gentoo resync : 18.11.2019

13 files changed, 457 insertions, 8 deletions

diff --git a/sci-mathematics/Manifest.gz b/sci-mathematics/Manifest.gz
index ae7060fa43ce..df905547d8fe 100644
--- a/sci-mathematics/Manifest.gz
+++ b/sci-mathematics/Manifest.gz
diff --git a/sci-mathematics/agda/Manifest b/sci-mathematics/agda/Manifest
index 5eb31b95bfed..084f0fb21e16 100644
--- a/sci-mathematics/agda/Manifest
+++ b/sci-mathematics/agda/Manifest
@@ -2,6 +2,6 @@ AUX 50agda2-gentoo.el 317 BLAKE2B c295509014fc7f254c5c0650b079d3827b182270c6e1aa
 AUX agda-2.4.2.5-hashtables.patch 558 BLAKE2B 88532103f488b643ac84ad37fae3776514034121624c43610910c44a67ac0e68cc5d5d8afece38e2fbf95dbaa3e268e2418d1c34ba4a8fbc60637d63765be42d SHA512 0297fc4605db3dc11f08ec068cfdce908d273c6d14f472e4d00b4416a8e5f671b3b77d4e0cb671671bafd07b39ec46e72eab6cab972145199b25b3c4cfb0b3a6
 DIST Agda-2.4.2.5.tar.gz 1031427 BLAKE2B bf64731e0c068c4f609e9651f0cb6ea763f1e02ddd8909269a140f8ebd036dbb5b36d9f1b038a32016447bbfbd4f9dd6a00a1cc34616efd7099a2b4ddcc7d3bc SHA512 c2e090a42f699200854c20dad868b4b67e99107f0cdbba20ed268f4618fcf80068ee31db37e4b6637f73128d9f652ef9276d8f7adea54628da759d79f5e4f4a2
 DIST Agda-2.5.2.tar.gz 1240885 BLAKE2B bccdaa0c40b8e116f44ee436171cec0a8e1366d7b1f0b469bf459eacf4256e29a00c60a371dcf7971c499e948ce6264861016bb51fcad3251f62cb3e7370c19c SHA512 39ec73316eb7409f7f2618e86a9a3a2c420c93470bf46a1c37a4c4753c6c831d2d6da9ba007086ddee9defd481a695bf142a0a7d360dfa01bdb1fb92467af164
-EBUILD agda-2.4.2.5-r2.ebuild 4430 BLAKE2B ada8a71a68e16bfcb23801d89438944f29140e68f40271280f8ce713c91d694f56ea9a8868f86067da61ec5ee8ffa299e482d4d57728f869878891cc385f73af SHA512 5af62713f088922724bd2356bb3fe9602d5af59a512b06eedbe2ee113858e7368830c8135aa7f10bc76502c69282e6151d9a18a4869f035f2ea098a5823f04ea
-EBUILD agda-2.5.2-r1.ebuild 5264 BLAKE2B 369150bdf77fde730bafb5d80a7bb7d7491de593e07a2f2708b5a69b530051ef65e3dae267e3d8e18ca297bffa04d7d0de7f1a1332f6419573ebb5de8a0566e0 SHA512 4c8e7b1cc863ee0df7924659772b3fb7fad5088514f4731ac33849eb9c3a5f9cf0871686775e595fbe841147dab96e1980f8155a6df1f8418b7498974120144d
+EBUILD agda-2.4.2.5-r2.ebuild 4422 BLAKE2B c5d222e5191cb21102965a280839b8d3d7c8dc8ddaeae239b03b09dfdf5fda4abea07a9df5690e0f986ffecc8632f9c7a6884c9f0e3ce8f80bbaf62622190def SHA512 709169949495bd804cd4fa45622e04856d6078d8b87c240415ec0effbbca69a2941aa8db67b1f5209484663ce2ca79a29d76fed79cf9f2a71ce1c7e3d8b76fe9
+EBUILD agda-2.5.2-r1.ebuild 5256 BLAKE2B fe72cecab078db6668a6796df896bef3383068a778a8360e991233e25dc947275a4a1745efe09065d0d66e53834de43e77a16e49941ef6f452607dd52bd8a41c SHA512 61dfdfc7c7072fcc509f4896387e9b7d5c81cd8db40ef29aa6ba2732d1aeedad0da4385ca8983d2ba1f341de130564747c83a5a57558339c5d1185f2552cafad
 MISC metadata.xml 907 BLAKE2B f4890d2c0e7c8d3eeb57ad9472ae3b5ae287fc7880fa853ec5d1a6c9867aa3e11ef71cd5b46ed5e9fd9e3c3307eea1260c4aa0d9f1598de64f48f43e0c2af137 SHA512 d48af119f929e739634165e1ece14ef2bf55eb996fd0852fd34783a18da04a156bf858b3f0a7ad3cd5c85e55c564bfb3e5552786161fd2ad66f86eb5d3d91426
diff --git a/sci-mathematics/agda/agda-2.4.2.5-r2.ebuild b/sci-mathematics/agda/agda-2.4.2.5-r2.ebuild
index 04d8026b58b3..35d86bd4e84c 100644
--- a/sci-mathematics/agda/agda-2.4.2.5-r2.ebuild
+++ b/sci-mathematics/agda/agda-2.4.2.5-r2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -13,7 +13,7 @@ MY_P="${MY_PN}-${PV}"
 
 DESCRIPTION="A dependently typed functional programming language and proof assistant"
 HOMEPAGE="http://wiki.portal.chalmers.se/agda/"
-SRC_URI="mirror://hackage/packages/archive/${MY_PN}/${PV}/${MY_P}.tar.gz"
+SRC_URI="https://hackage.haskell.org/package/${MY_P}/${MY_P}.tar.gz"
 
 LICENSE="MIT"
 SLOT="0/${PV}"
diff --git a/sci-mathematics/agda/agda-2.5.2-r1.ebuild b/sci-mathematics/agda/agda-2.5.2-r1.ebuild
