add setuptools scaffolding for windows

pybedtools/include/fileType.h

@@ -23,12 +23,19 @@
 #include <unistd.h>
 #include <sstream>
 
+#if !defined(S_ISREG) && defined(_S_IFMT) && defined(_S_IFREG)
+#define S_ISREG(m) (((m) & _S_IFMT) == _S_IFREG)
+#endif
+#if !defined(S_ISDIR) && defined(_S_IFMT) && defined(_S_IFDIR)
+#define S_ISDIR(m) (((m) & _S_IFMT) == _S_IFDIR)
+#endif
+
 using namespace std;
 
 /*****************************************************************************
-  Convenience functions to detect whether a given file is 
+  Convenience functions to detect whether a given file is
   "regular" and/or "gzipped".
-  
+
   Kindly contributed by Assaf Gordon.
 ******************************************************************************/
 string string_error(int errnum);

pybedtools/include/lineFileUtilities.h

@@ -18,9 +18,10 @@ std::string ToString(const T & value) {
     return ss.str();
 }
 
+#ifndef _MSVC_LANG
 // tokenize into a list of strings.
 inline
-void Tokenize(const string &str, vector<string> &elems, const string &delimiter = "\t") 
+void Tokenize(const string &str, vector<string> &elems, const string &delimiter = "\t")
 {
     char* tok;
     char cchars [str.size()+1];
@@ -46,6 +47,42 @@ void Tokenize(const string &str, vector<int> &elems, const string &delimiter = "
         tok = strtok(NULL, delimiter.c_str());
     }
 }
+#else
+inline void Tokenize(const string &str, vector<string> &tokens, const string &delimiter = "\t")
+{
+    // Skip delimiters at beginning.
+    string::size_type lastPos = str.find_first_not_of(delimiter, 0);
+    // Find first "non-delimiter".
+    string::size_type pos = str.find_first_of(delimiter, lastPos);
+
+    while (string::npos != pos || string::npos != lastPos)
+    {
+        // Found a token, add it to the vector.
+        tokens.push_back(str.substr(lastPos, pos - lastPos));
+        // Skip delimiters.  Note the "not_of"
+        lastPos = str.find_first_not_of(delimiter, pos);
+        // Find next "non-delimiter"
+        pos = str.find_first_of(delimiter, lastPos);
+    }
+}
+inline void Tokenize(const string &str, vector<int> &tokens, const string &delimiter = "\t")
+{
+    // Skip delimiters at beginning.
+    string::size_type lastPos = str.find_first_not_of(delimiter, 0);
+    // Find first "non-delimiter".
+    string::size_type pos = str.find_first_of(delimiter, lastPos);
+
+    while (string::npos != pos || string::npos != lastPos)
+    {
+        // Found a token, add it to the vector.
+        tokens.push_back(atoi(str.substr(lastPos, pos - lastPos).c_str()));
+        // Skip delimiters.  Note the "not_of"
+        lastPos = str.find_first_not_of(delimiter, pos);
+        // Find next "non-delimiter"
+        pos = str.find_first_of(delimiter, lastPos);
+    }
+}
+#endif
 
 #endif /* LINEFILEUTILITIES_H */
 

requirements-win.txt

@@ -0,0 +1,3 @@
+numpy
+pandas
+pysam @ "git+https://github.com/theAeon/pysam.git@pysam-mingw"

setup.py

@@ -234,24 +234,48 @@ def run(self):
 
 EXT = '.pyx' if USE_CYTHON else '.cpp'
 
-extensions = [
-    Extension(
-        'pybedtools.cbedtools',
-        depends=glob.glob('pybedtools/include/*h'),
-        libraries=['stdc++', 'z'],
-        include_dirs=['pybedtools/include/'],
-        sources=['pybedtools/cbedtools' + EXT] + sorted(glob.glob('pybedtools/include/*.cpp')),
-        language='c++'),
-
-    Extension(
-        'pybedtools.featurefuncs',
-        depends=glob.glob('pybedtools/include/*h'),
-        libraries=['stdc++', 'z'],
-        include_dirs=['pybedtools/include/'],
-        sources=['pybedtools/featurefuncs' + EXT] + sorted(glob.glob('pybedtools/include/*.cpp')),
-        language='c++'),
-]
-
+if sys.platform == "win32":
+    extensions = [
+        Extension(
+            'pybedtools.cbedtools',
+            depends=glob.glob('pybedtools/include/*h'),
+            library_dirs=[ os.environ.get("ZLIB_ROOT") + '/lib'],
+            libraries=['zlib'],
+            #extra_compile_args=["/std:c++17"],
+            include_dirs=['pybedtools/include/', os.environ.get("ZLIB_ROOT") + '/include', 'win32'],
+            sources=['pybedtools/cbedtools' + EXT] + sorted(glob.glob('pybedtools/include/*.cpp')),
+            language='c++'),
+
+        Extension(
+            'pybedtools.featurefuncs',
+            depends=glob.glob('pybedtools/include/*h'),
+            library_dirs=[ os.environ.get("ZLIB_ROOT") + '/lib'],
+            libraries=['zlib'],
+            include_dirs=['pybedtools/include/', os.environ.get("ZLIB_ROOT") + '/include', 'win32'],
+            sources=['pybedtools/featurefuncs' + EXT] + sorted(glob.glob('pybedtools/include/*.cpp')),
+            language='c++'),
+    ]
+else:
+    extensions = [
+        Extension(
+            "pybedtools.cbedtools",
+            depends=glob.glob("pybedtools/include/*h"),
+            libraries=["stdc++", "z"],
+            include_dirs=["pybedtools/include/"],
+            sources=["pybedtools/cbedtools" + EXT]
+            + sorted(glob.glob("pybedtools/include/*.cpp")),
+            language="c++",
+        ),
+        Extension(
+            "pybedtools.featurefuncs",
+            depends=glob.glob("pybedtools/include/*h"),
+            libraries=["stdc++", "z"],
+            include_dirs=["pybedtools/include/"],
+            sources=["pybedtools/featurefuncs" + EXT]
+            + sorted(glob.glob("pybedtools/include/*.cpp")),
+            language="c++",
+        ),
+    ]
 
 cmdclass = {
     'clean': CleanCommand,