From: "Anna Vyalkova" <cyber+gentoo@sysrq.in>
To: gentoo-commits@lists.gentoo.org
Subject: [gentoo-commits] repo/proj/guru:dev commit in: sci-biology/cmdock/, sci-biology/cmdock/files/
Date: Tue, 9 Jan 2024 10:19:59 +0000 (UTC) [thread overview]
Message-ID: <1704795590.bf5dd7c748cd41b6fa540780d668045d1836db0b.cybertailor@gentoo> (raw)
commit: bf5dd7c748cd41b6fa540780d668045d1836db0b
Author: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
AuthorDate: Tue Jan 9 10:19:33 2024 +0000
Commit: Anna Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
CommitDate: Tue Jan 9 10:19:50 2024 +0000
URL: https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=bf5dd7c7
sci-biology/cmdock: fix build
Closes: https://bugs.gentoo.org/901345
Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq.in>
sci-biology/cmdock/cmdock-0.2.0-r1.ebuild | 119 ++++++++++++++++++++
.../cmdock/files/cmdock-0.2.0-cxxopts.patch | 122 +++++++++++++++++++++
.../cmdock/files/cmdock-0.2.0-include.patch | 19 ++++
3 files changed, 260 insertions(+)
diff --git a/sci-biology/cmdock/cmdock-0.2.0-r1.ebuild b/sci-biology/cmdock/cmdock-0.2.0-r1.ebuild
new file mode 100644
index 0000000000..e01a7ecf70
--- /dev/null
+++ b/sci-biology/cmdock/cmdock-0.2.0-r1.ebuild
@@ -0,0 +1,119 @@
+# Copyright 2021-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+BOINC_APP_OPTIONAL="true"
+inherit boinc-app flag-o-matic meson optfeature python-any-r1
+
+DESCRIPTION="Program for docking ligands to proteins and nucleic acids"
+HOMEPAGE="https://gitlab.com/Jukic/cmdock"
+SRC_URI="https://gitlab.com/Jukic/${PN}/-/archive/v${PV}/${PN}-v${PV}.tar.bz2"
+S="${WORKDIR}/${PN}-v${PV}"
+
+LICENSE="LGPL-3 ZLIB"
+SLOT="0/${PV}"
+KEYWORDS="~amd64"
+IUSE="apidoc boinc cpu_flags_x86_sse2 doc test"
+
+# Flaky tests
+RESTRICT="test"
+
+RDEPEND="
+ boinc? ( sci-misc/boinc-wrapper )
+"
+DEPEND="
+ dev-cpp/eigen:3
+ >=dev-cpp/indicators-2.3-r1
+ >=dev-cpp/pcg-cpp-0.98.1_p20210406-r1
+ >=dev-libs/cxxopts-3
+"
+BDEPEND="
+ apidoc? (
+ app-doc/doxygen
+ dev-texlive/texlive-fontutils
+ )
+ doc? (
+ $(python_gen_any_dep '
+ dev-python/insipid-sphinx-theme[${PYTHON_USEDEP}]
+ dev-python/sphinx[${PYTHON_USEDEP}]
+ ')
+ )
+ test? ( ${PYTHON_DEPS} )
+"
+
+PATCHES=(
+ "${FILESDIR}"/${P}-include.patch
+ "${FILESDIR}"/${P}-cxxopts.patch
+)
+
+DOCS=( README.md changelog.md )
+
+BOINC_MASTER_URL="https://www.sidock.si/sidock/"
+BOINC_INVITATION_CODE="Crunch_4Science"
+BOINC_APP_HELPTEXT=\
+"The easiest way to do something useful with this application
+is to attach it to SiDock@home BOINC project."