index dcdb851153f5..630d67092eb1 100644
--- a/sci-mathematics/agda/agda-2.5.2-r1.ebuild
+++ b/sci-mathematics/agda/agda-2.5.2-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -23,7 +23,7 @@ MY_GENTOO_AGDA_STDLIB_V="${PV}.${MY_UPSTREAM_AGDA_STDLIB_V}"
 
 DESCRIPTION="A dependently typed functional programming language and proof assistant"
 HOMEPAGE="http://wiki.portal.chalmers.se/agda/"
-SRC_URI="mirror://hackage/packages/archive/${MY_PN}/${PV}/${MY_P}.tar.gz"
+SRC_URI="https://hackage.haskell.org/package/${MY_P}/${MY_P}.tar.gz"
 
 LICENSE="MIT"
 SLOT="0/${PV}"
diff --git a/sci-mathematics/petsc/Manifest b/sci-mathematics/petsc/Manifest
index a44ec7dfeb4e..126511a8fbea 100644
--- a/sci-mathematics/petsc/Manifest
+++ b/sci-mathematics/petsc/Manifest
@@ -1,5 +1,9 @@
+AUX petsc-3.12.1-do_not_run_mpiexec.patch 2648 BLAKE2B 521db3b12644ec692134f11e96d2ec633f3600199e2ac4da5cf2ee6be566fc6e65d0b6a67437752b0c1cf656561ba6c991d2ad603d3975f334b66362d275483c SHA512 b5eb5406203ae4df21d94755f8ccb996c7d6822ef93a60ebe3a82f404436f1aa314809f63bbcbdc15a5613ff143df80e3e69b3e3f48dc9521a2e2855dad73e25
+AUX petsc-3.12.1-make_hypre_configure.patch 3970 BLAKE2B 562cab7e3176acf2bce1b40d4a8563718d419be95881b7fb68fee563591db8bc9fac7444885139c9887e3ab8fe790c4568dbc58cff43f718dbace335564ec1fb SHA512 7f954e6a9a2e3eabe15c9eca6dd385a6a50a5cb7dcda8fd0de8fa2ff49667850fcad62a3b3caade0bc024a1eef1bf4f1f429385e9208b95badb77d814480357c
 AUX petsc-3.7.0-disable-rpath.patch 909 BLAKE2B b9b6064886d6c10b382982778398cb7fa254242e5ed0dfb86dd4cd6c094dc51eecfd625f6de5c2779bfc5b3beda351ac44145c69ac246d814a728d7565da8086 SHA512 8241c593d903615feb175bfe8213792ace739a18ac5f4c1d1890155ccea7de30b5ef5d97e2fa3b043e9a1e520e022abedeb038d0b4db671f89045e04edc65a68
 AUX petsc-3.9.0-fix_sandbox_violation.patch 916 BLAKE2B f58ba79c3082d253c9a95b0c9ce0bcc6373fa91b4155fac5a6d4688c21805d938f5c04a939ab9d8b810732e79699e7156bd4916717b9ab0217ab257ca64bb92e SHA512 cde22a54f0f6c73cfa326ea0c0026878b3099381ec703154bb8d2746a502ffc9ae82e65082f63579abce5b3d3f89bccf0cbc7db7d031e642c5c02ca8281e616c
 DIST petsc-3.11.3.tar.gz 33279017 BLAKE2B 870b8245e5e06d8538ea3ee1d01fa2cebade4a0bd79dfcf17d74e6201f41d21ca021e206744ece28847b434ece142a2789851b5514a8a1e3f82a8551288b695b SHA512 e545f69e87bc72950939ff3cec3e0ba225a5b3e7f1cb93b0fb6123194eb7240ac1d97ba397235d8ab872c653caab1427673124e5e1e706b796c0ae46ec1bcffa
-EBUILD petsc-3.11.3.ebuild 5339 BLAKE2B e864ef1479ee6bfc878e8ea5ba294d7987b0a810555d51ef2cfa3aa96fa07e3de4b2acbbea80c2bd80d0aaf2618636d18f916e2ccb990adb05a0f68bb7968039 SHA512 1e1ceacac2c4c03f1cb634f7695180832eb7042e21089df0f76a0fee2ae3a4c8935ed9286497f2ea8268a5d4b4179a9e535fadd4b61ab4982d8104843d3f2037
+DIST petsc-3.12.1.tar.gz 34592587 BLAKE2B b48056a1fe1d507338f7d145f5fceeab2b2f576470d8af90c9d7828de9b775daadf11198fecc46b5e48fcf1eb38addb366e3a908dab5c4ffaf7f9b71ff17b3d8 SHA512 df33170922c0b34136d2fd5bdc3c68a80d3a5873d66bfb03b2cea4a6456393c7181a8da673911b89ea0fcb51d5fd89b5b4c8b76ddb1df573180a92d029fbc1fb
+EBUILD petsc-3.11.3.ebuild 5337 BLAKE2B bdd7062ad5b5b55de97c676a30437901838749d9ee910d274711668de7b43d1f0c630b53e1f4f0b50442ea05b3a9900f5b3f2d5a7d10de3e124f7012ecd0b8b5 SHA512 2e67e5399c57a587e2afac1a412919faf383e4bfa00011ebf54bc3d4af6a353890500463b5f8a138fac7079eccec6b590c161be1419c5193d924fd1be1377f49
+EBUILD petsc-3.12.1.ebuild 5431 BLAKE2B 06e00d3f76c1eb2548fb2973014a7f674ecd2bb3b8928b12fa531acf3704fc8a85d22c194ad3d07c2ba470e228ccb4c5393b9f819e1a914d82dec6da2dd29e5b SHA512 2bfe62beb35946bf365925bc4b7b5c790f45fe6a3a37e45de420b69b983eba7d0d723a0eee3fa5e712a8abf87974baaf6120e8414f99a80dc5b353f5f90654e1
 MISC metadata.xml 1131 BLAKE2B db15101bb24374026158a0b45bab1b4b38ab6869bb13fc1df48eef96ca003cea0a8b9118033a3d53c735cefd5ca7563e074d458aee32e038a39e68a6a91b7364 SHA512 19cf1bcddd8bc1378bf85c47b090dd684474f29896c1877bfbeb53a24b1112ed4bb6e823cbc830ee40c886727c6c90d0852081488b1df63f8b4f071d3d453630
