Update Workflows (#35)

* add release-based workflows * update installation instructions * render README * use development mode for pages * Apply suggestions from code review Co-authored-by: Evan Ray <elray1@users.noreply.github.com> --------- Co-authored-by: Evan Ray <elray1@users.noreply.github.com>
hubverse-org · Sep 24, 2024 · 84ee0c5 · 84ee0c5
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -5,6 +5,9 @@ on:
     branches: [main, master]
   pull_request:
     branches: [main, master]
+  workflow_dispatch:
+  schedule:
+    - cron: "47 14 * * 1"   # <=== Set to run at 14:47 on Mondays (avoiding 00:00 and top of the hour runs gives us a better chance for getting server time)
 
 name: R-CMD-check
 
@@ -29,22 +32,35 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v4
+      - id: checkout
+        uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-pandoc@v2
+      - name: Setup for Hotfix/Release Testing
+        id: release-setup
+        if: "${{ contains(github.event.pull_request.head.ref, '/hotfix/') || contains(github.event.pull_request.head.ref, '/release/') }}"
+        run: |
+          # remove the remote declarations from the DESCRIPTION so that we
+          # test the released version
+          sed -i -e '/  hubverse-org/d' DESCRIPTION
 
-      - uses: r-lib/actions/setup-r@v2
+      - id: setup-pandoc
+        uses: r-lib/actions/setup-pandoc@v2
+
+      - id: setup-r
+        uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
+          extra-repositories: https://hubverse-org.r-universe.dev
 
-      - uses: r-lib/actions/setup-r-dependencies@v2
+      - id: fetch-dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::rcmdcheck
           needs: check
 
-      - uses: r-lib/actions/check-r-package@v2
+      - id: check
+        uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
-          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -20,6 +20,7 @@ jobs:
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
+          extra-repositories: https://hubverse-org.r-universe.dev
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:

diff --git a/README.Rmd b/README.Rmd
@@ -4,7 +4,7 @@ output: github_document
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
-```{r, include = FALSE}
+```{r, include=FALSE}
 knitr::opts_chunk$set(
   collapse = TRUE,
   comment = "#>",
@@ -13,13 +13,14 @@ knitr::opts_chunk$set(
 )
 ```
 
-
 # hubExamples <a href="https://hubverse-org.github.io/hubExamples/"><img src="man/figures/logo.png" align="right" height="131" alt="hubExamples website" /></a>
 
 <!-- badges: start -->
+
 [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
 [![CRAN status](https://www.r-pkg.org/badges/version/hubExamples)](https://CRAN.R-project.org/package=hubExamples)
 [![R-CMD-check](https://github.com/hubverse-org/hubExamples/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/hubverse-org/hubExamples/actions/workflows/R-CMD-check.yaml)
+
 <!-- badges: end -->
 
 The goal of hubExamples is to provide example data for forecasting and scenario modeling hubs in the hubverse format.
@@ -28,9 +29,19 @@ This package is part of the [hubverse](https://hubverse.io/en/latest/) ecosystem
 
 ## Installation
 
-You can install the development version of hubExamples from [GitHub](https://github.com/) with:
+### Latest
+
+You can install the [latest version of hubExamples from the R-universe](https://hubverse-org.r-universe.dev/hubExamples):
+
+```r
+install.packages("hubExamples", repos = c("https://hubverse-org.r-universe.dev", "https://cloud.r-project.org"))
+```
 
-``` r
+### Development
+
+If you want to test out new features that have not yet been released, you can install the development version of hubExamples from [GitHub](https://github.com/) with:
+
+```r
 # install.packages("remotes")
 remotes::install_github("hubverse-org/hubExamples")
 ```
@@ -64,8 +75,9 @@ head(scenario_target_ts)
 
 Please note that the hubExamples package is released with a [Contributor Code of Conduct](.github/CODE_OF_CONDUCT.md). By contributing to this project, you agree to abide by its terms.
 
