Merge branch 'develop' of https://github.com/SynBioDex/libSBOL into d…

…evelop

README.md

@@ -1,4 +1,4 @@
-# libSBOL 2.1.1
+# libSBOL 2.2.0
 
 [libSBOL](https://github.com/SynBioDex/libSBOL) is a C++ library for reading, writing, and constructing genetic designs according to the standardized specifications of the [Synthetic Biology Open Language (SBOL)](http://www.sbolstandard.org/).  
 

installer/Win32_installer.iss

@@ -2,7 +2,7 @@
 ; SEE THE DOCUMENTATION FOR DETAILS ON CREATING INNO SETUP SCRIPT FILES!
 
 #define MyAppName "libSBOL"
-#define MyAppVersion "2.1.1"
+#define MyAppVersion "2.2.0"
 #define MyAppSubVersion ""
 #define MyPlatform "Win"
 #define MyArchitecture "x86"

installer/Win64_installer.iss

@@ -2,7 +2,7 @@
 ; SEE THE DOCUMENTATION FOR DETAILS ON CREATING INNO SETUP SCRIPT FILES!
 
 #define MyAppName "libSBOL"
-#define MyAppVersion "2.1.1"
+#define MyAppVersion "2.2.0"
 #define MyAppSubVersion ""
 #define MyPlatform "Win"
 #define MyArchitecture "x64"

manual/Doxyfile

@@ -38,7 +38,7 @@ PROJECT_NAME           = libSBOL
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = 2.1.1
+PROJECT_NUMBER         = 2.2.0
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a