diff --git a/sci-mathematics/petsc/files/petsc-3.12.1-do_not_run_mpiexec.patch b/sci-mathematics/petsc/files/petsc-3.12.1-do_not_run_mpiexec.patch
new file mode 100644
index 000000000000..9c3d5047b0a6
--- /dev/null
+++ b/sci-mathematics/petsc/files/petsc-3.12.1-do_not_run_mpiexec.patch
@@ -0,0 +1,32 @@
+diff --git a/config/BuildSystem/config/packages/MPI.py b/config/BuildSystem/config/packages/MPI.py
+index c85bb504..7720eba9 100644
+--- a/config/BuildSystem/config/packages/MPI.py
++++ b/config/BuildSystem/config/packages/MPI.py
+@@ -209,26 +209,11 @@ shared libraries and run with --known-mpi-shared-libraries=1')
+           raise RuntimeError('Could not locate MPIEXEC - please specify --with-mpiexec option')
+       # Support for spaces and () in executable names; also needs to handle optional arguments at the end
+       # TODO: This support for spaces and () should be moved to core BuildSystem
+-      self.mpiexec = self.mpiexec.replace(' ', '\\ ').replace('(', '\\(').replace(')', '\\)').replace('\ -',' -')
+-      if (hasattr(self, 'ompi_major_version') and int(self.ompi_major_version) >= 3):
+-        (out, err, ret) = Configure.executeShellCommand(self.mpiexec+' -help all', checkCommand = noCheck, timeout = 10, log = self.log)
+-        if out.find('--oversubscribe') >=0:
+-          self.mpiexec = self.mpiexec + ' --oversubscribe'
++      self.mpiexec = self.mpiexec + ' --oversubscribe'
+ 
+     # using mpiexec environmental variables make sure mpiexec matches the MPI libraries and save the variables for testing in PetscInitialize()
+     # the variable HAVE_MPIEXEC_ENVIRONMENTAL_VARIABLE is not currently used. PetscInitialize() can check the existence of the environmental variable to
+     # determine if the program has been started with the correct mpiexec (will only be set for parallel runs so not clear how to check appropriately)
+-    (out, err, ret) = Configure.executeShellCommand(self.mpiexec+' -n 1 printenv', checkCommand = noCheck, timeout = 10, log = self.log)
+-    if ret: raise RuntimeError('Unable to run '+self.mpiexec+' with option "-n 1"\n'+err)
+-    if out.find('MPIR_CVAR_CH3') > -1:
+-      if hasattr(self,'ompi_major_version'): raise RuntimeError("Your libraries are from OpenMPI but it appears your mpiexec is from MPICH");
+-      self.addDefine('HAVE_MPIEXEC_ENVIRONMENTAL_VARIABLE', 'MPIR_CVAR_CH3')
+-    elif  out.find('MPIR_CVAR_CH3') > -1:
+-      if hasattr(self,'ompi_major_version'): raise RuntimeError("Your libraries are from OpenMPI but it appears your mpiexec is from MPICH");
+-      self.addDefine('HAVE_MPIEXEC_ENVIRONMENTAL_VARIABLE', 'MPICH')
+-    elif out.find('OMPI_COMM_WORLD_SIZE') > -1:
+-      if hasattr(self,'mpich_numversion'): raise RuntimeError("Your libraries are from MPICH but it appears your mpiexec is from OpenMPI");
+-      self.addDefine('HAVE_MPIEXEC_ENVIRONMENTAL_VARIABLE', 'OMP')
+     self.addMakeMacro('MPIEXEC', self.mpiexec)
+     self.mpiexec = self.mpiexec + ' -n 1'
+ 
diff --git a/sci-mathematics/petsc/files/petsc-3.12.1-make_hypre_configure.patch b/sci-mathematics/petsc/files/petsc-3.12.1-make_hypre_configure.patch
new file mode 100644
index 000000000000..9460d57e4617
--- /dev/null
+++ b/sci-mathematics/petsc/files/petsc-3.12.1-make_hypre_configure.patch
@@ -0,0 +1,90 @@
+diff --git a/config/BuildSystem/config/packages/hypre.py b/config/BuildSystem/config/packages/hypre.py
+index 869a1661..76067c8d 100644
+--- a/config/BuildSystem/config/packages/hypre.py
++++ b/config/BuildSystem/config/packages/hypre.py
+@@ -5,10 +5,6 @@ class Configure(config.package.GNUPackage):
