[med-svn] [Git][med-team/altree][master] 4 commits: Fix watch file
Vincent Danjean (@vdanjean)
gitlab at salsa.debian.org
Fri Sep 17 19:34:36 BST 2021
Vincent Danjean pushed to branch master at Debian Med / altree
Commits:
8d4aa5e1 by Vincent Danjean at 2021-09-17T18:25:48+02:00
Fix watch file
- - - - -
9dce5a6a by Vincent Danjean at 2021-09-17T18:26:05+02:00
New upstream version 1.3.2
- - - - -
00209d34 by Vincent Danjean at 2021-09-17T18:26:08+02:00
Update upstream source from tag 'upstream/1.3.2'
Update to upstream version '1.3.2'
with Debian dir da1910a27ca38d9eddaeedaf158f65c5a01146d1
- - - - -
69bffa04 by Vincent Danjean at 2021-09-17T18:28:12+02:00
New upstream version
remove patches (applied upstream)
- - - - -
26 changed files:
- ALTree/SitePerForet.pm
- CUtils/CUtils.xs
- − CUtils/MYMETA.json
- CUtils/Makefile.PL
- − CUtils/c_sources/MYMETA.json
- CUtils/c_sources/rhyper.c
- CUtils/const-xs.inc
- CUtils/fallback/const-c.inc
- CUtils/fallback/const-xs.inc
- CUtils/ppport.h
- Changes
- Documentation/manual.tex
- MANIFEST
- + MANIFEST.SKIP
- − META.json
- − META.yml
- − MYMETA.json
- debian/changelog
- − debian/patches/blas.patch
- − debian/patches/figlatex.patch
- − debian/patches/from-upstream-no-nested-functions.patch
- − debian/patches/no-quicksort.patch
- − debian/patches/series
- debian/watch
- + make-release
- progs/altree
Changes:
=====================================
ALTree/SitePerForet.pm
=====================================
@@ -7,7 +7,6 @@ package ALTree::SitePerForet;
################################################################
use base qw(ALTree::Base ALTree::Site);
-use sort '_quicksort';
sub New { # [classe] site_nb
my $class=shift;
=====================================
CUtils/CUtils.xs
=====================================
@@ -9,6 +9,7 @@
#include "double_permutation.h"
#include "resampling.h"
#include "stats.h"
+#include "rhyper.h"
#include "const-c.inc"
@@ -122,14 +123,14 @@ DoublePermutation(nb_sample, nb_chi2, data)
av_push(ra, newSVnv(rep[j]));
//fprintf(stderr, "chi2[%i]=%lf\n", j ,rep[j]);
}
- hv_store(RETVAL, "chi2", 4, newRV((SV *)ra), 0);
+ hv_store(RETVAL, "chi2", 4, newRV_inc((SV *)ra), 0);
ra = (AV *)sv_2mortal((SV *)newAV());
for (j=0; j<nb_sample; j++) {
av_push(ra, newSVnv(ens[j]));
//fprintf(stderr, "pmin[%i]=%lf\n", j ,rep[j]);
}
- hv_store(RETVAL, "distrib_pmin", 12, newRV((SV *)ra), 0);
+ hv_store(RETVAL, "distrib_pmin", 12, newRV_inc((SV *)ra), 0);
free_matrice(mat, nb_sample, nb_chi2);
free_replicat(rep);
@@ -220,7 +221,7 @@ ResamplingChi2(leaf_refs, leaf_depth, leaf_parent, nleaf_parent, max_depth, prol
av_push(ra, newSVnv(results[i]));
//fprintf(stderr, "chi2[%i]=%lf\n", i ,results[i]);
}
- hv_store(RETVAL, "chi2s", 5, newRV((SV *)ra), 0);
+ hv_store(RETVAL, "chi2s", 5, newRV_inc((SV *)ra), 0);
free(lcc);
free(tree.ld);
=====================================
CUtils/MYMETA.json deleted
=====================================
@@ -1,39 +0,0 @@
-{
- "abstract" : "Perl extension for blah blah blah",
- "author" : [
- "Claire Bardel <Claire.Bardel at univ-lyon1.fr>"
- ],
- "dynamic_config" : 0,
