From cda2bd3f047b23e20c75c4b7557e62cda6a0ad81 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Leonardo=20Hern=C3=A1ndez=20Hern=C3=A1ndez?= Date: Sun, 14 Jul 2024 00:19:55 -0600 Subject: [PATCH 01/11] sec-keys/openpgp-keys-emersion: add 20240714, drop 20230421 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Closes: https://bugs.gentoo.org/935881 Signed-off-by: Leonardo Hernández Hernández --- sec-keys/openpgp-keys-emersion/Manifest | 2 +- ...on-20230421.ebuild => openpgp-keys-emersion-20240714.ebuild} | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) rename sec-keys/openpgp-keys-emersion/{openpgp-keys-emersion-20230421.ebuild => openpgp-keys-emersion-20240714.ebuild} (93%) diff --git a/sec-keys/openpgp-keys-emersion/Manifest b/sec-keys/openpgp-keys-emersion/Manifest index 7090b4f883..422f34ba88 100644 --- a/sec-keys/openpgp-keys-emersion/Manifest +++ b/sec-keys/openpgp-keys-emersion/Manifest @@ -1 +1 @@ -DIST openpgp-keys-emersion-20230421.asc 2263 BLAKE2B 03d35a3daa24b811de36e34f5c7bf082b8a49438acd33080ce2f01d8db7b0e0cdbd03d254ebb0ca8b1608815092a6e6e42fe7b5cbdecfa6f310e9f8608f04d6f SHA512 5681bac74f6e7e34230ad9a0127161872eb77a237ac5534127467046d90bdff1abe96d269ca4f8ff8c076ccbb88a4e71feb1525196f9df19a03efe05a69cea6f +DIST openpgp-keys-emersion-20240714.asc 2263 BLAKE2B 2cee5af46ddfd374b94368c805f7a663015ebc90501f1ecb21e548ec209156ff658f6f8ad97eb0415fe74b6c0e30dd232872bfca28b5002ce130cdf590742550 SHA512 0033b669a58a63c256aa641178b9cbbbeef5bd8a017f0080f2a07c3fb393273e151931378b33724428491f7c537b26026781abede72d225a7d95e6b48bbd2dc5 diff --git a/sec-keys/openpgp-keys-emersion/openpgp-keys-emersion-20230421.ebuild b/sec-keys/openpgp-keys-emersion/openpgp-keys-emersion-20240714.ebuild similarity index 93% rename from sec-keys/openpgp-keys-emersion/openpgp-keys-emersion-20230421.ebuild rename to sec-keys/openpgp-keys-emersion/openpgp-keys-emersion-20240714.ebuild index 4d82653071..2f09a4af18 100644 --- a/sec-keys/openpgp-keys-emersion/openpgp-keys-emersion-20230421.ebuild +++ b/sec-keys/openpgp-keys-emersion/openpgp-keys-emersion-20240714.ebuild @@ -1,4 +1,4 @@ -# Copyright 2022 Gentoo Authors +# Copyright 2022-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 From dd9d541bf216715f4a3bbc426c38231db375717d Mon Sep 17 00:00:00 2001 From: "Anna (cybertailor) Vyalkova" Date: Tue, 9 Jul 2024 20:19:31 +0500 Subject: [PATCH 02/11] boinc-app.eclass: better wrapper install function MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit "dowrapper" had too much magic: it relied on specifically files being present in ${FILESDIR}, which is just… wrong. It will burn in flames without any backwards compatibility. New "boinc_install_wrapper" function replaces it. Signed-off-by: Anna (cybertailor) Vyalkova --- eclass/boinc-app.eclass | 62 ++++++++++++++++++++++------------------- 1 file changed, 34 insertions(+), 28 deletions(-) diff --git a/eclass/boinc-app.eclass b/eclass/boinc-app.eclass index 540fc8ea0a..6a386bf2f2 100644 --- a/eclass/boinc-app.eclass +++ b/eclass/boinc-app.eclass @@ -236,61 +236,67 @@ boinc-wrapper_foreach_wrapper_job() { || die "$(basename "$1") sed failed" } -# @FUNCTION: dowrapper -# @USAGE: [more apps...] +# @FUNCTION: boinc_install_wrapper +# @USAGE: [new name] # @DESCRIPTION: # This function provides a uniform way to install wrapper applications # for BOINC projects. It