gentoo resync : 14.05.2020

4 files changed, 191 insertions, 24 deletions

diff --git a/sci-libs/cantera/Manifest b/sci-libs/cantera/Manifest
index 9060984e7a0c..b4ee5e8a3304 100644
--- a/sci-libs/cantera/Manifest
+++ b/sci-libs/cantera/Manifest
@@ -1,7 +1,9 @@
 AUX cantera_2.4.0_env.patch 3559 BLAKE2B 07af1b751b653b1c92288286b9c82ef230ea0df7d9ea4036d23ac24338a221cc45c8e74f137fcf741bb9bb7148e7f3339f54234e9a92ac939956ba7c0ca8e157 SHA512 f2574c3de42d1666a2b64914c66d97045a2a3598f63678b3b60a701d111d7bfc9bd71031dd665a64e6791c9f311fb9514b1a0462a5713763a1b5f87fcd72e528
 AUX cantera_2.4.0_env_python_install.patch 1001 BLAKE2B bfe6e69332117526d8a7c330ae9610e26e72a9e250ce04beda564149fbd21f3262f36982971e5ec0c552e09f12804172b7f978ab03bfb98c0dbe92cd8c7d9401 SHA512 410a81b4ec69eb6eb2a60d55d142b266b836da5a7d4e4ae2fd8844fb87eff0f3544f6e370fc354d334c6cd5a61f8364842c8a9b3bd0dc2290f58ee7392a170f4
-AUX cantera_2.4.0_sundials4.patch 7504 BLAKE2B 55bfc58edaed97459a40a1adafcba545bc6513219e9ce1bbf4a529007c6c629ad295b4f85b9cac44da9a9399c721ca19547fa75948c0d0d518fc149862eb9b14 SHA512 4ddf7122df491f53bf67f299d8134b072751dc6f56ab0e4d7cfed733f35ad4b1fb7f005584b06f44d68dc2f29abc299bfb6a65b6b0b3daa828fc80fa52fac964
+AUX cantera_2.4.0_env_python_install_prefix.patch 943 BLAKE2B 06bc4ac2cc4aaa212325c3883b9cead668ed294f23a2ac768f28e593916d07f2322e21846b97b40e336dfc742ed45a9b95f8f49531cd82d2055499f810e13c2f SHA512 a7ebfd8f9a6fa406d5a5847ad98e91aa9cbf53d194ec87d8479b88ad322df13308947fae61574ebd6254eeaa1bcb49a4cd3e30db2981cebcbf13241ab8e050d6
+AUX cantera_2.4.0_sundials4.patch 8410 BLAKE2B dbee09305610bb0d74c1569d694782194c0cb3daf06b581fa385021faed9d54d8f900747bdcac64b0322dcc82fee20bc330b71bee1aa90fe9df68efc335427b7 SHA512 ec4b80b761c3d18cc03bb87ec59b7c860b6818c3a5503f3f7c759f0bfde7cc6c5ded3c64294f9844e28a649754f4a1c158738bc5a7c923bd4808a78c6a59c91a
 DIST cantera-2.4.0.tar.gz 2321316 BLAKE2B 40750e3864afa3d35817e6f5777a6ac235261e9d134ef749966dbd738a2af5efec2882e6dcc719851f88656b41469e2159d3bff3df32f6abdf57db3b0a2afcae SHA512 8bb0fee34fa5bc9ec78e6f21a100eaa77bdd966bd0b7f0fa27d452e4f122c69e61648beef847178490f5c5d56267a96f6081cac9ccd03cea153c32814e0e84e9
 EBUILD cantera-2.4.0-r1.ebuild 2929 BLAKE2B 57eb719f155c1c58024283cea0fd7a667888ce1749be056a644e80f466ac7ed66c854277ae67681a19f6d374ede9a3fb4394f80f4d5802bab77bc28e41807223 SHA512 f1d88be5b54a480735ae55da4a05267c3890abaa80776124234bb5dcb8dd539e6df9d3cf8dd29a1577f9008cc57581e0f6a575b14d1c432599e72f93cbd6967b
 EBUILD cantera-2.4.0-r4.ebuild 3028 BLAKE2B cacb43b61a63aba2ae8a55393ff8f0ea93c0bbea9266f182d3ac270e822b09a16865da60076e6ea059bc1c684c9a13e7291f3aed037ca2fa79c48d0844fd5051 SHA512 c3f361945f1d4756f8251fc3122a4b8ba36e5f5723c4d71742f8d089a41614669ecaf5462a8e2d5945b09611eda3a98f4d91736ca253202c44d1a6fd6cb22705
+EBUILD cantera-2.4.0-r5.ebuild 3072 BLAKE2B 44b04260688a25de14ad1bd53bc5831f4f3354bc0b9cda0c857f86456b7d64e644284e7748ac0949cc5a5b50e3c297bedfdd6f162621eeb8c5d32f3570e318d7 SHA512 a4f702e5a7f4e8bf7c1147bd6a96d2bc51ef99a7c60691deb1f24fd07a78ca8cfb6427a0758912611793272c58a8bf87d66dcaa47b888dc0a3204729c0bb8ecf
