Merge branch 'improve-setup'

MANIFEST.in

@@ -0,0 +1 @@
+recursive-include src *.cpp *.h *.inl

Makefile

@@ -53,35 +53,7 @@ SCRIPTS = bin/*
 PROGS = bin/arg-sample bin/arg-summarize bin/smc2bed
 BINARIES = $(PROGS) $(SCRIPTS)
 
-ARGWEAVER_SRC = \
-    src/compress.cpp \
-    src/emit.cpp \
-    src/est_popsize.cpp \
-    src/fs.cpp \
-    src/hmm.cpp \
-    src/IntervalIterator.cpp \
-    src/itree.cpp \
-    src/local_tree.cpp \
-    src/logging.cpp \
-    src/matrices.cpp \
-    src/mem.cpp \
-    src/model.cpp \
-    src/newick.cpp \
-    src/parsing.cpp \
-    src/ptree.cpp \
-    src/recomb.cpp \
-    src/sample_arg.cpp \
-    src/sample_thread.cpp \
-    src/seq.cpp \
-    src/states.cpp \
-    src/sequences.cpp \
-    src/tabix.cpp \
-    src/thread.cpp \
-    src/total_prob.cpp \
-    src/track.cpp \
-    src/trans.cpp \
-    src/Tree.cpp \
-    src/t2exp.cpp
+ARGWEAVER_SRC = $(shell ls src/argweaver/*.cpp)
 
 #    src/prior.cpp
 #    src/expm/matrix_exponential.cpp
@@ -195,7 +167,7 @@ gtest:
 #-----------------------------
 # install
 
-install: $(BINARIES) $(LIBARGWEAVER_SHARED_INSTALL)
+install: $(BINARIES)
 	mkdir -p $(prefix)/bin
 	cp $(BINARIES) $(prefix)/bin
 	$(PYTHON) setup.py install --prefix=$(prefix)
@@ -215,7 +187,7 @@ $(ALL_OBJS): %.o: %.cpp
 	$(CXX) -c $(CFLAGS) -o $@ $<
 
 clean:
-	rm -f $(ALL_OBJS) $(LIBARGWEAVER) $(LIBARGWEAVER_SHARED) $(TEST_OBJS)
+	rm -f $(ALL_OBJS) $(LIBARGWEAVER) $(LIBARGWEAVER_SHARED) $(TEST_OBJS) $(PROGS)
 
 clean-test:
 	rm -f $(TEST_OBJS)

README.md

@@ -36,7 +36,21 @@ ARGweaver:
 