makes symlinks to the BOINC wrapper and also # installs respective job.xml files. # -# When sci-misc/boinc-example-1.0 calls `dowrapper boinc-example` it: +# When `dowrapper boinc-example_wrapper A.xml B.xml` is called, it: # -# 1. Installs boinc-example_job_1.0.xml from ebuild's files/ directory -# to project's root directory +# 1. Installs A.xml in the project's root directory, renaming it to B.xml # -# 2. Installs boinc-example_wrapper_1.0 symlink, which points -# to /usr/bin/boinc-wrapper, to project's root directory +# 2. Installs boinc-example_wrapper symlink, which points +# to /usr/bin/boinc-wrapper, in the project's root directory # # Example: # @CODE # src_install() { # meson_src_install # -# dowrapper boinc-example boinc-sample +# boinc_install_wrapper boinc-example_wrapper "${FILESDIR}"/job.xml # doappinfo "${FILESDIR}"/app_info_${PV}.xml # } # @CODE # # Keep your job.xml files in sync with app_info.xml! -dowrapper() { +boinc_install_wrapper() { debug-print-function ${FUNCNAME} "${@}" - for app in "$@"; do - local wrapperjob="${app}_job_${PV}.xml" - local wrapperexe="${app}_wrapper_${PV}" + (( $# >= 2 && $# <= 3 )) || \ + die "${FUNCNAME} got wrong number of arguments" - [[ -f "${FILESDIR}/${wrapperjob}" ]] || \ - die "${wrapperjob} not found in ebuild's files/ directory" + local exe="${1:?}" + local job="${2:?}" + local job_dest="${3:-$(basename "${job:?}")}" - cp "${FILESDIR}/${wrapperjob}" "${T}" || die + cp "${job:?}" "${T:?}/${job_dest:?}" || die + if declare -f foreach_wrapper_job >/dev/null; then + foreach_wrapper_job "${T:?}/${job_dest:?}" + else + boinc-wrapper_foreach_wrapper_job "${T:?}/${job_dest:?}" + fi - if declare -f foreach_wrapper_job >/dev/null; then - foreach_wrapper_job "${T}/${wrapperjob}" - else - boinc-wrapper_foreach_wrapper_job "${T}/${wrapperjob}" - fi - - ( # subshell to avoid pollution of calling environment - insinto $(get_project_root) - insopts -m 0644 --owner root --group boinc - doins "${T}/${wrapperjob}" - dosym -r /usr/bin/boinc-wrapper "$(get_project_root)/${wrapperexe}" - ) || die "failed to install '${app}' wrapper app" - done + ( # subshell to avoid pollution of calling environment + insinto "$(get_project_root)" + insopts -m 0644 --owner root --group boinc + doins "${T:?}/${job_dest:?}" + ) || die "failed to install ${exe:?} wrapper job" + rm -f "${T:?}/${job_dest:?}" + dosym -r /usr/bin/boinc-wrapper "$(get_project_root)/${exe:?}" _boinc-app_fix_permissions } +# @FUNCTION: dowrapper +# @DEPRECATED: boinc_install_wrapper +# @DESCRIPTION: +# Install BOINC wrappers and job definitions. +dowrapper() { + die "${FUNCNAME} has been removed, please use boinc_install_wrapper instead" +} + # @FUNCTION: boinc-app_pkg_postinst # @DESCRIPTION: # Display helpful instructions on how to make the BOINC client use installed From 85e5d892dc80013893de85f9358db176b9757c5c Mon Sep 17 00:00:00 2001 From: "Anna (cybertailor) Vyalkova" Date: Tue, 9 Jul 2024 20:24:55 +0500 Subject: [PATCH 03/11] boinc-app.eclass: rename boinc-wrapper_foreach_wrapper_job This shouldn't have been like this in the first place. I must've been really sleepy when I was writing this eclass. Signed-off-by: Anna (cybertailor) Vyalkova --- eclass/boinc-app.eclass | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/eclass/boinc-app.eclass b/eclass/boinc-app.eclass index 6a386bf2f2..689be49923 