Initial repository

4 files changed, 148 insertions, 0 deletions

diff --git a/.SRCINFO b/.SRCINFO
new file mode 100644
index 000000000000..7ea2b5033167
--- /dev/null
+++ b/.SRCINFO
@@ -0,0 +1,27 @@
+pkgbase = nupack4
+	pkgdesc = Software suite for the analysis and design of nucleic acid structures, devices, and systems.
+	pkgver = 4.0.0.28
+	pkgrel = 1
+	url = https://nupack.org
+	arch = x86_64
+	license = Custom
+	depends = armadillo
+	depends = tbb2019
+	depends = gecode
+	depends = nlohmann-json
+	depends = jsoncpp
+	depends = tclap
+	depends = spdlog
+	depends = boost
+	depends = boost-libs
+	depends = python
+	depends = python-scipy
+	depends = python-pandas
+	source = nupack-4.0.0.28.zip::file://nupack-4.0.0.28.zip
+	source = disable-vcpkg.patch
+	source = disable-broken-logger.patch
+	sha256sums = 4b15e4773cbe9dd5bee6afaa1085170fc8e2cee9de711f8603d66575be83cbe1
+	sha256sums = f9dac1f4a8cb26f3c11fa5cbf39de4feee34f5914023cc8c93950c88dca5f12b
+	sha256sums = 9dd038b73b9d34050b208a93b4521ee661e7f4d7ccd49ba4ae40ff85b8d441d2
+
+pkgname = nupack4
diff --git a/PKGBUILD b/PKGBUILD
new file mode 100644
index 000000000000..867f6eebe9ac
--- /dev/null
+++ b/PKGBUILD
@@ -0,0 +1,93 @@
+# Maintainer: Constantine Evans <const@costi.eu>
+#
+# Note: you probably want to install the binary version of NUPACK 4, not this source build.  See below for
+# more details.
+#
+# NUPACK is available under a restricted license that is largely similar to the BSD 3-clause license, updated
+# to address web applications, but with the notable exception that it allows for use and redistribution 
+# "non-commercial academic purposes only".  Furthermore, access to the downloads requires requires a username
+# and password that can be obtained through (free) registration, and sources and binary wheels are intentionally
+# not in PyPI.  While the license appears to allow for redistribution, in the interest of following the authors' 
+# wishes, this PKGBUILD does provide the source code automatically.
+#
+# To use this PKGBUILD, if you can agree to the non-commercial academic license, register for a username and 
+# password at https://www.nupack.org/downloads, download the NUPACK 4 zip file there, and place the zip file 
+# in the same directory as this PKGBUILD.
+#
+# Note that this PKGBUILD is for *source* installation, which may be significantly more complicated than simply
+# installing a binary wheel, also available from the Nupack website.  The intention of this PKGBUILD is to attempt
+# to make source installation work smoothly in Arch Linux, using Arch and AUR packages as much as possible, and
+# allowing installation in circumstances (for example, more recent Python versions) where binary wheels may not
+# be suitable.  The PKGBUILD makes certain changes to the build process:
+#
+# - The default build process uses a bundled vcpkg to build and install a number of external dependencies.  This
+#   build process did not work on Arch the last time I tried it.  The PKGBUILD removes vcpkg from the build process
+#   entirely, and instead uses Arch and AUR packages.  In many cases, this means that newer versions of those
+#   dependencies are used than in the normal build process, which may cause breakages.
+# - NUPACK 4 relies on an older version of TBB, and newer versions removed parts of the API it uses.  This PKGBUILD
+#   thus requires an older version of TBB, which may cause problems for other packages on your system.
+# - One error message in NUPACK 4 does not work well with newer versions of spdlog and fmt, and so is commented out.
+# - SIMD support is currently disabled, as (a) libsimdpp is not currently in the AUR, and (b) when installed (I have
+#   a PKGBUILD for it locally), NUPACK 4 has build errors wwhen NUPACK_SIMD=ON that I don't currently understand.
+
+pkgname=nupack4
+pkgver=4.0.0.28
+pkgrel=1
+pkgdesc="Software suite for the analysis and design of nucleic acid structures, devices, and systems."