manual/installation.dox

@@ -8,7 +8,7 @@
 ///
 /// On Windows, installation through binary installers is the simplest way to obtain libSBOL. The installer contains pre-compiled libSBOL library. Simply install it to whichever path you want and use it.
 ///
-/// [Get the latest binary installers](https://sourceforge.net/projects/libsbol/files/v2.1.1.1/)
+/// [Get the latest binary installers](https://sourceforge.net/projects/libsbol/)
 ///
 /// @section use_brew Using Homebrew
 ///
@@ -45,7 +45,7 @@
 ///
 /// 3. Run CMake-gui. For "Where is the source code" enter the path to your libSBOL folder (not libSBOL/source folder). Choose build path by setting "Where to build the binaries". After setting the paths, click Configure, and choose what type of compiler you want to generate instructions for (e.g. Visual Studio 14 2015 for 32 bit and Visual Studio 14 2015 Win64 for 64 bit). See the screenshot above.
 ///
-/// 4. (optional) Set optional targets, e.g. examples, tests, manual, or Python wrapper. To add them check the appropriate boxes and then press Configure again. CMAKE_INSTALL_PREFIX is of particular interest, since it determines the path the output will be located. Building Python wrapper requires SWIG.
+/// 4. Set optional targets, e.g. examples, tests, manual, or Python wrapper. To add them check the appropriate boxes and then press Configure again. It is HIGHLY RECOMMENDED to change CMAKE_INSTALL_PREFIX from it's default path (Program Files) to somewhere else. This value determines the path the output files will be located. Building Python wrapper requires SWIG.
 ///
 ///   SBOL_BUILD_SHARED: Builds a dynamically linked library. The default is static.
 ///
@@ -74,7 +74,7 @@
 /// ```
 /// You will need administrator privileges for a make install.
 ///
-/// 7. (optional) For Python bindings, copy and paste the sbol folder with Python bindings to your local Python site-packages folder.
+/// 7. For Python bindings, copy and paste the sbol folder with Python bindings to your local Python site-packages folder.
 ///
 ///
 /// Mac
@@ -95,7 +95,7 @@
 ///
 /// 4. Run CMake-gui (type cmake in terminal or run cmake app). For "Where is the source code" enter the path to your libSBOL folder (not libSBOL/source folder). Choose build path by setting "Where to build the binaries". After setting the paths, click Configure, and choose what type of compiler you want to generate instructions for. 
 /// 
-/// 5. (optional) Set optional targets, e.g. examples, tests, manual, or Python wrapper. To add them check the appropriate boxes and then press Configure again. CMAKE_INSTALL_PREFIX is of particular interest, since it determines the path the output will be located. By default on Mac OSX, the library will be installed to /usr/local/lib. Building Python wrapper requires SWIG.
+/// 5. Set optional targets, e.g. examples, tests, manual, or Python wrapper. To add them check the appropriate boxes and then press Configure again. CMAKE_INSTALL_PREFIX is of particular interest, since it determines the path the output will be located. By default on Mac OSX, the library will be installed to /usr/local/lib. Building Python wrapper requires SWIG.
 ///
 ///   SBOL_BUILD_SHARED: Builds a dynamically linked library. The default is static.
 ///
@@ -134,7 +134,7 @@
 /// sudo apt-get install build-essential libxml2-dev gcc-multilib g++-multilib libraptor2-dev libjsoncpp-dev
 /// ```
 /// 
-/// 2. (optional) If you want to generate Python wrapper you will need SWIG. To install run:
+/// 2. If you want to generate Python wrapper you will need SWIG. To install run:
 /// ```
 /// sudo apt-get install swig python-dev
 /// ```
@@ -147,7 +147,7 @@
 ///
 /// 4. Run CMake-gui (type cmake-gui or cmake-qt-gui in terminal). For "Where is the source code" enter the path to your libSBOL folder (not libSBOL/source folder). Choose build path by setting "Where to build the binaries". After setting the paths, click Configure, and choose what type of compiler you want to generate instructions for. See the screenshot above.
 /// 
-/// 5. (optional) Set optional targets, e.g. examples, tests, manual, or Python wrapper. To add them check the appropriate boxes and then press Configure again. CMAKE_INSTALL_PREFIX is of particular interest, since it determines the path the output will be located. Building Python wrapper requires SWIG.
+/// 5. Set optional targets, e.g. examples, tests, manual, or Python wrapper. To add them check the appropriate boxes and then press Configure again. CMAKE_INSTALL_PREFIX is of particular interest, since it determines the path the output will be located. Building Python wrapper requires SWIG.
 ///
 ///   SBOL_BUILD_SHARED: Builds a dynamically linked library. The default is static.
 ///
@@ -177,7 +177,7 @@
 /// ```
 /// to compile. The library will be located under the folder you specified in CMAKE_INSTALL_PREFIX.
 ///
-/// 8. (optional) For Python bindings, you might want to add the path of Python bindings as part of PYTHONPATH environment. To do so, run:
+/// 8. For Python bindings, you might want to add the path of Python bindings as part of PYTHONPATH environment. To do so, run:
 /// ```
 /// export PYTHONPATH=$PYTHONPATH:/path-to-your-Python-bindings
 /// ```

manual/mainpage.dox

@@ -1,6 +1,6 @@
 //////////////////////////////////////////////////////////////////////
 /// @mainpage
-/// libSBOL 2.1.1
+/// libSBOL 2.2.0
 /// ======================================
 /// 
 /// [libSBOL](https://github.com/SynBioDex/libSBOL) is a C++ library for reading, writing, and constructing genetic designs according to the standardized specification of the [Synthetic Biology Open Language (SBOL)](http://www.sbolstandard.org/).  

manual/sequences.dox

@@ -18,10 +18,7 @@
 /// e0040 = doc.getComponentDefinition('http://synbiohub.org/public/igem/BBa_E0040/1');
 /// b0012 = doc.getComponentDefinition('http://synbiohub.org/public/igem/BBa_B0012/1')
 /// ```
-/// PySBOL supports several search options, including a general search, an exact search, and an advanced search. The easiest search is a general search.
-/// ```
 ///
-/// ```
 /// @section template_design Design Abstraction with SBOL
 /// Design abstraction enables the synthetic biologist to think about the high-level, functional characteristics of a biological system independently of its structural characteristics. This enables a computer-aided design (CAD) approach similar to electronics, in which the functional or schematic representation of an electronic circuit can be represented separately from the physical dimensions of the electronic components.
 /// One advantage of the SBOL standard over GenBank is the ability to represent DNA as abstract components without knowing their exact sequence. An abstract design can be used as a template, with sequence information filled in later. A ComponentDefinition represents a biological component whose general function is known while its sequence is currently either unknown or unspecified. The intended function of a component is specified using a term from the Sequence Ontology (SO), a standard vocabulary for describing genetic parts. As the following example shows, some common SO terms are built in to libSBOL as pre-defined constants (see @file constants.h ). This code example defines the new component as a gene.  Other terms may be found by browsing the [Sequence Ontology](http://www.sequenceontology.org/browser/obob.cgi) online.

