From e452e915ace207e28b02e5ef95d49a57c51f93a8 Mon Sep 17 00:00:00 2001
From: Rich FitzJohn <r.fitzjohn@imperial.ac.uk>
Date: Fri, 16 Aug 2024 14:59:21 +0100
Subject: [PATCH] Move to new packing structure

---
 DESCRIPTION        |  2 +-
 R/dust.R           |  2 +-
 inst/dust/cows.cpp | 11 ++++++++---
 src/cows.cpp       | 13 +++++++++----
 4 files changed, 19 insertions(+), 9 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index cc074c5..116cf22 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -18,7 +18,7 @@ Imports:
     dust2
 LinkingTo:
     cpp11,
-    dust2,
+    dust2 (>= 0.1.1),
     mcstate2
 Suggests:
     testthat (>= 3.0.0)
diff --git a/R/dust.R b/R/dust.R
index c1865f8..be67b27 100644
--- a/R/dust.R
+++ b/R/dust.R
@@ -1,4 +1,4 @@
-## Generated by dust2 (version 0.1.0) - do not edit
+## Generated by dust2 (version 0.1.1) - do not edit
 cows <- function() {
   dust2::dust_system_generator("cows", "discrete")
 }
diff --git a/inst/dust/cows.cpp b/inst/dust/cows.cpp
index a4983df..96e3f9a 100644
--- a/inst/dust/cows.cpp
+++ b/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
diff --git a/src/cows.cpp b/src/cows.cpp
index a050085..73e5034 100644
--- a/src/cows.cpp
+++ b/src/cows.cpp
@@ -1,4 +1,4 @@
-// Generated by dust2 (version 0.1.0) - do not edit
+// Generated by dust2 (version 0.1.1) - do not edit
 
 #include <dust2/common.hpp>
 #include <numeric>
@@ -62,8 +62,12 @@ 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,
@@ -73,7 +77,8 @@ 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