commit: fabb98163cb060a020c3894ad7729924aff6a6fc Author: Arthur Zamarin <arthurzam <AT> gentoo <DOT> org> AuthorDate: Mon Jun 2 16:35:30 2025 +0000 Commit: Arthur Zamarin <arthurzam <AT> gentoo <DOT> org> CommitDate: Mon Jun 2 16:39:04 2025 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=fabb9816
sci-chemistry/modeller: treeclean Closes: https://bugs.gentoo.org/692308 (pkgremoved) Closes: https://bugs.gentoo.org/727980 (pkgremoved) Closes: https://bugs.gentoo.org/765871 (pkgremoved) Closes: https://bugs.gentoo.org/777351 (pkgremoved) Closes: https://bugs.gentoo.org/829187 (pkgremoved) Closes: https://bugs.gentoo.org/832745 (pkgremoved) Closes: https://bugs.gentoo.org/835004 (pkgremoved) Closes: https://bugs.gentoo.org/851585 (pkgremoved) Closes: https://bugs.gentoo.org/923272 (pkgremoved) Closes: https://bugs.gentoo.org/927901 (pkgremoved) Closes: https://bugs.gentoo.org/932087 (pkgremoved) Closes: https://bugs.gentoo.org/933877 (pkgremoved) Closes: https://bugs.gentoo.org/950475 (pkgremoved) Closes: https://bugs.gentoo.org/222357 (pkgremoved) Closes: https://bugs.gentoo.org/952653 (pkgremoved) Signed-off-by: Arthur Zamarin <arthurzam <AT> gentoo.org> profiles/package.mask | 7 - sci-chemistry/modeller/Manifest | 1 - .../modeller/files/modeller-10.5-fix-except.patch | 29 ---- sci-chemistry/modeller/metadata.xml | 12 -- sci-chemistry/modeller/modeller-10.5.ebuild | 149 --------------------- 5 files changed, 198 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index d9bb800db804..21bfeee3fb67 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -226,13 +226,6 @@ dev-libs/libxml2-compat =dev-python/ensurepip-setuptools-80.3.0 =dev-python/setuptools-80.3.0 -# Michał Górny <[email protected]> (2025-05-03) -# Not actively maintained in ::gentoo. Last bumped a year ago. -# Still on EAPI 7, no Python 3.13 support, does not work with new -# dev-lang/swig. Lots of bugs open. -# Removal on 2025-06-02. Bug #950475, #952653. -sci-chemistry/modeller - # Matt Jolly <[email protected]> (2025-04-28) # Unmaintained in Gentoo, depends on masked x11-wm/fvwm, # SRC_URI uses mirror://gentoo and the files don't exist on mirrors. diff --git a/sci-chemistry/modeller/Manifest b/sci-chemistry/modeller/Manifest deleted file mode 100644 index 7f12b0817212..000000000000 --- a/sci-chemistry/modeller/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST modeller-10.5.tar.gz 38272541 BLAKE2B 9c71a9f1e4c34c91852db73ebf86f71cf355217d6889566ff6840dc6874d4906b989a36f3dd642ba4e4d1fe671c1a15753a33e7fabb53adc9182c76fe4fdb6c4 SHA512 666c5367a14084438c96b68ba0779ebd97ca831a4a6538f66e54b63657c8e13b85931c2de8300311f1df7d02907b2ec61f27f95b0704f2c6a313b6baee56febc diff --git a/sci-chemistry/modeller/files/modeller-10.5-fix-except.patch b/sci-chemistry/modeller/files/modeller-10.5-fix-except.patch deleted file mode 100644 index f480a8229bf9..000000000000 --- a/sci-chemistry/modeller/files/modeller-10.5-fix-except.patch +++ /dev/null @@ -1,29 +0,0 @@ ---- a/modlib/modeller/top_interpreter/__init__.py 2024-03-27 15:52:04.005550025 +0300 -+++ b/modlib/modeller/top_interpreter/__init__.py 2024-03-27 15:54:00.776897686 +0300 -@@ -65,7 +65,7 @@ - if len(line) > 0: - try: - self._parse_top_ini_line(line.split(None, 4), vars) -- except TypeError, detail: # noqa: E999 -+ except (TypeError, detail): # noqa: E999 - mod_log_write("read_top__E> " + str(detail)) - mod_log_write(" top.ini line: " + line) - raise -@@ -115,7 +115,7 @@ - try: - fh = self._open_include_file( - self.variables['include_file']) -- except IOError, detail: -+ except (IOError, detail): - mod_log_write("runlines__E> " + str(detail)) - mod_log_write(" TOP Command line: " + line) - raise -@@ -162,7 +162,7 @@ - indxca = self._run_top_cmd(cmd, indxca, lines, callstack, - subrout) - _modeller.mod_top_post() -- except (IndexError, SyntaxError, TypeError), detail: -+ except (IndexError, SyntaxError, TypeError, detail): - mod_log_write("runlines__E> " + str(detail)) - mod_log_write(" TOP Command line: " + line) - raise diff --git a/sci-chemistry/modeller/metadata.xml b/sci-chemistry/modeller/metadata.xml deleted file mode 100644 index 22631b58bc2b..000000000000 --- a/sci-chemistry/modeller/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="person"> - <email>[email