- "generated_by" : "ExtUtils::MakeMaker version 6.66, CPAN::Meta::Converter version 2.120921",
- "license" : [
- "unknown"
- ],
- "meta-spec" : {
- "url" : "http://search.cpan.org/perldoc?CPAN::Meta::Spec",
- "version" : "2"
- },
- "name" : "ALTree-CUtils",
- "no_index" : {
- "directory" : [
- "t",
- "inc"
- ]
- },
- "prereqs" : {
- "build" : {
- "requires" : {
- "ExtUtils::MakeMaker" : "0"
- }
- },
- "configure" : {
- "requires" : {
- "ExtUtils::MakeMaker" : "0"
- }
- },
- "runtime" : {
- "requires" : {}
- }
- },
- "release_status" : "stable",
- "version" : "1.1"
-}
=====================================
CUtils/Makefile.PL
=====================================
@@ -9,7 +9,7 @@ WriteMakefile(
($] >= 5.005 ? ## Add these new keywords supported since 5.005
(ABSTRACT_FROM => 'lib/ALTree/CUtils.pm', # retrieve abstract from module
AUTHOR => 'Claire Bardel <Claire.Bardel at univ-lyon1.fr>') : ()),
- LIBS => ['-lm -lpthread -lgsl -lcblas'], # e.g., '-lm'
+ LIBS => ['-lm -lpthread -lgsl -lblas'], # e.g., '-lm'
DEFINE => '', # e.g., '-DHAVE_SOMETHING'
INC => '-ggdb3 -I. -Ic_sources', # e.g., '-I. -I/usr/include/other'
# Un-comment this if you add C files to link with later:
=====================================
CUtils/c_sources/MYMETA.json deleted
=====================================
@@ -1,39 +0,0 @@
-{
- "abstract" : "unknown",
- "author" : [
- "unknown"
- ],
- "dynamic_config" : 0,
- "generated_by" : "ExtUtils::MakeMaker version 6.66, CPAN::Meta::Converter version 2.120921",
- "license" : [
- "unknown"
- ],
- "meta-spec" : {
- "url" : "http://search.cpan.org/perldoc?CPAN::Meta::Spec",
- "version" : "2"
- },
- "name" : "ALTree-CUtils",
- "no_index" : {
- "directory" : [
- "t",
- "inc"
- ]
- },
- "prereqs" : {
- "build" : {
- "requires" : {
- "ExtUtils::MakeMaker" : "0"
- }
- },
- "configure" : {
- "requires" : {
- "ExtUtils::MakeMaker" : "0"
- }
- },
- "runtime" : {
- "requires" : {}
- }
- },
- "release_status" : "stable",
- "version" : ""
-}
=====================================
CUtils/c_sources/rhyper.c
=====================================
@@ -52,55 +52,61 @@
* If (i > 7), use Stirling's approximation, otherwise use table lookup.
*/
-static double afc(int i)
-{
- static int computed=10;
- static double al[1756] =
- {
- 0.0,
- 0,/*ln(0!)*/
- 0,/*ln(1!)*/
- 0.693147180559945309,/*ln(2!)*/
- 1.791759469228055,/*ln(3!)*/
- 3.17805383034794562,/*ln(4!)*/
- 4.78749174278204599,/*ln(5!)*/
- 6.579251212010101,/*ln(6!)*/
- 8.5251613610654143,/*ln(7!)*/
- 10.6046029027452502,/*ln(8!)*/
- 12.8018274800814696,/*ln(9!)*/
- 15.1044125730755153,/*ln(10!)*/
- };
- double compute(int n) {
- static long double cur=3628800;
- static int i=11;
- static volatile int mutex=0;
-
- while (__sync_lock_test_and_set(&mutex, 1)) {
- /* Internal loop with only read to avoid cache line ping-pong
- on multi-processors */
- while(mutex) {
- /* spinlock */
- }
+struct afc_data {
+ int computed;
+ double al[1756];
+};
+
+double compute(int n, struct afc_data * __restrict__ data) {
+ static long double cur=3628800;
+ static int i=11;
+ static volatile int mutex=0;
+
+ while (__sync_lock_test_and_set(&mutex, 1)) {
