Merge branch 'release/v3.4.1-1'

3 files changed, 75 insertions, 140 deletions

diff --git a/.SRCINFO b/.SRCINFO
index ab312e74441f..632d8c4a2718 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,7 +1,7 @@
 pkgbase = apbs
 	pkgdesc = Software for biomolecular electrostatics and solvation calculations
-	pkgver = 3.0.0
-	pkgrel = 2
+	pkgver = 3.4.1
+	pkgrel = 1
 	url = http://www.poissonboltzmann.org/
 	arch = x86_64
 	license = custom
@@ -10,16 +10,21 @@ pkgbase = apbs
 	makedepends = git
 	makedepends = wget
 	depends = python
-	depends = termcap
-	depends = swig
+	depends = openblas
+	depends = suitesparse
+	depends = lapack
+	depends = arpack
+	depends = eigen
+	depends = boost
+	depends = boost-libs
+	depends = metis
+	depends = superlu
+	depends = gtest
 	provides = apbs
 	conflicts = apbs-bin
 	options = !makeflags
 	options = !buildflags
-	source = https://github.com/Electrostatics/apbs/releases/download/v3.0.0/APBS-3.0.0_Source-Code.tar.gz
-	source = globals_apbs.patch
-	sha256sums = 3cf8b227a205cdcbd13246489427606f256f2356343fc954734fd39975e5cbdb
-	sha256sums = 6bc1f2dc7a454aa8b0799641f78ee571ba04795821a9bcac356cbe496bdb3df6
+	source = https://github.com/Electrostatics/apbs/archive/refs/tags/v3.4.1.tar.gz
+	sha256sums = 644e6246fd37c9dd4172fc7be1763337082ab8584dbcd53e738c831b62c89bb2
 
 pkgname = apbs
-
diff --git a/PKGBUILD b/PKGBUILD
index ae0db43d1d28..2babdbb7f839 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,97 +1,96 @@
-# Maintainer: Viktor Drobot (aka dviktor) linux776 [at] gmail [dot] com
+# Maintainer: Kherim Willems <aur@kher.im>
+# Contributor: Viktor Drobot (aka dviktor) linux776 [at] gmail [dot] com
 
 pkgname=apbs
-pkgver=3.0.0
-pkgrel=2
+pkgver=3.4.1
+pkgrel=1
 pkgdesc="Software for biomolecular electrostatics and solvation calculations"
 arch=(x86_64)
 url="http://www.poissonboltzmann.org/"
 license=(custom)
-depends=(python termcap swig)
+depends=(python openblas suitesparse lapack arpack eigen boost boost-libs metis superlu gtest)
 makedepends=('cmake>=3.12' make git wget)
 provides=(apbs)
 conflicts=(apbs-bin)
-source=("https://github.com/Electrostatics/apbs/releases/download/v${pkgver}/APBS-${pkgver}_Source-Code.tar.gz"
-        "globals_apbs.patch")
-sha256sums=('3cf8b227a205cdcbd13246489427606f256f2356343fc954734fd39975e5cbdb'
-            '6bc1f2dc7a454aa8b0799641f78ee571ba04795821a9bcac356cbe496bdb3df6')
+source=("https://github.com/Electrostatics/apbs/archive/refs/tags/v${pkgver}.tar.gz")
+sha256sums=('644e6246fd37c9dd4172fc7be1763337082ab8584dbcd53e738c831b62c89bb2')
 options=(!makeflags !buildflags)
 