-
 ## Contributing
 
 Interested in contributing back to the open-source Hubverse project?
 Learn more about how to [get involved in the Hubverse Community](https://hubverse.io/en/latest/overview/contribute.html) or [how to contribute to the hubExamples package](.github/CONTRIBUTING.md).
+
+
diff --git a/README.md b/README.md
@@ -10,19 +10,31 @@ experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](h
 [![CRAN
 status](https://www.r-pkg.org/badges/version/hubExamples)](https://CRAN.R-project.org/package=hubExamples)
 [![R-CMD-check](https://github.com/hubverse-org/hubExamples/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/hubverse-org/hubExamples/actions/workflows/R-CMD-check.yaml)
+
 <!-- badges: end -->
 
 The goal of hubExamples is to provide example data for forecasting and
 scenario modeling hubs in the hubverse format.
 
-This package is part of the
-[hubverse](https://hubverse.io/en/latest/) ecosystem, which
-aims to provide a set of tools for infectious disease modeling hubs to
-share and collaborate on their work.
+This package is part of the [hubverse](https://hubverse.io/en/latest/)
+ecosystem, which aims to provide a set of tools for infectious disease
+modeling hubs to share and collaborate on their work.
 
 ## Installation
 
-You can install the development version of hubExamples from
+### Latest
+
+You can install the [latest version of hubExamples from the
+R-universe](https://hubverse-org.r-universe.dev/hubExamples):
+
+``` r
+install.packages("hubExamples", repos = c("https://hubverse-org.r-universe.dev", "https://cloud.r-project.org"))
+```
+
+### Development
+
+If you want to test out new features that have not yet been released,
+you can install the development version of hubExamples from
 [GitHub](https://github.com/) with:
 
 ``` r
@@ -40,20 +52,20 @@ package documentation for further information about these data objects.
 ``` r
 library(hubExamples)
 head(forecast_outputs)
-#>            model_id location reference_date horizon target_end_date
-#> 1 Flusight-baseline       48     2022-12-17       0      2022-12-17
-#> 2 Flusight-baseline       48     2022-12-17       0      2022-12-17
-#> 3 Flusight-baseline       48     2022-12-17       0      2022-12-17
-#> 4 Flusight-baseline       48     2022-12-17       0      2022-12-17
-#> 5 Flusight-baseline       48     2022-12-17       0      2022-12-17
-#> 6 Flusight-baseline       48     2022-12-17       0      2022-12-17
-#>             target output_type output_type_id        value
-#> 1 wk flu hosp rate         cdf           0.25 7.592233e-13
-#> 2 wk flu hosp rate         cdf            0.5 4.736251e-12
-#> 3 wk flu hosp rate         cdf           0.75 2.767176e-11
-#> 4 wk flu hosp rate         cdf              1 1.514312e-10
-#> 5 wk flu hosp rate         cdf           1.25 7.762725e-10
-#> 6 wk flu hosp rate         cdf            1.5 3.728055e-09
+#>            model_id reference_date          target horizon location
+#> 1 Flusight-baseline     2022-11-19 wk inc flu hosp       0       25
+#> 2 Flusight-baseline     2022-11-19 wk inc flu hosp       0       25
+#> 3 Flusight-baseline     2022-11-19 wk inc flu hosp       0       25
+#> 4 Flusight-baseline     2022-11-19 wk inc flu hosp       0       25
+#> 5 Flusight-baseline     2022-11-19 wk inc flu hosp       0       25
+#> 6 Flusight-baseline     2022-11-19 wk inc flu hosp       0       25
+#>   target_end_date output_type output_type_id value
+#> 1      2022-11-19    quantile           0.05    22
+#> 2      2022-11-19    quantile            0.1    31
+#> 3      2022-11-19    quantile           0.25    45
+#> 4      2022-11-19    quantile            0.5    51
+#> 5      2022-11-19    quantile           0.75    57
+#> 6      2022-11-19    quantile            0.9    71
 head(forecast_target_ts)
 #>         date location observation
 #> 1 2020-01-11       01           0
@@ -124,6 +136,5 @@ project, you agree to abide by its terms.
 
 Interested in contributing back to the open-source Hubverse project?
 Learn more about how to [get involved in the Hubverse
-Community](https://hubverse.io/en/latest/overview/contribute.html)
-or [how to contribute to the hubExamples
-package](.github/CONTRIBUTING.md).
+Community](https://hubverse.io/en/latest/overview/contribute.html) or
+[how to contribute to the hubExamples package](.github/CONTRIBUTING.md).
diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -1,3 +1,6 @@
 url: https://hubverse-org.github.io/hubExamples/
 template:
   package: hubStyle
+development:
+  mode: auto
+