+ /* Internal loop with only read to avoid cache line ping-pong
+ on multi-processors */
+ while(mutex) {
+ /* spinlock */
}
+ }
- for(; i<=n; i++) {
- cur*=i;
- al[i+1]=logl(cur);
- }
- computed=n;
- __sync_lock_release(&mutex);
- return al[i];
- };
+ for(; i<=n; i++) {
+ cur*=i;
+ data->al[i+1]=logl(cur);
+ }
+ data->computed=n;
+ __sync_lock_release(&mutex);
+ return data->al[i];
+};
+static double afc(int i)
+{
double di, value;
+ static struct afc_data data = {
+ .computed = 10,
+ .al = {
+ 0.0,
+ 0,/*ln(0!)*/
+ 0,/*ln(1!)*/
+ 0.693147180559945309,/*ln(2!)*/
+ 1.791759469228055,/*ln(3!)*/
+ 3.17805383034794562,/*ln(4!)*/
+ 4.78749174278204599,/*ln(5!)*/
+ 6.579251212010101,/*ln(6!)*/
+ 8.5251613610654143,/*ln(7!)*/
+ 10.6046029027452502,/*ln(8!)*/
+ 12.8018274800814696,/*ln(9!)*/
+ 15.1044125730755153,/*ln(10!)*/
+ }
+ };
if (i < 0) {
fprintf(stderr, "rhyper.c: afc(i), i=%d < 0 -- SHOULD NOT HAPPEN!\n", i);
exit(1);
- } else if (i <= computed) {
- value = al[i + 1];
+ } else if (i <= data.computed) {
+ value = data.al[i + 1];
} else if (i <= 1754) {
- value = compute(i);
+ value = compute(i, &data);
} else {
di = i;
value = (di + 0.5) * log(di) - di + 0.08333333333333 / di
=====================================
CUtils/const-xs.inc
=====================================
@@ -32,37 +32,37 @@ constant(sv)
break;
/* Uncomment this if you need to return IVs
case PERL_constant_ISIV:
- EXTEND(SP, 1);
+ EXTEND(SP, 2);
PUSHs(&PL_sv_undef);
PUSHi(iv);
break; */
/* Uncomment this if you need to return NOs
case PERL_constant_ISNO:
- EXTEND(SP, 1);
+ EXTEND(SP, 2);
PUSHs(&PL_sv_undef);
PUSHs(&PL_sv_no);
break; */
/* Uncomment this if you need to return NVs
case PERL_constant_ISNV:
- EXTEND(SP, 1);
+ EXTEND(SP, 2);
PUSHs(&PL_sv_undef);
PUSHn(nv);
break; */
/* Uncomment this if you need to return PVs
case PERL_constant_ISPV:
- EXTEND(SP, 1);
+ EXTEND(SP, 2);
PUSHs(&PL_sv_undef);
PUSHp(pv, strlen(pv));
break; */
/* Uncomment this if you need to return PVNs
case PERL_constant_ISPVN:
- EXTEND(SP, 1);
+ EXTEND(SP, 2);
PUSHs(&PL_sv_undef);
PUSHp(pv, iv);
break; */
/* Uncomment this if you need to return SVs
case PERL_constant_ISSV:
- EXTEND(SP, 1);
+ EXTEND(SP, 2);
PUSHs(&PL_sv_undef);
PUSHs(sv);
break; */
@@ -71,13 +71,13 @@ constant(sv)
break; */
/* Uncomment this if you need to return UVs
case PERL_constant_ISUV:
- EXTEND(SP, 1);
+ EXTEND(SP, 2);
PUSHs(&PL_sv_undef);
PUSHu((UV)iv);
break; */
/* Uncomment this if you need to return YESs
case PERL_constant_ISYES:
- EXTEND(SP, 1);
+ EXTEND(SP, 2);
PUSHs(&PL_sv_undef);
PUSHs(&PL_sv_yes);
break; */
=====================================
CUtils/fallback/const-c.inc
=====================================
@@ -1,3 +1,4 @@
+#include "ppport.h"
#define PERL_constant_NOTFOUND 1
#define PERL_constant_NOTDEF 2
#define PERL_constant_ISIV 3
=====================================
CUtils/fallback/const-xs.inc
=====================================
@@ -1,3 +1,4 @@
+#include "ppport.h"
void
constant(sv)
PREINIT:
=====================================
CUtils/ppport.h
=====================================
The diff for this file was not included because it is too large.
