[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/numbat/files/, sci-chemistry/numbat/, profiles/

[Jakov Smolić]

commit:     5f26b5938812d41ebfd3712a9c59ba8a49f13d1b
Author:     Jakov Smolić <jsmolic <AT> gentoo <DOT> org>
AuthorDate: Mon Aug 29 08:06:35 2022 +0000
Commit:     Jakov Smolić <jsmolic <AT> gentoo <DOT> org>
CommitDate: Mon Aug 29 08:07:22 2022 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=5f26b593

sci-chemistry/numbat: treeclean

Closes: https://bugs.gentoo.org/862486
Closes: https://bugs.gentoo.org/583038
Signed-off-by: Jakov Smolić <jsmolic <AT> gentoo.org>

 profiles/package.mask                              |  5 --
 sci-chemistry/numbat/Manifest                      |  1 -
 .../numbat/files/numbat-0.999-gnuplot.patch        | 42 ----------------
 sci-chemistry/numbat/metadata.xml                  | 19 --------
 sci-chemistry/numbat/numbat-0.999-r2.ebuild        | 56 ----------------------
 5 files changed, 123 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 802fbdab5660..e081bb867239 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -291,11 +291,6 @@ dev-qt/qtwebsockets:6
 # Removal in 30 days (Bug #)
 <net-analyzer/suricata-6.0.0
 
-# Matthew Smith <matthew@g.o> (2022-07-31)
-# No updates since 2010, dead homepage, and incompatible with newer
-# sci-libs/gsl. Bug #862486. Removal on 2022-08-31.
-sci-chemistry/numbat
-
 # Marek Szuba <marecki@g.o> (2022-07-13)
 # Upstream has switched from CMake to hand-crafted Makefiles (yes, TO them),
 # which have seriously messed up dependency handling and trigger several

diff --git a/sci-chemistry/numbat/Manifest b/sci-chemistry/numbat/Manifest
deleted file mode 100644
index 961584beeaaa..000000000000
--- a/sci-chemistry/numbat/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST Numbat-0.999.tar.gz 1791471 BLAKE2B 7f6536533fdf6bc3860dc1a7c03ade4896e782c5ecadf1c6a7d70896f4c6ef9f0571796c171012497d7b47b3342c215a5302ed210d7dde3ecdbef170c3f55dbc SHA512 0887f77905bbb476b0d12a7015d5d5745023740acc974ea9cd452de7d38a75a92e6090015127588b38ba62353d38c2be20f57be5df3011b51050c4934dfd206c

diff --git a/sci-chemistry/numbat/files/numbat-0.999-gnuplot.patch b/sci-chemistry/numbat/files/numbat-0.999-gnuplot.patch
deleted file mode 100644
index 942f5871e50b..000000000000
--- a/sci-chemistry/numbat/files/numbat-0.999-gnuplot.patch
+++ /dev/null
@@ -1,42 +0,0 @@
- src/error_analysis.c | 20 ++++++++++----------
- 1 file changed, 10 insertions(+), 10 deletions(-)
-
-diff --git a/src/error_analysis.c b/src/error_analysis.c
-index eb86a6f..c0edf5f 100644
---- a/src/error_analysis.c
-+++ b/src/error_analysis.c
-@@ -848,11 +848,11 @@ void write_sanson_mac(FILE * F, char * name_plot, char * name_world, int number_
-     }
- 
-     fprintf(F, "reset\n");
--    fprintf(F, "set noxtics\n");
--    fprintf(F, "set noytics\n");
-+    fprintf(F, "unset xtics\n");
-+    fprintf(F, "unset ytics\n");
-     fprintf(F, "set angles degrees\n");
--    fprintf(F, "set nogrid\n");
--    fprintf(F, "set noborder\n");
-+    fprintf(F, "unset grid\n");
-+    fprintf(F, "unset border\n");
-     //fprintf(F, "width=40\n");
-     //fprintf(F, "height=width*(3./4.)\n");
-     //fprintf(F, "set xrange [-width : width]\n");
-@@ -867,12 +867,12 @@ void write_sanson_mac(FILE * F, char * name_plot, char * name_world, int number_
-     fprintf(F, "YC(lat,lon)=(lon-long0)*cos(lat)\n");
-     fprintf(F, "plot '%s'  using (YC($2,$1)):(XC($2,$1)) t '' with lines lw 0.1 lt -1", name_world);
-     for(i = 0; i < number_of_tensor; i++){
--        fprintf(F, ", '%s' using (YC($%d,$%d)):(XC($%d,$%d)) t '' with points %d", name_plot,
--                6*i+2, 6*i+1, 6*i+2, 6*i+1, 3*i+1);
--        fprintf(F, ", '%s' using (YC($%d,$%d)):(XC($%d,$%d)) t '' with points %d", name_plot,
--                6*i+4, 6*i+3, 6*i+4, 6*i+3, 3*i+2);
--        fprintf(F, ", '%s' using (YC($%d,$%d)):(XC($%d,$%d)) t '' with points %d", name_plot,
--                6*i+6, 6*i+5, 6*i+6, 6*i+5, 3*i+3);
-+        fprintf(F, ", '%s' using (YC($%d,$%d)):(XC($%d,$%d)) t '' with points", name_plot,
-+                6*i+2, 6*i+1, 6*i+2, 6*i+1);
-+        fprintf(F, ", '%s' using (YC($%d,$%d)):(XC($%d,$%d)) t '' with points", name_plot,
-+                6*i+4, 6*i+3, 6*i+4, 6*i+3);
-+        fprintf(F, ", '%s' using (YC($%d,$%d)):(XC($%d,$%d)) t '' with points", name_plot,
-+                6*i+6, 6*i+5, 6*i+6, 6*i+5);
-     }
-     fprintf(F, "\n");
-     //fprintf(F, "pause 2\n");

