From fd58ea6454347f9e702803317e6a54dd12320f0c Mon Sep 17 00:00:00 2001
From: Peter Winskill <p.winskill@imperial.ac.uk>
Date: Wed, 12 Jul 2023 14:27:26 +0100
Subject: [PATCH] Specify timesteps in create process

---
 DESCRIPTION                               |  2 +-
 R/model.R                                 |  6 ++++--
 R/processes.R                             |  2 ++
 src/RcppExports.cpp                       |  2 +-
 tests/testthat/test-process-integration.R | 22 ++++++++++++++++++++++
 5 files changed, 30 insertions(+), 4 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 3396705b..1d971723 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: malariasimulation
 Title: An individual based model for malaria
-Version: 1.6.0
+Version: 1.6.1
 Authors@R: c(
   person(
     given = "Giovanni",
diff --git a/R/model.R b/R/model.R
index 48af9af9..fb6ffef9 100644
--- a/R/model.R
+++ b/R/model.R
@@ -115,7 +115,8 @@ run_simulation <- function(
       solvers,
       correlations,
       list(create_lagged_eir(variables, solvers, parameters)),
-      list(create_lagged_infectivity(variables, parameters))
+      list(create_lagged_infectivity(variables, parameters)),
+      timesteps
     ),
     variables = variables,
     events = unlist(events),
@@ -206,6 +207,7 @@ run_metapop_simulation <- function(
         correlations[[i]],
         lagged_eir,
         lagged_infectivity,
+        timesteps,
         mixing[i,],
         i
       )
@@ -248,4 +250,4 @@ run_simulation_with_repetitions <- function(
     }
   )
   do.call("rbind", dfs)
-}
\ No newline at end of file
+}
diff --git a/R/processes.R b/R/processes.R
index 6109490f..d3b11fda 100644
--- a/R/processes.R
+++ b/R/processes.R
@@ -14,6 +14,7 @@
 #' population and species in the simulation
 #' @param lagged_infectivity a list of LaggedValue objects for FOIM for each population
 #' in the simulation
+#' @param timesteps Number of timesteps
 #' @param mixing a vector of mixing coefficients for the lagged transmission
 #' values (default: 1)
 #' @param mixing_index an index for this population's position in the
@@ -29,6 +30,7 @@ create_processes <- function(
     correlations,
     lagged_eir,
     lagged_infectivity,
+    timesteps, 
     mixing = 1,
     mixing_index = 1
 ) {
diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp
index f5c226fd..affb233d 100644
--- a/src/RcppExports.cpp
+++ b/src/RcppExports.cpp
@@ -260,7 +260,7 @@ BEGIN_RCPP
 END_RCPP
 }
 
-RcppExport SEXP run_testthat_tests();
+RcppExport SEXP run_testthat_tests(void);
 
 static const R_CallMethodDef CallEntries[] = {
     {"_malariasimulation_create_adult_mosquito_model", (DL_FUNC) &_malariasimulation_create_adult_mosquito_model, 5},
diff --git a/tests/testthat/test-process-integration.R b/tests/testthat/test-process-integration.R
index f259be5e..1b07f127 100644
--- a/tests/testthat/test-process-integration.R
+++ b/tests/testthat/test-process-integration.R
@@ -19,6 +19,28 @@ test_that('create_processes makes valid process functions', {
   }
 })
 
+test_that('create_processes makes valid process functions when progress bar specified', {
+  parameters <- get_parameters()
+  parameters$progress_bar <- TRUE
+  events <- create_events(parameters)
+  variables <- create_variables(parameters)
+  vector_models <- parameterise_mosquito_models(parameters, 1)
+  solvers <- parameterise_solvers(vector_models, parameters)
+  renderer <- individual::Render$new(1)
+  processes <- create_processes(
+    renderer,
+    variables,
+    events,
+    parameters,
+    vector_models,
+    solvers,
+    timesteps = 100
+  )
+  for (process in processes) {
+    expect(is.function(process) || inherits(process, 'externalptr'), 'Process is not a function')
+  }
+})
+
 test_that('attach_event_listeners makes valid listeners', {
   parameters <- get_parameters()
   events <- create_events(parameters)