=====================================
Changes
=====================================
@@ -1,5 +1,29 @@
Revision history for Altree Perl program
+Version v1.3.2
+==============
+
+Vincent Danjean (6):
+ Avoid nested functions
+ Use figlatex instead of texgraphicx
+ Do not require atlas
+ Remove unused _quicksort sub-pragma, no longer supported in Perl 5.27
+ Add missing include file
+ Update perl XS files
+ Remove old CVS ignore files
+ New release
+
+Version v1.3.1
+==============
+
+Claire Bardel (1):
+ No RCS version anymore, using 1.00 version by default
+
+Vincent Danjean (3):
+ Avoid too precise tests with float datatypes
+ Do not compute more permutation than requested, even with lots of processors
+ New release
+
Version v1.3.0
==============
=====================================
Documentation/manual.tex
=====================================
@@ -4,7 +4,7 @@
\usepackage{a4wide}
\usepackage[nocolor]{pdfswitch}
-\usepackage{texgraphicx}% Pour inclure les pstex_t
+\usepackage{figlatex}% Pour inclure les pstex_t
\graphicspath{{fig/}{eps/}}
\usepackage[latin1]{inputenc}% pour pouvoir taper des accents directement
\usepackage[T1]{fontenc}% jolie fontes
=====================================
MANIFEST
=====================================
@@ -241,5 +241,3 @@ test/phylip/outgroup_present/association/outfile
test/phylip/outgroup_present/association/outtree
test/phylip/outgroup_present/association/run_altree
test/phylip/outgroup_present/association/trio.phy
-META.yml Module YAML meta-data (added by MakeMaker)
-META.json Module JSON meta-data (added by MakeMaker)
=====================================
MANIFEST.SKIP
=====================================
@@ -0,0 +1,40 @@
+# Version control files and dirs.
+\bRCS\b
+\bCVS\b
+,v$
+.cvsignore$
+^\.svn\b
+^\.git\b
+/\.svn\b
+
+# Makemaker generated files and dirs.
+^MANIFEST\.
+^Makefile$
+^CUtils.*/Makefile$
+blib/
+^MakeMaker-\d
+^MYMETA.yml$
+/MYMETA.yml$
+
+# Temp, old and emacs backup files.
+~$
+\.old$
+^#.*#$
+^\.#
+.*\.swp$
+
+# Distributions
+^altree-.*\.tar\.gz$
+
+# Documentation
+^Documentation/fig/.*\.pdftex(_t)?$
+^Documentation/fig/.*\.pstex(_t)?$
+^Documentation/fig/.*\.subfig\.mk$
+^Documentation/fig/.*_[0-9]+\.fig$
+
+# Other
+.*\.o$
+^make-release$
+^Documentation/example_files
+^altree_enleve$
+
=====================================
META.json deleted
=====================================
@@ -1,39 +0,0 @@
-{
- "abstract" : "Association and Localisation tests using phylogenetic Trees",
- "author" : [
- "Claire Bardel <Claire.Bardel at univ-lyon1.fr>"
- ],
- "dynamic_config" : 1,
- "generated_by" : "ExtUtils::MakeMaker version 6.66, CPAN::Meta::Converter version 2.120921",
- "license" : [
- "perl_5"
- ],
- "meta-spec" : {
- "url" : "http://search.cpan.org/perldoc?CPAN::Meta::Spec",
- "version" : "2"
- },
- "name" : "altree",
- "no_index" : {
- "directory" : [
- "t",
- "inc"
- ]
- },
- "prereqs" : {
- "build" : {
- "requires" : {
- "ExtUtils::MakeMaker" : "0"
- }
- },
- "configure" : {
- "requires" : {
- "ExtUtils::MakeMaker" : "0"
- }
- },
- "runtime" : {
- "requires" : {}
- }
- },
- "release_status" : "stable",
- "version" : "v1.3.1"
-}
=====================================
META.yml deleted
=====================================
@@ -1,21 +0,0 @@
----
-abstract: 'Association and Localisation tests using phylogenetic Trees'
-author:
- - 'Claire Bardel <Claire.Bardel at univ-lyon1.fr>'
-build_requires:
- ExtUtils::MakeMaker: 0
-configure_requires:
- ExtUtils::MakeMaker: 0
-dynamic_config: 1
-generated_by: 'ExtUtils::MakeMaker version 6.66, CPAN::Meta::Converter version 2.120921'
-license: perl
-meta-spec:
- url: http://module-build.sourceforge.net/META-spec-v1.4.html
