Commit 3861e37b authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 0.3.2

parent 89cb22dd

ChangeLog.md

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@@ -2,6 +2,17 @@ 
All notable changes to `libpll` will be documented in this file.

This project adheres to [Semantic Versioning](http://semver.org/).



## [0.3.2] - 2017-07-12

### Added

 - Optional per-rate category scalers for protein and generic kernels

 - Hardware detection for APPLE builds defaults to assembly code

### Fixed

 - Improved fix for negative p-matrix values.

 - Derivatives computation for Lewis/Felsenstein ascertainment bias correction

 - set_tipchars() for ascertainment bias correction with non-DNA sequences

 - Excessive memory allocation when compressing site patterns

 - Issue with PHYLIP parsing when header ends with CRLF



## [0.3.1] - 2017-05-17

### Added

 - Checks for older versions of clang and gcc to use assembly instructions

README.md

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File changed.

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configure.ac

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@@ -2,7 +2,7 @@ 
# Process this file with autoconf to produce a configure script.



AC_PREREQ([2.63])

AC_INIT([libpll], [0.3.1], [Tomas.Flouri@h-its.org])

AC_INIT([libpll], [0.3.2], [Tomas.Flouri@h-its.org])

AM_INIT_AUTOMAKE([subdir-objects])

AC_LANG([C])

AC_CONFIG_SRCDIR([src/pll.c])

examples/rooted-tacg/rooted-tacg.c

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@@ -228,23 +228,23 @@ int main(int argc, char * argv[]) 
  /* set the 5 tip CLVs, and use the pll_map_nt map for converting

     the sequences to CLVs */

  double * enc = encode_tacg("WAAAAB");

  assert(pll_set_tip_clv(partition, 0, enc));

  assert(pll_set_tip_clv(partition, 0, enc, PLL_FALSE));

  free(enc);



  enc = encode_tacg("CACACD");

  assert(pll_set_tip_clv(partition, 1, enc));

  assert(pll_set_tip_clv(partition, 1, enc, PLL_FALSE));

  free(enc);



  enc = encode_tacg("AGGACA");

  assert(pll_set_tip_clv(partition, 2, enc));

  assert(pll_set_tip_clv(partition, 2, enc, PLL_FALSE));

  free(enc);



  enc = encode_tacg("CGTAGT");

  assert(pll_set_tip_clv(partition, 3, enc));

  assert(pll_set_tip_clv(partition, 3, enc, PLL_FALSE));

  free(enc);



  enc = encode_tacg("CGAATT");

  assert(pll_set_tip_clv(partition, 4, enc));

  assert(pll_set_tip_clv(partition, 4, enc, PLL_FALSE));

  free(enc);



  /* update two probability matrices for the corresponding branch lengths */

man/libpll.3

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.\" -*- coding: utf-8 -*-

.\" ============================================================================

.TH libpll 3 "May 17, 2017" "libpll 0.3.1" "Library Functions Manual"

.TH libpll 3 "July 12, 2017" "libpll 0.3.2" "Library Functions Manual"

.\" ============================================================================

.SH NAME

libpll \(em Phylogenetic Likelihood Library
@@ -544,7 +544,7 @@ Source code and binaries are available at 
<https://github.com/xflouris/libpll>.

.\" ============================================================================

.SH COPYRIGHT

Copyright (C) 2015-2016, Tomas Flouri, Diego Darriba

Copyright (C) 2015-2017, Tomas Flouri, Diego Darriba

.PP

All rights reserved.

.PP
@@ -581,7 +581,7 @@ First public release. 
Added faster vectorizations for 20-state and arbitrary-state models, unweighted

parsimony functions, randomized stepwise addition, portable functions for

parsing trees from C-strings, per-rate category scalers for preventing

numberical underflows. Modified newick exporting function to accept callbacks

numerical underflows. Modified newick exporting function to accept callbacks

for custom printing. Fixed derivatives computation, parsing of branch lengths,

invariant sites computation, log-likelihood computation for cases where we have

scaling and patterns, ascertainment bias computation, per-site log-likelihood
@@ -591,5 +591,12 @@ computation, memory leaks. Added run-time detection of hardware. 
Correct updating of paddded eigen-decomposition arrays for models with a number

of states not being a power of two. Added portable hardware detection for clang

and GCC. 

.TP

.BR v0.3.2\~ "released July 12th, 2017"

Added optional per-rate category scalers for protein and generic kernels.

Improved fix for negative transition probability matrices caused by numerics.

Fixed initialization of tip CLVs when using ascertainment bias correction with

non-DNA sequences. Fixed excessive memory allocation when compressing site

patterns and issue with PHYLIP parsing when header ends with CRLF.

.RE

.LP