100644 --- a/eclass/boinc-app.eclass +++ b/eclass/boinc-app.eclass @@ -221,19 +221,19 @@ doappinfo() { _boinc-app_fix_permissions } -# @FUNCTION: boinc-wrapper_foreach_wrapper_job -# @USAGE: +# @FUNCTION: boinc-app_foreach_wrapper_job +# @USAGE: # @DESCRIPTION: # The default foreach_wrapper_job(). It replaces all occurences # of @PV@, @EPREFIX@ and @LIBDIR@ strings with their corresponding values. -boinc-wrapper_foreach_wrapper_job() { +boinc-app_foreach_wrapper_job() { debug-print-function ${FUNCNAME} "${@}" - sed -i "$1" \ + sed -i "${1:?}" \ -e "s:@PV@:${PV}:g" \ -e "s:@EPREFIX@:${EPREFIX}:g" \ -e "s:@LIBDIR@:$(get_libdir):g" \ - || die "$(basename "$1") sed failed" + || die "$(basename "${1}") sed failed" } # @FUNCTION: boinc_install_wrapper @@ -275,7 +275,7 @@ boinc_install_wrapper() { if declare -f foreach_wrapper_job >/dev/null; then foreach_wrapper_job "${T:?}/${job_dest:?}" else - boinc-wrapper_foreach_wrapper_job "${T:?}/${job_dest:?}" + boinc-app_foreach_wrapper_job "${T:?}/${job_dest:?}" fi ( # subshell to avoid pollution of calling environment From a681b42cacb145c2aa008c9ca8be15e89f3ac5a5 Mon Sep 17 00:00:00 2001 From: "Anna (cybertailor) Vyalkova" Date: Tue, 9 Jul 2024 20:33:40 +0500 Subject: [PATCH 04/11] =?UTF-8?q?boinc-app.eclass:=20rename=20doappinfo=20?= =?UTF-8?q?=E2=86=92=20boinc=5Finstall=5Fappinfo?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Use the same naming style as in "boinc_install_wrapper". "doappinfo" is kept for compatibility but deprecated and will be removed sooner or later. Signed-off-by: Anna (cybertailor) Vyalkova --- eclass/boinc-app.eclass | 31 ++++++++++++++++++++----------- 1 file changed, 20 insertions(+), 11 deletions(-) diff --git a/eclass/boinc-app.eclass b/eclass/boinc-app.eclass index 689be49923..a20c800cb8 100644 --- a/eclass/boinc-app.eclass +++ b/eclass/boinc-app.eclass @@ -173,8 +173,8 @@ boinc-app_appinfo_prepare() { || die "app_info.xml sed failed" } -# @FUNCTION: doappinfo -# @USAGE: +# @FUNCTION: boinc_install_appinfo +# @USAGE: # @DESCRIPTION: # Installs given app_info.xml file to the project root. # @@ -191,36 +191,45 @@ boinc-app_appinfo_prepare() { # } # # src_install() { -# doappinfo "${FILESDIR}"/app_info_${PV}.xml +# boinc_install_appinfo "${FILESDIR}"/app_info_1.0.xml # # exeinto $(get_project_root) # exeopts -m 0755 --owner root --group boinc -# newexe bin/${PN} example_app_v${PV} +# newexe bin/${PN} example_app_v1.0 # } # @CODE -doappinfo() { +boinc_install_appinfo() { debug-print-function ${FUNCNAME} "${@}" (( $# == 1 )) || \ die "${FUNCNAME} takes exactly one argument" - cp "$1" "${T}"/app_info.xml || die + cp "${1:?}" "${T:?}"/app_info.xml || die if declare -f appinfo_prepare >/dev/null; then - appinfo_prepare "${T}"/app_info.xml + appinfo_prepare "${T:?}"/app_info.xml else - boinc-app_appinfo_prepare "${T}"/app_info.xml + boinc-app_appinfo_prepare "${T:?}"/app_info.xml fi ( # subshell to avoid pollution of calling environment - insinto $(get_project_root) + insinto "$(get_project_root)" insopts -m 0644 --owner root --group boinc - doins "${T}"/app_info.xml + doins "${T:?