Commit 62913cc6 authored by Julien Y. Dutheil's avatar Julien Y. Dutheil
Browse files

New upstream version 1.1.0

parent 1fb8db55

CMakeLists.txt

+5 −4
Original line number Diff line number Diff line
@@ -59,6 +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)

    # -9 for maximum compression (lintian error)

    set (COMPRESS_ARGS -c9n)

  else ()

    set (COMPRESS_ARGS -c)
@@ -73,7 +74,7 @@ IF (CMAKE_INSTALL_PREFIX) 
ENDIF (CMAKE_INSTALL_PREFIX)



include (GNUInstallDirs)

find_package (bpp-phyl 11.0.0 REQUIRED)

find_package (bpp-phyl 12.0.0 REQUIRED)





# Subdirectories
@@ -86,10 +87,10 @@ ENDIF(NO_DEP_CHECK) 
# Packager

SET(CPACK_PACKAGE_NAME "physamp")

SET(CPACK_PACKAGE_VENDOR "Julien Y. Dutheil")

SET(CPACK_PACKAGE_VERSION "1.0.3")

SET(CPACK_PACKAGE_VERSION "1.1.0")

SET(CPACK_PACKAGE_VERSION_MAJOR "1")

SET(CPACK_PACKAGE_VERSION_MINOR "0")

SET(CPACK_PACKAGE_VERSION_PATCH "3")

SET(CPACK_PACKAGE_VERSION_MINOR "1")

SET(CPACK_PACKAGE_VERSION_PATCH "0")

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")

ChangeLog

+5 −0
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14/03/18 -*- Version 1.1.0 -*-



14/03/18 Julien Dutheil

* Compatibility update Bio++ 2.4.0.



30/03/15 -*- Version 0.2.0 -*-



30/03/15 Julien Dutheil

docs/_config.yml

+5 −1
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theme: jekyll-theme-slate

title: PhySamp

description: Phylogenetic Sampling and Optimization of Sequence Alignments

show_downloads: true

share: true

docs/physamp.texi

+3 −3
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\input texinfo   @c -*-texinfo-*-

@c %**start of header

@setfilename physamp.info

@settitle PhySamp Manual 1.0.3

@settitle PhySamp Manual 1.1.0

@documentencoding UTF-8

@afourpaper

@dircategory Science Biology Genetics
@@ -13,9 +13,9 @@ 




@copying

This is the manual of the PhySamp package, version 1.0.3.

This is the manual of the PhySamp package, version 1.1.0.



Copyright @copyright{} 2017 Julien Y. Dutheil

Copyright @copyright{} 2018 Julien Y. Dutheil

@end copying



@titlepage

physamp.spec

+18 −18
Original line number Diff line number Diff line 
%define _basename physamp

%define _version 1.0.1

%define _release 1

%define _prefix /usr



URL: https://github.com/jydu/maffilter

URL: https://github.com/jydu/physamp



Name: %{_basename}

Version: %{_version}

Release: %{_release}

Name: physamp

Version: 1.1.0

Release: 1%{?dist}

License: GPL-3.0

Vendor: Julien Dutheil

Source: %{_basename}-%{_version}.tar.gz

Source: %{name}-%{version}.tar.gz

Summary: The PhySamp package

Group: Productivity/Scientific/Other



Requires: libbpp-phyl11 = 2.3.1

Requires: libbpp-seq11 = 2.3.1

Requires: libbpp-core3 = 2.3.1

Requires: libbpp-phyl12 = 2.4.0

Requires: libbpp-seq12 = 2.4.0

Requires: libbpp-core4 = 2.4.0



BuildRoot: %{_builddir}/%{_basename}-root

BuildRoot: %{_builddir}/%{name}-root

BuildRequires: cmake >= 2.8.11

BuildRequires: gcc-c++ >= 4.7.0

BuildRequires: groff

BuildRequires: texinfo >= 4.0.0

BuildRequires: libbpp-core3 = 2.3.1

BuildRequires: libbpp-core-devel = 2.3.1

BuildRequires: libbpp-seq11 = 2.3.1

BuildRequires: libbpp-seq-devel = 2.3.1

BuildRequires: libbpp-phyl11 = 2.3.1

BuildRequires: libbpp-phyl-devel = 2.3.1

BuildRequires: libbpp-core4 = 2.4.0

BuildRequires: libbpp-core-devel = 2.4.0

BuildRequires: libbpp-seq12 = 2.4.0

BuildRequires: libbpp-seq-devel = 2.4.0

BuildRequires: libbpp-phyl12 = 2.4.0

BuildRequires: libbpp-phyl-devel = 2.4.0





AutoReq: yes
@@ -80,6 +77,9 @@ rm -rf $RPM_BUILD_ROOT 
%{_prefix}/share/man/man1/bppphysamp.1.*



%changelog

* Wed Mar 14 2018 Julien Dutheil <dutheil@evolbio.mpg.de> 1.1.0-1

- Compatibility update with Bio++ 2.4.0

- More options in branch panel

* Tue Jun 06 2017 Julien Dutheil <dutheil@evolbio.mpg.de> 1.0.1-1

- Compatibility update with Bio++ 2.3.1

* Fri May 26 2017 Julien Dutheil <dutheil@evolbio.mpg.de> 1.0.0-1