Small tweaks to merge before the workshop

.gitignore

@@ -14,4 +14,3 @@ docs
 *.gcov
 .valgrind_ignore
 inst/doc
-pkgdown

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: odin2
 Title: Next generation odin
-Version: 0.2.13
+Version: 0.3.0
 Authors@R: c(person("Rich", "FitzJohn", role = c("aut", "cre"),
                     email = "[email protected]"),
              person("Wes", "Hinsley", role = "aut"),
@@ -17,9 +17,9 @@ URL: https://mrc-ide.github.io/odin2, https://github.com/mrc-ide/odin2
 BugReports: https://github.com/mrc-ide/odin2/issues
 Imports:
     cli,
-    dust2 (>= 0.2.1),
+    dust2 (>= 0.3.0),
     glue,
-    monty (>= 0.2.39),
+    monty (>= 0.3.0),
     rlang
 Suggests:
     decor,

R/migrate.R

@@ -75,7 +75,8 @@ odin_migrate <- function(path, dest) {
       "{cli::qty(sum(is_error))}{?This statement has/These statements have}",
       "been preserved in the migrated code at '{dest}'"))
     cli::cli_alert_info(
-      "See {.vignette migrating} for information on updating these issues")
+      paste("See {.vignette odin2::migrating} for information on updating",
+            "these issues"))
   }
 
   if (!any(is_migratable) && identical(path, dest)) {

R/parse_compat.R

@@ -290,7 +290,7 @@ parse_compat_fix_assign_time <- function(expr, call) {
           x = paste(
             "Your code contains an assignment to 'time' that we can't",
             "automatically migrate"),
-          i = "Please see {.vignette migrating} for guidance"),
+          i = "Please see {.vignette odin2::migrating} for guidance"),
         "E1048", expr, call)
     }
   }
@@ -313,11 +313,11 @@ parse_compat_fix_assign_dt <- function(expr, call) {
       ## might look.  For now, this is not allowed.
       odin_parse_error(
         c("Don't assign to 'dt'",
-          i = "'dt' is now provided to {.help dust::dust_system_create}'",
+          i = "'dt' is now provided to {.fun dust2::dust_system_create}'",
           x = paste(
             "Your odin code contains an assignment to 'dt' that we can't",
             "automatically migrate"),
-          i = "Please see {.vignette migrating} for guidance"),
+          i = "Please see {.vignette odin2::migrating} for guidance"),
         "E1049", expr, call)
     }
   }
@@ -345,7 +345,7 @@ parse_compat_fix_use_step <- function(expr, call) {
       c("Use of 'step' is no longer allowed",
         i = paste("Previously, discrete-time models used 'step' as a measure",
                   "of time, but we have removed this in odin2"),
-        i = "Please see {.vignette migrating} for guidance"),
+        i = "Please see {.vignette odin2::migrating} for guidance"),
       "E1050", expr, call)
   }
   expr

R/parse_system.R

@@ -36,7 +36,7 @@ parse_system_overall <- function(exprs, call) {
       c("Can't use 'output()' in discrete time systems",
         i = paste("You should be able to do what you need using 'update()'.",
                   "If you are migrating from odin 1.x.x, you might find",
-                  'some advice in {.vignette "migrating"}')),
+                  'some advice in {.vignette odin2::migrating}')),
       "E2020", src, call)
   }
 

README.md

@@ -1,7 +1,7 @@
-# odin2 <img src='man/figures/logo.png' align="right" height="139" />
+# odin2 <a href="https://mrc-ide.github.io/odin2/"><img src="man/figures/logo.png" align="right" height="139" alt="odin2 website" /></a>
 
 <!-- badges: start -->
-[![Project Status: Concept – Minimal or no implementation has been done yet, or the repository is only intended to be a limited example, demo, or proof-of-concept.](https://www.repostatus.org/badges/latest/concept.svg)](https://www.repostatus.org/#concept)
+[![Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip)
 [![R build status](https://github.com/mrc-ide/odin2/workflows/R-CMD-check/badge.svg)](https://github.com/mrc-ide/odin2/actions)
 [![codecov.io](https://codecov.io/github/mrc-ide/odin2/coverage.svg?branch=main)](https://codecov.io/github/mrc-ide/odin2?branch=main)
 <!-- badges: end -->

pkgdown/favicon/site.webmanifest

@@ -0,0 +1,21 @@
+{
+  "name": "",
+  "short_name": "",
+  "icons": [
+    {
+      "src": "/web-app-manifest-192x192.png",
+      "sizes": "192x192",
+      "type": "image/png",
+      "purpose": "maskable"
+    },
+    {
+      "src": "/web-app-manifest-512x512.png",
+      "sizes": "512x512",
+      "type": "image/png",
+      "purpose": "maskable"
+    }
+  ],
+  "theme_color": "#ffffff",
+  "background_color": "#ffffff",
+  "display": "standalone"
+}