+   def __init__(self, framework):
+     config.package.GNUPackage.__init__(self, framework)
+     self.version         = '2.18.1'
+-    self.minversion      = '2.14'
+-    self.versionname     = 'HYPRE_RELEASE_VERSION'
+-    self.versioninclude  = 'HYPRE_config.h'
+-    self.requiresversion = 1
+     self.gitcommit       = 'v'+self.version
+     self.download        = ['git://https://github.com/hypre-space/hypre','https://github.com/hypre-space/hypre/archive/'+self.gitcommit+'.tar.gz']
+     self.functions       = ['HYPRE_IJMatrixCreate']
+diff --git a/include/petsc/private/petschypre.h b/include/petsc/private/petschypre.h
+index 81ca7136..b403e70e 100644
+--- a/include/petsc/private/petschypre.h
++++ b/include/petsc/private/petschypre.h
+@@ -6,12 +6,6 @@
+ #include <HYPRE_config.h>
+ #include <HYPRE_utilities.h>
+ 
+-/* from version 2.16 on, HYPRE_BigInt is 64 bit for 64bit installations
+-   and 32 bit for 32bit installations -> not the best name for a variable */
+-#if PETSC_PKG_HYPRE_VERSION_LT(2,16,0)
+-typedef PetscInt HYPRE_BigInt;
+-#endif
+-
+ /*
+   With scalar type == real, HYPRE_Complex == PetscScalar;
+   With scalar type == complex,  HYPRE_Complex is double __complex__ while PetscScalar may be std::complex<double>
+diff --git a/src/mat/impls/hypre/mhypre.c b/src/mat/impls/hypre/mhypre.c
+index 8e8fe678..3533b99a 100644
+--- a/src/mat/impls/hypre/mhypre.c
++++ b/src/mat/impls/hypre/mhypre.c
+@@ -15,10 +15,6 @@
+ #include <_hypre_parcsr_ls.h>
+ #include <_hypre_sstruct_ls.h>
+ 
+-#if PETSC_PKG_HYPRE_VERSION_LT(2,18,0)
+-#define  hypre_ParCSRMatrixClone(A,B) hypre_ParCSRMatrixCompleteClone(A)
+-#endif
+-
+ PETSC_INTERN PetscErrorCode MatPtAP_IS_XAIJ(Mat,Mat,MatReuse,PetscReal,Mat*);
+ 
+ static PetscErrorCode MatHYPRE_CreateFromMat(Mat,Mat_HYPRE*);
+@@ -65,7 +61,6 @@ static PetscErrorCode MatHYPRE_IJMatrixPreallocate(Mat A_d, Mat A_o, HYPRE_IJMat
+         nnz_o[i] = 0;
+       }
+     }
+-#if PETSC_PKG_HYPRE_VERSION_GE(2,16,0)
+     { /* If we don't do this, the columns of the matrix will be all zeros! */
+       hypre_AuxParCSRMatrix *aux_matrix;
+       aux_matrix = (hypre_AuxParCSRMatrix*)hypre_IJMatrixTranslator(ij);
+@@ -75,9 +70,6 @@ static PetscErrorCode MatHYPRE_IJMatrixPreallocate(Mat A_d, Mat A_o, HYPRE_IJMat
+       aux_matrix = (hypre_AuxParCSRMatrix*)hypre_IJMatrixTranslator(ij);
+       hypre_AuxParCSRMatrixNeedAux(aux_matrix) = 1;
+     }
+-#else
+-    PetscStackCallStandard(HYPRE_IJMatrixSetDiagOffdSizes,(ij,nnz_d,nnz_o));
+-#endif
+     ierr = PetscFree(nnz_d);CHKERRQ(ierr);
+     ierr = PetscFree(nnz_o);CHKERRQ(ierr);
+   }
+@@ -235,11 +227,7 @@ static PetscErrorCode MatHYPRE_IJMatrixFastCopy_MPIAIJ(Mat A, HYPRE_IJMatrix ij)
+   /* need to shift the diag column indices (hdiag->j) back to global numbering since hypre is expecting this */
+   hjj = hdiag->j;
+   pjj = pdiag->j;
+-#if PETSC_PKG_HYPRE_VERSION_GE(2,16,0)
+   for (i=0; i<pdiag->nz; i++) hjj[i] = pjj[i];
+-#else
+-  for (i=0; i<pdiag->nz; i++) hjj[i] = cstart + pjj[i];
+-#endif
+   ierr = PetscArraycpy(hdiag->data,pdiag->a,pdiag->nz);CHKERRQ(ierr);
+   if (sameint) {
+     ierr = PetscArraycpy(hoffd->i,poffd->i,pA->A->rmap->n + 1);CHKERRQ(ierr);
+@@ -249,12 +237,8 @@ static PetscErrorCode MatHYPRE_IJMatrixFastCopy_MPIAIJ(Mat A, HYPRE_IJMatrix ij)
+ 
+   /* need to move the offd column indices (hoffd->j) back to global numbering since hypre is expecting this
+      If we hacked a hypre a bit more we might be able to avoid this step */
+-#if PETSC_PKG_HYPRE_VERSION_GE(2,16,0)
+   PetscStackCallStandard(hypre_CSRMatrixBigInitialize,(hoffd));
+   jj  = (PetscInt*) hoffd->big_j;
+-#else
+-  jj  = (PetscInt*) hoffd->j;
+-#endif
+   pjj = poffd->j;
+   for (i=0; i<poffd->nz; i++) jj[i] = garray[pjj[i]];
