Renamed python module to dna_jellyfish. Deprecation not working.

configure.ac

@@ -138,6 +138,9 @@ AM_CONDITIONAL(PYTHON_BINDING, [test -n "$enable_python_binding" -a x$enable_pyt
 AM_COND_IF([PYTHON_BINDING],
            [AS_IF([test x$enable_python_binding != xyes], [PYTHON_SITE_PKG=$enable_python_binding])]
            [AX_PYTHON_DEVEL([], [$prefix])])
+AC_ARG_ENABLE([python-deprecated],
+              [AC_HELP_STRING([--enable-python-deprecated], [enable the deprecated 'jellyfish' module (in addition to 'dna_jellyfish')])])
+AM_CONDITIONAL([PYTHON_DEPRECATED], [test -z "$enable_python_deprecated" -o x$enable_python_deprecated != xno])
 
 # Ruby binding setup
 AS_IF([test -z "$enable_ruby_binding"], [enable_ruby_binding="$enable_all_binding"])

swig/Makefile.am

@@ -16,23 +16,27 @@ endif
 
 # Python support
 if PYTHON_BINDING
-PYTHON_BUILT = swig/python/swig_wrap.cpp swig/python/jellyfish.py
+PYTHON_BUILT = swig/python/swig_wrap.cpp swig/python/dna_jellyfish.py
 BUILT_SOURCES += $(PYTHON_BUILT)
 
-pythonextdir = $(PYTHON_SITE_PKG)/jellyfish
+if PYTHON_DEPRECATED
+pythonglobaldir = $(PYTHON_SITE_PKG)
+pythonglobal_SCRIPTS = swig/python/jellyfish.py
+endif
+pythonextdir = $(PYTHON_SITE_PKG)/dna_jellyfish
 pythonext_SCRIPTS = swig/python/__init__.pyc
-pythonext_LTLIBRARIES = swig/python/_jellyfish.la
-swig_python__jellyfish_la_SOURCES = swig/python/swig_wrap.cpp $(SWIG_SRC)
-swig_python__jellyfish_la_CPPFLAGS = $(PYTHON_CPPFLAGS) -I$(srcdir)/include
-swig_python__jellyfish_la_LDFLAGS = -module
-swig_python__jellyfish_la_LIBADD = libjellyfish-2.0.la
+pythonext_LTLIBRARIES = swig/python/_dna_jellyfish.la
+swig_python__dna_jellyfish_la_SOURCES = swig/python/swig_wrap.cpp $(SWIG_SRC)
+swig_python__dna_jellyfish_la_CPPFLAGS = $(PYTHON_CPPFLAGS) -I$(srcdir)/include
+swig_python__dna_jellyfish_la_LDFLAGS = -module
+swig_python__dna_jellyfish_la_LIBADD = libjellyfish-2.0.la
 CLEANFILES += $(PYTHON_BUILT) $(pythonext_SCRIPTS)
 PYTHONC_V_GEN = $(pythonc_v_GEN_$(V))
 pythonc_v_GEN_ = $(pythonc_v_GEN_$(AM_DEFAULT_VERBOSITY))
 pythonc_v_GEN_0 = @echo "  PYTHONC " $@;
-%/__init__.pyc: %/jellyfish.py
+%/__init__.pyc: %/dna_jellyfish.py
 	$(PYTHONC_V_GEN)$(PYTHON) -c 'import py_compile, sys; py_compile.compile(sys.argv[1], sys.argv[2])' $< $@
-swig/python/jellyfish.py: swig/python/swig_wrap.cpp
+swig/python/dna_jellyfish.py: swig/python/swig_wrap.cpp
 EXTRA_DIST += $(PYTHON_BUILT)
 endif
 

swig/jellyfish.i

@@ -1,14 +1,29 @@
+#ifdef SWIGPYTHON
+// Default Python loading code does not seem to work. Use our own.
+%define MODULEIMPORT
+"
+import os
+if os.path.basename(__file__) == \"__init__.pyc\" or os.path.basename(__file__) == \"__init__.py\":
+  import dna_jellyfish.$module
+else:
+  import $module
+"
+%enddef
+%module(docstring="Jellyfish binding", moduleimport=MODULEIMPORT) dna_jellyfish
+#else
 %module(docstring="Jellyfish binding") jellyfish
+#endif
+
 %naturalvar; // Use const reference instead of pointers
 %include "std_string.i"
+
 %include "exception.i"
 %include "std_except.i"
 %include "typemaps.i"
 %feature("autodoc", "2");
 
