gentoo resync : 25.08.2020

7 files changed, 0 insertions, 222 deletions

diff --git a/sci-chemistry/pdb2pqr/Manifest b/sci-chemistry/pdb2pqr/Manifest
deleted file mode 100644
index d057f25d651e..000000000000
--- a/sci-chemistry/pdb2pqr/Manifest
+++ /dev/null
@@ -1,7 +0,0 @@
-AUX pdb2pka 270 BLAKE2B c4b063cc22f416e5847ceec3377b43f2a7ddda7d204dd07c2870f499483d2ff9edada0632629336b268df904e960d4cb1dad92075ddf42b73d052e7214b20c45 SHA512 c6e66fa73a3119ea84a9bf304c9c8701a6eaf32870ba8c1755bfd8f2055e20af2f2ebc01fd2bf6a663e5873f3d6da7387a439efac3dcb7d4a415c176cb2f761b
-AUX pdb2pqr 263 BLAKE2B 3cbd33cf9fb9fd6469c71d8d167ed0fb85ad7b87b6caf27dabb2490b28950961eeffac1c9e4c67102924ecaad002fc5c3d9f2a6955f66eb0699139486caa5372 SHA512 5f8c963fc5addf782579b9312f601ec4547573c7ab88df5a6e38c71c9e31e7b7eea3cde99bdac8f8270f3646d933a0b510a94046e3a30736f75953af5d160b8d
-AUX pdb2pqr-1.9.0-flags.patch 1392 BLAKE2B b6b6ac64f98944d85fc93c076d7258c8f980a0391d2cf086edc46bca3f4ef15a5cb720ef8ae2dc38007962a462fb88e92eb4f439c4f3267a5d1d83de5a848dd6 SHA512 deed0aef88dc43515745204f2b4209bd6b42702d9004d48797d642b8f497229424bd0bb92017982cec54c448ea35de563bd42017cd5dc042840acae8495d135b
-AUX pdb2pqr-1.9.0-install-py.patch 578 BLAKE2B 91ad4b40ce3d13b574ad6d9ea84e55b08803fa018490a7327dae5621a371adfeda509188c049144301cbc023f4407f6c0daf7b57e7d3c10d95d78ab570a6f540 SHA512 902ad717e32790e9c691851dc4b92412f07ac79caf74b2b5794a10fa75cca7fa19e8814df4d8ba71bd2ecc98a3d777d0b79e6e43009171a32e8c99756d81d4d2
-DIST pdb2pqr-src-1.9.0.tar.gz 9051969 BLAKE2B bacb2c65d319fb918a7a15b772c250398ffa991a93ee731ec15c8ae907304daf57282bf83c24f84d11945349a7f93f6f934575c117d4ce24d6530f14e60f3730 SHA512 7f3f191cca9879a0e166e82700c706f8c99bb66558a218e54845f10c3324b6c45d413da80b0782d96a8d56df1463262609db075aba3768db3942cb928ee7b98f
-EBUILD pdb2pqr-1.9.0-r3.ebuild 2679 BLAKE2B 882e244c9764c317df96195e4c9049a8a23872c458487ed4e897263cc99b5e1fa8bb7a3a70bf34fda447d71767ee4eb59fa49c4beecbd04fd2577438bb8aaf8e SHA512 f5037488f9ecdc9be44fb1dcc15ec55db932fc4268b61db7d95375e0e22d9f54f0315a5c0eb4398919f8620c167adbdd5e632bcdb241724ebc77efb7e7442802
-MISC metadata.xml 511 BLAKE2B 70a1bf9ff6db44bdbae39b1f58ac5b80769738b2ce8fbb19b3bcb9fbf7cec2a9eab215a7a922025b9110673cb834255240adf10613fd78a8fea47fa7be4fbba9 SHA512 11a010eea3bbbaaf4150a23dadcd10c45737745d51a3341cd7e69cc8537215f313d1ab57059eff265e73e34aeaef435585bb652f5497508dd12b99f67b8580c0
diff --git a/sci-chemistry/pdb2pqr/files/pdb2pka b/sci-chemistry/pdb2pqr/files/pdb2pka
deleted file mode 100644
index 2406b0c4773f..000000000000
--- a/sci-chemistry/pdb2pqr/files/pdb2pka
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env python
-
-import subprocess
-import site
-import sys
-import os
-
-sitepackages = site.getsitepackages()[0]
-
-_cmd=[os.path.join(sitepackages, "pdb2pqr", "pdb2pka", "pka.py")]
-_cmd.extend(sys.argv[1:])
-
-subprocess.call(_cmd, stdout=sys.stdout, stderr=sys.stderr)
diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr b/sci-chemistry/pdb2pqr/files/pdb2pqr
deleted file mode 100644
index 8c0635aea94e..000000000000
--- a/sci-chemistry/pdb2pqr/files/pdb2pqr
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env python
-
-import subprocess
-import site
-import sys
-import os
-
-sitepackages = site.getsitepackages()[0]
-
-_cmd=[os.path.join(sitepackages, "pdb2pqr", "pdb2pqr.py")]
-_cmd.extend(sys.argv[1:])
-
-subprocess.call(_cmd, stdout=sys.stdout, stderr=sys.stderr)
diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.9.0-flags.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.9.0-flags.patch
deleted file mode 100644
index fac32b233e6b..000000000000
--- a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.9.0-flags.patch
+++ /dev/null
@@ -1,45 +0,0 @@
- pdb2pka/SConscript           | 9 ++++++++-
- pdb2pka/substruct/SConscript | 6 ++++++
- 2 files changed, 14 insertions(+), 1 deletion(-)
-
-diff --git a/pdb2pka/SConscript b/pdb2pka/SConscript
-index 583cdc5..6c30011 100644
---- a/pdb2pka/SConscript
-+++ b/pdb2pka/SConscript
-@@ -1,4 +1,11 @@
- Import('env')

