sci-chemistry/mdtraj: Remove last-rited pkg

Bug: https://bugs.gentoo.org/911646
Signed-off-by: Michał Górny <mgorny@gentoo.org>

profiles/package.mask

@@ -319,7 +319,6 @@ dev-java/failureaccess
 # dev-python/python-efl: econnman as revdep, bug #925692.
 # dev-python/pygame_sdl2: also py3.12, bug #911781
 # games-engines/renpy: also py3.12, bug #925693
-# sci-chemistry/mdtraj: also py3.12, PEP517, bug #911646.
 #
 # Includes their few reverse dependencies and their exclusive
 # dependencies without Python 3.12 support.
@@ -330,7 +329,6 @@ dev-python/pygame_sdl2
 dev-python/python-efl
 games-engines/renpy
 net-misc/econnman
-sci-chemistry/mdtraj
 
 # Eray Aslan <eras@gentoo.org> (2024-03-10)
 # Mask experimental software

sci-chemistry/mdtraj/Manifest

@@ -1 +0,0 @@
-DIST mdtraj-1.9.7.tar.gz 2087085 BLAKE2B 430b42eddee0be8beba47994efd16515727970ac7acb36007c9b153cdb474551e5ea228f78a194fa9672d5b169753a9db3c090412bf749b3f1e9323bad9f52de SHA512 5dc9d474909a160e0b1d7989325e8190d1c593087f0130854094eb9c49bc00fd631ea19142d396d49aa7a3dadddaf535b5e811f7574ffff36f0cd22f14691067

sci-chemistry/mdtraj/files/mdtraj-1.9.7-python311.patch

@@ -1,16 +0,0 @@
-Index: mdtraj/setup.py
-===================================================================
---- mdtraj.orig/setup.py	2023-01-18 15:26:51.424826255 +0100
-+++ mdtraj/setup.py	2023-01-18 15:26:51.420826223 +0100
-@@ -298,6 +298,10 @@
- 
-         for e in extensions:
-             e.include_dirs.append(np.get_include())
--        metadata['ext_modules'] = cythonize(extensions, language_level=sys.version_info[0])
-+        metadata['ext_modules'] = cythonize(
-+            extensions,
-+            language_level=sys.version_info[0],
-+            force=True,
-+        )
- 
-     setup(**metadata)

sci-chemistry/mdtraj/mdtraj-1.9.7.ebuild

@@ -1,49 +0,0 @@
-# Copyright 1999-2024 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-PYTHON_COMPAT=( python3_{10..11} )
-
-inherit distutils-r1 pypi
-
-DESCRIPTION="Read, write and analyze MD trajectories with only a few lines of Python code"
-HOMEPAGE="https://mdtraj.org"
-
-SLOT="0"
-LICENSE="LGPL-2.1+"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-RDEPEND="
-	dev-python/astunparse[${PYTHON_USEDEP}]
-	dev-python/astor[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/pandas[${PYTHON_USEDEP}]
-	dev-python/pyparsing[${PYTHON_USEDEP}]
-	dev-python/networkx[${PYTHON_USEDEP}]
-	dev-python/scipy[${PYTHON_USEDEP}]
-	dev-python/tables[${PYTHON_USEDEP}]
-"
-DEPEND="${RDEPEND}
-	test? (
-		dev-python/ipykernel[${PYTHON_USEDEP}]
-		dev-python/jupyter-client[${PYTHON_USEDEP}]
-		dev-python/nbformat[${PYTHON_USEDEP}]
-		dev-python/scikit-learn[${PYTHON_USEDEP}]
-	)
-"
-# <cython-3 for bug #911646
-BDEPEND="
-	<dev-python/cython-3[${PYTHON_USEDEP}]
-"
-
-distutils_enable_tests --install pytest
-
-PATCHES=(
-	"${FILESDIR}/${P}-python311.patch"
-)
-
-python_prepare_all() {
-	sed -e "s:re.match('build.*(mdtraj.*)', output_dir).group(1):'.':g" \
-		-i basesetup.py || die
-	distutils-r1_python_prepare_all
-}

sci-chemistry/mdtraj/metadata.xml

@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">mdtraj/mdtraj</remote-id>
-		<remote-id type="pypi">mdtraj</remote-id>
-	</upstream>
-</pkgmetadata>