Better subprocess handling

• PaDEL's native timeout functionality causes some compounds to "hang" during calculation
  • for higher-level functions, from_smiles and from_mdl, supplied timeout now controls subprocess.Popen's timeout instead of PaDEL's

This change reduces the chance of a compound to fail during calculation.

Bug fix

• Upon a successful conversion in "from_smiles" and "from_mdl", attempt loop is exited

Bug Fix for Unix Systems

• subprocess.Popen call required a list of arguments instead of a string on Unix-based systems, therefore the command was .split() to form a list

Function timeouts, process attempts

• "from_smiles" and "from_mdl" now accept an optional timeout argument
• "from_smiles" and "from_mdl" will now attempt conversion three times before throwing an exception
  • this should reduce indeterminate failures caused by PaDEL-Descriptor
• exceptions thrown by PaDEL-Descriptor are now decoded to UTF-8

Cleanup when RuntimeError encountered

• If a RuntimeError is encountered, temporary files (.smi, CSV if not saving) are removed

Max Run-time per Molecule for "from_smiles", "from_mdl"

• Added maximum run-time per molecule for "from_smiles" and "from_mdl" functions
  • set to 10 seconds per molecule
  • does not affect default wrapper maximum run-time, just these functions

Initial Release

• Initial upload of source code and documentation