+
+INSTALL_PREFIX="${EPREFIX}/opt/${P}"
+
+python_check_deps() {
+ use doc || return 0
+
+ python_has_version "dev-python/sphinx[${PYTHON_USEDEP}]" &&
+ python_has_version "dev-python/insipid-sphinx-theme[${PYTHON_USEDEP}]"
+}
+
+foreach_wrapper_job() {
+ sed -e "s:@PREFIX@:${INSTALL_PREFIX}:g" -i "${1}" || die
+}
+
+src_prepare() {
+ default
+ python_fix_shebang "${S}"/bin
+}
+
+src_configure() {
+ # very weird directory layout
+ local emesonargs=(
+ --prefix="${INSTALL_PREFIX}"
+ $(meson_use apidoc)
+ $(meson_use doc)
+ $(meson_use test tests)
+ -Ddocdir="${EPREFIX}"/usr/share/doc/${PF}
+ )
+ meson_src_configure
+
+ use cpu_flags_x86_sse2 || append-cppflags "-DBUNDLE_NO_SSE"
+}
+
+src_install() {
+ meson_src_install
+ python_optimize "${D}${INSTALL_PREFIX}"/bin
+
+ if use boinc; then
+ doappinfo "${FILESDIR}"/app_info_${PV}.xml
+ dowrapper cmdock-l
+
+ # install cmdock executable
+ exeinto "$(get_project_root)"
+ exeopts --owner root --group boinc
+ newexe "${D}${INSTALL_PREFIX}"/bin/cmdock cmdock-${PV}
+
+ # install a blank file
+ touch "${T}"/docking_out || die
+ insinto "$(get_project_root)"
+ insopts --owner root --group boinc
+ doins "${T}"/docking_out
+ fi
+}
+
+pkg_postinst() {
+ optfeature "sdtether.py and sdrmsd.py scripts" "dev-python/numpy sci-chemistry/openbabel[python]"
+ use boinc && boinc-app_pkg_postinst
+}
+
+pkg_postrm() {
+ use boinc && boinc-app_pkg_postrm
+}
diff --git a/sci-biology/cmdock/files/cmdock-0.2.0-cxxopts.patch b/sci-biology/cmdock/files/cmdock-0.2.0-cxxopts.patch
new file mode 100644
index 0000000000..4d7f227957
--- /dev/null
+++ b/sci-biology/cmdock/files/cmdock-0.2.0-cxxopts.patch
@@ -0,0 +1,122 @@
+Update to cxxopts 3.0
+
+--- a/meson.build
++++ b/meson.build
+@@ -40,7 +40,7 @@ if cpp_compiler.get_id() == 'msvc'
+ message('Applying workaround for MSVC by adding flag /Zc:twoPhase-: https://stackoverflow.com/questions/56782470/why-do-i-have-warning-c4199-two-phase-name-lookup-is-not-supported-for-c-cli')
+ endif
+
+-cxxopts_dep = dependency('cxxopts', fallback : ['cxxopts', 'cxxopts_dep'])
++cxxopts_dep = dependency('cxxopts', version : '>=3.0', fallback : ['cxxopts', 'cxxopts_dep'])
+ eigen3_dep = dependency('eigen3', fallback : ['eigen', 'eigen_dep'])
+ openmp_dep = dependency('openmp', required : false)
+
+diff --git a/src/exe/cmcavity.cxx b/src/exe/cmcavity.cxx
+index 427d3c0..3a5c747 100644
+--- a/src/exe/cmcavity.cxx
++++ b/src/exe/cmcavity.cxx
+@@ -41,7 +41,7 @@ void PrintHeaderAddon(std::ostream &outputStream) {
+ // MAIN PROGRAM STARTS HERE
+ /////////////////////////////////////////////////////////////////////
+
+-int main(int argc, char *argv[]) {
++int main(const int argc, const char *argv[]) {
+ // Handle obsolete arguments, if any
+ for (int i = 0; i < argc; i++) {
+ std::string opt = argv[i];
+@@ -451,7 +451,7 @@ int main(int argc, char *argv[]) {
+
+ logFile.close();
+ }
+- } catch (const cxxopts::OptionException &e) {
++ } catch (const cxxopts::exceptions::exception &e) {
+ std::cout << "Error parsing options: " << e.what() << std::endl;
+ return 1;
+ } catch (RbtError &e) {
+@@ -463,4 +463,4 @@ int main(int argc, char *argv[]) {
+ _RBTOBJECTCOUNTER_DUMP_(std::cout)
+
+ return 0;
+-}
+\ No newline at end of file
++}
+diff --git a/src/exe/cmdock.cxx b/src/exe/cmdock.cxx
+index 10e18ca..86bbff1 100644
+--- a/src/exe/cmdock.cxx
++++ b/src/exe/cmdock.cxx
+@@ -80,7 +80,7 @@ void printHelpFooter() {
+ // MAIN PROGRAM STARTS HERE
+ /////////////////////////////////////////////////////////////////////
+
+-int main(int argc, char *argv[]) {
++int main(const int argc, const char *argv[]) {
+ // Handle premature termination
