[med-svn] [indelible] 02/04: Rebased patches

Sun Feb 7 18:07:06 UTC 2016

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kloetzl-guest pushed a commit to branch master
in repository indelible.

commit 9ee4931d930acd0d557247ee4d63581abe760591
Author: Fabian Klötzl <fabian at kloetzl.info>
Date:   Sun Feb 7 16:29:08 2016 +0100

    Rebased patches
    
    Changed to a sane order of patches.
---
 .../0002-added-auto-tools-build-system.patch       | 54 -------------------
 ...h => 0002-added-documentation-index-page.patch} |  0
 ...dded-manpage.patch => 0003-added-manpage.patch} |  0
 ...ch => 0004-added-auto-tools-build-system.patch} | 62 ++++++++++++++++++----
 .../patches/0005-Ensure-docs-are-distributed.patch | 21 --------
 debian/patches/series                              |  8 ++-
 6 files changed, 54 insertions(+), 91 deletions(-)

diff --git a/debian/patches/0002-added-auto-tools-build-system.patch b/debian/patches/0002-added-auto-tools-build-system.patch
deleted file mode 100644
index 0cc970e..0000000
--- a/debian/patches/0002-added-auto-tools-build-system.patch
+++ /dev/null
@@ -1,54 +0,0 @@
-From: =?utf-8?q?Fabian_Kl=C3=B6tzl?= <fabian at kloetzl.info>
-Date: Mon, 21 Dec 2015 13:39:45 +0100
-Subject: added auto tools build system
-
-Upstream did not provide a makefile or any more advanced build system. Thus,
-I added files for autoconf and automake to help with the installation.
----
- Makefile.am  |  6 ++++++
- configure.ac | 23 +++++++++++++++++++++++
- 2 files changed, 29 insertions(+)
- create mode 100644 Makefile.am
- create mode 100644 configure.ac
-
-diff --git a/Makefile.am b/Makefile.am
-new file mode 100644
-index 0000000..ba9c4ba
---- /dev/null
-+++ b/Makefile.am
-@@ -0,0 +1,6 @@
-+bin_PROGRAMS= indelible
-+indelible_SOURCES= src/indelible.cpp
-+indelible_CPPFLAGS= -Isrc
-+
-+# The following files are #included by indelible.cpp
-+EXTRA_indelible_SOURCES= src/control.cpp src/models.cpp src/paml.cpp src/randoms.cpp src/MersenneTwister.h
-diff --git a/configure.ac b/configure.ac
-new file mode 100644
-index 0000000..3d34e72
---- /dev/null
-+++ b/configure.ac
-@@ -0,0 +1,23 @@
-+AC_INIT([indelible], [1.03])
-+AM_INIT_AUTOMAKE([-Wall foreign])
-+
-+AC_PROG_CPP
-+AC_PROG_CXX
-+
-+AC_LANG(C++)
-+
-+AC_CHECK_LIB([m],[cos])
-+
-+AC_TYPE_SIZE_T
-+AC_TYPE_INT32_T
-+AC_TYPE_UINT32_T
-+AC_HEADER_STDBOOL
-+
-+AC_FUNC_MALLOC
-+AC_CHECK_HEADERS([limits.h])
-+AC_CHECK_FUNCS([floor pow sqrt])
-+
-+AC_CONFIG_FILES([
-+ Makefile
-+])
-+AC_OUTPUT
diff --git a/debian/patches/0003-added-documentation-index-page.patch b/debian/patches/0002-added-documentation-index-page.patch
similarity index 100%
rename from debian/patches/0003-added-documentation-index-page.patch
rename to debian/patches/0002-added-documentation-index-page.patch
diff --git a/debian/patches/0006-added-manpage.patch b/debian/patches/0003-added-manpage.patch
similarity index 100%
rename from debian/patches/0006-added-manpage.patch
rename to debian/patches/0003-added-manpage.patch
diff --git a/debian/patches/0004-Install-HTML-docs.patch b/debian/patches/0004-added-auto-tools-build-system.patch
similarity index 54%
rename from debian/patches/0004-Install-HTML-docs.patch
rename to debian/patches/0004-added-auto-tools-build-system.patch
index fec52a3..3378893 100644
--- a/debian/patches/0004-Install-HTML-docs.patch
+++ b/debian/patches/0004-added-auto-tools-build-system.patch
@@ -1,21 +1,32 @@
 From: =?utf-8?q?Fabian_Kl=C3=B6tzl?= <fabian at kloetzl.info>
-Date: Tue, 22 Dec 2015 10:42:35 +0100
-Subject: Install HTML docs
+Date: Mon, 21 Dec 2015 13:39:45 +0100
+Subject: added auto tools build system
 