 MISC metadata.xml 794 BLAKE2B 4a92fb553aad7d87d4b7a8d77974dbd67d593b4010783f96324979d9c01067bccc60d2faedf604bd8d44a8ac4316356879301899af8bc08d0fcd548df6d3762d SHA512 a9e6f4e161519d0b3618fe8da7065195bc760ba889fa4356358d4047ea1970eb5fd78bdc5fbeb7c660f1bee48a68ab20ced636514e6f12848e88f6f4dabc9705
diff --git a/sci-libs/cantera/cantera-2.4.0-r5.ebuild b/sci-libs/cantera/cantera-2.4.0-r5.ebuild
new file mode 100644
index 000000000000..ac2a89b4ddd4
--- /dev/null
+++ b/sci-libs/cantera/cantera-2.4.0-r5.ebuild
@@ -0,0 +1,131 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{6,7,8} )
+
+FORTRAN_NEEDED=fortran
+FORTRAN_STANDARD=90
+
+inherit desktop fortran-2 python-single-r1 scons-utils toolchain-funcs
+
+DESCRIPTION="Object-oriented tool suite for chemical kinetics, thermodynamics, and transport"
+HOMEPAGE="https://www.cantera.org"
+SRC_URI="https://github.com/Cantera/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="+cti fortran pch +python test"
+RESTRICT="!test? ( test )"
+
+REQUIRED_USE="
+	python? ( cti )
+	${PYTHON_REQUIRED_USE}
+	"
+
+RDEPEND="
+	${PYTHON_DEPS}
+	python? (
+		$(python_gen_cond_dep '
+			dev-python/numpy[${PYTHON_MULTI_USEDEP}]
+		')
+	)
+	<sci-libs/sundials-5.3.0:0=
+"
+
+DEPEND="
+	${RDEPEND}
+	dev-cpp/eigen:3
+	dev-libs/boost
+	dev-libs/libfmt
+	python? (
+		$(python_gen_cond_dep '
+			dev-python/cython[${PYTHON_MULTI_USEDEP}]
+		')
+	)
+	test? (
+		>=dev-cpp/gtest-1.8.0
+	)
+"
+
+PATCHES=(
+	"${FILESDIR}/${PN}_${PV}_env.patch"
+	"${FILESDIR}/${PN}_${PV}_env_python_install_prefix.patch"
+	"${FILESDIR}/${PN}_${PV}_sundials4.patch"
+)
+
+pkg_setup() {
+	fortran-2_pkg_setup
+	python-single-r1_pkg_setup
+}
+
+## Full list of configuration options of Cantera is presented here:
+## http://cantera.org/docs/sphinx/html/compiling/config-options.html
+
+src_configure() {
+	scons_vars=(
+		CC="$(tc-getCC)"
+		CXX="$(tc-getCXX)"
+		cc_flags="${CXXFLAGS}"
+		cxx_flags="-std=c++11"
+		debug="no"
+		FORTRAN="$(tc-getFC)"
+		FORTRANFLAGS="${FFLAGS}"
+		optimize_flags="-Wno-inline"
+		renamed_shared_libraries="no"
+		use_pch=$(usex pch)
+## In some cases other order can break the detection of right location of Boost: ##
+		system_fmt="y"
+		system_sundials="y"
+		system_eigen="y"
+		env_vars="all"
+		extra_inc_dirs="/usr/include/eigen3"
+	)
+	use test || scons_vars+=( googletest="none" )
+
+	scons_targets=(
+		f90_interface=$(usex fortran y n)
+		python2_package="none"
+	)
+
+	if use cti ; then
+		local scons_python=$(usex python full minimal)
+		scons_targets+=( python3_package="${scons_python}" python3_cmd="${EPYTHON}" )
+	else
+		scons_targets+=( python3_package="none" )
+	fi
+}
+
+src_compile() {
+	escons build "${scons_vars[@]}" "${scons_targets[@]}" prefix="/usr"
+}
+
+src_test() {
+	escons test
+}
+
+src_install() {
+	escons install stage_dir="${D}" libdirname="$(get_libdir)" python3_prefix="$(python_get_sitedir)"
+	if ! use cti ; then
+		rm -r "${D}/usr/share/man" || die "Can't remove man files."
