[gentoo-dev] Last rites: sci-biology/diya

2021-04-05 Thread David Seifert
# David Seifert  (2021-04-05)
# Tests broken since perl 5.22, last release in 2008,
# Bug #625492, removal in 30 days.
sci-biology/diya


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[gentoo-dev] [PATCH v2 1/3] autotools.eclass: eclassdoc, cosmetic changes, drop old EAPIs, configure.ac rename

2021-04-05 Thread Sam James
(Relatively) significant changes:
* inherit eutils for < EAPI 7 for eqawarn
* rename configure.in -> configure.ac in >= EAPI 8 (to avoid retroactive 
breakage)
* convert phase test to EBUILD_PHASE_FUNC
* use gnuconfig.eclass for finding gnuconfig logic for consistency and
avoiding duplication
* add explicit GNU awk BDEPEND as we use it in the eclass
* drop support for < EAPI 5 officially
[Needed for the EBUILD_PHASE_FUNC change.
< EAPI 5 is no longer in ::gentoo (since December).

Note that we were using ${EPREFIX} which isn't defined
< EAPI 3 so we were wrong about which EAPIs we supported
anyway.]

eclassdoc fixes:
* explicitly blank and mark variables as @DEFAULT_UNSET
* add @DESCRIPTION for _at_uses_pkg
* document AUTOTOOLS_DEPEND

Cosmetic changes:
* minor cosmetic changes to various elogs
* fix whitespace/phrasing in comment
* convert ewarn to eqawarn
* consistent 'case' style
* consistent variable references
* consistent references to bugs in comments
* consistent use of ${ECLASS}, not "autotools.eclass"
* use same ${WANT_AUTOCONF} comparison test throughout

Bug: https://bugs.gentoo.org/426262
Closes: https://bugs.gentoo.org/584254
Signed-off-by: Sam James 
---
 eclass/autotools.eclass | 118 ++--
 1 file changed, 65 insertions(+), 53 deletions(-)

diff --git a/eclass/autotools.eclass b/eclass/autotools.eclass
index 3e6906cb469..455fe38f466 100644
--- a/eclass/autotools.eclass
+++ b/eclass/autotools.eclass
@@ -4,7 +4,7 @@
 # @ECLASS: autotools.eclass
 # @MAINTAINER:
 # base-sys...@gentoo.org
-# @SUPPORTED_EAPIS: 0 1 2 3 4 5 6 7
+# @SUPPORTED_EAPIS: 5 6 7
 # @BLURB: Regenerates auto* build scripts
 # @DESCRIPTION:
 # This eclass is for safely handling autotooled software packages that need to
@@ -19,19 +19,23 @@ if [[ ${__AUTOTOOLS_AUTO_DEPEND+set} == "set" ]] ; then
# eclass at that point, but that adds overhead, and it's trivial
# to re-order inherit in eclasses/ebuilds instead.  #409611
if [[ ${__AUTOTOOLS_AUTO_DEPEND} != ${AUTOTOOLS_AUTO_DEPEND} ]] ; then
-   die "AUTOTOOLS_AUTO_DEPEND changed value between inherits; 
please inherit autotools.eclass first! ${__AUTOTOOLS_AUTO_DEPEND} -> 
${AUTOTOOLS_AUTO_DEPEND}"
+   die "AUTOTOOLS_AUTO_DEPEND changed value between inherits; 
please inherit ${ECLASS} first! ${__AUTOTOOLS_AUTO_DEPEND} -> 
${AUTOTOOLS_AUTO_DEPEND}"
fi
 fi
 
-if [[ -z ${_AUTOTOOLS_ECLASS} ]]; then
+if [[ -z ${_AUTOTOOLS_ECLASS} ]] ; then
 _AUTOTOOLS_ECLASS=1
 
 case ${EAPI:-0} in
-   0|1|2|3|4|5|6|7) ;;
+   5|6)
+   # Needed for eqawarn
+   inherit eutils
+   ;;
+   7) ;;
*) die "${ECLASS}: EAPI ${EAPI} not supported" ;;
 esac
 