 prepare() {
-    # patch APBS building issues
-    cd "${srcdir}/${pkgname}-${pkgver}/apbs"
-    patch -Np0 -i "${srcdir}/globals_apbs.patch"
-
-    # get external modules
-    cd "${srcdir}/${pkgname}-${pkgver}/apbs/externals"
-
-    # mesh_routines
-    mkdir -p mesh_routines/NanoShaper/Linux64
-    mkdir -p mesh_routines/msms/msms_i86_64Linux2_2.6.1
-    wget https://github.com/lwwilson1/mesh_routines/releases/download/v1.5/NanoShaper_Linux64 -O mesh_routines/NanoShaper/Linux64/NanoShaper
-    wget https://github.com/lwwilson1/mesh_routines/releases/download/v1.5/msms.x86_64Linux2.2.6.1.staticgcc -O mesh_routines/msms/msms_i86_64Linux2_2.6.1/msms.x86_64Linux2.2.6.1.staticgcc
-
-    # PBAM/PBSAM
-    git clone https://github.com/Electrostatics/pb_solvers.git pb_s_am
-    cd pb_s_am
-    git checkout 7ca2a8a491c0cf746074053005fcae026acc4da5
-    cd ..
-
-    # FETK
-    git clone https://github.com/Electrostatics/FETK.git fetk
-    cd fetk
-    git checkout 0c6fdeabe8929acea7481cb1480b5706b343b7e0
-    cd ..
-
-    # Geometric Flow
-    git clone https://github.com/Electrostatics/geoflow_c.git geoflow_c
-    cd geoflow_c
-    git checkout 99446ec841647419411d23bad632d50405913a06
-    cd ..
-
-    # TABI-PB (BEM)
-    git clone https://github.com/Electrostatics/TABIPB.git bem
-    cd bem
-    git checkout 322a8d66180285250cd2f01e6b60584efcba9b65
-    cd ..
+    echo "Nothing to do here"
 }
 
 build() {
-    cd "${srcdir}/${pkgname}-${pkgver}/apbs"
+    cd "${srcdir}/${pkgname}-${pkgver}"
 
-    mkdir build
+    # Create empty build directory
+    mkdir -p build
     cd build
-
+    rm -rf *
+
+    # APBS compilation flags
+    APBS_STATIC_BUILD=OFF
+    BLA_VENDOR="OpenBLAS"
+    BUILD_DOC=ON
+    BUILD_TOOLS=ON
+    INSTALL_DIR=/usr
+    RELEASE_TYPE=Debug
+    ENABLE_PYGBE=ON
+    ENABLE_BEM=ON
+    ENABLE_GEOFLOW=ON
+    FETK_VERSION=57195e55351e04ce6ee0ef56a143c996a9aee7e2
+    ENABLE_iAPBS=ON
+    ENABLE_OPENMP=OFF
+    ENABLE_PBAM=OFF
+    ENABLE_PBSAM=OFF
+    ENABLE_PYTHON=OFF
+    ENABLE_TESTS=ON
+    GET_NanoShaper=ON
+    PYTHON_VERSION="3.10"
+
+    # Configure and compile
     cmake \
-        -DCMAKE_INSTALL_PREFIX=/usr \
-        -DCMAKE_BUILD_TYPE=Release \
-        -DENABLE_GEOFLOW=ON \
-        -DENABLE_BEM=ON \
-        -DENABLE_FETK=ON \
-        -DENABLE_OPENMP=ON \
-        -DENABLE_PBAM=ON \
-        -DENABLE_PBSAM=ON \
-        -DENABLE_PYTHON=ON \
-        -DENABLE_TESTS=OFF \
-        -DBUILD_SHARED_LIBS=ON \
-        -DBUILD_DOC=OFF \
-        -Wno-dev \
+        -DCMAKE_INSTALL_INCLUDEDIR="include" \
+        -DBUILD_DOC=${BUILD_DOC} \
+        -DAPBS_STATIC_BUILD=${APBS_STATIC_BUILD}  \
+        -DBUILD_TOOLS=O${BUILD_TOOLS} \
+        -DCMAKE_BUILD_TYPE=$RELEASE_TYPE \
+        -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR \
+        -DENABLE_PYGBE=${ENABLE_PYGBE} \
+        -DENABLE_BEM=${ENABLE_BEM} \
+        -DENABLE_iAPBS=${ENABLE_iAPBS} \
+        -DENABLE_GEOFLOW=${ENABLE_GEOFLOW} \
+        -DENABLE_OPENMP=${ENABLE_OPENMP} \
+        -DENABLE_PBAM=${ENABLE_PBAM} \
+        -DENABLE_PBSAM=${ENABLE_PBSAM} \
+        -DENABLE_PYTHON=${ENABLE_PYTHON} \
+        -DENABLE_TESTS=${ENABLE_TESTS} \
+        -DFETK_VERSION=${FETK_VERSION} \
+        -DGET_NanoShaper=${GET_NanoShaper} \
+        -DPYTHON_VERSION="${PYTHON_VERSION}" \
         ..
 
