Migrations are not being applied

I am trying to apply migrations programmatically using Entity Framework Core 2.0, in a Code-First ASP.Net Core 2.0 project. If I run the migrations manually through a terminal, they're applied without issue. Applying the migrations in my Startup class though results in the database model never changing.

Am I doing this wrong?

public Startup(IConfiguration configuration)
{
    Configuration = configuration;
}

public IConfiguration Configuration { get; }

// This method gets called by the runtime. Use this method to add services to the container.
public void ConfigureServices(IServiceCollection services)
{
    services.AddMvc();
    services.AddEntityFrameworkSqlite();
    services.AddDbContext<ApplicationContext>(options => options.UseSqlite("Data Source=blogging.db"));
    services.AddDbContext<UserContext>(options => options.UseSqlite("Data Source=blogging.db"));
}

// This method gets called by the runtime. Use this method to configure the HTTP request pipeline.
public void Configure(IApplicationBuilder app, IHostingEnvironment env)
{
    if (env.IsDevelopment())
    {
        app.UseDeveloperExceptionPage();
    }

    app.UseMvc();
    var services = app.ApplicationServices.GetService<IServiceScopeFactory>();
    var context = services.CreateScope().ServiceProvider.GetRequiredService<ApplicationContext>();
    context.Database.Migrate();
}

I can run this from the terminal and it works fine:

dotnet ef migrations add FourthMigration --context EFCore_Test.DataAccess.ApplicationContext

I have multiple DataContext Types; only one represents the entire data model and the rest are used just to access the database in a more domain specific manor. The ApplicationContext represents my "everything + kitchen sink" data context. It's this context that I perform my migrations and updates with.

In preparation for deploying to Azure, I want to have the web-app migrate itself with each deployment, instead of having to wire up powershell scripts to run the dotnet core tooling commands.