 ## Install
 
-To compile the ARGweaver commands and library use the Makefile:
+ARGweaver can be installed using any of the normal Python mechanisms.
+For example, to install from [PyPI](https://pypi.python.org/pypi) you
+can use [pip](https://github.com/pypa/pip) with the following command:
+
+```
+pip install argweaver
+```
+
+Alternatively, ARGweaver can be install using the `setup.py` file:
+
+```
+python setup.py install
+```
+
+Lastly, ARGweaver can be installed using the `Makefile`:
 
 ```
 make

argweaver/__init__.py

@@ -76,7 +76,7 @@
 PROGRAM_NAME = u"argweaver"
 PROGRAM_VERSION_MAJOR = 0
 PROGRAM_VERSION_MINOR = 8
-PROGRAM_VERSION_RELEASE = 0
+PROGRAM_VERSION_RELEASE = 1
 PROGRAM_VERSION = (PROGRAM_VERSION_MAJOR,
                    PROGRAM_VERSION_MINOR,
                    PROGRAM_VERSION_RELEASE)

argweaver/ctypes_export.py

@@ -144,15 +144,31 @@ def wrapper(*args):
 
 
 def load_library(path, lib):
+    errors = []
+
     try:
         # use library from source path
         libdir = os.path.join(os.path.dirname(__file__), *path)
         return cdll.LoadLibrary(os.path.join(libdir, lib))
-    except Exception, e:
-        # search for lib in library path
-        try:
-            return cdll.LoadLibrary(lib)
-        except Exception, e2:
-            print >>sys.stderr, e
-            print >>sys.stderr, e2
-            return None
+    except Exception as error:
+        errors.append(error)
+
+    # Search for lib in library path.
+    try:
+        return cdll.LoadLibrary(lib)
+    except Exception as error:
+        errors.append(error)
+
+    # Search PYTHONPATH for shared library.
+    for path in sys.path:
+        filename = os.path.join(path, lib)
+        if os.path.exists(filename):
+            try:
+                return cdll.LoadLibrary(filename)
+            except Exception as error:
+                errors.append(error)
+
+    # Display import errors.
+    for error in errors:
+        print >>sys.stderr, error
+    return None

requirements-dev.txt

@@ -1,4 +1,4 @@
-nose
-pyflakes
-pep8
+nose=1.3.7
+pyflakes=0.9.2
+pep8=1.5.6
 

setup.py

@@ -6,13 +6,131 @@
 #   python setup.py install
 #
 
-from distutils.core import setup, Extension
+from distutils import log
+from distutils.core import Command
+from distutils.core import Extension
+from distutils.core import setup
+from distutils.command.build import build as _build
+from distutils.command.build_clib import build_clib as _build_clib
+from distutils.dep_util import newer_group
+from distutils.sysconfig import customize_compiler
 import os
 
 import argweaver
+
+
 VERSION = argweaver.PROGRAM_VERSION_TEXT
 
-scripts = [os.path.join('bin', x) for x in os.listdir('bin')]
+
+def get_files(path, ext=''):
+    """
+    Get all files in a directory with a extension.
+    """
+    files = []
+    for filename in os.listdir(path):
+        if filename.endswith(ext):
+            files.append(os.path.join(path, filename))
+    return files
+
+
+scripts = get_files('bin')
+lib_src = get_files('src/argweaver', '.cpp')
+
+
+# Default to a C++ compiler, if possible.
+if os.system('which g++') == 0:
+    os.environ.setdefault('CC', 'g++')
+    os.environ.setdefault('CXX', 'g++')
+
+
+class build(_build):
+    """
+    Add more subcommands to the build command.
+    """
+    sub_commands = _build.sub_commands + [('build_prog', lambda cmd: True)]
+
+
+class build_prog(_build_clib):
+    """
+    Build subcommand for compiling programs.
+
+    This is implemented as subclass of build_clib since compiling a
+    C/C++ program is very similar to compiling C/C++ library.
+    """
+
+    description = 'build compiled programs'
+
+    # Config. Ideally, we could add this to setup().
+    progs = [
+        (
+            'arg-sample',
+            {
+                'sources': lib_src + ['src/arg-sample.cpp'],
+            }
+        ),
+        (
+            'arg-summarize',
+            {
+                'sources': lib_src + ['src/arg-summarize.cpp'],
+            }
+        ),
+        (
+            'smc2bed',
+            {
+                'sources': lib_src + ['src/smc2bed.cpp'],
+            }
+        ),
+    ]
+
+    def initialize_options(self):
+        # Call super class.
+        _build_clib.initialize_options(self)
+
+        # Directory for built binaries.
+        self.build_bin = None
+
+    def finalize_options(self):
+        # Call super class.
+        _build_clib.finalize_options(self)
+
+        self.set_undefined_options('build', ('build_scripts', 'build_bin'))
