[med-svn] [physamp] 01/03: New upstream version 1.0.3

[Julien Dutheil]

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jdutheil-guest pushed a commit to branch master
in repository physamp.

commit cc19710929c637685b70aa09bec154c86c1ef674
Author: Julien Y. Dutheil <dutheil at evolbio.mpg.de>
Date:   Sun Sep 3 21:07:04 2017 +0200

    New upstream version 1.0.3
---
 CMakeLists.txt    |  6 +++---
 docs/physamp.texi |  5 +++--
 man/bppphysamp.1  | 37 +++++++++++++++++++++++++++++++++++++
 3 files changed, 43 insertions(+), 5 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 77ca39e..1f87e7e 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -59,7 +59,7 @@ else ()
   # Generate command line args (always add -c to output compressed file to stdout)
   if (${COMPRESS_PROGRAM} STREQUAL "gzip")
     # -n for no timestamp in files (reproducible builds)
-    set (COMPRESS_ARGS -c -n)
+    set (COMPRESS_ARGS -c9n)
   else ()
     set (COMPRESS_ARGS -c)
   endif ()
@@ -86,10 +86,10 @@ ENDIF(NO_DEP_CHECK)
 # Packager
 SET(CPACK_PACKAGE_NAME "physamp")
 SET(CPACK_PACKAGE_VENDOR "Julien Y. Dutheil")
-SET(CPACK_PACKAGE_VERSION "1.0.2")
+SET(CPACK_PACKAGE_VERSION "1.0.3")
 SET(CPACK_PACKAGE_VERSION_MAJOR "1")
 SET(CPACK_PACKAGE_VERSION_MINOR "0")
-SET(CPACK_PACKAGE_VERSION_PATCH "2")
+SET(CPACK_PACKAGE_VERSION_PATCH "3")
 SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "The Phylogenetic Sampler package")
 SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/LICENSE")
 SET(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS")
diff --git a/docs/physamp.texi b/docs/physamp.texi
index f6b7656..1974c21 100644
--- a/docs/physamp.texi
+++ b/docs/physamp.texi
@@ -1,18 +1,19 @@
 \input texinfo   @c -*-texinfo-*-
 @c %**start of header
 @setfilename physamp.info
- at settitle PhySamp Manual 1.0.1
+ at settitle PhySamp Manual 1.0.3
 @documentencoding UTF-8
 @afourpaper
 @dircategory Science Biology Genetics
 @direntry
 * bppalnoptim: (bppalnoptim)    Alignment Optimizer.
+* bppphysamp: (bppphysamp)      Phylogenetic Sampling.
 @end direntry
 @c %**end of header
 
 
 @copying
-This is the manual of the PhySamp package, version 1.0.1.
+This is the manual of the PhySamp package, version 1.0.3.
 
 Copyright @copyright{} 2017 Julien Y. Dutheil
 @end copying
diff --git a/man/bppphysamp.1 b/man/bppphysamp.1
new file mode 100644
index 0000000..0669d3d
--- /dev/null
+++ b/man/bppphysamp.1
@@ -0,0 +1,37 @@
+.TH BPPPHYSAMP 1 LOCAL
+
+.SH NAME
+
+bppphysamp - Phylogenetic Sampling
+
+.SH SYNOPSIS
+
+.B bppphysamp [options]
+
+.SH AVAILABILITY
+
+All UNIX flavors
+
+.SH DESCRIPTION
+
+bppphysamp samples a sequence alignment according to a given phylogenetic tree, in order to control the set of redundancy in the data.
+
+.SH OPTIONS
+
+You should refer to 'info physamp' or to the online manual of bppsuite for a complete list of available options.
+
+.TP 5
+
+--noninteractive
+
+generates output for redirection in a file.
+
+.TP
+
+param=file
+
+reads a file for loading options
+
+.SH AUTHOR
+
+Julien Y. Dutheil.

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