Merge pull request #229 from bpuchala/v0.2a2_install

0.2a2 bug fixes and 'casm-calc'

Author: bpuchala

SConstruct

@@ -1,7 +1,7 @@
 # http://www.scons.org/doc/production/HTML/scons-user.html
 # This is: Sconstruct
 
-import os, glob, copy, shutil, subprocess, imp, re
+import sys, os, glob, copy, shutil, subprocess, imp, re
 
 from os.path import join
 
@@ -575,13 +575,24 @@ if 'configure' in COMMAND_LINE_TARGETS:
   def check_module(module_name):
     print "Checking for Python module '" + module_name + "'... ",
     try:
-      imp.find_module(module_name)
-      res = 1
-      print "yes"
-    except:
-      res = 0
-      print "no"
-    return res
+      res = imp.find_module(module_name)
+      if res:
+        print "yes"
+        return 1
+    except ImportError:
+      pass
+    for item in sys.path:
+      importer = sys.path_importer_cache.get(item)
+      if importer:
+        try:
+          result = importer.find_module(module_name, [item])
+          if result:
+            print "yes"
+            return 1
+        except ImportError:
+          pass
+    print "no"
+    return 0
 
   conf = Configure(
     env.Clone(LIBPATH=install_lib_paths,
@@ -619,12 +630,12 @@ if 'configure' in COMMAND_LINE_TARGETS:
     if not check_module(module_name):
       if_failed("Python module '" + module_name + "' is not installed")
   if not check_module('pbs'):
-      if_failed("""
-      Python module '%s' is not installed
+      print """
+      Python module 'pbs' is not installed
         This module is only necessary for setting up and submitting DFT jobs
         **It is not the module available from pip**"
         It is available from: https://github.com/prisms-center/pbs
-      """ % module_name)
+      """
 
 
   print "Configuration checks passed."

apps/casm/casm.cpp

@@ -9,7 +9,7 @@ using namespace CASM;
 int main(int argc, char *argv[]) {
 
   PrimClex *_primclex = nullptr;
-  CommandArgs args(argc, argv, _primclex, default_log(), default_err_log());
+  CommandArgs args(argc, argv, _primclex, fs::path(), default_log(), default_err_log());
 
   return casm_api(args);
 

include/casm/app/DirectoryStructure.hh

@@ -65,7 +65,7 @@ namespace CASM {
       return _all_settings("ref", calc_settings_dir(calctype));
     }
 
-    /// \brief Check filesystem directory structure and return list of all cluster expansion names
+    /// \brief Check filesystem directory structure and return list of all property names
     std::vector<std::string> all_property() const {
       return _all_settings("clex", m_root / m_clex_dir);
     }
@@ -272,13 +272,13 @@ namespace CASM {
     }
 
     /// \brief Returns path to eci directory
-    fs::path eci_dir(std::string clex, std::string calctype, std::string ref, std::string bset, std::string eci) const {
-      return clex_dir(clex) / _calctype(calctype) / _ref(ref) / _bset(bset) / _eci(eci);
+    fs::path eci_dir(std::string property, std::string calctype, std::string ref, std::string bset, std::string eci) const {
+      return clex_dir(property) / _calctype(calctype) / _ref(ref) / _bset(bset) / _eci(eci);
     }
 
     /// \brief Returns path to eci.json
-    fs::path eci(std::string clex, std::string calctype, std::string ref, std::string bset, std::string eci) const {
-      return eci_dir(clex, calctype, ref, bset, eci) / "eci.json";
+    fs::path eci(std::string property, std::string calctype, std::string ref, std::string bset, std::string eci) const {
+      return eci_dir(property, calctype, ref, bset, eci) / "eci.json";
     }
 
 
@@ -297,8 +297,8 @@ namespace CASM {
     // -- deprecated ------------------------------------
 