protected]</email> - <name>Alexey Shvetsov</name> - </maintainer> - <maintainer type="project"> - <email>[email protected]</email> - <name>Gentoo Chemistry Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-chemistry/modeller/modeller-10.5.ebuild b/sci-chemistry/modeller/modeller-10.5.ebuild deleted file mode 100644 index 8f3bbb408910..000000000000 --- a/sci-chemistry/modeller/modeller-10.5.ebuild +++ /dev/null @@ -1,149 +0,0 @@ -# Copyright 1999-2025 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{10..12} ) -DISTUTILS_USE_PEP517=setuptools -DISTUTILS_EXT=1 - -inherit distutils-r1 - -DESCRIPTION="Homology or comparative modeling of protein three-dimensional structures" -HOMEPAGE="https://salilab.org/modeller/"; -SRC_URI="https://salilab.org/${PN}/${PV}/${P}.tar.gz"; - -LICENSE="modeller" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="doc examples" - -RESTRICT="mirror" - -# <swig-4.3.0 for https://bugs.gentoo.org/950475 -BDEPEND="<dev-lang/swig-4.3.0" - -PATCHES=( "${FILESDIR}/${P}-fix-except.patch" ) - -INPATH="${EPREFIX}"/opt/modeller${ver} - -QA_PREBUILT="/opt/*" - -pkg_setup() { - case ${ARCH} in - x86) - EXECTYPE="i386-intel8";; - amd64) - EXECTYPE="x86_64-intel8";; - *) - die "Your arch "${ARCH}" does not appear supported at this time.";; - esac -} - -python_prepare_all() { - sed "s:i386-intel8:${EXECTYPE}:g" -i src/swig/setup.py || die - rm -rf modlib/modeller/python_library || die - distutils-r1_python_prepare_all -} - -python_compile() { - cd src/swig || die - swig -python -keyword -nodefaultctor -nodefaultdtor -noproxy modeller.i || die - distutils-r1_python_compile -} - -python_install() { - cd src/swig || die - distutils-r1_python_install -} - -python_install_all() { - cd "${S}" || die - sed \ - -e "/^EXECUTABLE_TYPE/s:xxx:${EXECTYPE}:g" \ - -e "/MODINSTALL/s:xxx:\"${INPATH}\":g" \ - -i bin/modscript || die - - sed -e "s;@TOPDIR\@;\"${INPATH}\";" \ - -e "s;@EXETYPE\@;${EXECTYPE};" \ - bin/modpy.sh.in > "${T}/modpy.sh" - - insinto ${INPATH} - doins -r modlib - python_foreach_impl python_domodule modlib/modeller - - insinto ${INPATH}/bin - doins -r bin/{lib,*top} - - exeinto ${INPATH}/bin - doexe bin/{modscript,mod${PV}_${EXECTYPE}} "${T}"/modpy.sh - - dosym ${INPATH}/bin/modscript /opt/bin/mod${PV} - dosym ${INPATH}/bin/modpy.sh /opt/bin/modpy.sh - - exeinto ${INPATH}/lib/${EXECTYPE}/ - doexe lib/${EXECTYPE}/lib* - dosym libmodeller.so.12 ${INPATH}/lib/${EXECTYPE}/libmodeller.so - dosym ../../${INPATH}/lib/${EXECTYPE}/libmodeller.so.12 /usr/$(get_libdir)/libmodeller.so.12 - - use doc && HTML_DOCS=( doc/. ) - distutils-r1_python_install_all - - if use examples; then - insinto /usr/share/${PN}/ - doins -r examples - fi - - insinto /etc/revdep-rebuild - cat >> "${T}"/40-${PN} <<- EOF - SEARCH_DIRS_MASK="${EPREFIX}/opt/modeller/lib/" - EOF - doins "${T}"/40-${PN} -} - -pkg_postinst() { - if [[ ! -e "${INPATH}/modlib/modeller/config.py" ]]; then - echo install_dir = \"${INPATH}/\"> ${INPATH}/modlib/modeller/config.py - fi - - if grep -q license ${INPATH}/modlib/modeller/config.py; then - einfo "A license key file is already present in ${INPATH}/modlib/modeller/config.py" - else - ewarn "Obtain a license Key from" - ewarn "http://salilab.org/modeller/registration.html"; - ewarn "And run this before using modeller:" - ewarn "emerge --config =${CATEGORY}/${PF}" - ewarn "That way you can [re]enter your license key." - fi -} - -pkg_postrm() { - ewarn "This package leaves a license Key file in ${INPATH}/modlib/modeller/config.py" - ewarn "that you need to remove to completely get rid of modeller." -} - -pkg_config() { - ewarn "Your license key is NOT checked for validity here." - ewarn " Make sure you type it in correctly." - eerror "If you CTRL+C out of this, modeller will not run!" - while true - do - einfo "Please enter your license key:" - read license_key1 - einfo "Please re-enter your license key:" - read license_key2 - if [[ "$license_key1" == "" ]] - then - echo "You entered a blank license key. Try again." - else - if [[ "$license_key1" == "$license_key2" ]] - then - echo license = '"'$license_key1'"' >> "${INPATH}/modlib/modeller/config.py" - einfo "Thank you!" - break - else - eerror "Your license key entries do not match. Try again." - fi - fi - done -}