+ signal (SIGINT, terminator);
+
+@@ -941,7 +941,7 @@ int main(int argc, char *argv[]) {
+ log << "Thank you for using " << Rbt::GetProgramName() << " "
+ << Rbt::GetVersion() << "." << std::endl;
+ logFile.close();
+- } catch (const cxxopts::OptionException &e) {
++ } catch (const cxxopts::exceptions::exception &e) {
+ std::cout << "Error parsing options: " << e.what() << std::endl;
+ return 1;
+ } catch (RbtError &e) {
+@@ -953,4 +953,4 @@ int main(int argc, char *argv[]) {
+ _RBTOBJECTCOUNTER_DUMP_(std::cout)
+
+ return 0;
+-}
+\ No newline at end of file
++}
+diff --git a/src/exe/cmmoegrid.cxx b/src/exe/cmmoegrid.cxx
+index 4bff8f3..bf74b52 100644
+--- a/src/exe/cmmoegrid.cxx
++++ b/src/exe/cmmoegrid.cxx
+@@ -57,7 +57,7 @@ RbtModelList CreateProbes(std::string anAtomTypeStr) {
+ // MAIN PROGRAM STARTS HERE
+ /////////////////////////////////////////////////////////////////////
+
+-int main(int argc, char *argv[]) {
++int main(const int argc, const char *argv[]) {
+ std::cout.setf(std::ios_base::left, std::ios_base::adjustfield);
+
+ // Strip off the path to the executable, leaving just the file name
+@@ -268,7 +268,7 @@ int main(int argc, char *argv[]) {
+ }
+ std::cout << "done." << std::endl;
+ }
+- } catch (const cxxopts::OptionException &e) {
++ } catch (const cxxopts::exceptions::exception &e) {
+ std::cout << "Error parsing options: " << e.what() << std::endl;
+ return 1;
+ } catch (RbtError &e) {
+diff --git a/src/exe/cmzip.cxx b/src/exe/cmzip.cxx
+index 1d1f69a..043d7be 100644
+--- a/src/exe/cmzip.cxx
++++ b/src/exe/cmzip.cxx
+@@ -504,7 +504,7 @@ void rescue(cxxopts::ParseResult result){
+ }
+
+ // ENTRY POINT
+-int main(int argc, char *argv[]) {
++int main(const int argc, const char *argv[]) {
+ // Handle premature termination
+ signal (SIGINT, terminator);
+
+@@ -580,7 +580,7 @@ Use this if CmDock terminates prematurely. CmZIP will search for records in the
+ return 0;
+ }
+
+- } catch (const cxxopts::OptionException &e) {
++ } catch (const cxxopts::exceptions::exception &e) {
+ std::cout << "Error parsing options: " << e.what() << std::endl;
+ return 1;
+ } catch (const std::exception &exc) {
+@@ -589,4 +589,4 @@ Use this if CmDock terminates prematurely. CmZIP will search for records in the
+ /*} catch (...) {
+ std::cout << "Unknown exception" << std::endl;
+ }*/
+-}
+\ No newline at end of file
++}
diff --git a/sci-biology/cmdock/files/cmdock-0.2.0-include.patch b/sci-biology/cmdock/files/cmdock-0.2.0-include.patch
new file mode 100644
index 0000000000..b4a6e80bb0
--- /dev/null
+++ b/sci-biology/cmdock/files/cmdock-0.2.0-include.patch
@@ -0,0 +1,19 @@
+Rbt.cxx: Add missing include
+
+--- a/src/lib/Rbt.cxx
++++ b/src/lib/Rbt.cxx
+@@ -15,6 +15,7 @@
+ #include <algorithm> //For sort
+ #include <climits> //For PATH_MAX
+ #include <cstdlib> //For getenv
++#include <cstdint> //For int types
+ #include <ctime> //For time functions
+ #include <dirent.h> //For directory handling
+ #include <fstream> //For ifstream
+@@ -581,4 +582,4 @@ bool Rbt::endsWith (std::string const &fullString, std::string const &ending) {
+ } else {
+ return false;
+ }
+-}
+\ No newline at end of file
++}
next reply other threads:[~2024-01-09 10:20 UTC|newest]
Thread overview: 8+ messages / expand[flat|nested] mbox.gz Atom feed top
2024-01-09 10:19 Anna Vyalkova [this message]
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2024-01-09 9:06 [gentoo-commits] repo/proj/guru:dev commit in: sci-biology/cmdock/, sci-biology/cmdock/files/ Anna Vyalkova
2022-12-12 11:44 Anna Vyalkova
2022-06-02 4:55 Anna Vyalkova
2021-11-25 7:16 Anna Vyalkova
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