If you are using a sqlproj based project in .NET 4 and above, you can build and publish it programatically fairly easily using classes in the Microsoft.Build namespace. Taken from my answer here:
using Microsoft.Build.Framework;
using Microsoft.Build.Execution;
public void UpdateSchema() {
    var props = new Dictionary<string, string> {
        { "UpdateDatabase", "True" },
        { "PublishScriptFileName", "schema-update.sql" },
        { "SqlPublishProfilePath", "path/to/publish.xml") }
    };
    var projPath = "path/to/database.sqlproj";
    var result = BuildManager.DefaultBuildManager.Build(
        new BuildParameters { Loggers = new[] { new ConsoleLogger() } },
        new BuildRequestData(new ProjectInstance(projPath, props, null), new[] { "Publish" }));
    if (result.OverallResult == BuildResultCode.Success) {
        Console.WriteLine("Schema update succeeded!");
    }
    else {
        Console.ForegroundColor = ConsoleColor.Red;
        Console.WriteLine("Schema update failed!");
        Console.ResetColor();
    }
}
private class ConsoleLogger : ILogger
{
    public void Initialize(IEventSource eventSource) {
        eventSource.ErrorRaised += (sender, e) => {
            Console.ForegroundColor = ConsoleColor.Red;
            Console.WriteLine(e.Message);
            Console.ResetColor();
        };
        eventSource.MessageRaised += (sender, e) => {
            if (e.Importance != MessageImportance.Low)
                Console.WriteLine(e.Message);
        };
    }
    public void Shutdown() { }
    public LoggerVerbosity Verbosity { get; set; }
    public string Parameters { get; set; }
}
This is for .NET 4 and above. Be sure and include assembly references to Microsoft.Build and Microsoft.Build.Framework.