Merge pull request #63 from epiforecasts/i56_timeout

I56 timeout

.github/workflows/pr-commands.yaml

@@ -0,0 +1,55 @@
+on:
+  issue_comment:
+    types: [created]
+name: Commands
+jobs:
+  document:
+    if: startsWith(github.event.comment.body, '/document')
+    name: document
+    runs-on: macOS-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+      - uses: r-lib/actions/pr-fetch@master
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+      - uses: r-lib/actions/setup-r@master
+      - name: Install dependencies
+        run: Rscript -e 'install.packages(c("remotes", "roxygen2"))' -e 'remotes::install_deps(dependencies = TRUE)'
+      - name: Document
+        run: Rscript -e 'roxygen2::roxygenise()'
+      - name: commit
+        run: |
+          git config --local user.email "actions@github.com"
+          git config --local user.name "GitHub Actions"
+          git add man/\* NAMESPACE
+          git commit -m 'Document'
+      - uses: r-lib/actions/pr-push@master
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+  style:
+    if: startsWith(github.event.comment.body, '/style')
+    name: style
+    runs-on: macOS-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+      - uses: r-lib/actions/pr-fetch@master
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+      - uses: r-lib/actions/setup-r@master
+      - name: Install dependencies
+        run: Rscript -e 'install.packages("styler")'
+      - name: Style
+        run: Rscript -e 'styler::style_pkg()'
+      - name: commit
+        run: |
+          git config --local user.email "actions@github.com"
+          git config --local user.name "GitHub Actions"
+          git add \*.R
+          git commit -m 'Style'
+      - uses: r-lib/actions/pr-push@master
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}

.gitignore

@@ -3,6 +3,7 @@
 .RData
 .Ruserdata
 .cache
+.idea
 src/*.so
 src/*.dll
 src/*.o

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: EpiNow2
 Type: Package
 Title: Estimate Real-Time Case Counts and Time-Varying Epidemiological Parameters
-Version: 1.1.0
+Version: 1.2.0
 Authors@R: c(
     person(given = "Sam Abbott",
            role = c("aut", "cre"),
@@ -61,7 +61,9 @@ Imports:
     methods,
     patchwork,
     purrr,
+    R.utils (>= 2.0.0),
     Rcpp (>= 0.12.0),
+    rlang (>= 0.4.7),
     rstan (>= 2.18.1),
     rstantools (>= 2.0.0),
     scales,

NAMESPACE

@@ -34,6 +34,7 @@ export(theme_map)
 import(Rcpp)
 import(methods)
 importFrom(HDInterval,hdi)
+importFrom(R.utils,withTimeout)
 importFrom(cowplot,get_legend)
 importFrom(cowplot,panel_border)
 importFrom(cowplot,theme_cowplot)
@@ -57,6 +58,7 @@ importFrom(futile.logger,flog.debug)
 importFrom(futile.logger,flog.fatal)
 importFrom(futile.logger,flog.info)
 importFrom(futile.logger,flog.threshold)
+importFrom(futile.logger,flog.trace)
 importFrom(futile.logger,flog.warn)
 importFrom(future.apply,future_lapply)
 importFrom(ggplot2,.data)
@@ -91,6 +93,7 @@ importFrom(lubridate,days)
 importFrom(lubridate,wday)
 importFrom(patchwork,plot_layout)
 importFrom(purrr,compact)
+importFrom(purrr,keep)
 importFrom(purrr,map)
 importFrom(purrr,map_chr)
 importFrom(purrr,map_dbl)
@@ -99,6 +102,7 @@ importFrom(purrr,partial)
 importFrom(purrr,safely)
 importFrom(purrr,transpose)
 importFrom(purrr,walk)
+importFrom(rlang,cnd_muffle)
 importFrom(rstan,extract)
 importFrom(rstan,sampling)
 importFrom(scales,comma)

NEWS.md

@@ -1,3 +1,7 @@
+# EpiNow2 1.2.0
+* Added timeout and timing option to `regional_epinow`
+* Improved logging of warnings in `regional_epinow`
+
 # EpiNow2 1.1.0
 
 * Implemented reporting templates