+ 
diff --git a/sci-mathematics/petsc/petsc-3.11.3.ebuild b/sci-mathematics/petsc/petsc-3.11.3.ebuild
index 88fb1f58da1c..50ce3b7f6631 100644
--- a/sci-mathematics/petsc/petsc-3.11.3.ebuild
+++ b/sci-mathematics/petsc/petsc-3.11.3.ebuild
@@ -154,7 +154,7 @@ src_configure() {
 		$(petsc_enable threads pthread) \
 		$(petsc_with afterimage afterimage \
 			/usr/include/libAfterImage -lAfterImage) \
-		$(petsc_with hdf5) \
+		$(use_with hdf5) \
 		$(petsc_with hypre hypre \
 			/usr/include/hypre -lHYPRE) \
 		$(petsc_with sparse suitesparse) \
diff --git a/sci-mathematics/petsc/petsc-3.12.1.ebuild b/sci-mathematics/petsc/petsc-3.12.1.ebuild
new file mode 100644
index 000000000000..845d7ff75d69
--- /dev/null
+++ b/sci-mathematics/petsc/petsc-3.12.1.ebuild
@@ -0,0 +1,195 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit flag-o-matic fortran-2 python-any-r1 toolchain-funcs
+
+DESCRIPTION="Portable, Extensible Toolkit for Scientific Computation"
+HOMEPAGE="http://www.mcs.anl.gov/petsc/"
+SRC_URI="http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/${P}.tar.gz"
+
+LICENSE="BSD-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="afterimage boost complex-scalars cxx debug doc fftw
+	fortran hdf5 hypre mpi metis mumps scotch sparse superlu threads X"
+
+# hypre and superlu curretly exclude each other due to missing linking to hypre
+# if both are enabled
+REQUIRED_USE="
+	afterimage? ( X )
+	complex-scalars? ( !hypre !superlu )
+	hdf5? ( mpi )
+	hypre? ( cxx mpi !superlu )
+	mumps? ( mpi scotch )
+	scotch? ( mpi )
+	superlu? ( !hypre )
+"
+
+RDEPEND="
+	virtual/blas
+	virtual/lapack
+	afterimage? ( media-libs/libafterimage )
+	boost? ( dev-libs/boost )
+	fftw? ( sci-libs/fftw:3.0[mpi?] )
+	hdf5? ( sci-libs/hdf5[mpi?] )
+	hypre? ( >=sci-libs/hypre-2.18.0[mpi?] )
+	metis? ( >=sci-libs/parmetis-4 )
+	mpi? ( virtual/mpi[cxx?,fortran?] )
+	mumps? ( sci-libs/mumps[mpi?] sci-libs/scalapack )
+	scotch? ( sci-libs/scotch[mpi?] )
+	sparse? ( sci-libs/suitesparse >=sci-libs/cholmod-1.7.0 )
+	superlu? ( >=sci-libs/superlu-5 )
+	X? ( x11-libs/libX11 )
+"
+
+DEPEND="${RDEPEND}
+	${PYTHON_DEPS}
+	virtual/pkgconfig
+	dev-util/cmake
+"
+
+PATCHES=(
+	"${FILESDIR}"/${PN}-3.7.0-disable-rpath.patch
+	"${FILESDIR}"/${PN}-3.9.0-fix_sandbox_violation.patch
+	"${FILESDIR}"/${PN}-3.12.1-make_hypre_configure.patch
+	"${FILESDIR}"/${PN}-3.12.1-do_not_run_mpiexec.patch
+)
+
+src_prepare() {
+	default
+
+	sed -i -e 's%/usr/bin/env python%/usr/bin/env python2%' configure || die
+}
+
+# petsc uses --with-blah=1 and --with-blah=0 to en/disable options
+petsc_enable() {
+	use "$1" && echo "--with-${2:-$1}=1" || echo "--with-${2:-$1}=0"
+}
+# add external library:
+# petsc_with use_flag libname libdir
+# petsc_with use_flag libname include linking_libs
+petsc_with() {
+	local myuse p=${2:-${1}}
+	if use ${1}; then
+		myuse="--with-${p}=1"
+		if [[ $# -ge 4 ]]; then
+			myuse="${myuse} --with-${p}-include=${EPREFIX}${3}"
+			shift 3
+			myuse="${myuse} --with-${p}-lib=$@"
+		else
+			myuse="${myuse} --with-${p}-dir=${EPREFIX}${3:-/usr}"
+		fi
+	else
+		myuse="--with-${p}=0"
+	fi
+	echo ${myuse}
+}
+
+# select between configure options depending on use flag
+petsc_select() {
+	use "$1" && echo "--with-$2=$3" || echo "--with-$2=$4"
+}
+
+src_configure() {
+	# bug 548498
+	# PETSc runs mpi processes during configure that result in a sandbox
+	# violation by trying to open /proc/mtrr rw. This is not easy to
+	# mitigate because it happens in libpciaccess.so called by libhwloc.so,
+	# which is used by libmpi.so.
+	addpredict /proc/mtrr
+	# if mpi is built with knem support it needs /dev/knem too
+	addpredict /dev/knem
+
+	# configureMPITypes with openmpi-2* insists on accessing the scaling
+	# governor rw.
