[med-svn] [genometools] 01/01: reproducibility and housekeeping
Sascha Steinbiss
sascha at steinbiss.name
Wed Apr 27 10:34:30 UTC 2016
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sascha-guest pushed a commit to branch master
in repository genometools.
commit 51805def3431be743d199440666257ed488e43f2
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date: Wed Apr 27 10:34:11 2016 +0000
reproducibility and housekeeping
---
debian/changelog | 9 ++
debian/patches/ignore-m32-m64.patch | 27 ++++++
debian/patches/manual_fixed_dates.patch | 150 ++++++++++++++++++++++++++++++++
debian/patches/series | 2 +
4 files changed, 188 insertions(+)
diff --git a/debian/changelog b/debian/changelog
index 7ed98ab..b742bfe 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,12 @@
+genometools (1.5.8+ds-3) unstable; urgency=medium
+
+ * Remove explicit -m32 and -m64.
+ * Fix dates in manuals (cf upstream PR #780) for reproducibility.
+ * Remove unnecessary maintainer scripts.
+ * Update upstream metadata.
+
+ -- Sascha Steinbiss <sascha at steinbiss.name> Wed, 27 Apr 2016 09:25:08 +0000
+
genometools (1.5.8+ds-2) unstable; urgency=medium
* Fix locale (LC_PAPER) for LaTeX runs (reproducibility).
diff --git a/debian/patches/ignore-m32-m64.patch b/debian/patches/ignore-m32-m64.patch
new file mode 100644
index 0000000..76a64f3
--- /dev/null
+++ b/debian/patches/ignore-m32-m64.patch
@@ -0,0 +1,27 @@
+Description: remove explicit -m32 and -m64
+Author: Sascha Steinbiss <sascha at steinbiss.name>
+--- a/Makefile
++++ b/Makefile
+@@ -360,22 +360,6 @@
+ endif
+ endif
+
+-ifneq ($(x32),yes)
+- ifeq ($(m32),yes)
+- GT_CFLAGS += -m32
+- GT_LDFLAGS += -m32
+- SQLITE_CFLAGS += -m32
+- endif
+-
+- ifeq ($(m64),yes)
+- ifeq (,$(filter $(MACHINE),ia64 alpha mips64 mips64el aarch64))
+- GT_CFLAGS += -m64
+- GT_LDFLAGS += -m64
+- SQLITE_CFLAGS += -m64
+- endif
+- endif
+-endif
+-
+ ifeq ($(findstring clang,$(CC)),clang)
+ # do not complain about unnecessary options
+ GT_CFLAGS += -Qunused-arguments -Wno-parentheses
diff --git a/debian/patches/manual_fixed_dates.patch b/debian/patches/manual_fixed_dates.patch
new file mode 100644
index 0000000..cd38847
--- /dev/null
+++ b/debian/patches/manual_fixed_dates.patch
@@ -0,0 +1,150 @@
+From 3bf0e31b3a020c415d99d8661c5aca32647c7a6f Mon Sep 17 00:00:00 2001
+From: Sascha Steinbiss <ss34 at sanger.ac.uk>
+Date: Thu, 7 Apr 2016 10:25:25 +0100
+Subject: [PATCH] introduce dates for manuals
+
+IMHO manuals should have a specific date, and the build date should not be
+relevant here. This commit initialises the date fields in the manuals by
+setting the date to the last modification date of the file in git, as
+given by:
+
+for f in doc/manuals/*.tex; do
+ export OUT=`TZ=UTC LC_ALL=C date -d "$(git log -1 --format='%aD' -- $f )" +'%d\/%m\/%Y'`;
+ sed -ri "s/.begin.document./\\\date{$OUT}\n\\\begin{document}/g" $f;
+ unset OUT;
+done
+---
+ doc/manuals/annotationsketch.tex | 1 +
+ doc/manuals/genomediff.tex | 1 +
+ doc/manuals/hop.tex | 1 +
+ doc/manuals/ltrdigest.tex | 1 +
+ doc/manuals/ltrharvest.tex | 1 +
+ doc/manuals/mgth.tex | 1 +
