Loading .gitmodules +0 −4 Original line number Diff line number Diff line [submodule "testiphy"] path = testiphy url = https://gitlab.com/testiphy/testiphy.git ignore = untracked .travis.yml +12 −2 Original line number Diff line number Diff line Loading @@ -53,15 +53,25 @@ matrix: before_install: # We need to re-export CC and CXX here, because travis exports CXX=g++ or clang++ AFTER we set CXX. - PATH=$HOME/local/bin:$PATH - echo $PATH - if [ -n "${C_COMPILER}" ]; then export CC="${C_COMPILER}"; fi - if [ -n "${CXX_COMPILER}" ]; then export CXX="${CXX_COMPILER}"; fi - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew update && brew install meson; fi - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then wget https://github.com/ninja-build/ninja/releases/download/v1.8.2/ninja-linux.zip && unzip -q ninja-linux.zip -d ~/bin && pyenv local 3.6 && pip3 install meson; fi script: - meson build --prefix=$HOME/bali-phy - ninja -C build test - meson build --prefix=$HOME/local - ninja -C build install # Run internal test suite - cd tests - ./run-tests.py bali-phy # Run testiphy test suite - cd - git clone https://gitlab.com/testiphy/testiphy.git - cd $HOME/testiphy - which bali-phy || true - ./testiphy bali-phy env: global: Loading NEWS +140 −8 Original line number Diff line number Diff line * 3.2.0 UNRELEASED - Fixes - * 3.3 (Aug 6, 2018) - Fixes - make bp-analyze able to parse output files from 3.0-beta. - rename Goldman & Yang codon model to gy94 from incorrect yn94. - fix run file for f81 model. - fix incorrect LG model. - normalize WAG and LG standard frequencies. - Codon models - gy94 and mg94 now have no submodels and are rate matrices. - f1x4, f3x4, and f61 now compute named codon frequencies. - 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 - add +dNdS function so we can do e.g. hky85+x3+dNdS - Functions in models - Add new syntax function[x,...] for specifying models. - new functions map, zip, zipWith. - m1a,m2a,..,m8a_test,branch-site, etc. now take functions as arguments. - let-bind names for lambda-dependent arguments, but inside the lambda. - Model framework - +fe as synonym for +f[Frequencies.uniform] - +f and +gwF now take exchange models like wag as a submodel. - logging now returns an object that can change shape dynamically. - function calls can now look like f[g[x],y] instead of just f[x,y] - arguments now referenced with @arg to fix function[x,add[x,x]] - fixes to unification and constraints. - suppress gamma:shift and exponential:shift - Haskell - modules can now re-export imported modules. - refactor module SModel into SModel.Codons, SModel.ReversibleMarkov, etc. - remove hky85', etc now that models can call hky85 directly. - add lazy IO - make sampling in the Random monad lazy - correctly set rates in sample' - do normal 0 1 => do sample $ normal 0 1 - Docs - Reorganize docs on substitution models. - Move docs on partitions to new section. - Etc - Allow specifying alphabet for --print. - Allow running gy94 from --print. - Testing - Find out why different package disagree on wag+f[wag_freq] * 3.2 (Jun 25, 2018) - Fixes - Increase test timeout for internal testsuite and testiphy. - HTML report: don't hide header behind top-bar in Chrome. - alignment-smc improvements. * 3.1.5 - change alignment-diff back to red - Add NEWS file. * 3.1.5 (Jun 13, 2018) - Fixes - Make all programs use shipped libstdc++ - Make MDS plots handle bp-analyze --subsample - Increase test timeouts - Correctly write initial alignment for fixed alignment partitions. - Don't write "file:" for MDS URLs in HTML report - Help - Print citations with pmid and pmcid in help. - Add Frequencies.uniform[] function. - Print help for 0-argument functions like 'dna' - Improve help for fMutSel and fMutSel0 - Add Frequencies.uniform[] function. - Make SEV handle site-compression. - HTML report: print version number + lots of cosmetic improvements. - Add new tool tree-tool (and map page, etc.) - Change alignments-diff highlight color back to red. - Clean up DP matrix code. * 3.1.4 * 3.1.4 (Jun 9, 2018) - Fix prior on alpha in Rates.gamma * 3.1.3 * 3.1.3 (Jun 9, 2018) - Fix mean_length prior in RS05 model. - Add some more color-schemes for drawing alignments-diff output. - Add ferns exon/intro data set. * 3.1.2 * 3.1.2 (May 6, 2018) - Fix a testsuite bug * 3.1.1 - Haskell - parse exports list * 3.1.1 (May 5, 2018 - Fixes - Don't require testiphy - Print priors on models in their own section. * 3.1 (May 2, 2018) - Fixes - Build alignment-thin and alignments-diff - Show model and priors readably - bali-phy accepted into