+
+        self.libraries = self.progs
+        if self.libraries:
+            self.check_library_list(self.libraries)
+
+    def build_libraries(self, libraries):
+        if not os.path.exists(self.build_bin):
+            os.makedirs(self.build_bin)
+
+        for (prog_name, build_info) in libraries:
+            sources = build_info.get('sources')
+            if sources is None or not isinstance(sources, (list, tuple)):
+                raise DistutilsSetupError, \
+                      ("in 'libraries' option ('%s'), " +
+                       "'sources' must be present and must be " +
+                       "a list of source filenames") % prog_name
+            sources = list(sources)
+
+            # Skip build, if program already built.
+            prog_path = os.path.join(self.build_bin, prog_name)
+            if not (self.force or newer_group(sources, prog_path, 'newer')):
+                log.debug("skipping '%s' program (up-to-date)", prog_name)
+                return
+
+            log.info("building '%s' program", prog_name)
+
+            macros = build_info.get('macros')
+            include_dirs = build_info.get('include_dirs')
+            objects = self.compiler.compile(sources,
+                                            output_dir=self.build_temp,
+                                            macros=macros,
+                                            include_dirs=include_dirs,
+                                            debug=self.debug)
+            self.compiler.link_executable(objects, prog_name,
+                                          output_dir=self.build_bin,
+                                          debug=self.debug)
+
 
 setup(
     name='argweaver',
@@ -22,7 +140,20 @@
             """,
     author='Matt Rasmussen',
     author_email='[email protected]',
-
-    packages=['argweaver', 'argweaver.deps.rasmus', 'argweaver.deps.compbio'],
+    cmdclass={
+        'build': build,
+        'build_prog': build_prog,
+    },
+    packages=[
+        'argweaver',
+        'argweaver.deps.rasmus',
+        'argweaver.deps.compbio',
+    ],
     scripts=scripts,
+    ext_modules=[
+        Extension(
+            'libargweaver',
+            lib_src,
+        )
+    ],
 )

src/arg-sample.cpp

@@ -7,24 +7,24 @@
 #include <unistd.h>
 
 // arghmm includes
-#include "compress.h"
-#include "ConfigParam.h"
-#include "emit.h"
-#include "fs.h"
-#include "logging.h"
-#include "mem.h"
-#include "parsing.h"
-#include "sample_arg.h"
-#include "sequences.h"
-#include "total_prob.h"
-#include "track.h"
+#include "argweaver/compress.h"
+#include "argweaver/ConfigParam.h"
+#include "argweaver/emit.h"
+#include "argweaver/fs.h"
+#include "argweaver/logging.h"
+#include "argweaver/mem.h"
+#include "argweaver/parsing.h"
+#include "argweaver/sample_arg.h"
+#include "argweaver/sequences.h"
+#include "argweaver/total_prob.h"
+#include "argweaver/track.h"
 
 
 using namespace argweaver;
 
 
 // version info
-#define VERSION_TEXT "0.8"
+#define VERSION_TEXT "0.8.1"
 #define VERSION_INFO  "\
 ARGweaver " VERSION_TEXT " \n\
 Matt Rasmussen\n\

src/arg-summarize.cpp

@@ -11,21 +11,21 @@
 #include <vector>
 #include <math.h>
 #include <queue>
-#include <map>
-
-// arghmm includes
-#include "ConfigParam.h"
-#include "logging.h"
-#include "parsing.h"
-#include "track.h"
-#include "Tree.h"
-#include "tabix.h"
-#include "compress.h"
-#include "IntervalIterator.h"
 #include <set>
+#include <map>
 
+// argweaver includes
+#include "argweaver/ConfigParam.h"
+#include "argweaver/logging.h"
+#include "argweaver/parsing.h"
+#include "argweaver/track.h"
+#include "argweaver/Tree.h"
+#include "argweaver/tabix.h"
+#include "argweaver/compress.h"
+#include "argweaver/IntervalIterator.h"
 //#include "allele_age.h"
 
+
 using namespace argweaver;
 using namespace spidir;
 

src/prior.cpp → src/argweaver/prior.cpp

@@ -8,6 +8,9 @@
 
 namespace argweaver {
 
+/*
+// Currently, disabled.
+
 
 static inline double H(int i, int j, double n)
 {
@@ -53,5 +56,7 @@ double prob_coal_counts_matrix(int a, int b, double t, double n)
 
 } // extern "C"
 
+*/
+
 } // namespace argweaver
 

src/smc2bed.cpp

@@ -1,11 +1,13 @@
+#include "getopt.h"
 #include <iostream>
 #include <fstream>
 #include <assert.h>
 
-#include "Tree.h"
-#include "compress.h"
-#include "getopt.h"
-#include "parsing.h"
+// argweaver includes
+#include "argweaver/Tree.h"
+#include "argweaver/compress.h"
+#include "argweaver/parsing.h"
+
 
 using namespace spidir;
 using namespace argweaver;