-inherit libtool
+inherit gnuconfig libtool
 
 # @ECLASS-VARIABLE: WANT_AUTOCONF
 # @PRE_INHERIT
@@ -74,21 +78,14 @@ _LATEST_AUTOMAKE=( 1.16.2-r1:1.16 )
 
 _automake_atom="sys-devel/automake"
 _autoconf_atom="sys-devel/autoconf"
-if [[ -n ${WANT_AUTOMAKE} ]]; then
+if [[ -n ${WANT_AUTOMAKE} ]] ; then
case ${WANT_AUTOMAKE} in
# Even if the package doesn't use automake, we still need to 
depend
# on it because we run aclocal to process m4 macros.  This 
matches
# the autoreconf tool, so this requirement is correct, bug 
#401605.
none) ;;
-   latest)
-   # Use SLOT deps if we can.  For EAPI=0, we get pretty 
close.
-   if [[ ${EAPI:-0} != 0 ]] ; then
-   _automake_atom="|| ( `printf 
'>=sys-devel/automake-%s:%s ' ${_LATEST_AUTOMAKE[@]/:/ }` )"
-   else
-   _automake_atom="|| ( `printf 
'>=sys-devel/automake-%s ' ${_LATEST_AUTOMAKE[@]/%:*}` )"
-   fi
-   ;;
-   *)  _automake_atom="=sys-devel/automake-${WANT_AUTOMAKE}*" 
;;
+   latest) _automake_atom="|| ( `printf 
'>=sys-devel/automake-%s:%s ' ${_LATEST_AUTOMAKE[@]/:/ }` )" ;;
+   *) _automake_atom="=sys-devel/automake-${WANT_AUTOMAKE}*" ;;
esac
export WANT_AUTOMAKE
 fi
@@ -114,9 +111,16 @@ if [[ -n ${WANT_LIBTOOL} ]] ; then
export WANT_LIBTOOL
 fi
 
+# @ECLASS-VARIABLE: AUTOTOOLS_DEPEND
+# @INTERNAL
+# @DESCRIPTION:
+# Contains the combination of requested automake/autoconf/libtool
+# versions in *DEPEND format.
 AUTOTOOLS_DEPEND="${_automake_atom}
${_autoconf_atom}
-   ${_libtool_atom}"
+   ${_libtool_atom}
+   sys-apps/gawk
+"
 RDEPEND=""
 
 # @ECLASS-VARIABLE: AUTOTOOLS_AUTO_DEPEND
@@ -128,7 +132,7 @@ RDEPEND=""
 : ${AUTOTOOLS_AUTO_DEPEND:=yes}
 if [[ ${AUTOTOOLS_AUTO_DEPEND} != "no" ]] ; then
case ${EAPI:-0} in
-   0|1|2|3|4|5|6) DEPEND=${AUTOTOOLS_DEPEND} ;;
+   4|5|6) DEPEND=${AUTOTOOLS_DEPEND} ;;
7) BDEPEND=${AUTOTOOLS_DEPEND} ;;
esac
 fi
@@ -141,12 +145,14 @@ unset _automake_atom _autoc

[gentoo-dev] [PATCH v2 2/3] gnuconfig.eclass: provide basic @ECLASS block, docs

2021-04-05 Thread Sam James
Signed-off-by: Sam James 
---
 eclass/gnuconfig.eclass | 33 +++--
 1 file changed, 23 insertions(+), 10 deletions(-)

diff --git a/eclass/gnuconfig.eclass b/eclass/gnuconfig.eclass
index 3433837787c..f679441445f 100644
--- a/eclass/gnuconfig.eclass
+++ b/eclass/gnuconfig.eclass
@@ -1,25 +1,32 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
-#
-# Author: Will Woods 
-#
+
+# @ECLASS: gnuconfig.eclass
+# @MAINTAINER:
+# maintainer-nee...@gentoo.org
+# @AUTHOR:
+# Will Woods 
+# @BLURB: Eclass to make PCF font generator from BDF uniform and optimal
+# @DESCRIPTION:
 # This eclass is used to automatically update files that typically come with
 # automake to the newest version available on the system. The most common use
 # of this is to update config.guess and config.sub when configure dies from
 # misguessing your canonical system name (CHOST). It can also be used to update
 # other files that come with automake, e.g. depcomp, mkinstalldirs, etc.
 #
-# usage: gnuconfig_update [file1 file2 ...]
+
+DEPEND="sys-devel/gnuconfig"
+
+# @FUNCTION: gnuconfig_update
+# @USAGE: [file1 file2 ...]
+# @DESCRIPTION:
 # if called without arguments, config.guess and config.sub will be updated.
 # All files in the source tree ($S) with the given name(s) will be replaced
 # with the newest available versions chosen from the list of locations in
 # gnuconfig_findnewest(), below.
 #
 # gnuconfig_update should generally be called from src_unpack()
-
-
-DEPEND="sys-devel/gnuconfig"
-
+#
 # Wrapper function for gnuconfig_do_update. If no arguments are given, update
 # config.sub and config.guess (old default behavior), otherwise update the
 # named files.
@@ -42,6 +49,9 @@ gnuconfig_update() {
return $?
 }
 