+	addpredict /sys/devices/system/cpu/
+
+	local mylang
+	local myopt
+
+	use cxx && mylang="cxx" || mylang="c"
+	use debug && myopt="debug" || myopt="opt"
+
+	# environmental variables expected by petsc during build
+
+	export PETSC_DIR="${S}"
+	export PETSC_ARCH="linux-gnu-${mylang}-${myopt}"
+
+	if use debug; then
+		strip-flags
+		filter-flags -O*
+	fi
+
+	# C Support on CXX builds is enabled if possible i.e. when not using
+	# complex scalars (no complex type for both available at the same time)
+
+	econf \
+		scrollOutput=1 \
+		FFLAGS="${FFLAGS} -fPIC" \
+		CFLAGS="${CFLAGS} -fPIC" \
+		CXXFLAGS="${CXXFLAGS} -fPIC" \
+		LDFLAGS="${LDFLAGS}" \
+		--prefix="${EPREFIX}/usr/$(get_libdir)/petsc" \
+		--with-shared-libraries \
+		--with-single-library \
+		--with-clanguage=${mylang} \
+		$(use cxx && ! use complex-scalars && echo "with-c-support=1") \
+		--with-petsc-arch=${PETSC_ARCH} \
+		--with-precision=double \
+		--with-gnu-compilers \
+		--with-blas-lapack-lib="$($(tc-getPKG_CONFIG) --libs blas lapack)" \
+		$(petsc_enable debug debugging) \
+		$(petsc_enable mpi) \
+		$(petsc_select mpi cc mpicc $(tc-getCC)) \
+		$(petsc_select mpi cxx mpicxx $(tc-getCXX)) \
+		$(petsc_enable fortran) \
+		$(use fortran && echo "$(petsc_select mpi fc mpif77 $(tc-getF77))") \
+		$(petsc_enable mpi mpi-compilers) \
+		$(petsc_select complex-scalars scalar-type complex real) \
+		--with-windows-graphics=0 \
+		--with-matlab=0 \
+		--with-cmake:BOOL=1 \
+		$(petsc_enable threads pthread) \
+		$(petsc_with afterimage afterimage \
+			/usr/include/libAfterImage -lAfterImage) \
+		$(use_with hdf5) \
+		$(petsc_with hypre hypre \
+			/usr/include/hypre -lHYPRE) \
+		$(use_with sparse suitesparse) \
+		$(petsc_with superlu superlu \
+			/usr/include/superlu -lsuperlu) \
+		$(use_with X x) \
+		$(use_with X x11) \
+		$(petsc_with scotch ptscotch \
+			/usr/include/scotch \
+		[-lptesmumps,-lptscotch,-lptscotcherr,-lscotch,-lscotcherr]) \
+		$(petsc_with mumps scalapack \
+			/usr/include/scalapack -lscalapack) \
+		$(use_with mumps mumps \
+			/usr/include \
+			[-lcmumps,-ldmumps,-lsmumps,-lzmumps,-lmumps_common,-lpord]) \
+		--with-imagemagick=0 \
+		--with-python=0 \
+		$(use_with boost) \
+		$(use_with fftw)
+}
+
+src_install() {
+	emake DESTDIR="${ED}" install
+
+	# add PETSC_DIR to environmental variables
+	cat >> 99petsc <<- EOF
+		PETSC_DIR=${EPREFIX}/usr/$(get_libdir)/petsc
+		LDPATH=${EPREFIX}/usr/$(get_libdir)/petsc/lib
+	EOF
+	doenvd 99petsc
+
+	if use doc ; then
+		docinto html
+		dodoc -r docs/*.html docs/changes docs/manualpages
+	fi
+}
diff --git a/sci-mathematics/slepc/Manifest b/sci-mathematics/slepc/Manifest
index 414735747532..c8fc5c686237 100644
--- a/sci-mathematics/slepc/Manifest
+++ b/sci-mathematics/slepc/Manifest
@@ -1,3 +1,5 @@
 DIST slepc-3.11.1.tar.gz 4700643 BLAKE2B a624050aad0128d7ef53f27f72484e078e62d8edf9298995dda71a9e8d804dddc7e433542eccf95b2d896be80e8795b1664375e68a4c02c18c56d78d490bffb7 SHA512 a941c2a955953ed2344de7f7d9eaaed79504c3559e27920c633bc09cfb192f883b26fd4aa5dc3bd9909a2fc045f3a34e514feca0e074ca36bc3166aa9c059235
+DIST slepc-3.12.1.tar.gz 4757436 BLAKE2B 607e7b28730ff16fa995768e23fd9861e180c078d2f06e8f65324b1e1761f0688fe5a4c4420983b521583cb2b3fe28b606baea604daf5253c30131f9f54c5572 SHA512 0254ea1a521cf150f9f0402bb936c9d1aa32765264e055ecdd058e44aaa7e87c3df1b63b1889c1989c4a691c652eb0f248a1bbbe6d555ce16f9f8f28d6765b50
 EBUILD slepc-3.11.1.ebuild 1661 BLAKE2B 6844c1e110d47bf7620e5a1712bbd265d6d0a40f65e8961ec3818c0eeb5b56c95b35bf4b76fdeab1a144a4561f549e4be1ad8a4cb27fcd623add77fd3e33af97 SHA512 e827d09af4082f3b6e6a96ae1880042a292f7cc1d44729c2efc77cfac91a554dde8f19ea8210dbc5d532e9f09786ec87d6a92ad379e18326181eee35e6f33d2d