- version: 1.4
-name: altree
-no_index:
- directory:
- - t
- - inc
-requires: {}
-version: v1.3.1
=====================================
MYMETA.json deleted
=====================================
@@ -1,39 +0,0 @@
-{
- "abstract" : "Association and Localisation tests using phylogenetic Trees",
- "author" : [
- "Claire Bardel <Claire.Bardel at univ-lyon1.fr>"
- ],
- "dynamic_config" : 0,
- "generated_by" : "ExtUtils::MakeMaker version 6.66, CPAN::Meta::Converter version 2.120921",
- "license" : [
- "perl_5"
- ],
- "meta-spec" : {
- "url" : "http://search.cpan.org/perldoc?CPAN::Meta::Spec",
- "version" : "2"
- },
- "name" : "altree",
- "no_index" : {
- "directory" : [
- "t",
- "inc"
- ]
- },
- "prereqs" : {
- "build" : {
- "requires" : {
- "ExtUtils::MakeMaker" : "0"
- }
- },
- "configure" : {
- "requires" : {
- "ExtUtils::MakeMaker" : "0"
- }
- },
- "runtime" : {
- "requires" : {}
- }
- },
- "release_status" : "stable",
- "version" : "v1.3.1"
-}
=====================================
debian/changelog
=====================================
@@ -1,5 +1,6 @@
-altree (1.3.1-11) UNRELEASED; urgency=medium
+altree (1.3.2-1) unstable; urgency=medium
+ [ Andreas Tille ]
* Replace dummy package libopenblas-base by libopenblas0
Closes: #994474
* Fix watch file
@@ -10,7 +11,12 @@ altree (1.3.1-11) UNRELEASED; urgency=medium
* Do not fail in clean target if latex-make is not installed on local
machine
- -- Andreas Tille <tille at debian.org> Fri, 17 Sep 2021 12:18:39 +0200
+ [ Vincent Danjean ]
+ * New upstream version
+ - debian patches applied
+ - XS files refreshed
+
+ -- Vincent Danjean <vdanjean at debian.org> Fri, 17 Sep 2021 18:26:18 +0200
altree (1.3.1-10) unstable; urgency=medium
=====================================
debian/patches/blas.patch deleted
=====================================
@@ -1,16 +0,0 @@
-Author: Mo Zhou <lumin at debian.org>
-Last-Update: Wed, 30 Oct 2019 13:08:31 +0000
-Bug-Debian: https://bugs.debian.org/943828
-Description: Do not require atlas
-
---- a/CUtils/Makefile.PL
-+++ b/CUtils/Makefile.PL
-@@ -9,7 +9,7 @@ WriteMakefile(
- ($] >= 5.005 ? ## Add these new keywords supported since 5.005
- (ABSTRACT_FROM => 'lib/ALTree/CUtils.pm', # retrieve abstract from module
- AUTHOR => 'Claire Bardel <Claire.Bardel at univ-lyon1.fr>') : ()),
-- LIBS => ['-lm -lpthread -lgsl -lcblas'], # e.g., '-lm'
-+ LIBS => ['-lm -lpthread -lgsl -lblas'], # e.g., '-lm'
- DEFINE => '', # e.g., '-DHAVE_SOMETHING'
- INC => '-ggdb3 -I. -Ic_sources', # e.g., '-I. -I/usr/include/other'
- # Un-comment this if you add C files to link with later:
=====================================
debian/patches/figlatex.patch deleted
=====================================
@@ -1,16 +0,0 @@
-Description: Use figlatex instead of texgraphicx
-Bug-Debian: https://bugs.debian.org/963418
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Mon, 22 Jun 2020 13:12:19 +0200
-
---- a/Documentation/manual.tex
-+++ b/Documentation/manual.tex
-@@ -4,7 +4,7 @@
-
- \usepackage{a4wide}
- \usepackage[nocolor]{pdfswitch}
--\usepackage{texgraphicx}% Pour inclure les pstex_t
-+\usepackage{figlatex}% Pour inclure les pstex_t
- \graphicspath{{fig/}{eps/}}
- \usepackage[latin1]{inputenc}% pour pouvoir taper des accents directement
- \usepackage[T1]{fontenc}% jolie fontes
=====================================
debian/patches/from-upstream-no-nested-functions.patch deleted
=====================================
@@ -1,105 +0,0 @@
-Description: From upstream, avoid nested C functions
---- a/CUtils/c_sources/rhyper.c
-+++ b/CUtils/c_sources/rhyper.c
-@@ -52,55 +52,61 @@
- * If (i > 7), use Stirling's approximation, otherwise use table lookup.