-+import os

-+

-+env['CCFLAGS'].extend(os.environ['CXXFLAGS'].split())

-+env['LINKFLAGS'].extend(os.environ['LDFLAGS'].split())

-+env['CXX'] = os.environ['CXX']

-+env['LINK'] = os.environ['CXX']

-+

- 

- if env['REBUILD_SWIG']:

-     pyc = env.LoadableModule('_pMC_mult', ['pMC_mult.cpp', 'pMC_mult.i'])

-@@ -9,4 +16,4 @@ Default(pyc)
-     

- algorithms_module = SConscript('substruct/SConscript')

- 

--Return('pyc algorithms_module')
-\ No newline at end of file
-+Return('pyc algorithms_module')

-diff --git a/pdb2pka/substruct/SConscript b/pdb2pka/substruct/SConscript
-index 7dbcdb0..56fb577 100644
---- a/pdb2pka/substruct/SConscript
-+++ b/pdb2pka/substruct/SConscript
-@@ -1,7 +1,13 @@
- import distutils

- import numpy

-+import os

- Import('env')

- 

-+env['CCFLAGS'].extend(os.environ['CXXFLAGS'].split())

-+env['LINKFLAGS'].extend(os.environ['LDFLAGS'].split())

-+env['CXX'] = os.environ['CXX']

-+env['LINK'] = os.environ['CXX']

-+

- env.Append(CPPPATH=[distutils.sysconfig.get_python_inc(), numpy.get_include()])

- 

- algorithms_pyc = env.LoadableModule('Algorithms', ['Algorithms.cpp'])

diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.9.0-install-py.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.9.0-install-py.patch
deleted file mode 100644
index 2695b013c66a..000000000000
--- a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.9.0-install-py.patch
+++ /dev/null
@@ -1,15 +0,0 @@
- SConscript-install.py | 1 +
- 1 file changed, 1 insertion(+)
-
-diff --git a/SConscript-install.py b/SConscript-install.py
-index e2f9f09..1fdf1a8 100644
---- a/SConscript-install.py
-+++ b/SConscript-install.py
-@@ -41,6 +41,7 @@ def installFile(file_name, build_target='install'):
- 		if GetOption("clean"):

- 			env.Default(result)

- 		Alias(build_target, env.Install(env['PREFIX']+dirname(file_name), result))

-+		Alias(build_target, env.Install(env['PREFIX']+dirname(file_name), target))

- 	else:

- 		Alias(build_target, env.Install(env['PREFIX']+dirname(file_name), target))