+	else
+		# Run the byte-compile of modules
+		python_optimize "${D}/$(python_get_sitedir)/${PN}"
+	fi
+}
+
+pkg_postinst() {
+	if use cti && ! use python ; then
+		elog "Cantera was build without 'python' use-flag therefore the CTI tool 'ck2cti'"
+		elog "will convert Chemkin files to Cantera format without verification of kinetic mechanism."
+	fi
+
+	local post_msg=$(usex fortran "and Fortran " "")
+	elog "C++ ${post_msg}samples are installed to '/usr/share/${PN}/samples/' directory."
+
+	if use python ; then
+		elog "Python examples are installed to '$(python_get_sitedir)/${PN}/examples/' directories."
+	fi
+}
diff --git a/sci-libs/cantera/files/cantera_2.4.0_env_python_install_prefix.patch b/sci-libs/cantera/files/cantera_2.4.0_env_python_install_prefix.patch
new file mode 100644
index 000000000000..838907996361
--- /dev/null
+++ b/sci-libs/cantera/files/cantera_2.4.0_env_python_install_prefix.patch
@@ -0,0 +1,17 @@
+diff -Nur old/interfaces/cython/SConscript new/interfaces/cython/SConscript
+--- old/interfaces/cython/SConscript	2018-08-24 16:24:45.000000000 +0300
++++ new/interfaces/cython/SConscript	2019-08-14 04:28:41.000000000 +0300
+@@ -83,10 +83,10 @@
+             extra = ''
+         elif localenv['OS'] == 'Darwin':
+             extra = localenv.subst(' --prefix=${python%s_prefix}' % major)
+-        elif localenv['libdirname'] == 'lib64':
+-            # 64-bit RHEL / Fedora
++        elif localenv['libdirname'] != 'lib':
++            # 64-bit RHEL / Fedora etc. or e.g. x32 Gentoo profile
+             extra = localenv.subst(
+-                ' --prefix=${python%s_prefix} --install-lib=${python%s_prefix}/lib64/python%s.%s/site-packages' % (major, major, major, minor))
++                ' --prefix=${stage_dir}${prefix} --install-lib=${python%s_prefix}' % (major))
+         else:
+             extra = '--user'
+             localenv.AppendENVPath(
diff --git a/sci-libs/cantera/files/cantera_2.4.0_sundials4.patch b/sci-libs/cantera/files/cantera_2.4.0_sundials4.patch
index 8c44228019b8..0b4d3abf8541 100644
--- a/sci-libs/cantera/files/cantera_2.4.0_sundials4.patch
+++ b/sci-libs/cantera/files/cantera_2.4.0_sundials4.patch
@@ -1,6 +1,6 @@
-diff -Nur old/SConstruct new/SConstruct
---- old/SConstruct	2019-08-14 04:12:50.000000000 +0300
-+++ new/SConstruct	2019-08-14 04:38:55.000000000 +0300
+diff -Naur a/SConstruct b/SConstruct
+--- a/SConstruct	2020-04-21 13:55:06.000000000 +0300
++++ b/SConstruct	2020-04-21 13:55:54.000000000 +0300
 @@ -1013,23 +1013,29 @@
  
  import SCons.Conftest, SCons.SConf
@@ -42,18 +42,35 @@ diff -Nur old/SConstruct new/SConstruct
  
  # Checkout Sundials submodule if needed
  if (env['system_sundials'] == 'n' and
-@@ -1066,7 +1072,7 @@
+@@ -1066,13 +1072,14 @@
  
      # Ignore the minor version, e.g. 2.4.x -> 2.4
      env['sundials_version'] = '.'.join(sundials_version.split('.')[:2])
 -    if env['sundials_version'] not in ('2.4','2.5','2.6','2.7','3.0','3.1','3.2'):
