improved setup.py for installing python extension

mdrasmus · Jul 6, 2015 · 2bc6004 · 2bc6004
1 parent c119b40
commit 2bc6004
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Showing 74 changed files with 113 additions and 73 deletions.
diff --git a/Makefile b/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)

diff --git a/argweaver/ctypes_export.py b/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
diff --git a/requirements-dev.txt b/requirements-dev.txt
@@ -1,4 +1,4 @@
-nose
-pyflakes
-pep8
+nose=1.3.7
+pyflakes=0.9.2
+pep8=1.5.6
 
diff --git a/setup.py b/setup.py
@@ -12,7 +12,21 @@
 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')
+
 
 setup(
     name='argweaver',
@@ -25,4 +39,11 @@
 
     packages=['argweaver', 'argweaver.deps.rasmus', 'argweaver.deps.compbio'],
     scripts=scripts,
+
+    ext_modules=[
+        Extension(
+            'libargweaver',
+            lib_src,
+        )
+    ],
 )
diff --git a/src/arg-sample.cpp b/src/arg-sample.cpp
@@ -7,17 +7,17 @@
 #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;

diff --git a/src/arg-summarize.cpp b/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;
 

diff --git a/src/ConfigParam.h → src/argweaver/ConfigParam.h b/src/ConfigParam.h → src/argweaver/ConfigParam.h
diff --git a/src/ExtendArray.h → src/argweaver/ExtendArray.h b/src/ExtendArray.h → src/argweaver/ExtendArray.h
diff --git a/src/IntervalIterator.cpp → src/argweaver/IntervalIterator.cpp b/src/IntervalIterator.cpp → src/argweaver/IntervalIterator.cpp
diff --git a/src/IntervalIterator.h → src/argweaver/IntervalIterator.h b/src/IntervalIterator.h → src/argweaver/IntervalIterator.h
diff --git a/src/Tree.cpp → src/argweaver/Tree.cpp b/src/Tree.cpp → src/argweaver/Tree.cpp
diff --git a/src/Tree.h → src/argweaver/Tree.h b/src/Tree.h → src/argweaver/Tree.h
diff --git a/src/common.h → src/argweaver/common.h b/src/common.h → src/argweaver/common.h
diff --git a/src/compress.cpp → src/argweaver/compress.cpp b/src/compress.cpp → src/argweaver/compress.cpp
diff --git a/src/compress.h → src/argweaver/compress.h b/src/compress.h → src/argweaver/compress.h
diff --git a/src/emit.cpp → src/argweaver/emit.cpp b/src/emit.cpp → src/argweaver/emit.cpp
diff --git a/src/emit.h → src/argweaver/emit.h b/src/emit.h → src/argweaver/emit.h
diff --git a/src/est_popsize.cpp → src/argweaver/est_popsize.cpp b/src/est_popsize.cpp → src/argweaver/est_popsize.cpp
diff --git a/src/est_popsize.h → src/argweaver/est_popsize.h b/src/est_popsize.h → src/argweaver/est_popsize.h
diff --git a/src/expm/matrix_exponential.cpp → src/argweaver/expm/matrix_exponential.cpp b/src/expm/matrix_exponential.cpp → src/argweaver/expm/matrix_exponential.cpp
diff --git a/src/expm/matrix_exponential.h → src/argweaver/expm/matrix_exponential.h b/src/expm/matrix_exponential.h → src/argweaver/expm/matrix_exponential.h
diff --git a/src/expm/r8lib.cpp → src/argweaver/expm/r8lib.cpp b/src/expm/r8lib.cpp → src/argweaver/expm/r8lib.cpp
diff --git a/src/expm/r8lib.h → src/argweaver/expm/r8lib.h b/src/expm/r8lib.h → src/argweaver/expm/r8lib.h
diff --git a/src/fs.cpp → src/argweaver/fs.cpp b/src/fs.cpp → src/argweaver/fs.cpp
diff --git a/src/fs.h → src/argweaver/fs.h b/src/fs.h → src/argweaver/fs.h
diff --git a/src/hmm.cpp → src/argweaver/hmm.cpp b/src/hmm.cpp → src/argweaver/hmm.cpp
diff --git a/src/hmm.h → src/argweaver/hmm.h b/src/hmm.h → src/argweaver/hmm.h
diff --git a/src/itree.cpp → src/argweaver/itree.cpp b/src/itree.cpp → src/argweaver/itree.cpp
diff --git a/src/itree.h → src/argweaver/itree.h b/src/itree.h → src/argweaver/itree.h
diff --git a/src/local_tree.cpp → src/argweaver/local_tree.cpp b/src/local_tree.cpp → src/argweaver/local_tree.cpp
diff --git a/src/local_tree.h → src/argweaver/local_tree.h b/src/local_tree.h → src/argweaver/local_tree.h
diff --git a/src/logging.cpp → src/argweaver/logging.cpp b/src/logging.cpp → src/argweaver/logging.cpp
diff --git a/src/logging.h → src/argweaver/logging.h b/src/logging.h → src/argweaver/logging.h
diff --git a/src/matrices.cpp → src/argweaver/matrices.cpp b/src/matrices.cpp → src/argweaver/matrices.cpp
diff --git a/src/matrices.h → src/argweaver/matrices.h b/src/matrices.h → src/argweaver/matrices.h
diff --git a/src/mem.cpp → src/argweaver/mem.cpp b/src/mem.cpp → src/argweaver/mem.cpp
diff --git a/src/mem.h → src/argweaver/mem.h b/src/mem.h → src/argweaver/mem.h
diff --git a/src/model.cpp → src/argweaver/model.cpp b/src/model.cpp → src/argweaver/model.cpp
diff --git a/src/model.h → src/argweaver/model.h b/src/model.h → src/argweaver/model.h
diff --git a/src/newick.cpp → src/argweaver/newick.cpp b/src/newick.cpp → src/argweaver/newick.cpp
diff --git a/src/newick.h → src/argweaver/newick.h b/src/newick.h → src/argweaver/newick.h
diff --git a/src/parsing.cpp → src/argweaver/parsing.cpp b/src/parsing.cpp → src/argweaver/parsing.cpp
diff --git a/src/parsing.h → src/argweaver/parsing.h b/src/parsing.h → src/argweaver/parsing.h
diff --git a/src/prior.cpp → src/argweaver/prior.cpp b/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
 