+url="https://nupack.org"
+license=('Custom')
+
+arch=('x86_64')
+
+depends=(
+    'armadillo'
+    'tbb2019'
+    'gecode'
+    'nlohmann-json'
+    'jsoncpp'
+    'tclap'
+    'spdlog'
+    'boost'
+    'boost-libs'
+    'python'
+    'python-scipy'
+    'python-pandas'
+)
+
+DLAGENTS=("file::/usr/bin/echo ${BOLD}${RED} Unable to find %u, please read the PKGBUILD ${ALL_OFF}" $DLAGENTS[@])
+
+source=("nupack-4.0.0.28.zip::file://nupack-4.0.0.28.zip" "disable-vcpkg.patch" "disable-broken-logger.patch")
+
+sha256sums=('4b15e4773cbe9dd5bee6afaa1085170fc8e2cee9de711f8603d66575be83cbe1'
+            'f9dac1f4a8cb26f3c11fa5cbf39de4feee34f5914023cc8c93950c88dca5f12b'
+            '9dd038b73b9d34050b208a93b4521ee661e7f4d7ccd49ba4ae40ff85b8d441d2')
+
+prepare() {
+	cd "nupack-$pkgver"
+    patch --forward --strip=1 --input=../disable-vcpkg.patch
+    patch --forward --strip=1 --input=../disable-broken-logger.patch
+}
+
+build() {
+    cmake -B build -S "nupack-${pkgver}/source" \
+        -DCMAKE_BUILD_TYPE='None' \
+        -DCMAKE_INSTALL_PREFIX='/usr' \
+        -DNUPACK_SIMD=OFF \
+        -DCMAKE_C_COMPILER=clang \
+        -DCMAKE_CXX_COMPILER=clang++ \
+        -DCMAKE_POSITION_INDEPENDENT_CODE=ON \
+        -Wno-dev
+    cmake --build build --target nupack-python
+}
+
+# check() {
+# 	cd "$pkgname-$pkgver/source"
+# 	make -k check
+# }
+
+package() {
+    cd "build"
+    python setup.py install --root="$pkgdir" --optimize=1
+    cd ..
+    install -Dm644 "nupack-${pkgver}/source/LICENSE.txt" "$pkgdir/usr/share/licenses/$pkgname/LICENSE"
+}
diff --git a/disable-broken-logger.patch b/disable-broken-logger.patch
new file mode 100644
index 000000000000..cf474b84cff9
--- /dev/null
+++ b/disable-broken-logger.patch
@@ -0,0 +1,14 @@
+diff '--color=auto' -U3 -r nupack-4.0.0.28/source/include/nupack/concentration/Solve.h nu-edit/source/include/nupack/concentration/Solve.h
+--- nupack-4.0.0.28/source/include/nupack/concentration/Solve.h	2022-06-09 16:19:40.000000000 +0100
++++ nu-edit/source/include/nupack/concentration/Solve.h	2022-09-07 17:51:54.179141241 +0100
+@@ -360,8 +360,8 @@
+     // Run trust region with initial radius 1000
+     auto ret = trust_region(std::move(sys), gradient, hessian, direction, condition, adjust_delta, ops.delta_max);
+ 
+-    if (!good && logger)
+-        logger->error("A:\n{}\northo A:\n{}\nx0:\n{}\ng:\n{}\nx:\n{}\n", orig_A, A, x0, q, ret.primal);
++    //if (!good && logger)
++    //    logger->error("A:\n{}\northo A:\n{}\nx0:\n{}\ng:\n{}\nx:\n{}\n", orig_A, A, x0, q, ret.primal);
+ 
+     if (logger) logger->info("equilibrate finished. Number of iterations: {}", n - 1);
+ 
diff --git a/disable-vcpkg.patch b/disable-vcpkg.patch
new file mode 100644
index 000000000000..bcb35fb82242
--- /dev/null
+++ b/disable-vcpkg.patch
@@ -0,0 +1,14 @@
+diff '--color=auto' -U3 -r nupack-4.0.0.28/source/CMakeLists.txt nu-edit/source/CMakeLists.txt
+--- nupack-4.0.0.28/source/CMakeLists.txt	2022-06-09 16:19:40.000000000 +0100
++++ nu-edit/source/CMakeLists.txt	2022-09-07 17:05:31.926023038 +0100
+@@ -22,8 +22,8 @@
+ 
+ ################################################################################
+ 
+-set(CMAKE_TOOLCHAIN_FILE ${CMAKE_CURRENT_SOURCE_DIR}/external/vcpkg/scripts/buildsystems/vcpkg.cmake
+-  CACHE STRING "Vcpkg toolchain file")
++#set(CMAKE_TOOLCHAIN_FILE ${CMAKE_CURRENT_SOURCE_DIR}/external/vcpkg/scripts/buildsystems/vcpkg.cmake
++#  CACHE STRING "Vcpkg toolchain file")
+ 
+ ################################################################################
+