source/CMakeLists.txt

@@ -8,12 +8,12 @@ include_directories( ${CURL_INCLUDE_DIR})
 if( SBOL_BUILD_PYTHON2 )
     find_package( SWIG REQUIRED )
     find_package( PythonLibs 2 EXACT)
-    include_directories( ${PYTHON_INCLUDE_DIRS} )
+    include_directories( ${PYTHON_INCLUDE_DIR} )
 endif()
 if( SBOL_BUILD_PYTHON3 )
     find_package( SWIG REQUIRED )
     find_package( PythonLibs 3)
-    include_directories( ${PYTHON_INCLUDE_DIRS} )
+    include_directories( ${PYTHON_INCLUDE_DIR} )
 endif()
 
 # gather source files

source/assembly.cpp

@@ -660,7 +660,7 @@ void Participation::define(ComponentDefinition& species, string role)
 
 ComponentDefinition& ComponentDefinition::build()
 {
-    
+	return *new ComponentDefinition();
 };
 
 void ComponentDefinition::participate(Participation& species)

source/document.h

@@ -275,9 +275,6 @@ namespace sbol {
         }
 	};
 
-
-
-
     template < class SBOLClass > void Document::add(std::vector < SBOLClass* > sbol_objects)
     {
         for (auto i_obj = sbol_objects.begin(); i_obj != sbol_objects.end(); ++i_obj)
@@ -791,7 +788,6 @@ namespace sbol {
             target_doc->add < SBOLClass > (new_obj);
         return new_obj;
     };
-
 }
 
 

source/object.h

@@ -36,7 +36,9 @@
 #include <map>
 #include <unordered_map>
 
+#if defined(SBOL_BUILD_PYTHON2) || defined(SBOL_BUILD_PYTHON3)
 #include "Python.h"
+#endif
 
 namespace sbol
 {
@@ -207,6 +209,7 @@ namespace sbol
 
         std::vector<std::string>::iterator python_iter;
 
+		#if defined(SBOL_BUILD_PYTHON2) || defined(SBOL_BUILD_PYTHON3)
         std::string __getitem__(const int nIndex)
         {
             return this->operator[](nIndex);
@@ -258,6 +261,7 @@ namespace sbol
         {
             return this->size();
         }
+		#endif
 
     };
     bool operator !=(const SBOLObject &a, const SBOLObject &b);

source/properties.cpp

@@ -139,7 +139,7 @@ void VersionProperty::incrementMinor()
 
     // Concatenate new version string
     string new_version;
-    int i_v = 0;
+    unsigned int i_v = 0;
     do
     {
         new_version += v_tokens[i_v] + v_delimiters[i_v];
@@ -180,7 +180,7 @@ void VersionProperty::incrementMajor()
 
     // Concatenate new version string
     string new_version;
-    int i_v = 0;
+    unsigned int i_v = 0;
     do
     {
         new_version += v_tokens[i_v] + v_delimiters[i_v];
@@ -220,7 +220,7 @@ void VersionProperty::incrementPatch()
 
     // Concatenate new version string
     string new_version;
-    int i_v = 0;
+    unsigned int i_v = 0;
     do
     {
         new_version += v_tokens[i_v] + v_delimiters[i_v];

source/properties.h

@@ -37,7 +37,9 @@
 #include <utility>
 #include <regex>
 
+#if defined(SBOL_BUILD_PYTHON2) || defined(SBOL_BUILD_PYTHON3)
 #include "Python.h"
+#endif
 
 namespace sbol
 {
@@ -55,6 +57,8 @@ namespace sbol
 		{
 		}
 
+		#if defined(SBOL_BUILD_PYTHON2) || defined(SBOL_BUILD_PYTHON3)
+
         std::string __getitem__(const int nIndex)
         {
             return this->operator[](nIndex);
@@ -103,11 +107,13 @@ namespace sbol
             throw SBOLError(END_OF_LIST, "");
             return NULL;
         }
-        
+
         int __len__()
         {
             return this->size();
         }
+		#endif
+
 	};
 
     /// @ingroup extension_layer
@@ -117,6 +123,7 @@ namespace sbol
 	public:
         virtual std::string get();                  ///< Basic getter for all SBOL literal properties.
 