diff --git a/src/prior.h → src/argweaver/prior.h b/src/prior.h → src/argweaver/prior.h
diff --git a/src/ptree.cpp → src/argweaver/ptree.cpp b/src/ptree.cpp → src/argweaver/ptree.cpp
diff --git a/src/ptree.h → src/argweaver/ptree.h b/src/ptree.h → src/argweaver/ptree.h
diff --git a/src/recomb.cpp → src/argweaver/recomb.cpp b/src/recomb.cpp → src/argweaver/recomb.cpp
diff --git a/src/recomb.h → src/argweaver/recomb.h b/src/recomb.h → src/argweaver/recomb.h
diff --git a/src/sample_arg.cpp → src/argweaver/sample_arg.cpp b/src/sample_arg.cpp → src/argweaver/sample_arg.cpp
diff --git a/src/sample_arg.h → src/argweaver/sample_arg.h b/src/sample_arg.h → src/argweaver/sample_arg.h
diff --git a/src/sample_thread.cpp → src/argweaver/sample_thread.cpp b/src/sample_thread.cpp → src/argweaver/sample_thread.cpp
diff --git a/src/sample_thread.h → src/argweaver/sample_thread.h b/src/sample_thread.h → src/argweaver/sample_thread.h
diff --git a/src/seq.cpp → src/argweaver/seq.cpp b/src/seq.cpp → src/argweaver/seq.cpp
diff --git a/src/seq.h → src/argweaver/seq.h b/src/seq.h → src/argweaver/seq.h
diff --git a/src/sequences.cpp → src/argweaver/sequences.cpp b/src/sequences.cpp → src/argweaver/sequences.cpp
diff --git a/src/sequences.h → src/argweaver/sequences.h b/src/sequences.h → src/argweaver/sequences.h
diff --git a/src/states.cpp → src/argweaver/states.cpp b/src/states.cpp → src/argweaver/states.cpp
diff --git a/src/states.h → src/argweaver/states.h b/src/states.h → src/argweaver/states.h
diff --git a/src/t2exp.cpp → src/argweaver/t2exp.cpp b/src/t2exp.cpp → src/argweaver/t2exp.cpp
diff --git a/src/t2exp.h → src/argweaver/t2exp.h b/src/t2exp.h → src/argweaver/t2exp.h
diff --git a/src/t2exp.inl → src/argweaver/t2exp.inl b/src/t2exp.inl → src/argweaver/t2exp.inl
diff --git a/src/tabix.cpp → src/argweaver/tabix.cpp b/src/tabix.cpp → src/argweaver/tabix.cpp
diff --git a/src/tabix.h → src/argweaver/tabix.h b/src/tabix.h → src/argweaver/tabix.h
diff --git a/src/thread.cpp → src/argweaver/thread.cpp b/src/thread.cpp → src/argweaver/thread.cpp
diff --git a/src/thread.h → src/argweaver/thread.h b/src/thread.h → src/argweaver/thread.h
diff --git a/src/total_prob.cpp → src/argweaver/total_prob.cpp b/src/total_prob.cpp → src/argweaver/total_prob.cpp
diff --git a/src/total_prob.h → src/argweaver/total_prob.h b/src/total_prob.h → src/argweaver/total_prob.h
diff --git a/src/track.cpp → src/argweaver/track.cpp b/src/track.cpp → src/argweaver/track.cpp
diff --git a/src/track.h → src/argweaver/track.h b/src/track.h → src/argweaver/track.h
diff --git a/src/trans.cpp → src/argweaver/trans.cpp b/src/trans.cpp → src/argweaver/trans.cpp
diff --git a/src/trans.h → src/argweaver/trans.h b/src/trans.h → src/argweaver/trans.h
diff --git a/src/smc2bed.cpp b/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;