+# @FUNCTION: gnuconfig_do_update
+# @INTERNAL
+# @DESCRIPTION:
 # Copy the newest available version of specified files over any old ones in the
 # source dir. This function shouldn't be called directly - use gnuconfig_update
 #
@@ -75,7 +85,10 @@ gnuconfig_do_update() {
return 0
 }
 
-# this searches the standard locations for the newest config.{sub|guess}, and
+# @FUNCTION: gnuconfig_findnewest
+# @INTERNAL
+# @DESCRIPTION:
+# This searches the standard locations for the newest config.{sub|guess}, and
 # returns the directory where they can be found.
 gnuconfig_findnewest() {
local locations=(
-- 
2.31.1




[gentoo-dev] [PATCH v2 3/3] gnuconfig.eclass: use BDEPEND, BROOT where available (drop support for EAPI <4)

2021-04-05 Thread Sam James
EPREFIX is only available in > EAPI 2 but let's take the opportuinty
to clean up in general. We don't want to keep worrying about
*very* old EAPI cases, especially given other eclasses
either barely - or don't - support it.

Signed-off-by: Sam James 
---
 eclass/gnuconfig.eclass | 41 +++--
 1 file changed, 35 insertions(+), 6 deletions(-)

diff --git a/eclass/gnuconfig.eclass b/eclass/gnuconfig.eclass
index f679441445f..865bc9fcb70 100644
--- a/eclass/gnuconfig.eclass
+++ b/eclass/gnuconfig.eclass
@@ -15,7 +15,23 @@
 # other files that come with automake, e.g. depcomp, mkinstalldirs, etc.
 #
 
-DEPEND="sys-devel/gnuconfig"
+case ${EAPI:-0} in
+   4|5|6)
+   DEPEND="
+   sys-apps/grep
+   sys-devel/gnuconfig
+   "
+   ;;
+   7)
+   BDEPEND="
+   sys-apps/grep
+   sys-devel/gnuconfig
+   "
+   ;;
+   *)
+   die "EAPI ${EAPI} is unsupported!"
+   ;;
+esac
 
 # @FUNCTION: gnuconfig_update
 # @USAGE: [file1 file2 ...]
@@ -91,12 +107,25 @@ gnuconfig_do_update() {
 # This searches the standard locations for the newest config.{sub|guess}, and
 # returns the directory where they can be found.
 gnuconfig_findnewest() {
-   local locations=(
-   "${EPREFIX}"/usr/share/misc/config.sub
-   "${EPREFIX}"/usr/share/gnuconfig/config.sub
-   "${EPREFIX}"/usr/share/automake*/config.sub
-   "${EPREFIX}"/usr/share/libtool/config.sub
+   local locations=()
+   local prefix
+
+   case ${EAPI:-0} in
+   4|5|6)
+   prefix="${EPREFIX}"
+   ;;
+   *)
+   prefix="${BROOT}"
+   ;;
+   esac
+
+   locations+=(
+   "${prefix}"/usr/share/misc/config.sub
+   "${prefix}"/usr/share/gnuconfig/config.sub
+   "${prefix}"/usr/share/automake*/config.sub
+   "${prefix}"/usr/share/libtool/config.sub
)
+
grep -s '^timestamp' "${locations[@]}" | \
sort -r -n -t\' -k2 | \
sed -n '1{s,/config.sub:.*$,,;p;q}'
-- 
2.31.1




Re: [gentoo-dev] [PATCH v2 3/3] gnuconfig.eclass: use BDEPEND, BROOT where available (drop support for EAPI <4)

2021-04-05 Thread Ulrich Mueller
> On Mon, 05 Apr 2021, Sam James wrote:
 
> + 4|5|6)
> + DEPEND="
> + sys-apps/grep
> + sys-devel/gnuconfig
> + "
> + ;;
> + 7)
> + BDEPEND="
> + sys-apps/grep

We usually don't add basic tools like grep to dependencies.


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[gentoo-dev] Last rites: sci-biology/gatk

2021-04-05 Thread David Seifert
# David Seifert  (2021-04-05)
# Completely broken, unmaintained, does not build. Newer versions
# use Maven, good luck with that. Bugs #418625, #431644, #515816
# #542940, #574632, #780396, removal in 30 days.
sci-biology/gatk


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[gentoo-dev] Maintainer needed on a few packages

2021-04-05 Thread Mike Gilbert
I recently dropped base-system as a maintainer on the following
packages. Feel free to pick them up.

dev-util/makepp
sys-apps/ucspi-proxy
sys-devel/dev86
sys-devel/bin86