-+    if env['sundials_version'] not in ('2.4','2.5','2.6','2.7','3.0','3.1','3.2','4.0','4.1','5.0','5.1'):
++    sundials_ver = LooseVersion(env['sundials_version'])
++    if sundials_ver < LooseVersion('2.4') or sundials_ver >= LooseVersion('6.0'):
          print("""ERROR: Sundials version %r is not supported.""" % env['sundials_version'])
          sys.exit(1)
      print("""INFO: Using system installation of Sundials version %s.""" % sundials_version)
-diff -Nur old/include/cantera/numerics/CVodesIntegrator.h new/include/cantera/numerics/CVodesIntegrator.h
---- old/include/cantera/numerics/CVodesIntegrator.h	2018-08-24 16:24:45.000000000 +0300
-+++ new/include/cantera/numerics/CVodesIntegrator.h	2019-08-14 04:39:50.000000000 +0300
+ 
+     #Determine whether or not Sundials was built with BLAS/LAPACK
+-    if LooseVersion(env['sundials_version']) < LooseVersion('2.6'):
++    if sundials_ver < LooseVersion('2.6'):
+         # In Sundials 2.4 / 2.5, SUNDIALS_BLAS_LAPACK is either 0 or 1
+         sundials_blas_lapack = get_expression_value(['"sundials/sundials_config.h"'],
+                                                        'SUNDIALS_BLAS_LAPACK')
+@@ -1690,7 +1697,7 @@
+ 
+ if env['system_sundials'] == 'y':
+     env['sundials_libs'] = ['sundials_cvodes', 'sundials_ida', 'sundials_nvecserial']
+-    if env['use_lapack'] and LooseVersion(env['sundials_version']) >= LooseVersion('3.0'):
++    if env['use_lapack'] and sundials_ver >= LooseVersion('3.0'):
+         if env.get('has_sundials_lapack'):
+             env['sundials_libs'].extend(('sundials_sunlinsollapackdense',
+                                          'sundials_sunlinsollapackband'))
+diff -Naur a/include/cantera/numerics/CVodesIntegrator.h b/include/cantera/numerics/CVodesIntegrator.h
+--- a/include/cantera/numerics/CVodesIntegrator.h	2018-08-24 16:24:45.000000000 +0300
++++ b/include/cantera/numerics/CVodesIntegrator.h	2020-04-21 13:55:54.000000000 +0300
 @@ -49,7 +49,6 @@
          m_maxord = n;
      }
@@ -62,9 +79,9 @@ diff -Nur old/include/cantera/numerics/CVodesIntegrator.h new/include/cantera/nu
      virtual void setMaxStepSize(double hmax);
      virtual void setMinStepSize(double hmin);
      virtual void setMaxSteps(int nmax);
-diff -Nur old/include/cantera/numerics/Integrator.h new/include/cantera/numerics/Integrator.h
---- old/include/cantera/numerics/Integrator.h	2018-08-24 16:24:45.000000000 +0300
-+++ new/include/cantera/numerics/Integrator.h	2019-08-14 04:44:27.000000000 +0300
+diff -Naur a/include/cantera/numerics/Integrator.h b/include/cantera/numerics/Integrator.h
+--- a/include/cantera/numerics/Integrator.h	2018-08-24 16:24:45.000000000 +0300
++++ b/include/cantera/numerics/Integrator.h	2020-04-21 13:55:54.000000000 +0300
 @@ -34,17 +34,6 @@
      Adams_Method //! Adams
  };
@@ -95,9 +112,9 @@ diff -Nur old/include/cantera/numerics/Integrator.h new/include/cantera/numerics
