +30,6 @@
#--- END OF EXAMPLES ---
-# Andrew Ammerlaan <[email protected]> (29 Dec 2023)
-# Depends on removed llvm:14, at the time of writing no llvm:15
-# update available.
-dev-python/llvmlite
-dev-python/numba
-dev-python/numba-dpex
-dev-python/pynndescent
-# Reverse dep of numba
-dev-python/tridesclous
-dev-python/umap-learn
-
# Andrew Ammerlaan <[email protected]> (26 Jun 2023)
# Depends on removed dev-python/toml.
# Alternatives are tomli or tomlkit
