Add meson+setuptools as alternative build system

X-Thanks: David Seifert <SoapZA@users.noreply.github.com>
X-Thanks: Ivan Blagoev Topolsky <ivan.topolsky@bsse.ethz.ch>

.gitignore

@@ -4,6 +4,7 @@
 # Autotools cruft (NEVER check this into VCS)
 Makefile
 Makefile.in
+.version
 aclocal.m4
 .deps/
 .dirstamp
@@ -17,37 +18,36 @@ configure
 depcomp
 install-sh
 missing
+py-compile
+ar-lib
+/shorah
 
 # generated tarball
 shorah*.tar.bz2
 
 # executables
 b2w
-contain
 diri_sampler
 fil
-freqEst
 
 # samtools lib
 libbam.a
 
-# python/perl scripts are generated by Autoconf from *.{py,pl}.in
-# files, replacing the shebang in the process
-fas2read.pl
-src/scripts/amplian.py
-src/scripts/dec.py
-src/scripts/mm.py
-src/scripts/shorah.py
-src/scripts/snv.py
-
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
 *$py.class
-py-compile
 
 # OS X temporary files that should never be committed
 .DS_Store
 *.swp
 *.lock
 profile
+
+# other intermediate stuff
+build
+.eggs
+src/ShoRAH.egg-info/
+
+# shorah output
+shorah.log

.travis.yml

@@ -1,13 +1,17 @@
-language: c cpp
+language: c cpp python
+
+python:
+  - "3.6"
 
 # GSL and Autotools needed
 before_install:
   - sudo add-apt-repository ppa:ondrej/autotools -y
   - sudo apt-get update -qq
   - sudo apt-get install -y gsl-bin libgsl0-dev autoconf automake-1.15 pkg-config m4
+  - source ~/virtualenv/python3.6/bin/activate
 
 compiler:
   - gcc
 
 before_script: autoreconf -vif
-script: ./configure && make -j1 && make distcheck
+script: ./configure && make -j1 distcheck

Makefile.am

@@ -1,48 +1,38 @@
 # install scripts in ${bindir}
 bin_SCRIPTS = \
-	src/scripts/amplian.py \
-	src/scripts/dec.py \
-	src/scripts/mm.py \
-	src/scripts/shorah.py \
-	src/scripts/snv.py \
-	fas2read.pl
+	shorah
 CLEANFILES = $(bin_SCRIPTS)
 EXTRA_DIST = \
-	src/scripts/amplian.py.in \
-	src/scripts/dec.py.in \
-	src/scripts/mm.py.in \
-	src/scripts/shorah.py.in \
-	src/scripts/snv.py.in \
-	src/scripts/fas2read.pl.in \
-	src/samtools/COPYING
+	.version \
+	meson.build \
+	setup.py \
+	src/meson.build \
+	src/cpp/meson.build \
+	src/samtools/COPYING \
+	src/samtools/meson.build
+BUILT_SOURCES = .version
 
-fas2read.pl: src/scripts/fas2read.pl.in Makefile
-	$(SED) 's,[@]perldir[@],$(perldir),g' $< > $@
+shorah: $(top_srcdir)/src/shorah/__main__.py Makefile
+	$(SED) 's,#!/usr/bin/env python3,#!/usr/bin/env $(PYTHON),g' $(top_srcdir)/src/shorah/__main__.py > $@
 
 # actual C/C++ programs doing the real computation
-bin_PROGRAMS = diri_sampler contain freqEst b2w fil
+bin_PROGRAMS = diri_sampler b2w fil
 
 diri_sampler_SOURCES = \
-	src/shorah/data_structures.hpp \
-	src/shorah/dpm_sampler.hpp \
-	src/shorah/dpm_sampler.cpp
+	src/cpp/data_structures.hpp \
+	src/cpp/dpm_sampler.hpp \
+	src/cpp/dpm_sampler.cpp
 diri_sampler_CPPFLAGS = $(GSL_CFLAGS)
 diri_sampler_LDADD = $(GSL_LIBS)
 
-contain_SOURCES = \
-	src/shorah/contain.cpp
-
-freqEst_SOURCES = \
-	src/shorah/freqEst.cpp
-
 b2w_SOURCES = \
-	src/shorah/b2w.cpp
+	src/cpp/b2w.cpp
 b2w_CXXFLAGS = $(PTHREAD_CFLAGS)
 b2w_CPPFLAGS = -I$(top_srcdir)/src/samtools
 b2w_LDADD = libbam.a $(ZLIB_LIBS) $(PTHREAD_LIBS)
 
 fil_SOURCES = \
-	src/shorah/fil.cpp
+	src/cpp/fil.cpp
 fil_CXXFLAGS = $(PTHREAD_CFLAGS)
 fil_CPPFLAGS = $(GSL_CFLAGS) -I$(top_srcdir)/src/samtools
 fil_LDADD = libbam.a $(ZLIB_LIBS) $(GSL_LIBS) $(PTHREAD_LIBS)
@@ -85,19 +75,14 @@ libbam_a_SOURCES = \
 libbam_a_CPPFLAGS = $(ZLIB_CFLAGS) -D_USE_KNETFILE
 libbam_a_CFLAGS = $(PTHREAD_CFLAGS)
 
-# perl modules
-dist_perl_DATA = \
-	src/perl/DNA.pm \
-	src/perl/NikoUtil.pm \
-	src/perl/ReadUtil.pm \
-	src/perl/Util.pm
-
 # python modules
-python_PYTHON = \
-	src/python/shorah_dec.py \
-	src/python/shorah_matching.py \
-	src/python/shorah_mm.py \
-	src/python/shorah_snv.py
+dist_pkgpython_PYTHON = \
+	src/shorah/__main__.py \
+	src/shorah/amplicon.py \
+	src/shorah/cli.py \
+	src/shorah/shorah_snv.py \
+	src/shorah/shotgun.py
+pkgpython_PYTHON = .version
 
 # example files
 dist_pkgdata_DATA = \
@@ -110,3 +95,9 @@ dist_ampliconpkgdata_DATA = \
 	examples/amplicon_test/ampli_sorted.bam \
 	examples/amplicon_test/amplicon_reads.fastq \
 	examples/amplicon_test/reference.fasta
+
+# version handling
+$(top_srcdir)/.version:
+	echo $(VERSION) > $@-t && mv $@-t $@
+dist-hook:
+	echo $(VERSION) > $(distdir)/.tarball-version

README.md

@@ -132,10 +132,10 @@ These can be run one after the other, or one can invoke `shorah.py`, that runs
 the whole process from bam file to frequency estimation and SNV calling.
 
 ## Coding style
-All changes to the C++ code in `src/shorah` should always be formatted according to the included `.clang-format` style by doing
+All changes to the C++ code in `src/cpp` should always be formatted according to the included `.clang-format` style by doing
 
-	clang-format -style=file -i src/shorah/*.[ch]pp
+	clang-format -style=file -i src/cpp/*.[ch]pp
 
 in the root of the repository.
 
-All changes to the python code in `src/python` and `src/scripts` should always be formatted conforming to the [PEP 8](https://www.python.org/dev/peps/pep-0008/) style guide. To this end, we advise to use [autopep8](https://pypi.python.org/pypi/autopep8). 
+All changes to the python code in `src/shorah` should always be formatted conforming to the [PEP 8](https://www.python.org/dev/peps/pep-0008/) style guide. To this end, we advise to use [autopep8](https://pypi.python.org/pypi/autopep8).