- */
-
--static double afc(int i)
--{
-- static int computed=10;
-- static double al[1756] =
-- {
-- 0.0,
-- 0,/*ln(0!)*/
-- 0,/*ln(1!)*/
-- 0.693147180559945309,/*ln(2!)*/
-- 1.791759469228055,/*ln(3!)*/
-- 3.17805383034794562,/*ln(4!)*/
-- 4.78749174278204599,/*ln(5!)*/
-- 6.579251212010101,/*ln(6!)*/
-- 8.5251613610654143,/*ln(7!)*/
-- 10.6046029027452502,/*ln(8!)*/
-- 12.8018274800814696,/*ln(9!)*/
-- 15.1044125730755153,/*ln(10!)*/
-- };
-- double compute(int n) {
-- static long double cur=3628800;
-- static int i=11;
-- static volatile int mutex=0;
--
-- while (__sync_lock_test_and_set(&mutex, 1)) {
-- /* Internal loop with only read to avoid cache line ping-pong
-- on multi-processors */
-- while(mutex) {
-- /* spinlock */
-- }
-- }
-+struct afc_data {
-+ int computed;
-+ double al[1756];
-+};
-+
-+double compute(int n, struct afc_data * __restrict__ data) {
-+ static long double cur=3628800;
-+ static int i=11;
-+ static volatile int mutex=0;
-
-- for(; i<=n; i++) {
-- cur*=i;
-- al[i+1]=logl(cur);
-+ while (__sync_lock_test_and_set(&mutex, 1)) {
-+ /* Internal loop with only read to avoid cache line ping-pong
-+ on multi-processors */
-+ while(mutex) {
-+ /* spinlock */
- }
-- computed=n;
-- __sync_lock_release(&mutex);
-- return al[i];
-- };
-+ }
-
-+ for(; i<=n; i++) {
-+ cur*=i;
-+ data->al[i+1]=logl(cur);
-+ }
-+ data->computed=n;
-+ __sync_lock_release(&mutex);
-+ return data->al[i];
-+};
-+
-+static double afc(int i)
-+{
- double di, value;
-+ static struct afc_data data = {
-+ .computed = 10,
-+ .al = {
-+ 0.0,
-+ 0,/*ln(0!)*/
-+ 0,/*ln(1!)*/
-+ 0.693147180559945309,/*ln(2!)*/
-+ 1.791759469228055,/*ln(3!)*/
-+ 3.17805383034794562,/*ln(4!)*/
-+ 4.78749174278204599,/*ln(5!)*/
-+ 6.579251212010101,/*ln(6!)*/
-+ 8.5251613610654143,/*ln(7!)*/
-+ 10.6046029027452502,/*ln(8!)*/
-+ 12.8018274800814696,/*ln(9!)*/
-+ 15.1044125730755153,/*ln(10!)*/
-+ }
-+ };
-
- if (i < 0) {
- fprintf(stderr, "rhyper.c: afc(i), i=%d < 0 -- SHOULD NOT HAPPEN!\n", i);
- exit(1);
-- } else if (i <= computed) {
-- value = al[i + 1];
-+ } else if (i <= data.computed) {
-+ value = data.al[i + 1];
- } else if (i <= 1754) {
-- value = compute(i);
-+ value = compute(i, &data);
- } else {
- di = i;
- value = (di + 0.5) * log(di) - di + 0.08333333333333 / di
=====================================
debian/patches/no-quicksort.patch deleted
=====================================
@@ -1,15 +0,0 @@
-Author: Dominic Hargreaves <dom at earth.li>
-Last-Update: Fri, 18 May 2018 11:20:24 +0200
-Bug-Debian: https://bugs.debian.org/898989
-Description: Remove unused _quicksort sub-pragma, no longer supported in Perl 5.27
-
---- a/ALTree/SitePerForet.pm
-+++ b/ALTree/SitePerForet.pm
-@@ -7,7 +7,6 @@ package ALTree::SitePerForet;
- ################################################################
-
- use base qw(ALTree::Base ALTree::Site);
--use sort '_quicksort';
-
- sub New { # [classe] site_nb
- my $class=shift;
=====================================
debian/patches/series deleted
=====================================
@@ -1,4 +0,0 @@
-from-upstream-no-nested-functions.patch
-no-quicksort.patch
-blas.patch
-figlatex.patch
=====================================
debian/watch
=====================================
@@ -1,6 +1,5 @@
version=4
-opts=filenamemangle=s/.*\.tar\.gz\?ref=v?(\d\S*)/ALTree-$1\.tar\.gz/g \
- https://gitlab.inria.fr/NGS/ALTree/tags .*/v at ANY_VERSION@/ALTree-v at ANY_VERSION@\.tar\.gz
+https://gitlab.inria.fr/NGS/ALTree/tags .*/v[0-9.]*/ALTree-v at ANY_VERSION@\.tar\.gz
-# https://gitlab.inria.fr/NGS/ALTree/repository/v1.3.1/archive.tar.gz
\ No newline at end of file
+# https://gitlab.inria.fr/NGS/ALTree/repository/v1.3.1/archive.tar.gz
=====================================
make-release
=====================================
@@ -0,0 +1,96 @@
+#!/bin/sh
+
+set -e
+
+VERSION=$(cat progs/altree | \
+ sed -e '/our.*VERSION/s/.*qv(\([0-9.]\+\)).*/\1/p;d')
+
+if [ "$VERSION" = "" ]; then
+ echo "Unable to read current version. Aborting."