+EBUILD slepc-3.12.1.ebuild 1661 BLAKE2B 6844c1e110d47bf7620e5a1712bbd265d6d0a40f65e8961ec3818c0eeb5b56c95b35bf4b76fdeab1a144a4561f549e4be1ad8a4cb27fcd623add77fd3e33af97 SHA512 e827d09af4082f3b6e6a96ae1880042a292f7cc1d44729c2efc77cfac91a554dde8f19ea8210dbc5d532e9f09786ec87d6a92ad379e18326181eee35e6f33d2d
 MISC metadata.xml 451 BLAKE2B 5268292011dffcbc322504b29332ae20a4e775238e201ffe793e1ebfb8d8c13a836ca1f8eba44b38bc63ba7b21a3634a03df9990e8b801def0152316d1539960 SHA512 7bf6d4cdedaa48f96e9b1d3e237b795f7cbfd840cece0c0181c9efa05ec833477191e8d12cf2b7737a921b85fb5af055d5868e1173415fc70802eb515959c9d5
diff --git a/sci-mathematics/slepc/slepc-3.12.1.ebuild b/sci-mathematics/slepc/slepc-3.12.1.ebuild
new file mode 100644
index 000000000000..52212cabfd52
--- /dev/null
+++ b/sci-mathematics/slepc/slepc-3.12.1.ebuild
@@ -0,0 +1,75 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit eutils flag-o-matic python-any-r1 toolchain-funcs
+
+DESCRIPTION="Scalable Library for Eigenvalue Problem Computations"
+HOMEPAGE="http://slepc.upv.es/"
+SRC_URI="http://slepc.upv.es/download/distrib/${P}.tar.gz"
+
+LICENSE="LGPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="complex-scalars doc mpi"
+
+RDEPEND="
+	=sci-mathematics/petsc-$(ver_cut 1-2)*:=[mpi=,complex-scalars=]
+	sci-libs/arpack[mpi=]
+	mpi? ( virtual/mpi )
+"
+
+DEPEND="${RDEPEND}
+	${PYTHON_DEPS}
+	virtual/pkgconfig
+	dev-util/cmake
+"
+
+MAKEOPTS="${MAKEOPTS} V=1"
+
+src_prepare() {
+	default
+
+	sed -i -e 's%/usr/bin/env python%/usr/bin/env python2%' configure || die
+}
+
+src_configure() {
+	# *sigh*
+	addpredict "${PETSC_DIR}"/.nagged
+
+	# Make sure that the environment is set up correctly:
+	unset PETSC_DIR
+	unset PETSC_ARCH
+	unset SLEPC_DIR
+	source "${EPREFIX}"/etc/env.d/99petsc
+	export PETSC_DIR
+
+	# configure is a custom python script and doesn't want to have default
+	# configure arguments that we set with econf
+	./configure \
+		--prefix="${EPREFIX}/usr/$(get_libdir)/slepc" \
+		--with-arpack=1 \
+		--with-arpack-dir="${EPREFIX}/usr/$(get_libdir)" \
+		--with-arpack-flags="$(usex mpi "-lparpack,-larpack" "-larpack")"
+
+}
+
+src_install() {
+	emake DESTDIR="${ED}" install
+
+	# add PETSC_DIR to environmental variables
+	cat >> 99slepc <<- EOF
+		SLEPC_DIR=${EPREFIX}/usr/$(get_libdir)/slepc
+		LDPATH=${EPREFIX}/usr/$(get_libdir)/slepc/lib
+	EOF
+	doenvd 99slepc
+
+	if use doc ; then
+		dodoc docs/slepc.pdf
+		docinto html
+		dodoc -r docs/*.html docs/manualpages
+	fi
+}
diff --git a/sci-mathematics/wxmaxima/Manifest b/sci-mathematics/wxmaxima/Manifest
index bb2df91b05f2..4b74e98ed822 100644
--- a/sci-mathematics/wxmaxima/Manifest
+++ b/sci-mathematics/wxmaxima/Manifest
@@ -3,9 +3,11 @@ DIST wxmaxima-19.05.7.tar.gz 13832202 BLAKE2B 6afe37dfcefe3f1711cc1cc89e4c61071d
 DIST wxmaxima-19.08.1.tar.gz 15153254 BLAKE2B 1bd48735ab95b078b9f35d7be623c1a16da6764649254579a2c2252ff858adb05e9408a85e5ed84dba6f15f879db761472276a5da77fa15e1c1823c678160aa3 SHA512 07f650144b8acd8295a45411185805185078f5236b67b33dac0f12308fc3b7522a6a46dfd2df35397c1d2fd5a357fb8d12473be4af576fcf09bda1e34352ae68
 DIST wxmaxima-19.09.0.tar.gz 15153282 BLAKE2B 96cb2db8938b73fb2dc3547310109df581a780a0372687aed9957cd3434fcbec8fef23467543f854f7e6b2c302dba6f3d5a411b17ab83e886175a62dc3fac385 SHA512 fad35fa118e49834d2ff6d54fb1f7cb8675ca1caadbb43c526b7a313479412c1a6c69959a0820c17af0119fc926f66c31368598c9e212fac56305a96d7a39838
 DIST wxmaxima-19.10.0.tar.gz 16573758 BLAKE2B 9bee3f8822e9c9ed28058496f7c5c6b2358feeafad39d08d92f3e6ff382817a8a7fd3e33b821f6faba3863f4c8871bc3bebee2b9d97ec6ccfdbfd7c0f7d44940 SHA512 39681cefb81a3816b7daeef7df5b23f57f3a4572ff34396fd447829ceaf6505d09f730255d3c44dd48232879b9994f26a9f86801fe333e15483026d864efdf14
+DIST wxmaxima-19.11.0.tar.gz 15304346 BLAKE2B 3a8038f4b67cee261d261f64671227963f91b55969b922282c3b2057029617a5989dc44dc8c28ab17a74e57c2547381dab98b07bf2a1f2f01a5d3c838d6d8a68 SHA512 bb0701ad2be71463ab412649164b2040e5fe95bd6fadb5332fbe5712dc4b65ef30fc86f2ff375e14f1879156fd77e1b8431f15794a136d7e6ee4e6a9393b903a