}"/app_info.xml ) || die "failed to install app_info.xml" _boinc-app_fix_permissions } +# @FUNCTION: doappinfo +# @DEPRECATED: boinc_install_appinfo +# @USAGE: +# @DESCRIPTION: +# Installs given app_info.xml file to the project root. +doappinfo() { + boinc_install_appinfo "${@}" +} + # @FUNCTION: boinc-app_foreach_wrapper_job # @USAGE: # @DESCRIPTION: @@ -256,7 +265,7 @@ boinc-app_foreach_wrapper_job() { # meson_src_install # # boinc_install_wrapper boinc-example_wrapper "${FILESDIR}"/job.xml -# doappinfo "${FILESDIR}"/app_info_${PV}.xml +# boinc_install_appinfo "${FILESDIR}"/app_info_1.0.xml # } # @CODE # From 3a44a689c61265e859ff37a535c2c87a2359757d Mon Sep 17 00:00:00 2001 From: "Anna (cybertailor) Vyalkova" Date: Tue, 9 Jul 2024 20:38:31 +0500 Subject: [PATCH 05/11] boinc-app.eclass: allow non-standard runtime dir Signed-off-by: Anna (cybertailor) Vyalkova --- eclass/boinc-app.eclass | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/eclass/boinc-app.eclass b/eclass/boinc-app.eclass index a20c800cb8..00ffd39ed7 100644 --- a/eclass/boinc-app.eclass +++ b/eclass/boinc-app.eclass @@ -71,6 +71,12 @@ if [[ ! ${_BOINC_APP_ECLASS} ]]; then You have to attach to the corresponding project in order to use this application with BOINC.} +# @ECLASS_VARIABLE: BOINC_RUNTIMEDIR +# @USER_VARIABLE +# @DEFAULT_UNSET +# @DESCRIPTION: +# Directory with BOINC runtime data. + # @FUNCTION: boinc-app_add_deps # @USAGE: [--wrapper] # @DESCRIPTION: @@ -104,11 +110,9 @@ boinc_master_url_check() { # @FUNCTION: get_boincdir # @USAGE: -# @RETURN: non-prefixed default BOINC runtime directory +# @RETURN: non-prefixed BOINC runtime directory get_boincdir() { - debug-print-function ${FUNCNAME} "${@}" - - echo /var/lib/boinc + echo "${BOINC_RUNTIMEDIR:-/var/lib/boinc}" } # @FUNCTION: get_project_dirname From ce227aa165920d92198c2ca24be6e33b77f470c7 Mon Sep 17 00:00:00 2001 From: "Anna (cybertailor) Vyalkova" Date: Fri, 12 Jul 2024 13:36:36 +0500 Subject: [PATCH 06/11] boinc-app.eclass: allow to set deps for boinc-optional apps Signed-off-by: Anna (cybertailor) Vyalkova --- eclass/boinc-app.eclass | 27 ++++++++++++++++++++------- 1 file changed, 20 insertions(+), 7 deletions(-) diff --git a/eclass/boinc-app.eclass b/eclass/boinc-app.eclass index 00ffd39ed7..3a26e6738b 100644 --- a/eclass/boinc-app.eclass +++ b/eclass/boinc-app.eclass @@ -80,20 +80,33 @@ in order to use this application with BOINC.} # @FUNCTION: boinc-app_add_deps # @USAGE: [--wrapper] # @DESCRIPTION: -# Generate appropriate (R)DEPEND for wrapper-enabled or +# Generate appropriate IUSE and (R)DEPEND for wrapper-enabled or # native application. +# +# If BOINC_APP_OPTIONAL is set to a non-null value, dependencies +# will be added for "boinc" USE-flag. boinc-app_add_deps() { debug-print-function ${FUNCNAME} "${@}" - if [[ $1 == "--wrapper" ]]; then - RDEPEND="sci-misc/boinc-wrapper" + local depend rdepend + if [[ ${1} == "--wrapper" ]]; then + rdepend="sci-misc/boinc-wrapper" else - DEPEND="sci-misc/boinc" - RDEPEND="sci-misc/boinc" + depend="sci-misc/boinc" + rdepend="sci-misc/boinc" fi - DEPEND="${DEPEND} acct-user/boinc" - RDEPEND="${RDEPEND} acct-user/boinc" + depend+=" acct-user/boinc" + rdepend+=" acct-user/boinc" + + if [[ ${BOINC_APP_OPTIONAL} ]]; then + IUSE+=" boinc" + DEPEND+=" boinc? ( ${depend} )" + RDEPEND+=" boinc? ( ${rdepend} )" + else + DEPEND+=" ${depend}" + RDEPEND+=" ${rdepend}" + fi } # @FUNCTION: boinc_master_url_check From 50b84aa2d1160992a84dcfeefd7748a491147ccc Mon Sep 17 00:00:00 2001 From: "Anna (cybertailor) Vyalkova" Date: Fri, 12 Jul 2024 13:40:43 +0500 Subject: [PATCH 07/11] boinc-app.eclass: use standard inherit guard style Signed-off-by: Anna (cybertailor) Vyalkova --- eclass/boinc-app.eclass | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/eclass/boinc-app.eclass b/eclass/boinc-app.eclass index 3a26e6738b..f6fb82034b 100644 --- a/eclass/boinc-app.eclass +++ b/eclass/boinc-app.eclass @@ -22,7 +22,7 @@ case ${EAPI} in 8) ;; - *) die "${ECLASS}: EAPI ${EAPI} unsupported." + *) die "${ECLASS}: EAPI ${EAPI:-0} unsupported" esac # @ECLASS_VARIABLE: BOINC_APP_OPTIONAL @@ -34,10 +34,6 @@ esac # If you enable BOINC_APP_OPTIONAL, you have to call boinc-app # default phase functions and add dependencies manually. -if [[ ! ${BOINC_APP_OPTIONAL} ]]; then - EXPORT_FUNCTIONS pkg_postinst pkg_postrm -fi - if [[ ! ${_BOINC_APP_ECLASS} ]]; then # @ECLASS_VARIABLE: BOINC_MASTER_URL @@ -382,3 +378,7 @@ boinc-app_pkg_postrm() { _BOINC_APP_ECLASS=1 fi + +if [[ ! ${BOINC_APP_OPTIONAL} ]]; then + EXPORT_FUNCTIONS pkg_postinst pkg_postrm +fi From 9cd4309b1e2f97a9d037a365639b8cb2049a26f0 Mon Sep 17 00:00:00 2001 From: "Anna (cybertailor) Vyalkova" Date: Fri, 12 Jul 2024 13:54:47 +0500 Subject: [PATCH 08/11] boinc-app.eclass: remove excess and fix style Signed-off-by: Anna (cybertailor) Vyalkova --- eclass/boinc-app.eclass | 56 ++++++++++++++++------------------------- 1 file changed, 21 insertions(+), 35 deletions(-) diff --git a/eclass/boinc-app.eclass b/eclass/boinc-app.eclass index f6fb82034b..822c843974 100644 --- a/eclass/boinc-app.eclass +++ b/eclass/boinc-app.eclass @@ -26,6 +26,7 @@ case ${EAPI} in esac # @ECLASS_VARIABLE: BOINC_APP_OPTIONAL +# @PRE_INHERIT # @DEFAULT_UNSET # @DESCRIPTION: # If set to a non-null value, BOINC part in the ebuild will be @@ -55,6 +56,7 @@ if [[ ! ${_BOINC_APP_ECLASS} ]]; then # it's published on project's website. # @ECLASS_VARIABLE: HOMEPAGE +# @OUTPUT_VARIABLE # @DESCRIPTION: # This variable defines the HOMEPAGE for BOINC projects if BOINC_MASTER_URL # was set before inherit. @@ -105,20 +107,7 @@ boinc-app_add_deps() { fi } -# @FUNCTION: boinc_master_url_check -# @USAGE: -# @DESCRIPTION: -# Make sure BOINC_MASTER_URL has a value. -boinc_master_url_check() { - debug-print-function ${FUNCNAME} "${@}" - - [[ -n ${BOINC_MASTER_URL} ]] || \ - die "BOINC_MASTER_URL is not set" - return 0 -} - # @FUNCTION: get_boincdir -# @USAGE: # @RETURN: non-prefixed BOINC runtime directory get_boincdir() { echo "${BOINC_RUNTIMEDIR:-/var/lib/boinc}" @@ -126,7 +115,6 @@ get_boincdir() { # @FUNCTION: get_project_dirname # @INTERNAL -# @USAGE: # @RETURN: project's dirname, derived from BOINC_MASTER_URL # @DESCRIPTION: # Example: @@ -137,9 +125,8 @@ get_boincdir() { # -> boinc.berkeley.edu_example # @CODE get_project_dirname() { - debug-print-function ${FUNCNAME} "${@}" - - boinc_master_url_check + [[ ${BOINC_MASTER_URL} ]] || \ + die "BOINC_MASTER_URL is not set" local dirname dirname=${BOINC_MASTER_URL#*://} # strip http[s]:// @@ -150,16 +137,12 @@ get_project_dirname() { } # @FUNCTION: get_project_root -# @USAGE: # @RETURN: non-prefixed directory where applications and files should be installed get_project_root() { - debug-print-function ${FUNCNAME} "${@}" - echo "$(get_boincdir)/projects/$(get_project_dirname)" } # @FUNCTION: _boinc-app_fix_permissions -# @USAGE: # @INTERNAL # @DESCRIPTION: # Fix owner and permissions for the project root. @@ -174,14 +157,17 @@ _boinc-app_fix_permissions() { } # @FUNCTION: boinc-app_appinfo_prepare -# @USAGE: +# @USAGE: # @DESCRIPTION: # The default appinfo_prepare(). It replaces all occurences # of @PV@ with its corresponding value. boinc-app_appinfo_prepare() { debug-print-function ${FUNCNAME} "${@}" - sed -i "$1" \ + (( $# == 1 )) || \ + die "${FUNCNAME} takes exactly one argument" + + sed -i "${1:?