Debian - Change 'logp' => 'posterior' * 3.0.2 (Mar 10, 2018) - Docs - man pages for bali-phy and tools - man pages online * 3.0.1 (Mar 6, 2018) - Fixes - Fix crash in alignment-thin * 3.0 (Feb 12, 2018) - Models - Mixture models now work. - MultiRate[model,dist,n_bins] also works - let[var=E1,E2] now works - Rename RA[a] to RevCTMC[a] - Stop representing integer, double, and bool as strings. - Report - subsample trees when running trees-distances for MDS plot - Docs - Add help for more functions. - MCMC - Implement SPR+A - Destroy SPR_by_NNI with fire. * 3.0-beta6 (Jan 5, 2018) - Fixes - Make sorting of DP:rates and M3:omegas work again. - sample branch lengths from prior -- fixes very long initial tree. - specify branch lengths as a List[Double] - Models - Make lists into a collection of Cons[ ] functions.h + Speedup on 25-muscle because we aren't proposing the branch lengths badly - Eliminate compiler warnings. * Print expressions - Allow non-modifiable branch lengths if we aren't doing MCMC. - Improve pre-burnin - read parameter values as json - write out run parameters as json. - Improve help, add help for more functions. * stop finding branch lengths by parameter name * stop finding scales by parameter name * print parameter values that are data structures * meson build infrastructure * Read json using nlohmann::json * Switch to new ptree structure. 3.0-beta5 (Dec 6, 2018) - Fixes - Don't crash on --smodel=GTR+x3 - Short parameter names - Add --link option. - Complain if linking non-existant attributes. - Logging * Logging of [(String,a)] * Rationalize logging of frequencies and exchangabilities * DirichletOn prior for frequencies and exchangabilities. * Loading functions from files. - Allow expressing the branch length prior in terms of the tree. - Automatically convert integers to double when needed, and hide the conversions. - Help - Make simple|advanced|expert|(developer) options. - Help for all commands. No newline at end of file README.md +22 −12 Original line number Diff line number Diff line Loading @@ -7,7 +7,7 @@ Install Please visit the [releases page](http://www.bali-phy.org/download.php) to download official binaries. You can also install via homebrew on a Mac. You can also install via homebrew on a Mac, and using `apt-get` on recent version of Debian or Ubuntu. Documentation ------------ Loading @@ -30,25 +30,35 @@ You will need a C++ compiler that understands C++14. You will also need to install * cairo graphics library (optional, but required to build the `draw-tree` program) If you build with meson and ninja, you need You will also need * python3 * ninja * meson >= 0.45 You need meson version >= 0.45 to build bali-phy. Build with meson ---------------- Install Prerequisites --------------------- ```bash sudo apt-get install g++ libcairo2-dev ninja-build python3 ``` You also need to install meson. First try: ```bash sudo apt-get install meson ``` git clone https://github.com/bredelings/BAli-Phy.git cd BAli-Phy/ git submodule update --init # We need a recent version of meson If the version of meson is not at least 0.45, then you need to install meson through pip: ```bash python3 -m venv meson source meson/bin/activate pip3 install meson ``` 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 meson build --prefix=$HOME/Applications/bali-phy ninja -C install Loading @@ -58,7 +68,7 @@ ninja -C test Adding bali-phy to your `$PATH` ------------------------------ In order to run the installed software, you should [add bali-phy to your $PATH](http://bali-phy.org/README.xhtml#installation). In order to run the installed software, you should [add bali-phy to your $PATH](http://bali-phy.org/README.xhtml#path). Installed locations ------------------ Loading doc/GNUmakefile +4 −1 Original line number Diff line number Diff line all: README.html README.xhtml README.pdf Tutorial.html Tutorial.xhtml Tutorial.pdf Tutorial2.html Tutorial2.xhtml Tutorial2.pdf Tutorial3.html Tutorial3.xhtml Tutorial3.pdf Tutorial4.html Tutorial4.xhtml Tutorial4.pdf all: README.html README.xhtml README.pdf Tutorial.html Tutorial.xhtml Tutorial.pdf Tutorial2.html Tutorial2.xhtml Tutorial2.pdf Tutorial3.html Tutorial3.xhtml Tutorial3.pdf Tutorial4.html Tutorial4.xhtml Tutorial4.pdf developer.html clean: -@rm -f *.html *.xhtml REAMDE.xml *.fo *.pdf *~ Loading @@ -13,6 +13,9 @@ clean: %.html: %.xml docbook-html.xsl xsltproc --nonet --xinclude docbook-html.xsl $*.xml > $@ %.html: %.md pandoc -s $*.md --css doc.css --toc -N > $@ %.xhtml: %.xml docbook-xhtml.xsl xsltproc --nonet --xinclude docbook-xhtml.xsl $*.xml > $@ Loading Loading
