From 898c1f78af8afa898f93a392c4a5ec045d0c50d0 Mon Sep 17 00:00:00 2001
From: Rich FitzJohn <r.fitzjohn@imperial.ac.uk>
Date: Tue, 11 Jul 2023 09:55:58 +0100
Subject: [PATCH 1/2] Implement str for pmcmc_samples objects

Fixes #226
---
 DESCRIPTION                 |  2 +-
 NAMESPACE                   |  1 +
 R/pmcmc_utils.R             |  7 +++++++
 tests/testthat/test-pmcmc.R | 11 +++++++++++
 4 files changed, 20 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 8042b0ab..5c758864 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: mcstate
 Title: Monte Carlo Methods for State Space Models
-Version: 0.9.15
+Version: 0.9.16
 Authors@R: c(person("Rich", "FitzJohn", role = c("aut", "cre"),
                     email = "rich.fitzjohn@gmail.com"),
              person("Marc", "Baguelin", role = "aut"),
diff --git a/NAMESPACE b/NAMESPACE
index 97306f80..38c556a0 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -7,6 +7,7 @@ S3method(format,mcstate_pmcmc)
 S3method(predict,mcstate_pmcmc)
 S3method(predict,smc2_result)
 S3method(print,mcstate_pmcmc)
+S3method(str,mcstate_pmcmc)
 export(adaptive_proposal_control)
 export(array_bind)
 export(array_drop)
diff --git a/R/pmcmc_utils.R b/R/pmcmc_utils.R
index 7c68e9ad..d73218f5 100644
--- a/R/pmcmc_utils.R
+++ b/R/pmcmc_utils.R
@@ -126,6 +126,13 @@ print.mcstate_pmcmc <- function(x, ...) {
 }
 
 
+##' @export
+str.mcstate_pmcmc <- function(object, ...) {
+  object <- unclass(object)
+  NextMethod("str")
+}
+
+
 ## NOTE: we need to expose a 'force' argument here for testing, as
 ## otherwise under R CMD check the progress bar does not run.
 pmcmc_progress <- function(n_steps, progress, simple = FALSE, force = FALSE) {
diff --git a/tests/testthat/test-pmcmc.R b/tests/testthat/test-pmcmc.R
index c6d022ec..a1c06daf 100644
--- a/tests/testthat/test-pmcmc.R
+++ b/tests/testthat/test-pmcmc.R
@@ -785,3 +785,14 @@ test_that("can run pmcmc for ode models", {
   expect_equal(results1$predict$model_time, results1$predict$time)
   expect_identical(results1$predict$filter, p1$inputs())
 })
+
+
+test_that("can use str() without error on samples object", {
+  dat <- example_uniform()
+  control <- pmcmc_control(10, save_state = FALSE, save_trajectories = FALSE)
+  res <- pmcmc(dat$pars, dat$filter, control = control)
+  cmp <- structure(res, class = NULL)
+  expect_output(str(res),
+                paste(capture.output(str(cmp)), collapse = "\n"),
+                fixed = TRUE)
+})

From 7832a7c93c7bf73ea56bc0a7d38e72c586540f4f Mon Sep 17 00:00:00 2001
From: Rich FitzJohn <r.fitzjohn@imperial.ac.uk>
Date: Tue, 11 Jul 2023 09:59:49 +0100
Subject: [PATCH 2/2] Minimal gha updates

---
 .github/workflows/R-CMD-check.yaml   | 2 +-
 .github/workflows/make-release.yaml  | 2 +-
 .github/workflows/pkgdown.yaml       | 2 +-
 .github/workflows/test-coverage.yaml | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 56bcba0b..cb779963 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -34,7 +34,7 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
 
diff --git a/.github/workflows/make-release.yaml b/.github/workflows/make-release.yaml
index 5f2ada55..6044d392 100644
--- a/.github/workflows/make-release.yaml
+++ b/.github/workflows/make-release.yaml
@@ -27,7 +27,7 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
 
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
index 0f8079bb..ffe21ba3 100644
--- a/.github/workflows/pkgdown.yaml
+++ b/.github/workflows/pkgdown.yaml
@@ -12,7 +12,7 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
 
       - uses: r-lib/actions/setup-pandoc@v1
 
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index 05cc58ec..a4739db1 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -17,7 +17,7 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
 
       - uses: r-lib/actions/setup-pandoc@v1