+		#if defined(SBOL_BUILD_PYTHON2) || defined(SBOL_BUILD_PYTHON3)
         std::string __getitem__(const int nIndex)
         {
             return this->operator[](nIndex);
@@ -170,7 +177,8 @@ namespace sbol
         {
             return this->size();
         }
-
+		#endif
+
         TextProperty(sbol_type type_uri, void *property_owner, std::string initial_value = "", ValidationRules validation_rules = {}) :
 			Property(type_uri, property_owner, "\"" + initial_value + "\"", validation_rules)
 
@@ -185,6 +193,7 @@ namespace sbol
 	public:
         virtual int get();                  ///< Basic getter for all SBOL literal properties.
 
+		#if defined(SBOL_BUILD_PYTHON2) || defined(SBOL_BUILD_PYTHON3)
         std::string __getitem__(const int nIndex)
         {
             return this->operator[](nIndex);
@@ -238,7 +247,8 @@ namespace sbol
         {
             return this->size();
         }
-
+		#endif
+
 		IntProperty(sbol_type type_uri, void *property_owner, int initial_value = 0) :
 			Property(type_uri, property_owner, initial_value)
 		{

source/validation.cpp

@@ -92,7 +92,10 @@ void sbol::libsbol_rule_1(void *sbol_obj, void *arg)
 void sbol::libsbol_rule_2(void *sbol_obj, void *arg)
 {
 
-        string& date_time = (string&)*arg;
+        //string& date_time = (string&)*arg;
+		//char *date_time[] = (char *[])arg;
+		const char *c_date_time = (const char *)arg;
+		string date_time = string(c_date_time);
 
         bool DATETIME_MATCH_1 = false;
         bool DATETIME_MATCH_2 = false;

wrapper/CMakeLists.txt

@@ -307,18 +307,18 @@ IF (SBOL_BUILD_PYTHON3)
     endif()
 endif()
 
-unset( PYTHON_LIBRARIES CACHE  )
-unset( PYTHONLIBS_FOUND CACHE  )
-unset(PYTHON_INCLUDE_DIRS CACHE  )
-unset(PYTHON_INCLUDE_DIR CACHE  )
-unset(PYTHONLIBS_VERSION_STRING CACHE )
-unset(PYTHON_INCLUDE_PATH CACHE)
-unset( PYTHON_LIBRARIES   )
-unset( PYTHONLIBS_FOUND   )
-unset(PYTHON_INCLUDE_DIRS   )
-unset(PYTHON_INCLUDE_DIR   )
-unset(PYTHONLIBS_VERSION_STRING  )
-unset(PYTHON_INCLUDE_PATH )
+#unset( PYTHON_LIBRARIES CACHE  )
+#unset( PYTHONLIBS_FOUND CACHE  )
+#unset(PYTHON_INCLUDE_DIRS CACHE  )
+#unset(PYTHON_INCLUDE_DIR CACHE  )
+#unset(PYTHONLIBS_VERSION_STRING CACHE )
+#unset(PYTHON_INCLUDE_PATH CACHE)
+#unset( PYTHON_LIBRARIES   )
+#unset( PYTHONLIBS_FOUND   )
+#unset(PYTHON_INCLUDE_DIRS   )
+#unset(PYTHON_INCLUDE_DIR   )
+#unset(PYTHONLIBS_VERSION_STRING  )
+#unset(PYTHON_INCLUDE_PATH )
 
 IF (SBOL_BUILD_PYTHON2)
     find_package( PythonLibs 2 EXACT)

wrapper/__init__.py

@@ -1,4 +1,4 @@
-__version__ = '2.1.1'
+__version__ = '2.2.0'
 
 from libsbol import *
 import unit_tests