     /// \brief Returns path to eci.out
-    fs::path eci_out(std::string clex, std::string calctype, std::string ref, std::string bset, std::string eci) const {
-      return eci_dir(clex, calctype, ref, bset, eci) / "eci.out";
+    fs::path eci_out(std::string property, std::string calctype, std::string ref, std::string bset, std::string eci) const {
+      return eci_dir(property, calctype, ref, bset, eci) / "eci.out";
     }
 
     /// \brief Query aliases file

include/casm/app/ProjectSettings.hh

@@ -36,6 +36,8 @@ namespace CASM {
                     std::string _eci) :
       name(_name), property(_property), calctype(_calctype), ref(_ref), bset(_bset), eci(_eci) {}
 
+    void print(std::ostream &sout, bool is_default, int indent = 0) const;
+
     std::string name;
     std::string property;
     std::string calctype;

include/casm/app/casm_functions.hh

@@ -1,6 +1,7 @@
 #ifndef CASM_FUNCTIONS_HH
 #define CASM_FUNCTIONS_HH
 
+#include <wordexp.h>
 #include "casm/CASM_global_definitions.hh"
 #include "casm/casm_io/Log.hh"
 
@@ -37,23 +38,51 @@ namespace CASM {
   /// \brief Data structure holding basic CASM command info
   struct CommandArgs {
 
+    /// \brief CommandArgs constructor
     CommandArgs(int _argc,
                 char *_argv[],
                 PrimClex *_primclex = nullptr,
+                fs::path _root = fs::path(),
                 Log &_log = default_log(),
                 Log &_err_log = default_err_log());
 
+    /// \brief CommandArgs constructor
+    CommandArgs(std::string _args,
+                PrimClex *_primclex = nullptr,
+                fs::path _root = fs::path(),
+                Log &_log = default_log(),
+                Log &_err_log = default_err_log());
+
+    CommandArgs(const CommandArgs &other) = delete;
+    CommandArgs(CommandArgs &&other) = delete;
+    CommandArgs &operator=(const CommandArgs &) = delete;
+    CommandArgs &operator=(CommandArgs &&) = delete;
+
+    /// \brief CommandArgs destructor
+    ~CommandArgs();
+
     int argc;
     char **argv;
     PrimClex *primclex;
+    fs::path root;
     Log &log;
     Log &err_log;
 
-    fs::path root;
+    /// stores error codes when attempting to parse std::string _args -> argc, argv
+    int parse_result;
+
     bool is_help;
     bool write_log;
     std::string command;
 
+  private:
+
+    void _init();
+
+    /// Used when parsing std::string args -> argc, argv
+    bool m_free_p;
+    wordexp_t m_p;
+
   };
 
   typedef std::function<int (const CommandArgs &)> Command;
@@ -65,6 +94,9 @@ namespace CASM {
   /// \brief Executes CASM commands specified by args
   int casm_api(const CommandArgs &args);
 
+  // /// \brief Executes casm_api in specified working directory
+  // int casm_api(const CommandArgs &args, fs::path working_dir);
+
 
 
   /// \brief If !_primclex, construct new PrimClex stored in uniq_primclex, then

include/ccasm/api.hh

@@ -38,6 +38,6 @@ extern "C" {
                              bool clear_clex);
 
 
-  int casm_capi(char *args, cPrimClex *primclex, costream *log, costream *debug_log, costream *err_log);
+  int casm_capi(char *args, cPrimClex *primclex, char *root, costream *log, costream *debug_log, costream *err_log);
 
 }

python/casm/casm/__init__.py

@@ -1,4 +1,10 @@
 """A package of wrappers for running input codes to casm"""
-from casm import *
-from noindent import *
-__all__ = dir()
+from casm import API, project_path, jobname
+from noindent import NoIndent, NoIndentEncoder
+__all__ = [
+  'API',
+  'project_path',
+  'jobname',
+  'NoIndent',
+  'NoIndentEncoder'
+]