      //! Set the maximum step size
      virtual void setMaxStepSize(double hmax) {
          warn("setMaxStepSize");
-diff -Nur old/src/kinetics/ImplicitSurfChem.cpp new/src/kinetics/ImplicitSurfChem.cpp
---- old/src/kinetics/ImplicitSurfChem.cpp	2018-08-24 16:24:45.000000000 +0300
-+++ new/src/kinetics/ImplicitSurfChem.cpp	2019-08-14 04:45:57.000000000 +0300
+diff -Naur a/src/kinetics/ImplicitSurfChem.cpp b/src/kinetics/ImplicitSurfChem.cpp
+--- a/src/kinetics/ImplicitSurfChem.cpp	2018-08-24 16:24:45.000000000 +0300
++++ b/src/kinetics/ImplicitSurfChem.cpp	2020-04-21 13:55:54.000000000 +0300
 @@ -79,7 +79,6 @@
      // numerically, and use a Newton linear iterator
      m_integ->setMethod(BDF_Method);
@@ -106,9 +123,9 @@ diff -Nur old/src/kinetics/ImplicitSurfChem.cpp new/src/kinetics/ImplicitSurfChe
      m_work.resize(ntmax);
  }
  
-diff -Nur old/src/numerics/CVodesIntegrator.cpp new/src/numerics/CVodesIntegrator.cpp
---- old/src/numerics/CVodesIntegrator.cpp	2018-08-24 16:24:45.000000000 +0300
-+++ new/src/numerics/CVodesIntegrator.cpp	2019-08-14 04:49:02.000000000 +0300
+diff -Naur a/src/numerics/CVodesIntegrator.cpp b/src/numerics/CVodesIntegrator.cpp
+--- a/src/numerics/CVodesIntegrator.cpp	2018-08-24 16:24:45.000000000 +0300
++++ b/src/numerics/CVodesIntegrator.cpp	2020-04-21 13:55:54.000000000 +0300
 @@ -88,7 +88,6 @@
      m_type(DENSE+NOJAC),
      m_itol(CV_SS),
@@ -161,9 +178,9 @@ diff -Nur old/src/numerics/CVodesIntegrator.cpp new/src/numerics/CVodesIntegrato
              #if CT_SUNDIALS_USE_LAPACK
                  m_linsol = SUNLapackBand(m_y, (SUNMatrix) m_linsol_matrix);
              #else
-diff -Nur old/src/numerics/IDA_Solver.cpp new/src/numerics/IDA_Solver.cpp
---- old/src/numerics/IDA_Solver.cpp	2018-08-24 16:24:45.000000000 +0300
-+++ new/src/numerics/IDA_Solver.cpp	2019-08-14 04:51:01.000000000 +0300
+diff -Naur a/src/numerics/IDA_Solver.cpp b/src/numerics/IDA_Solver.cpp
+--- a/src/numerics/IDA_Solver.cpp	2018-08-24 16:24:45.000000000 +0300
++++ b/src/numerics/IDA_Solver.cpp	2020-04-21 13:55:54.000000000 +0300
 @@ -442,7 +442,11 @@
          #if CT_SUNDIALS_VERSION >= 30
              SUNLinSolFree((SUNLinearSolver) m_linsol);
@@ -177,9 +194,9 @@ diff -Nur old/src/numerics/IDA_Solver.cpp new/src/numerics/IDA_Solver.cpp
              #if CT_SUNDIALS_USE_LAPACK
                  m_linsol = SUNLapackBand(m_y, (SUNMatrix) m_linsol_matrix);
              #else
-diff -Nur old/src/zeroD/ReactorNet.cpp new/src/zeroD/ReactorNet.cpp
---- old/src/zeroD/ReactorNet.cpp	2018-08-24 16:24:45.000000000 +0300
-+++ new/src/zeroD/ReactorNet.cpp	2019-08-14 04:51:35.000000000 +0300
+diff -Naur a/src/zeroD/ReactorNet.cpp b/src/zeroD/ReactorNet.cpp
+--- a/src/zeroD/ReactorNet.cpp	2018-08-24 16:24:45.000000000 +0300
++++ b/src/zeroD/ReactorNet.cpp	2020-04-21 13:55:54.000000000 +0300
 @@ -28,7 +28,6 @@
      // numerically, and use a Newton linear iterator
      m_integ->setMethod(BDF_Method);