diff --git a/sci-chemistry/numbat/metadata.xml b/sci-chemistry/numbat/metadata.xml
deleted file mode 100644
index 273753c203e5..000000000000
--- a/sci-chemistry/numbat/metadata.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-chemistry@g.o</email>
-    <name>Gentoo Chemistry Project</name>
-  </maintainer>
-  <longdescription>
-Numbat is a user friendly software that fits dX-tensor to a set of PCS 
-measurements and a structure from a PDB file. It has also been designed to 
-assist in the semi automatic process of PCS assignment. A detailed description 
-of the software can be found in this publication: 
-
-Christophe Schmitz, Mitchell J. Stanton-Cook, Xun-Cheng Su, Gottfried Otting, 
-and Thomas Huber (2008). Numbat: an interactive software tool for fitting 
-Δχ-tensors to molecular coordinates using pseudocontact shifts. Journal of 
-Biomolecular NMR. 41:179-189.
-</longdescription>
-</pkgmetadata>

diff --git a/sci-chemistry/numbat/numbat-0.999-r2.ebuild b/sci-chemistry/numbat/numbat-0.999-r2.ebuild
deleted file mode 100644
index ddfec41ed12b..000000000000
--- a/sci-chemistry/numbat/numbat-0.999-r2.ebuild
+++ /dev/null
@@ -1,56 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit autotools
-
-MY_PN="Numbat"
-MY_P="${MY_PN}-${PV}"
-
-DESCRIPTION="New user-friendly method built for automatic dX-tensor determination"
-HOMEPAGE="http://www.nmr.chem.uu.nl/~christophe/numbat.html"
-SRC_URI="http://comp-bio.anu.edu.au/private/downloads/Numbat/${MY_P}.tar.gz"
-S="${WORKDIR}"/${MY_P}
-
-SLOT="0"
-LICENSE="GPL-3"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-DEPEND="
-	gnome-base/libglade:2.0
-	sci-libs/gsl:=
-	x11-libs/gtk+:2
-"
-RDEPEND="
-	${DEPEND}
-	sci-chemistry/molmol
-	sci-chemistry/pymol
-	sci-visualization/gnuplot
-"
-BDEPEND="virtual/pkgconfig"
-
-PATCHES=(
-#	"${FILESDIR}"/${P}-glade.patch
-	"${FILESDIR}"/${P}-gnuplot.patch
-)
-
-src_prepare() {
-	default
-
-	sed \
-		-e '/COPYING/d' \
-		-e "s:doc/numbat:share/doc/${PF}:g" \
-		-i Makefile.am src/common.h || die
-
-	rm missing || die
-
-	emake distclean
-	eautoreconf
-}
-
-src_install() {
-	docompress -x /usr/share/doc/${PF}
-
-	default
-}