- 

diff --git a/sci-chemistry/pdb2pqr/metadata.xml b/sci-chemistry/pdb2pqr/metadata.xml
deleted file mode 100644
index 36fd8c04ac52..000000000000
--- a/sci-chemistry/pdb2pqr/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="project">
-    <email>sci-chemistry@gentoo.org</email>
-    <name>Gentoo Chemistry Project</name>
-  </maintainer>
-  <use>
-    <flag name="opal">Add web interface via opal</flag>
-    <flag name="pdb2pka">Install experimental pdb2pka interface</flag>
-  </use>
-  <upstream>
-    <remote-id type="github">Electrostatics/apbs-pdb2pqr</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r3.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r3.ebuild
deleted file mode 100644
index 179e6448d605..000000000000
--- a/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r3.ebuild
+++ /dev/null
@@ -1,114 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit scons-utils fortran-2 flag-o-matic python-single-r1 toolchain-funcs
-
-DESCRIPTION="Automated pipeline for performing Poisson-Boltzmann electrostatics calculations"
-HOMEPAGE="https://www.poissonboltzmann.org/"
-SRC_URI="https://github.com/Electrostatics/apbs-${PN}/releases/download/${P}/${PN}-src-${PV}.tar.gz"
-
-SLOT="0"
-LICENSE="BSD"
-IUSE="doc examples opal +pdb2pka"
-KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="${PYTHON_DEPS}
-	$(python_gen_cond_dep '
-		|| (
-			dev-python/numpy-python2[${PYTHON_MULTI_USEDEP}]
-			dev-python/numpy[${PYTHON_MULTI_USEDEP}]
-		)
-		sci-chemistry/openbabel-python[${PYTHON_MULTI_USEDEP}]
-		opal? ( dev-python/zsi[${PYTHON_MULTI_USEDEP}] )
-	')
-	pdb2pka? ( sci-chemistry/apbs[${PYTHON_SINGLE_USEDEP},-mpi] )"
-DEPEND="${RDEPEND}
-	dev-lang/swig:0"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-flags.patch
-	"${FILESDIR}"/${P}-install-py.patch
-)
-
-pkg_setup() {
-	if [[ -z ${MAXATOMS} ]]; then
-		einfo "If you like to have support for more then 10000 atoms,"
-		einfo "export MAXATOMS=\"your value\""
-		export MAXATOMS=10000
-	else
-		einfo "Allow usage of ${MAXATOMS} during calculations"
-	fi
-	fortran-2_pkg_setup
-	python-single-r1_pkg_setup
-}
-
-src_prepare() {
-	find -type f \( -name "*\.pyc" -o -name "*\.pyo" \) -delete || die
-
-	export CXXFLAGS="${CXXFLAGS}"
-	export LDFLAGS="${LDFLAGS}"
-
-	epatch "${PATCHES[@]}"
-	tc-export CXX
-	rm -rf scons || die
-}
-
-src_configure() {
-	cat > build_config.py <<- EOF
-		PREFIX="${D}/$(python_get_sitedir)/${PN}"
-		#URL="http://<COMPUTER NAME>/pdb2pqr/"
-		APBS="${EPREFIX}/usr/bin/apbs"
-		#OPAL="http://nbcr-222.ucsd.edu/opal2/services/pdb2pqr_1.8"
-		#APBS_OPAL="http://nbcr-222.ucsd.edu/opal2/services/apbs_1.3"
-		MAX_ATOMS=${MAXATOMS}
-		BUILD_PDB2PKA=$(usex pdb2pka True False)
-		REBUILD_SWIG=True
-	EOF
-}
-
-src_compile() {
-	escons
-}
-
-src_test() {
-	local myesconsargs=( -j1 )
-	escons test
-	escons advtest
-	escons complete-test
-}
-
-src_install() {
-	dodir /usr/share/doc/${PF}/html
-	local lib
-
-	escons install
-
-	find "${D}$(python_get_sitedir)"/${PN}/{jmol,examples,doc,contrib} -delete || die
-
-	python_doscript "${FILESDIR}"/{${PN},pdb2pka}
-
-	for lib in apbslib.py{,c,o}; do
-		dosym ../../apbs/${lib} $(python_get_sitedir)/${PN}/pdb2pka/${lib}
-	done
-	dosym ../../_apbslib.so $(python_get_sitedir)/${PN}/pdb2pka/_apbslib.so
-	python_optimize
-
-	if use doc; then
-		pushd doc > /dev/null
-		docinto html
-		dodoc -r *.html images pydoc
-		popd > /dev/null
-	fi
-
-	use examples && \
-		insinto /usr/share/${PN}/ && \
-		doins -r examples
-
-	dodoc *md NEWS
-}