 %{
 #ifdef SWIGPYTHON
-#define SWIG_FILE_WITH_INIT
 #endif
 
 #ifdef SWIGPERL

swig/python/setup.py

@@ -29,17 +29,17 @@
 jf_ldflags = os.popen("pkg-config --libs-only-other jellyfish-2.0").read().rstrip().split()
 
 
-jellyfish_module = Extension('_jellyfish',
+jellyfish_module = Extension('_dna_jellyfish',
                              sources = ['jellyfish_wrap.cxx'],
                              include_dirs = jf_include,
                              libraries = jf_libs,
                              library_dirs = jf_libdir,
                              extra_compile_args = ["-std=c++0x"] + jf_cflags,
                              extra_link_args = jf_ldflags + jf_rpath,
                              language = "c++")
-setup(name = 'jellyfish',
+setup(name = 'dna_jellyfish',
       version = '0.0.1',
       author = 'Guillaume Marcais',
       description = 'Access to jellyfish k-mer counting',
       ext_modules = [jellyfish_module],
-      py_modules = ["jellyfish"])
+      py_modules = ["dna_jellyfish"])

swig/python/test_hash_counter.py

@@ -1,20 +1,22 @@
 import unittest
 import sys
 import random
-import jellyfish
+
+
+import dna_jellyfish as jf
 
 class TestHashCounter(unittest.TestCase):
     def setUp(self):
-        jellyfish.MerDNA.k(100)
-        self.hash = jellyfish.HashCounter(1024, 5)
+        jf.MerDNA.k(100)
+        self.hash = jf.HashCounter(1024, 5)
 
     def test_info(self):
-        self.assertEqual(100, jellyfish.MerDNA.k())
+        self.assertEqual(100, jf.MerDNA.k())
         self.assertEqual(1024, self.hash.size())
         self.assertEqual(5, self.hash.val_len())
 
     def test_add(self):
-        mer  = jellyfish.MerDNA()
+        mer  = jf.MerDNA()
         good = True
         for i in range(1000):
             mer.randomize()

swig/python/test_mer_file.py

@@ -1,12 +1,14 @@
-import jellyfish
 import unittest
 import sys
 import os
 from collections import Counter
 
+import dna_jellyfish as jf
+
+
 class TestMerFile(unittest.TestCase):
     def setUp(self):
-        self.mf = jellyfish.ReadMerFile(os.path.join(data, "swig_python.jf"))
+        self.mf = jf.ReadMerFile(os.path.join(data, "swig_python.jf"))
 
     def test_histo(self):
         histo = Counter()
@@ -46,7 +48,7 @@ def test_iter(self):
 
     def test_query(self):
         good = True
-        qf   = jellyfish.QueryMerFile(os.path.join(data, "swig_python.jf"))
+        qf   = jf.QueryMerFile(os.path.join(data, "swig_python.jf"))
         for mer, count in self.mf:
             good = good and count == qf[mer]
             if not good: break

swig/python/test_string_mers.py

@@ -1,31 +1,32 @@
 import unittest
 import sys
 import random
-import jellyfish
+
+import dna_jellyfish as jf
 
 class TestStringMers(unittest.TestCase):
     def setUp(self):
         bases = "ACGTacgt"
         self.str = ''.join(random.choice(bases) for _ in range(1000))
         self.k = random.randint(10, 110)
-        jellyfish.MerDNA.k(self.k)
+        jf.MerDNA.k(self.k)
 
     def test_all_mers(self):
         count = 0
         good = True
-        mers = jellyfish.string_mers(self.str)
+        mers = jf.string_mers(self.str)
         for m in mers:
-            m2 = jellyfish.MerDNA(self.str[count:count+self.k])
+            m2 = jf.MerDNA(self.str[count:count+self.k])
             good = good and m == m2
             count += 1
         self.assertTrue(good)
         self.assertEqual(len(self.str) - self.k + 1, count)
 
     def test_canonical_mers(self):
         good = True
-        mers = jellyfish.string_canonicals(self.str)
+        mers = jf.string_canonicals(self.str)
         for count, m in enumerate(mers):
-            m2 = jellyfish.MerDNA(self.str[count:count+self.k])
+            m2 = jf.MerDNA(self.str[count:count+self.k])
             rm2 = m2.get_reverse_complement()
             good = good and (m == m2 or m == rm2)
             good = good and (not (m > m2)) and (not (m > rm2))