.gitmodules +0 −4 Original line number Diff line number Diff line [submodule "testiphy"] path = testiphy url = https://gitlab.com/testiphy/testiphy.git ignore = untracked
.travis.yml +12 −2 Original line number Diff line number Diff line Loading @@ -53,15 +53,25 @@ matrix: before_install: # We need to re-export CC and CXX here, because travis exports CXX=g++ or clang++ AFTER we set CXX. - PATH=$HOME/local/bin:$PATH - echo $PATH - if [ -n "${C_COMPILER}" ]; then export CC="${C_COMPILER}"; fi - if [ -n "${CXX_COMPILER}" ]; then export CXX="${CXX_COMPILER}"; fi - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew update && brew install meson; fi - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then wget https://github.com/ninja-build/ninja/releases/download/v1.8.2/ninja-linux.zip && unzip -q ninja-linux.zip -d ~/bin && pyenv local 3.6 && pip3 install meson; fi script: - meson build --prefix=$HOME/bali-phy - ninja -C build test - meson build --prefix=$HOME/local - ninja -C build install # Run internal test suite - cd tests - ./run-tests.py bali-phy # Run testiphy test suite - cd - git clone https://gitlab.com/testiphy/testiphy.git - cd $HOME/testiphy - which bali-phy || true - ./testiphy bali-phy env: global: Loading
NEWS +140 −8 Original line number Diff line number Diff line * 3.2.0 UNRELEASED - Fixes - * 3.3 (Aug 6, 2018) - Fixes - make bp-analyze able to parse output files from 3.0-beta. - rename Goldman & Yang codon model to gy94 from incorrect yn94. - fix run file for f81 model. - fix incorrect LG model. - normalize WAG and LG standard frequencies. - Codon models - gy94 and mg94 now have no submodels and are rate matrices. - f1x4, f3x4, and f61 now compute named codon frequencies. - 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 - add +dNdS function so we can do e.g. hky85+x3+dNdS - Functions in models - Add new syntax function[x,...] for specifying models. - new functions map, zip, zipWith. - m1a,m2a,..,m8a_test,branch-site, etc. now take functions as arguments. - let-bind names for lambda-dependent arguments, but inside the lambda. - Model framework - +fe as synonym for +f[Frequencies.uniform] - +f and +gwF now take exchange models like wag as a submodel. - logging now returns an object that can change shape dynamically. - function calls can now look like f[g[x],y] instead of just f[x,y] - arguments now referenced with @arg to fix function[x,add[x,x]] - fixes to unification and constraints. - suppress gamma:shift and exponential:shift - Haskell - modules can now re-export imported modules. - refactor module SModel into SModel.Codons, SModel.ReversibleMarkov, etc. - remove hky85', etc now that models can call hky85 directly. - add lazy IO - make sampling in the Random monad lazy - correctly set rates in sample' - do normal 0 1 => do sample $ normal 0 1 - Docs - Reorganize docs on substitution models. - Move docs on partitions to new section. - Etc - Allow specifying alphabet for --print. - Allow running gy94 from --print. - Testing - Find out why different package disagree on wag+f[wag_freq] * 3.2 (Jun 25, 2018) - Fixes - Increase test timeout for internal testsuite and testiphy. - HTML report: don't hide header behind top-bar in Chrome. - alignment-smc improvements. * 3.1.5 - change alignment-diff back to red - Add NEWS file. * 3.1.5 (Jun 13, 2018) - Fixes - Make all programs use shipped libstdc++ - Make MDS plots handle bp-analyze --subsample - Increase test timeouts - Correctly write initial alignment for fixed alignment partitions. - Don't write "file:" for MDS URLs in HTML report - Help - Print citations with pmid and pmcid in help. - Add Frequencies.uniform[] function. - Print help for 0-argument functions like 'dna' - Improve help for fMutSel and fMutSel0 - Add Frequencies.uniform[] function. - Make SEV handle site-compression. - HTML report: print version number + lots of cosmetic improvements. - Add new tool tree-tool (and map page, etc.) - Change alignments-diff highlight color back to red. - Clean up DP matrix code. * 3.1.4 * 3.1.4 (Jun 9, 2018) - Fix prior on alpha in Rates.gamma * 3.1.3 * 3.1.3 (Jun 9, 2018) - Fix mean_length prior in RS05 model. - Add some more color-schemes for drawing alignments-diff output. - Add ferns exon/intro data set. * 3.1.2 * 3.1.2 (May 6, 2018) - Fix a testsuite bug * 3.1.1 - Haskell - parse exports list * 3.1.1 (May 5, 2018 - Fixes - Don't require testiphy - Print priors on models in their own section. * 3.1 (May 2, 2018) - Fixes - Build alignment-thin and alignments-diff - Show model and priors readably - bali-phy accepted into