+ exit 1
+fi
+
+FORCE=""
+
+while [ $# != 0 ]; do
+ case "$1" in
+ --force)
+ echo "--force enabled. Disabling sanity check..."
+ FORCE=yes
+ ;;
+ --dry-run|-n)
+ echo "--dry-run enabled. No real release will be done."
+ DRYRUN="echo DRY-RUN: "
+ ;;
+ --)
+ shift
+ break
+ ;;
+ -*)
+ echo "Unknown option $1"
+ echo "Aborting"
+ exit 1
+ ;;
+ *)
+ break;
+ ;;
+ esac
+ shift
+done
+
+echo "Creating version '$VERSION'"
+
+set -x
+[ -f Makefile ] || perl Makefile.PL
+make Makefile || true
+make realclean
+make -C Documentation distclean
+set +x
+
+if [ "$(git status --short --untracked)" != "" ]; then
+ echo "************************************"
+ echo "* Not all files are commited/cleaned"
+ echo "* Please correct before creating a release"
+ echo "* (use 'git status --short --untracked' to look for problematic files)"
+ echo "* (use 'git stash -a' to remove them temporarely)"
+ echo "************************************"
+ if [ "$FORCE" ]; then
+ echo "* !!! WARNING: --force enabled : type 'ENTER to continue'"
+ echo "************************************"
+ read a
+ else
+ exit 1
+ fi
+fi
+
+perl Makefile.PL
+
+if [ "$(make distcheck 2>&1 1>/dev/null | grep -v "^No such file: META.yml$")" != "" ]; then
+ echo "************************************"
+ echo "* Not all files are in MANIFEST (or removed from it)"
+ echo "* Please correct before creating a release"
+ echo "* (use 'make distcheck' to look for problematic files"
+ echo "************************************"
+ if [ "$FORCE" ]; then
+ echo "* !!! WARNING: --force enabled : type 'ENTER to continue'"
+ echo "************************************"
+ read a
+ else
+ exit 1
+ fi
+fi
+
+make disttest
+make dist
+
+echo "************************************"
+echo "* SUCCESS !"
+echo "************************************"
+echo "* Release created in altree-$VERSION.tar.gz"
+echo "* Do not forget to create a git tag and push it"
+echo "* You need to copy this file to the web site"
+echo "* and tell Vince to update the debian package"
+echo "************************************"
+
+
+
=====================================
progs/altree
=====================================
@@ -10,7 +10,7 @@ use Data::Dumper;
srand(654321);
-use version; our $VERSION = qv(1.3.1);
+use version; our $VERSION = qv(1.3.2);
# Positionner la variable PERL5LIB si besoin
View it on GitLab: https://salsa.debian.org/med-team/altree/-/compare/194cbf9e650a3915d7b372b2fae9a6373f305b8c...69bffa04e8159e2bf980f0b5ef95ff0788cf08a2
--
View it on GitLab: https://salsa.debian.org/med-team/altree/-/compare/194cbf9e650a3915d7b372b2fae9a6373f305b8c...69bffa04e8159e2bf980f0b5ef95ff0788cf08a2
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