Merge pull request #9 from mrc-ide/update-dust-0-1-0

Move to new packing structure

DESCRIPTION

@@ -18,7 +18,7 @@ Imports:
     dust2
 LinkingTo:
     cpp11,
-    dust2,
+    dust2 (>= 0.1.1),
     mcstate2
 Suggests:
     testthat (>= 3.0.0)

inst/dust/cows.cpp

@@ -60,8 +60,12 @@ class cows {
 
   using rng_state_type = mcstate::random::generator<real_type>;
 
-  static size_t size_state(const shared_state& shared) {
-    return 4 * (shared.n_herds + shared.n_regions);
+  static auto packing_state(const shared_state& shared) {
+    return dust2::packing{{"S_herd", {shared.n_herds}}, {"S_region", {shared.n_regions}}, {"E_herd", {shared.n_herds}}, {"E_region", {shared.n_regions}}, {"I_herd", {shared.n_herds}}, {"I_region", {shared.n_regions}}, {"R_herd", {shared.n_herds}}, {"R_region", {shared.n_regions}}};
+  }
+
+  static auto packing_gradient(const shared_state& shared) {
+    return dust2::packing{};
   }
 
   static void initial(real_type time,
@@ -71,7 +75,8 @@ class cows {
                       rng_state_type& rng_state,
                       real_type * state_next) {
     // Start by zeroing everything
-    std::fill(state_next, state_next + size_state(shared), 0);
+    const auto len_state = 4 * (shared.n_herds + shared.n_regions);
+    std::fill(state_next, state_next + len_state, 0);
     // Then fill in susceptibles from the mean herd size
     //
     // Thom: should this be drawn from some distribution?  If so that