+Upstream did not provide a makefile or any more advanced build system. Thus,
+I added files for autoconf and automake to help with the installation.
 ---
- Makefile.am | 22 ++++++++++++++++++++++
- 1 file changed, 22 insertions(+)
+ Makefile.am  | 30 ++++++++++++++++++++++++++++++
+ configure.ac | 23 +++++++++++++++++++++++
+ 2 files changed, 53 insertions(+)
+ create mode 100644 Makefile.am
+ create mode 100644 configure.ac
 
 diff --git a/Makefile.am b/Makefile.am
-index ba9c4ba..6e13155 100644
---- a/Makefile.am
+new file mode 100644
+index 0000000..26441f1
+--- /dev/null
 +++ b/Makefile.am
-@@ -4,3 +4,25 @@ indelible_CPPFLAGS= -Isrc
- 
- # The following files are #included by indelible.cpp
- EXTRA_indelible_SOURCES= src/control.cpp src/models.cpp src/paml.cpp src/randoms.cpp src/MersenneTwister.h
+@@ -0,0 +1,30 @@
++bin_PROGRAMS= indelible
++indelible_SOURCES= src/indelible.cpp
++indelible_CPPFLAGS= -Isrc
 +
-+nobase_html_DATA= help/index.html help/examples.shtml help/manual.shtml \
++dist_man_MAN= indelible.1
++
++# The following files are #included by indelible.cpp
++EXTRA_indelible_SOURCES= src/control.cpp src/models.cpp src/paml.cpp src/randoms.cpp src/MersenneTwister.h
++
++nobase_dist_html_DATA= help/index.html help/examples.shtml help/manual.shtml \
 +	help/example_files/AMINOACID.shtml help/example_files/basicaminoacid.shtml \
 +	help/example_files/basiccodon.shtml help/example_files/basicnucleotide.shtml \
 +	help/example_files/basic.shtml help/example_files/branch2.shtml \
@@ -36,3 +47,32 @@ index ba9c4ba..6e13155 100644
 +	help/manual_files/settings.shtml help/manual_files/symQmatrix.gif \
 +	help/manual_files/tree.shtml help/manual_files/trees.txt \
 +	help/manual_files/type.shtml help/manual_files/userAAmodel.txt
+diff --git a/configure.ac b/configure.ac
+new file mode 100644
+index 0000000..3d34e72
+--- /dev/null
++++ b/configure.ac
+@@ -0,0 +1,23 @@
++AC_INIT([indelible], [1.03])
++AM_INIT_AUTOMAKE([-Wall foreign])
++
++AC_PROG_CPP
++AC_PROG_CXX
++
++AC_LANG(C++)
++
++AC_CHECK_LIB([m],[cos])
++
++AC_TYPE_SIZE_T
++AC_TYPE_INT32_T
++AC_TYPE_UINT32_T
++AC_HEADER_STDBOOL
++
++AC_FUNC_MALLOC
++AC_CHECK_HEADERS([limits.h])
++AC_CHECK_FUNCS([floor pow sqrt])
++
++AC_CONFIG_FILES([
++ Makefile
++])
++AC_OUTPUT
diff --git a/debian/patches/0005-Ensure-docs-are-distributed.patch b/debian/patches/0005-Ensure-docs-are-distributed.patch
deleted file mode 100644
index 9e41d36..0000000
--- a/debian/patches/0005-Ensure-docs-are-distributed.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-From: =?utf-8?q?Fabian_Kl=C3=B6tzl?= <fabian at kloetzl.info>
-Date: Tue, 22 Dec 2015 10:56:01 +0100
-Subject: Ensure docs are distributed
-
----
- Makefile.am | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/Makefile.am b/Makefile.am
-index 6e13155..ba5eb2e 100644
---- a/Makefile.am
-+++ b/Makefile.am
-@@ -5,7 +5,7 @@ indelible_CPPFLAGS= -Isrc
- # The following files are #included by indelible.cpp
- EXTRA_indelible_SOURCES= src/control.cpp src/models.cpp src/paml.cpp src/randoms.cpp src/MersenneTwister.h
- 
--nobase_html_DATA= help/index.html help/examples.shtml help/manual.shtml \
-+nobase_dist_html_DATA= help/index.html help/examples.shtml help/manual.shtml \
- 	help/example_files/AMINOACID.shtml help/example_files/basicaminoacid.shtml \
- 	help/example_files/basiccodon.shtml help/example_files/basicnucleotide.shtml \
- 	help/example_files/basic.shtml help/example_files/branch2.shtml \
diff --git a/debian/patches/series b/debian/patches/series
index 367cf89..5cf56d6 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,6 +1,4 @@
 0001-added-headers-for-getpid-2.patch
-0002-added-auto-tools-build-system.patch
-0003-added-documentation-index-page.patch
-0004-Install-HTML-docs.patch
-0005-Ensure-docs-are-distributed.patch
-0006-added-manpage.patch
+0002-added-documentation-index-page.patch
+0003-added-manpage.patch
+0004-added-auto-tools-build-system.patch

-- 
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