diff --git a/test/test_install.py b/test/test_install.py
@@ -11,17 +11,41 @@
 from rasmus.testing import make_clean_dir
 
 
-def run_cmd(cmd):
-    assert os.system(cmd) == 0
+def run_cmd(cmd, ret_code=0):
+    """
+    Run shell command and assert success exit code.
+    """
+    assert os.system(cmd) == ret_code
 
 
-def test_install():
+def test_install_prog():
     """
-    Test installing ARGweaver.
+    Test installing ARGweaver program.
+
+    Use Makefile to install.
     """
 
     make_clean_dir("test/tmp/install")
     run_cmd("python setup.py clean > /dev/null")
     run_cmd("make install prefix=test/tmp/install > /dev/null")
-    run_cmd("PYTHONPATH=test/tmp/install python -c 'import argweaver'")
+    run_cmd("PYTHONPATH=test/tmp/install python -c 'import argweaver; "
+            "assert argweaver.argweaverc.argweaverclib'")
     assert os.path.exists("test/tmp/install/bin/arg-sample")
+
+
+def test_install_lib():
+    """
+    Test installing ARGweaver python lib.
+
+    Use setup.py to install and check that module can be imported.
+    Also ensure that c library is installed.
+    """
+
+    make_clean_dir("test/tmp/install")
+    run_cmd("python setup.py clean > /dev/null")
+    run_cmd(
+        "python setup.py install --prefix=test/tmp/install "
+        "--install-lib=test/tmp/install/lib/python/site-packages > /dev/null")
+    run_cmd("cd test; PYTHONPATH=tmp/install/lib/python/site-packages "
+            "python -c 'import argweaver; "
+            "assert argweaver.argweaverc.argweaverclib'")