New upstream version 3.4+dfsg (0bc915a8) · Commits · Debian Med / bali-phy

.appveyor.yml

+1 −1

Original line number	Diff line number	Diff line
		@@ -15,7 +15,7 @@ install:

		build_script:
		- bash -lc "cd $APPVEYOR_BUILD_FOLDER/ && git submodule update --init"
		- bash -lc "cd $APPVEYOR_BUILD_FOLDER/ && meson.py build --prefix=$APPVEYOR_BUILD_FOLDER/local"
		- bash -lc "cd $APPVEYOR_BUILD_FOLDER/ && meson build --prefix=$APPVEYOR_BUILD_FOLDER/local"
		- bash -lc "cd $APPVEYOR_BUILD_FOLDER/build && ninja install
		# - bash -lc "cd $APPVEYOR_BUILD_FOLDER/build && ninja test"

.gitignore

+1 −0

Original line number	Diff line number	Diff line
		@@ -3,3 +3,4 @@ doc/html
		doc/latex
		\#*#
		*.orig
		build*/

.travis.yml

+12 −12

Original line number	Diff line number	Diff line
		@@ -5,37 +5,37 @@ language: cpp
		matrix:
		include:
		- os: linux
		dist: trusty
		env: CXX_COMPILER=g++-5
		dist: xenial
		env: CXX_COMPILER=g++-6
		addons:
		apt:
		sources:
		- ubuntu-toolchain-r-test
		packages:
		- g++-5
		- g++-6
		- pandoc
		- os: linux
		dist: trusty
		env: CXX_COMPILER=g++-6
		dist: xenial
		env: CXX_COMPILER=g++-7
		addons:
		apt:
		sources:
		- ubuntu-toolchain-r-test
		packages:
		- g++-6
		- g++-7
		- pandoc
		- os: linux
		dist: trusty
		env: CXX_COMPILER=g++-7
		dist: xenial
		env: CXX_COMPILER=g++-8
		addons:
		apt:
		sources:
		- ubuntu-toolchain-r-test
		packages:
		- g++-7
		- g++-8
		- pandoc
		- os: linux
		dist: trusty
		dist: xenial
		compiler: clang++
		addons:
		apt:
		@@ -44,12 +44,12 @@ matrix:
		packages:
		- g++-7
		- pandoc
		- os: osx
		osx_image: xcode10.1
		- os: osx
		osx_image: xcode9.2
		- os: osx
		osx_image: xcode8.3
		- os: osx
		osx_image: xcode7.3

		before_install:
		# We need to re-export CC and CXX here, because travis exports CXX=g++ or clang++ AFTER we set CXX.

NEWS

+51 −4

Original line number	Diff line number	Diff line
		UNRELEASED
		* 3.4 (Dec 13, 2018)
		- Evolutionary models
		- Add Doublet alphabet for RNA stems.
		- Add generic +mut_sel model modifier.
		+ Add models x2, x2_sym, x2x2 for RNA stems.
		+ Add RNA.m16a model for RNA stems.
		- Fixes
		-
		- "--" should not become a single long dash (en-dash) in man pages.
		+ Don't crash if --scale is set to a constant (e.g. --scale=1).
		- Allow reading (a,b):1.0; by ignoring the root branch length.
		+ Properly translate newick labels with quotes or _.
		+ Don't replace W with A in observed sequences unless --set infer-ambiguous-observed=true
		- Misc
		- Correctly log things inside a let binding.
		+ Allow selecting character ranges from a file: "sequences.fasta:100-240,300-900"
		+ Rename subsample to bali-subsample (to avoid conflicts with other software).
		+ Install bali-phy-pkg.
		+ Make BES package work again.
		+ Reorganize fields on C1.log
		- Hold Numeric[k] or Doublets[DNA/RNA] alignments fixed.
		- Allow writing alignments every iteration.
		- tree-tool: add scaling, pruning, computing diameter, etc.
		- cut-range: allow selection samples from more than 1 alignment file
		- alignment-thin: clean up options and man page.
		- alignment-distances: new tool, add accuracy and recall metrics.
		- MCMC
		- Only compute probability ratios
		+ Allow recovery from initial -infinity.
		- Improved mixing for [0,1] random variables.
		- Graphical model framework
		- Interpreted models now separate the likelihood from the prior in logged output.
		- Interpreted models (e.g. LinearRegression.hs) are now a lot faster.
		- Simplify constructing loggers.
		- Allow using poisson distribution.
		- Haskell
		- Allow "import modid ( .... )" and "import modid hiding ( .... )"
		- Add Data.JSON module
		- Implement quot, rem, div, mod.
		- Implement -X NoImplicitPrelude
		- Refactored functions out of Prelude into Data.List, etc.
		- Implement layout-sensitive parsing.
		- Implement pattern bindings (i.e. let (x,y) = E1 in E2)
		- Implement @-patterns (i.e. x@(y,z) )
		- Implement lazy patterns (i.e. ~(y,z) )
		- Implement guards for functions and case.
		- Allow modules with no "module Name where" clause.
		- Implement running a module with --run-module
		- Encode strings as (listFromString String)
		- Add flags for dumping parsed, renamed, desugared, etc. code.
		- [FIX] float let out of let if it reveals a constant.

		* 3.3 (Aug 6, 2018)
		- Fixes
		@@ -15,7 +62,7 @@ UNRELEASED
		- add gy94_ext and mg94_ext for using any nucleotide rate matrix.
		- add mg94k for mg94_ext[hky85]
		- Triplet models
		- fix up x3, x3_xym, x3x3
		- fix up x3, x3_sym, x3x3
		- add +dNdS function so we can do e.g. hky85+x3+dNdS
		- Functions in models
		- Add new syntax function[x,...] for specifying models.
		@@ -144,7 +191,7 @@ UNRELEASED
		* Read json using nlohmann::json
		* Switch to new ptree structure.

		3.0-beta5 (Dec 6, 2018)
		3.0-beta5 (Dec 6, 2017)
		- Fixes
		- Don't crash on --smodel=GTR+x3
		- Short parameter names

README.md

+3 −5

Original line number	Diff line number	Diff line
		@@ -57,12 +57,10 @@ Build BAli-Phy
		--------------
		```
		git clone https://github.com/bredelings/BAli-Phy.git
		cd BAli-Phy/
		git submodule update --init # This is optional, it allows running the testiphy testsuite

		cd BAli-Phy
		meson build --prefix=$HOME/Applications/bali-phy
		ninja -C install
		ninja -C test
		ninja -C build install
		ninja -C build test
		```

		Adding bali-phy to your `$PATH`