}" \ -e "s:@PV@:${PV}:g" \ || die "app_info.xml sed failed" } @@ -251,6 +237,9 @@ doappinfo() { boinc-app_foreach_wrapper_job() { debug-print-function ${FUNCNAME} "${@}" + (( $# == 1 )) || \ + die "${FUNCNAME} takes exactly one argument" + sed -i "${1:?}" \ -e "s:@PV@:${PV}:g" \ -e "s:@EPREFIX@:${EPREFIX}:g" \ @@ -327,16 +316,13 @@ boinc-app_pkg_postinst() { debug-print-function ${FUNCNAME} "${@}" if [[ -f "${EROOT}/$(get_boincdir)/master_$(get_project_dirname).xml" ]]; then - if [[ -z ${REPLACING_VERSIONS} ]]; then + if [[ ! ${REPLACING_VERSIONS} ]]; then # most likely replacing applications downloaded # by the BOINC client from project's website elog "Restart the BOINC daemon for changes to take place:" elog "# rc-service boinc restart" - return - else - # applications are already in use - return fi + return fi elog @@ -347,10 +333,10 @@ boinc-app_pkg_postinst() { if [[ ! ${BOINC_INVITATION_CODE} ]]; then elog "# rc-service boinc attach" - elog " Enter the Project URL: ${BOINC_MASTER_URL}" + elog " Enter the Project URL: ${BOINC_MASTER_URL:?}" else - elog "- Master URL: ${BOINC_MASTER_URL}" - elog "- Invitation code: ${BOINC_INVITATION_CODE}" + elog "- Master URL: ${BOINC_MASTER_URL:?}" + elog "- Invitation code: ${BOINC_INVITATION_CODE:?}" fi } @@ -361,17 +347,17 @@ boinc-app_pkg_postinst() { boinc-app_pkg_postrm() { debug-print-function ${FUNCNAME} "${@}" - if [[ -z ${REPLACED_BY_VERSION} ]]; then + if [[ ! ${REPLACED_BY_VERSION} ]]; then local gui_rpc_auth="$(get_boincdir)/gui_rpc_auth.cfg" local passwd=$(cat "${EROOT}/${gui_rpc_auth}" 2>/dev/null) - if [[ -z ${passwd} ]]; then - passwd="\$(cat ${gui_rpc_auth})" + if [[ ! ${passwd?} ]]; then + passwd="\$(cat ${gui_rpc_auth:?})" fi elog "You should detach this project from the BOINC client" elog "to stop current tasks and delete remaining project files:" elog - elog "$ boinccmd --passwd ${passwd} --project ${BOINC_MASTER_URL} detach" + elog "$ boinccmd --passwd ${passwd:?} --project ${BOINC_MASTER_URL:?} detach" elog fi } From e9427f8954a1efb68fa1c95e9e111f226e9500a1 Mon Sep 17 00:00:00 2001 From: "Anna (cybertailor) Vyalkova" Date: Tue, 9 Jul 2024 20:47:57 +0500 Subject: [PATCH 09/11] sci-biology/cmdock: drop 0.2.0-r0 Signed-off-by: Anna (cybertailor) Vyalkova --- sci-biology/cmdock/cmdock-0.2.0.ebuild | 112 ------------------------- 1 file changed, 112 deletions(-) delete mode 100644 sci-biology/cmdock/cmdock-0.2.0.ebuild diff --git a/sci-biology/cmdock/cmdock-0.2.0.ebuild b/sci-biology/cmdock/cmdock-0.2.0.ebuild deleted file mode 100644 index 3d1c2f0359..0000000000 --- a/sci-biology/cmdock/cmdock-0.2.0.ebuild +++ /dev/null @@ -1,112 +0,0 @@ -# Copyright 2021-2024 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{10..12} ) -BOINC_APP_OPTIONAL="true" -inherit boinc-app flag-o-matic meson optfeature python-any-r1 - -DESCRIPTION="Program for docking ligands to proteins and nucleic acids" -HOMEPAGE="https://gitlab.com/Jukic/cmdock" -SRC_URI="https://gitlab.com/Jukic/${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" -RESTRICT="!test? ( test )" - -RDEPEND=" - boinc? ( sci-misc/boinc-wrapper ) -" -DEPEND=" - dev-cpp/eigen:3 - dev-cpp/indicators - >=dev-cpp/pcg-cpp-0.98.1_p20210406-r1 - dev-libs/cxxopts -" -BDEPEND=" - apidoc? ( - app-text/doxygen - dev-texlive/texlive-fontutils - ) - doc? ( - $(python_gen_any_dep ' - dev-python/insipid-sphinx-theme[${PYTHON_USEDEP}] - dev-python/sphinx[${PYTHON_USEDEP}] - ') - ) - test? ( ${PYTHON_DEPS} ) -" - -DOCS=( README.md changelog.md ) - -BOINC_MASTER_URL="https://www.sidock.si/sidock/" -BOINC_INVITATION_CODE="Crunch_4Science" -BOINC_APP_HELPTEXT=\ -"The easiest way to do something useful with this application -is to attach it to SiDock@home BOINC project." - -INSTALL_PREFIX="${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 -} From 1a76004eaaa74e01bdbe8f2afacac8306fbe6d6f Mon Sep 17 00:00:00 2001 From: "Anna (cybertailor) Vyalkova" Date: Tue, 9 Jul 2024 20:56:46 +0500 Subject: [PATCH 10/11] sci-biology/cmdock: boinc fixes * Update cmdline to the upstream current. Particularly, the option that causes CmDock to get stuck in an infinite loop in 1-5% of runs is removed. * Sync with boinc-app.eclass updates. Closes: https://bugs.gentoo.org/935231 Signed-off-by: Anna (cybertailor) Vyalkova --- ...0.2.0-r1.ebuild => cmdock-0.2.0-r2.ebuild} | 25 +++++++++---------- ...p_info_0.2.0.xml => app_info_0.2.0-r1.xml} | 14 +++++------ ...ob_0.2.0.xml => cmdock-l_job_0.2.0-r1.xml} | 2 +- 3 files changed, 20 insertions(+), 21 deletions(-) rename sci-biology/cmdock/{cmdock-0.2.0-r1.ebuild => cmdock-0.2.0-r2.ebuild} (83%) rename sci-biology/cmdock/files/{app_info_0.2.0.xml => app_info_0.2.0-r1.xml} (68%) rename sci-biology/cmdock/files/{cmdock-l_job_0.2.0.xml => cmdock-l_job_0.2.0-r1.xml} (77%) diff --git a/sci-biology/cmdock/cmdock-0.2.0-r1.ebuild b/sci-biology/cmdock/cmdock-0.2.0-r2.ebuild similarity index 83% rename from sci-biology/cmdock/cmdock-0.2.0-r1.ebuild rename to sci-biology/cmdock/cmdock-0.2.0-r2.ebuild index f46747447a..55e83bffb6 100644 --- a/sci-biology/cmdock/cmdock-0.2.0-r1.ebuild +++ b/sci-biology/cmdock/cmdock-0.2.0-r2.ebuild @@ -4,7 +4,7 @@ EAPI=8 PYTHON_COMPAT=( python3_{10..12} ) -BOINC_APP_OPTIONAL="true" +BOINC_APP_OPTIONAL=1 inherit boinc-app flag-o-matic meson optfeature python-any-r1 DESCRIPTION="Program for docking ligands to proteins and nucleic acids" @@ -15,14 +15,11 @@ S="${WORKDIR}/${PN}-v${PV}" LICENSE="LGPL-3 ZLIB" SLOT="0/${PV}" KEYWORDS="~amd64" -IUSE="apidoc boinc cpu_flags_x86_sse2 doc test" +IUSE="apidoc 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 @@ -58,6 +55,8 @@ is to attach it to SiDock@home BOINC project." INSTALL_PREFIX="${EPREFIX}/opt/${P}" +boinc-app_add_deps + python_check_deps() { use doc || return 0 @@ -77,7 +76,7 @@ src_prepare() { src_configure() { # very weird directory layout local emesonargs=( - --prefix="${INSTALL_PREFIX}" + --prefix="${INSTALL_PREFIX:?}" $(meson_use apidoc) $(meson_use doc) $(meson_use test tests) @@ -90,22 +89,22 @@ src_configure() { src_install() { meson_src_install - python_optimize "${D}${INSTALL_PREFIX}"/bin + python_optimize "${D}${INSTALL_PREFIX:?