Codecov

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/test-coverage.yml

@@ -1,29 +1,14 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [master]
-    paths:
-      - DESCRIPTION
-      - NAMESPACE
-      - R/**
-      - src/**
-      - tests/**
-      - man/**
-      - data/**
+    branches: [master, codecov]
   pull_request:
-    branches: [master]
-    paths:
-      - DESCRIPTION
-      - NAMESPACE
-      - R/**
-      - src/**
-      - tests/**
-      - man/**
-      - data/**
-  workflow_dispatch:
-
-name: test-coverage
+    branches: [master, codecov]
+
+name: Test-Coverage
+
+permissions: read-all
 
 jobs:
   test-coverage:
@@ -40,10 +25,24 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: |
-            any::covr
-            kingaa/pomp
+          extra-packages: any::covr, any::xml2
+          needs: coverage
 
       - name: Test coverage
-        run: covr::codecov()
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          covr::to_cobertura(cov)
         shell: Rscript {0}
+
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+

R/panelPomp.R

@@ -121,8 +121,8 @@ setClass(
 #' @examples
 #' ## recreate the 'panelRandomWalk()' example
 #' prw <- panelRandomWalk()
-#' prw2 <- panelPomp(unit_objects(prw),params=coef(prw))
-#' identical(prw,prw2) # TRUE
+#' prw2 <- panelPomp(unit_objects(prw), params = coef(prw))
+#' identical(prw, prw2) # TRUE
 #' @author Carles \Breto
 #' @export
 panelPomp <- function (object, shared, specific, params) {

README.md

@@ -4,7 +4,7 @@
 
 ### an *R* package for inference on panel partially observed Markov processes
 
-[![Project Status: Active -- The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) [![CRAN Status](https://www.r-pkg.org/badges/version/panelPomp)](https://cran.r-project.org/package=panelPomp) [![Last CRAN release date](https://www.r-pkg.org/badges/last-release/panelPomp)](https://cran.r-project.org/package=panelPomp) [![R-CMD-check](https://github.com/panelPomp-org/panelPomp/actions/workflows/r-cmd-check.yml/badge.svg)](https://github.com/panelPomp-org/panelPomp/actions/workflows/r-cmd-check.yml) [![binary-build](https://github.com/panelPomp-org/panelPomp/actions/workflows/binary-build.yml/badge.svg)](https://github.com/panelPomp-org/panelPomp/actions/workflows/binary-build.yml) [![test-coverage](https://github.com/panelPomp-org/panelPomp/actions/workflows/test-coverage.yml/badge.svg)](https://github.com/panelPomp-org/panelPomp/actions/workflows/test-coverage.yml)
+[![Project Status: Active -- The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) [![CRAN Status](https://www.r-pkg.org/badges/version/panelPomp)](https://cran.r-project.org/package=panelPomp) [![Last CRAN release date](https://www.r-pkg.org/badges/last-release/panelPomp)](https://cran.r-project.org/package=panelPomp) [![R-CMD-check](https://github.com/panelPomp-org/panelPomp/actions/workflows/r-cmd-check.yml/badge.svg)](https://github.com/panelPomp-org/panelPomp/actions/workflows/r-cmd-check.yml) [![binary-build](https://github.com/panelPomp-org/panelPomp/actions/workflows/binary-build.yml/badge.svg)](https://github.com/panelPomp-org/panelPomp/actions/workflows/binary-build.yml) [![test-coverage](https://github.com/panelPomp-org/panelPomp/actions/workflows/test-coverage.yml/badge.svg)](https://github.com/panelPomp-org/panelPomp/actions/workflows/test-coverage.yml)[![codecov](https://codecov.io/gh/panelPomp-org/panelPomp/graph/badge.svg?token=NI3KX6NIUN)](https://codecov.io/gh/panelPomp-org/panelPomp)
 
 This package allows performing data analysis based on panel partially-observed Markov process (PanelPOMP) models. To implement such models, simulate them and fit them to panel data, 'panelPomp' extends some of the facilities provided for time series data by the 'pomp' package. Implemented methods include filtering (panel particle filtering) and maximum likelihood estimation (Panel Iterated Filtering) as proposed in Bretó, Ionides and King (2020) "Panel Data Analysis via Mechanistic Models" [\<doi:10.1080/01621459.2019.1604367\>](https://doi.org/10.1080/01621459.2019.1604367).
 

tests/panelPomp.R

@@ -42,8 +42,11 @@ noparams <- lapply(unit_objects(ppo),pomp,params=numeric(0))
 
 ep <- "Error : in ''panelPomp'': "
 ## test checks for missing arguments in panelPomp function
-test(wQuotes(ep,"''object'' is a required argument.\n"),
-     panelPomp())
+test(
+  wQuotes(ep, "''object'' is a required argument.\n"),
+  panelPomp()
+)
+
 test(wQuotes(ep,"''object'' must be either a ''panelPomp'' object or a list of",
              " ''pomp'' objects.","\n"),
      panelPomp(list(a=1)))

tests/panelPomp.Rout.save

@@ -102,9 +102,12 @@ Error : in ‘panelPomp’: ‘object’ must be either a ‘panelPomp’ object
 > 
 > ep <- "Error : in ''panelPomp'': "
 > ## test checks for missing arguments in panelPomp function
-> test(wQuotes(ep,"''object'' is a required argument.\n"),
-+      panelPomp())
+> test(
++   wQuotes(ep, "''object'' is a required argument.\n"),
++   panelPomp()
++ )
 [1] TRUE
+> 
 > test(wQuotes(ep,"''object'' must be either a ''panelPomp'' object or a list of",
 +              " ''pomp'' objects.","\n"),
 +      panelPomp(list(a=1)))