From 7fa8a1e3f149eea4c844c47cfe26136ed7614c58 Mon Sep 17 00:00:00 2001
From: V3n3RiX <venerix@koprulu.sector>
Date: Mon, 15 Apr 2024 12:04:03 +0100
Subject: gentoo auto-resync : 15:04:2024 - 12:04:02

---
 sci-chemistry/Manifest.gz                          | Bin 9366 -> 9197 bytes
 sci-chemistry/mdtraj/Manifest                      |   4 --
 .../mdtraj/files/mdtraj-1.9.7-python311.patch      |  16 -------
 sci-chemistry/mdtraj/mdtraj-1.9.7.ebuild           |  49 ---------------------
 sci-chemistry/mdtraj/metadata.xml                  |  12 -----
 5 files changed, 81 deletions(-)
 delete mode 100644 sci-chemistry/mdtraj/Manifest
 delete mode 100644 sci-chemistry/mdtraj/files/mdtraj-1.9.7-python311.patch
 delete mode 100644 sci-chemistry/mdtraj/mdtraj-1.9.7.ebuild
 delete mode 100644 sci-chemistry/mdtraj/metadata.xml

(limited to 'sci-chemistry')

diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index aba8f109a3d6..bb4ee1b8daac 100644
Binary files a/sci-chemistry/Manifest.gz and b/sci-chemistry/Manifest.gz differ
diff --git a/sci-chemistry/mdtraj/Manifest b/sci-chemistry/mdtraj/Manifest
deleted file mode 100644
index c968c31ee89a..000000000000
--- a/sci-chemistry/mdtraj/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-AUX mdtraj-1.9.7-python311.patch 588 BLAKE2B 74d4b4ead237ffe0c1cfbd8f006e31c8faed2ef91f2d3fcf92d6ea2c6edc593815558fac0485bdefd80d6cacc7459979b96da314c2f7d18e0d614e31a4547d52 SHA512 f540d34fe9824e2a871dd891b4b3fbbfc5a9e6851c41083a0d2f7da4e412029cad0d6ad0fb60c923070dd696e99d9a93c5c5e535cf581cafe7419e18b96fc75b
-DIST mdtraj-1.9.7.tar.gz 2087085 BLAKE2B 430b42eddee0be8beba47994efd16515727970ac7acb36007c9b153cdb474551e5ea228f78a194fa9672d5b169753a9db3c090412bf749b3f1e9323bad9f52de SHA512 5dc9d474909a160e0b1d7989325e8190d1c593087f0130854094eb9c49bc00fd631ea19142d396d49aa7a3dadddaf535b5e811f7574ffff36f0cd22f14691067
-EBUILD mdtraj-1.9.7.ebuild 1217 BLAKE2B 95991ab3a3697b1b00dc3d1e6b5bfb4e7ab66e1672c466e23e16681ddcc2a62ee5cd04130b0050d18e6a4ed18b8a917708822c125c5c188cdcad64028e21bef1 SHA512 07ab8716aaf4dab09407ad0351ddc65f3597dad6d1449722c6a6a984c0dcab5886b5f4fed67293c3df0de1ed41a7313d77e5b58d0f32877c5049379ec210234b
-MISC metadata.xml 376 BLAKE2B 9fae78491c72370939157fcbf6f452831a46f919ffe0894d404cebff2d095735aaacfdbcae8e8500872ae69bfc790dfb8e788b9a904b9f44f82c873ed678299e SHA512 cce4d328ee75176dc53c4d8b7d1b74e153aeec929eeb15158054c557ddbaa2206b9bf3a7d729629bf8abfa0d8ce7f01206f9f240c2e78b390987cf014ee63669
diff --git a/sci-chemistry/mdtraj/files/mdtraj-1.9.7-python311.patch b/sci-chemistry/mdtraj/files/mdtraj-1.9.7-python311.patch
deleted file mode 100644
index 303c819aaee4..000000000000
--- a/sci-chemistry/mdtraj/files/mdtraj-1.9.7-python311.patch
+++ /dev/null
@@ -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)
diff --git a/sci-chemistry/mdtraj/mdtraj-1.9.7.ebuild b/sci-chemistry/mdtraj/mdtraj-1.9.7.ebuild
deleted file mode 100644
index 75356685592c..000000000000
--- a/sci-chemistry/mdtraj/mdtraj-1.9.7.ebuild
+++ /dev/null
@@ -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
-}
diff --git a/sci-chemistry/mdtraj/metadata.xml b/sci-chemistry/mdtraj/metadata.xml
deleted file mode 100644
index b91aca7d360a..000000000000
--- a/sci-chemistry/mdtraj/metadata.xml
+++ /dev/null
@@ -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>
-- 
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