 EBUILD wxmaxima-18.11.4.ebuild 1324 BLAKE2B 1f6c20362bc7403da290ae6ae0bfa898b611d2986f770523d24780682562fa5c60a853697dda8507fe1ede01410b140bd6518cf1f5b0a65502fc36a9f0486a7d SHA512 e6102de11417007556f36485d8c37c100c0bc2f5df0cb39750ef5bda82d4c7a71d4036f7879e066dc407f45eab3e92122ae2c0494cbc94e607daf3982ea1702a
 EBUILD wxmaxima-19.05.7.ebuild 1460 BLAKE2B 1137943c8725f8a47b31404ff691f4d865f419b9bdc224a851decc4d76c067c4b7dec561039c6b6efa9c6fc8b2643bb8f57f4c94dec60db954b8a02a3d049f65 SHA512 7437cacffb38ce11970036778acb916aadec00ad84e8d8de0f9627bb935e96caac30ede0f6b08ea72539fb3e93d96879796773741d95402df239536418e6dff4
 EBUILD wxmaxima-19.08.1.ebuild 1460 BLAKE2B 1137943c8725f8a47b31404ff691f4d865f419b9bdc224a851decc4d76c067c4b7dec561039c6b6efa9c6fc8b2643bb8f57f4c94dec60db954b8a02a3d049f65 SHA512 7437cacffb38ce11970036778acb916aadec00ad84e8d8de0f9627bb935e96caac30ede0f6b08ea72539fb3e93d96879796773741d95402df239536418e6dff4
 EBUILD wxmaxima-19.09.0.ebuild 1234 BLAKE2B 8cd862e12a583116859213c861d120095b88f5a815fcf8aed15499eaadaedcc5c0eae3c1e5b40e5bd4beae165fba68408c1c0772bf69ed28651264e214a82bf8 SHA512 f544e092e687134e312791a7b4d003bcc15b42aded3bc9e464ab1271c6e626fdb5fbdd87ae52c189a5e901099d3f8d47a9431b46c449f499081488b39d0e5218
 EBUILD wxmaxima-19.10.0.ebuild 1397 BLAKE2B fbd3c30213c726d0aeeb9a32c4f87c3d747343421c19330336cf132875cc84ad84b1b9b33b92961dbc54330bc02e33753d9e6f58eeeb069eca5d7a12559c773d SHA512 2ca45bc6831052fa7b6a0f8d6e628394419c46b040adab85878ff79acb6b19da710add34c5dcc17ea9bc397c41cd84597451340c2d68f6511cdeeecdf4715412
+EBUILD wxmaxima-19.11.0.ebuild 1397 BLAKE2B fbd3c30213c726d0aeeb9a32c4f87c3d747343421c19330336cf132875cc84ad84b1b9b33b92961dbc54330bc02e33753d9e6f58eeeb069eca5d7a12559c773d SHA512 2ca45bc6831052fa7b6a0f8d6e628394419c46b040adab85878ff79acb6b19da710add34c5dcc17ea9bc397c41cd84597451340c2d68f6511cdeeecdf4715412
 MISC metadata.xml 711 BLAKE2B 00c54141e803d86fb20dc4f058fe99f6bbc2fd067175af6d0a5f893dc5a0b523fdd9116341ba33f991b11538989869337e1ce36c2259cfdb284725fed1aeaf60 SHA512 30a578958cbc4813e2615d0c3d7c4a1349f408933f285d3a43a382bf90bdf5c985ef1b844c4f8391205be643961de0335536ee800e1be24bf358bb4ead736fe5
diff --git a/sci-mathematics/wxmaxima/wxmaxima-19.11.0.ebuild b/sci-mathematics/wxmaxima/wxmaxima-19.11.0.ebuild
new file mode 100644
index 000000000000..b22b9bbbbd26
--- /dev/null
+++ b/sci-mathematics/wxmaxima/wxmaxima-19.11.0.ebuild
@@ -0,0 +1,49 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+WX_GTK_VER="3.0"
+PLOCALES="ca cs da de el en es fi fr gl hu it ja kab nb pl pt_BR ru tr uk zh_CN zh_TW"
+inherit cmake-utils wxwidgets l10n xdg
+
+DESCRIPTION="Graphical frontend to Maxima, using the wxWidgets toolkit"
+HOMEPAGE="https://wxmaxima-developers.github.io/wxmaxima/"
+SRC_URI="https://github.com/wxMaxima-developers/wxmaxima/archive/Version-${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86"
+IUSE=""
+S="${WORKDIR}"/${PN}-Version-${PV}
+
+DEPEND="
+	dev-libs/libxml2:2
+	x11-libs/wxGTK:${WX_GTK_VER}"
+RDEPEND="${DEPEND}
+	media-fonts/jsmath
+	sci-visualization/gnuplot[wxwidgets]
+	sci-mathematics/maxima"
+
+src_prepare() {
+	setup-wxwidgets
+	cmake-utils_src_prepare
+
+	sed -e "s|share/doc/${PN}|share/doc/${PF}|g" -i "${S}"/info/CMakeLists.txt \
+		|| die "sed info/CMakeLists.txt failed"
+
+	# locales
+	rm_po() {
+		rm "${S}"/locales/wxMaxima/${1}.po || die "rm ${1}.po failed"
+		rm -f "${S}"/locales/manual/${1}.po
+		rm -f "${S}"/locales/wxwin/${1}.po
+		rm -f "${S}"/info/${PN}.${1}.md
+		rm -f "${S}"/info/${PN}.${1}.html
+	}
+	l10n_find_plocales_changes "${S}"/locales/wxMaxima '' '.po'
+	l10n_for_each_disabled_locale_do rm_po
+}
+
+src_install() {
+	docompress -x /usr/share/doc/${PF}/wxmaxima.hhp /usr/share/doc/${PF}/wxmaxima_tr.hhp
+	cmake-utils_src_install
+}