}"/bin if use boinc; then - doappinfo "${FILESDIR}"/app_info_${PV}.xml - dowrapper cmdock-l + boinc_install_appinfo "${FILESDIR}"/app_info_0.2.0-r1.xml + boinc_install_wrapper cmdock-l_wrapper \ + "${FILESDIR}"/cmdock-l_job_0.2.0-r1.xml cmdock-l_job.xml # install cmdock executable exeinto "$(get_project_root)" exeopts --owner root --group boinc - newexe "${D}${INSTALL_PREFIX}"/bin/cmdock cmdock-${PV} + doexe "${D}${INSTALL_PREFIX:?}"/bin/cmdock # install a blank file - touch "${T}"/docking_out || die insinto "$(get_project_root)" - insopts --owner root --group boinc - doins "${T}"/docking_out + insopts -m 0644 --owner root --group boinc + newins - docking_out fi } diff --git a/sci-biology/cmdock/files/app_info_0.2.0.xml b/sci-biology/cmdock/files/app_info_0.2.0-r1.xml similarity index 68% rename from sci-biology/cmdock/files/app_info_0.2.0.xml rename to sci-biology/cmdock/files/app_info_0.2.0-r1.xml index ad23f78901..b9eb040fbd 100644 --- a/sci-biology/cmdock/files/app_info_0.2.0.xml +++ b/sci-biology/cmdock/files/app_info_0.2.0-r1.xml @@ -1,22 +1,22 @@ cmdock-l - CurieMarieDock 0.2.0 long tasks + CurieMarieDock @PV@ long tasks - cmdock-l_wrapper_@PV@ + cmdock-l_wrapper - cmdock-@PV@ + cmdock - cmdock-l_job_@PV@.xml + cmdock-l_job.xml @@ -28,16 +28,16 @@ cmdock-l 100 - cmdock-l_wrapper_@PV@ + cmdock-l_wrapper - cmdock-@PV@ + cmdock cmdock - cmdock-l_job_@PV@.xml + cmdock-l_job.xml job.xml diff --git a/sci-biology/cmdock/files/cmdock-l_job_0.2.0.xml b/sci-biology/cmdock/files/cmdock-l_job_0.2.0-r1.xml similarity index 77% rename from sci-biology/cmdock/files/cmdock-l_job_0.2.0.xml rename to sci-biology/cmdock/files/cmdock-l_job_0.2.0-r1.xml index a163eb29cf..6d626fb826 100644 --- a/sci-biology/cmdock/files/cmdock-l_job_0.2.0.xml +++ b/sci-biology/cmdock/files/cmdock-l_job_0.2.0-r1.xml @@ -2,7 +2,7 @@ cmdock docking_log - -c -j 1 -b 1 -x -r target.prm -p "@PREFIX@/data/scripts/dock.prm" -f htvs.ptc -i ligands.sdf -o docking_out + -c -j 1 -b 1 -r target.prm -p "@PREFIX@/data/scripts/dock.prm" -f htvs.ptc -i ligands.sdf -o docking_out docking_out.chk docking_out.progress CMDOCK_ROOT=@PREFIX@ From 73d60c47026d0c17f871bdcac164f2d8f9a54068 Mon Sep 17 00:00:00 2001 From: Mark Harmstone Date: Sun, 14 Jul 2024 14:47:01 +0100 Subject: [PATCH 11/11] dev-db/tdscpp: add 20240707, drop 20240629 Signed-off-by: Mark Harmstone --- dev-db/tdscpp/Manifest | 2 +- .../tdscpp/{tdscpp-20240629.ebuild => tdscpp-20240707.ebuild} | 0 2 files changed, 1 insertion(+), 1 deletion(-) rename dev-db/tdscpp/{tdscpp-20240629.ebuild => tdscpp-20240707.ebuild} (100%) diff --git a/dev-db/tdscpp/Manifest b/dev-db/tdscpp/Manifest index 6b3401e77a..2436974beb 100644 --- a/dev-db/tdscpp/Manifest +++ b/dev-db/tdscpp/Manifest @@ -1 +1 @@ -DIST tdscpp-20240629.tar.gz 726330 BLAKE2B 61d3de2cf991d109cd58e3fc5cbdb2e5d5503fedba40431fff7eb01483e06e6d5ace737f650d44e1033f778cfcb893fd6f1f0506bc848ebebbb9e152332cc4ee SHA512 96ccfe86ecbe34fa7c55115d33ceb277c065f3ffef8600e1cf5df5daf458fedf35e994d3d335b5724436bf283622d32252616d4e9336fcf0123af5edb3f32bf1 +DIST tdscpp-20240707.tar.gz 728339 BLAKE2B 1a5cc1410b87872e59ca64a01900c1cdde550aadf12f7f4bc954b34d4bee9d266eb634e7e6cdc12281060baa8c7a267d2d8b9ba84e1d542ada23522fe71decf6 SHA512 62cab90e17394a5f1c4058bc3a606c1f9542fbad4a749032964ae76dfbcf903f7ff1b20a459c2b3d784c4abb31b5abe7e582b30eaebd83ac9887629221f4a694 diff --git a/dev-db/tdscpp/tdscpp-20240629.ebuild b/dev-db/tdscpp/tdscpp-20240707.ebuild similarity index 100% rename from dev-db/tdscpp/tdscpp-20240629.ebuild rename to dev-db/tdscpp/tdscpp-20240707.ebuild