Debian - Change 'logp' => 'posterior' * 3.0.2 (Mar 10, 2018) - Docs - man pages for bali-phy and tools - man pages online * 3.0.1 (Mar 6, 2018) - Fixes - Fix crash in alignment-thin * 3.0 (Feb 12, 2018) - Models - Mixture models now work. - MultiRate[model,dist,n_bins] also works - let[var=E1,E2] now works - Rename RA[a] to RevCTMC[a] - Stop representing integer, double, and bool as strings. - Report - subsample trees when running trees-distances for MDS plot - Docs - Add help for more functions. - MCMC - Implement SPR+A - Destroy SPR_by_NNI with fire. * 3.0-beta6 (Jan 5, 2018) - Fixes - Make sorting of DP:rates and M3:omegas work again. - sample branch lengths from prior -- fixes very long initial tree. - specify branch lengths as a List[Double] - Models - Make lists into a collection of Cons[ ] functions.h + Speedup on 25-muscle because we aren't proposing the branch lengths badly - Eliminate compiler warnings. * Print expressions - Allow non-modifiable branch lengths if we aren't doing MCMC. - Improve pre-burnin - read parameter values as json - write out run parameters as json. - Improve help, add help for more functions. * stop finding branch lengths by parameter name * stop finding scales by parameter name * print parameter values that are data structures * meson build infrastructure * Read json using nlohmann::json * Switch to new ptree structure. 3.0-beta5 (Dec 6, 2018) - Fixes - Don't crash on --smodel=GTR+x3 - Short parameter names - Add --link option. - Complain if linking non-existant attributes. - Logging * Logging of [(String,a)] * Rationalize logging of frequencies and exchangabilities * DirichletOn prior for frequencies and exchangabilities. * Loading functions from files. - Allow expressing the branch length prior in terms of the tree. - Automatically convert integers to double when needed, and hide the conversions. - Help - Make simple|advanced|expert|(developer) options. - Help for all commands. No newline at end of file
README.md +22 −12 Original line number Diff line number Diff line Loading @@ -7,7 +7,7 @@ Install Please visit the [releases page](http://www.bali-phy.org/download.php) to download official binaries. You can also install via homebrew on a Mac. You can also install via homebrew on a Mac, and using `apt-get` on recent version of Debian or Ubuntu. Documentation ------------ Loading @@ -30,25 +30,35 @@ You will need a C++ compiler that understands C++14. You will also need to install * cairo graphics library (optional, but required to build the `draw-tree` program) If you build with meson and ninja, you need You will also need * python3 * ninja * meson >= 0.45 You need meson version >= 0.45 to build bali-phy. Build with meson ---------------- Install Prerequisites --------------------- ```bash sudo apt-get install g++ libcairo2-dev ninja-build python3 ``` You also need to install meson. First try: ```bash sudo apt-get install meson ``` git clone https://github.com/bredelings/BAli-Phy.git cd BAli-Phy/ git submodule update --init # We need a recent version of meson If the version of meson is not at least 0.45, then you need to install meson through pip: ```bash python3 -m venv meson source meson/bin/activate pip3 install meson ``` 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 meson build --prefix=$HOME/Applications/bali-phy ninja -C install Loading @@ -58,7 +68,7 @@ ninja -C test Adding bali-phy to your `$PATH` ------------------------------ In order to run the installed software, you should [add bali-phy to your $PATH](http://bali-phy.org/README.xhtml#installation). In order to run the installed software, you should [add bali-phy to your $PATH](http://bali-phy.org/README.xhtml#path). Installed locations ------------------ Loading
doc/GNUmakefile +4 −1 Original line number Diff line number Diff line all: README.html README.xhtml README.pdf Tutorial.html Tutorial.xhtml Tutorial.pdf Tutorial2.html Tutorial2.xhtml Tutorial2.pdf Tutorial3.html Tutorial3.xhtml Tutorial3.pdf Tutorial4.html Tutorial4.xhtml Tutorial4.pdf all: README.html README.xhtml README.pdf Tutorial.html Tutorial.xhtml Tutorial.pdf Tutorial2.html Tutorial2.xhtml Tutorial2.pdf Tutorial3.html Tutorial3.xhtml Tutorial3.pdf Tutorial4.html Tutorial4.xhtml Tutorial4.pdf developer.html clean: -@rm -f *.html *.xhtml REAMDE.xml *.fo *.pdf *~ Loading @@ -13,6 +13,9 @@ clean: %.html: %.xml docbook-html.xsl xsltproc --nonet --xinclude docbook-html.xsl $*.xml > $@ %.html: %.md pandoc -s $*.md --css doc.css --toc -N > $@ %.xhtml: %.xml docbook-xhtml.xsl xsltproc --nonet --xinclude docbook-xhtml.xsl $*.xml > $@ Loading