     make
 }
 
 package() {
-    cd "${srcdir}/${pkgname}-${pkgver}/apbs/build"
+    cd "${srcdir}/${pkgname}-${pkgver}/build"
 
     # install base components
     make DESTDIR="$pkgdir" install
 
     # install license
-    install -Dm644 "${srcdir}/${pkgname}-${pkgver}/apbs/LICENSE.md" "${pkgdir}/usr/share/licenses/${pkgname}/LICENSE"
+    install -Dm644 "${srcdir}/${pkgname}-${pkgver}/LICENSE.md" "${pkgdir}/usr/share/licenses/${pkgname}/LICENSE"
 
     # cleanup conflicting symlinks
     cd "${pkgdir}/usr/lib"
 
     rm -f libamd.so libblas.so libsuperlu.so libumfpack.so
+
+    # Remove conflicting gtest headers
+    cd "${pkgdir}/usr/include"
+    rm -rf gmock gtest
+    cd "${pkgdir}/usr/lib"
+    rm -rf cmake pkgconfig
+    rm -rf libgmock.so libgmock_main.so libgtest.so libgtest_main.so
 }
diff --git a/globals_apbs.patch b/globals_apbs.patch
deleted file mode 100644
index b5756c7747a2..000000000000
--- a/globals_apbs.patch
+++ /dev/null
@@ -1,69 +0,0 @@
---- src/pmgc/mgsubd.c	2020-05-30 04:47:30.000000000 +0300
-+++ src/pmgc/mgsubd.c	2020-08-19 13:08:27.503698756 +0300
-@@ -52,10 +52,12 @@
-  * @endverbatim

-  */

- 

- #include "mgsubd.h"

- 

-+double bf, oh, cputme;

-+

- VPUBLIC void Vbuildops(

-         int *nx, int *ny, int *nz,

-         int *nlev, int *ipkey, int *iinfo,

-         int *ido, int *iz,

-         int *mgprol, int *mgcoar, int *mgsolv, int *mgdisc, int *ipc,

---- src/pmgc/mgsubd.h	2020-05-30 04:47:30.000000000 +0300
-+++ src/pmgc/mgsubd.h	2020-08-19 13:08:54.266813098 +0300
-@@ -253,11 +253,11 @@
-         int n3  ///< The third grid size

-         );

- 

- 

- /// @todo  Get rid of these globals in refactor

--double bf, oh, cputme;

-+extern double bf, oh, cputme;

- 

- /** @brief   This routine prints out some info and such from inside multigrid.

-  *  @author  Tucker Beck [C Translation], Michael Holst [Original]

-  *  @note    Replaces prtstp from mgsubd.f

-  */

---- src/pmgc/mypdec.c	2020-05-30 04:47:30.000000000 +0300
-+++ src/pmgc/mypdec.c	2020-08-19 13:09:34.939813105 +0300
-@@ -52,10 +52,15 @@
-  * @endverbatim

-  */

- 

- #include "mypdec.h"

- 

-+double v1, v2, v3, conc1, conc2, conc3, vol, relSize;

-+int nion;

-+double charge[MAXIONS];

-+double sconc[MAXIONS];

-+

- VPUBLIC void Vmypdefinitlpbe(int *tnion, double *tcharge, double *tsconc) {

- 

-     int i;

- 

-     nion = *tnion;

---- src/pmgc/mypdec.h	2020-05-30 04:47:30.000000000 +0300
-+++ src/pmgc/mypdec.h	2020-08-19 13:09:56.172972195 +0300
-@@ -65,14 +65,14 @@
- #define ZLARGE     1.0e20

- #define SINH_MIN -85.0

- #define SINH_MAX  85.0

- 

- /// @todo  Remove dependencies on global variables

--double v1, v2, v3, conc1, conc2, conc3, vol, relSize;

--int nion;

--double charge[MAXIONS];

--double sconc[MAXIONS];

-+extern double v1, v2, v3, conc1, conc2, conc3, vol, relSize;

-+extern int nion;

-+extern double charge[MAXIONS];

-+extern double sconc[MAXIONS];

- 

- #define Na 6.022045000e-04

- 

- /** @brief   Set up the ionic species to be used in later calculations.  This

-  *           must be called before any other of the routines in this file.