+ doc/manuals/packedindex.tex | 1 +
+ doc/manuals/readjoiner.tex | 1 +
+ doc/manuals/repfind.tex | 1 +
+ doc/manuals/tagerator.tex | 1 +
+ doc/manuals/tallymer.tex | 1 +
+ doc/manuals/uniquesub.tex | 1 +
+ 12 files changed, 12 insertions(+)
+
+--- a/doc/manuals/annotationsketch.tex
++++ b/doc/manuals/annotationsketch.tex
+@@ -50,6 +50,7 @@
+ \subject{Supplementary Information}
+ \author{Sascha Steinbiss, Gordon Gremme, Christin Sch\"arfer, Malte Mader\\ and Stefan Kurtz}
+
++\date{11/07/2012}
+ \begin{document}
+
+ \maketitle
+--- a/doc/manuals/genomediff.tex
++++ b/doc/manuals/genomediff.tex
+@@ -59,6 +59,7 @@
+ \url{willrodt at zbh.uni-hamburg.de}\\
+ \end{tabular}}
+
++\date{02/10/2012}
+ \begin{document}
+ %\tsuhhfamily
+ \maketitle
+--- a/doc/manuals/hop.tex
++++ b/doc/manuals/hop.tex
+@@ -32,6 +32,7 @@
+ \url{kurtz at zbh.uni-hamburg.de}\\[1cm]
+ \end{tabular}}
+
++\date{15/05/2014}
+ \begin{document}
+ \maketitle
+
+--- a/doc/manuals/ltrdigest.tex
++++ b/doc/manuals/ltrdigest.tex
+@@ -41,6 +41,7 @@
+ \end{tabular}
+ \end{tabular}}
+
++\date{26/08/2013}
+ \begin{document}
+ \maketitle
+
+--- a/doc/manuals/ltrharvest.tex
++++ b/doc/manuals/ltrharvest.tex
+@@ -41,6 +41,7 @@
+ \url{http://www.biomedcentral.com/1471-2105/9/18}
+ \end{tabular}
+ \end{tabular}}
++\date{26/08/2013}
+ \begin{document}
+ \maketitle
+
+--- a/doc/manuals/mgth.tex
++++ b/doc/manuals/mgth.tex
+@@ -37,6 +37,7 @@
+ 20146 Hamburg\\
+ Germany\\[1cm]
+ \end{tabular}}
++\date{26/08/2013}
+ \begin{document}
+ \maketitle
+
+--- a/doc/manuals/packedindex.tex
++++ b/doc/manuals/packedindex.tex
+@@ -38,6 +38,7 @@
+ % BMC Bioinformatics 2008, 9:18
+ \end{tabular}
+ \end{tabular}}
++\date{26/08/2013}
+ \begin{document}
+ \maketitle
+
+--- a/doc/manuals/readjoiner.tex
++++ b/doc/manuals/readjoiner.tex
+@@ -45,6 +45,7 @@
+ \url{kurtz at zbh.uni-hamburg.de}\\[1cm]
+ \end{tabular}}
+
++\date{18/02/2014}
+ \begin{document}
+ \maketitle
+
+--- a/doc/manuals/repfind.tex
++++ b/doc/manuals/repfind.tex
+@@ -28,6 +28,7 @@
+ University of Hamburg
+ \end{tabular}}
+
++\date{26/08/2013}
+ \begin{document}
+ \maketitle
+ This manual describes the options of the program \Repfind. It also gives
+--- a/doc/manuals/tagerator.tex
++++ b/doc/manuals/tagerator.tex
+@@ -22,6 +22,7 @@
+ University of Hamburg
+ \end{tabular}}
+
++\date{26/08/2013}
+ \begin{document}
+ \maketitle
+
+--- a/doc/manuals/tallymer.tex
++++ b/doc/manuals/tallymer.tex
+@@ -95,6 +95,7 @@
+ University of Hamburg
+ \end{tabular}}
+
++\date{26/08/2013}
+ \begin{document}
+ \maketitle
+ This manual describes the \textit{Tallymer}-software, a collection of programs
+--- a/doc/manuals/uniquesub.tex
++++ b/doc/manuals/uniquesub.tex
+@@ -24,6 +24,7 @@
+ University of Hamburg
+ \end{tabular}}
+
++\date{26/08/2013}
+ \begin{document}
+ \maketitle
+
diff --git a/debian/patches/series b/debian/patches/series
index 4b330ba..3fd76a2 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -8,3 +8,5 @@ fix-exports
split-manuals
use-mx32
gtdoc-traverse-sorted
+manual_fixed_dates.patch
+ignore-m32-m64.patch
--
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