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Update Workflows #55

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merged 5 commits into from
Sep 24, 2024
Merged

Update Workflows #55

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f9e599b
add release-based workflows
zkamvar Sep 20, 2024
a7da337
update installation instructions
zkamvar Sep 20, 2024
95eb59b
render README
zkamvar Sep 20, 2024
e40a1a8
use development mode for pages
zkamvar Sep 20, 2024
9aaa502
Apply suggestions from code review
zkamvar Sep 24, 2024
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27 changes: 22 additions & 5 deletions .github/workflows/R-CMD-check.yaml
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Expand Up @@ -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

Expand All @@ -29,21 +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
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For my own understanding: if there's a hotfix/release for this package (hubEvals), why do we need to remove the remote references for dependencies like hubUtils?

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This is because these packages are in the Remotes: field, which will pull the development versions of the packages when standing up the infrastructure for testing (see https://r-pkgs.org/dependencies-in-practice.html#depending-on-the-development-version-of-a-package).

By removing these from the DESCRIPTION, we force the workflow to pull the released versions of the dependent packages.


- 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
3 changes: 2 additions & 1 deletion .github/workflows/test-coverage.yaml
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Expand Up @@ -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:
Expand All @@ -39,7 +40,7 @@ jobs:
if: always()
run: |
## --------------------------------------------------------------------
find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
shell: bash

- name: Upload test results
Expand Down
22 changes: 17 additions & 5 deletions README.Rmd
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Expand Up @@ -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$set(
collapse = TRUE,
comment = "#>",
Expand All @@ -13,22 +13,33 @@ knitr::opts_chunk$set(
)
```


# hubEvals <a href="https://hubverse-org.github.io/hubEvals/"><img src="man/figures/logo.svg" align="right" height="131" alt="hubEvals 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/hubEvals)](https://CRAN.R-project.org/package=hubEvals)
[![R-CMD-check](https://github.com/hubverse-org/hubEvals/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/hubverse-org/hubEvals/actions/workflows/R-CMD-check.yaml)

<!-- badges: end -->

The goal of hubEvals is to provide tools for evaluating infectious disease model outputs. This package is part of the [Hubverse](https://hubverse.org) project, which aims to provide a suite of tools for infectious disease modeling hubs.

## Installation

You can install the development version of hubEvals from [GitHub](https://github.com/) with:
### Latest

You can install the [latest version of hubEvals from the R-universe](https://hubverse-org.r-universe.dev/hubEvals):

```r
install.packages("hubEvals", 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 hubEvals from [GitHub](https://github.com/) with:

```r
# install.packages("remotes")
remotes::install_github("hubverse-org/hubEvals")
```
Expand All @@ -48,8 +59,9 @@ library(hubEvals)

Please note that the hubEvals 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 hubEvals package](.github/CONTRIBUTING.md).


25 changes: 19 additions & 6 deletions README.md
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@@ -1,15 +1,16 @@

<!-- README.md is generated from README.Rmd. Please edit that file -->

# hubEvals <a href="https://Infectious-Disease-Modeling-Hubs.github.io/hubEvals/"><img src="man/figures/logo.svg" align="right" height="131" alt="hubEvals website" /></a>
# hubEvals <a href="https://hubverse-org.github.io/hubEvals/"><img src="man/figures/logo.svg" align="right" height="131" alt="hubEvals 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/hubEvals)](https://CRAN.R-project.org/package=hubEvals)
[![R-CMD-check](https://github.com/Infectious-Disease-Modeling-Hubs/hubEvals/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/Infectious-Disease-Modeling-Hubs/hubEvals/actions/workflows/R-CMD-check.yaml)
[![R-CMD-check](https://github.com/hubverse-org/hubEvals/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/hubverse-org/hubEvals/actions/workflows/R-CMD-check.yaml)

<!-- badges: end -->

The goal of hubEvals is to provide tools for evaluating infectious
Expand All @@ -19,12 +20,24 @@ of tools for infectious disease modeling hubs.

## Installation

You can install the development version of hubEvals from
### Latest

You can install the [latest version of hubEvals from the
R-universe](https://hubverse-org.r-universe.dev/hubEvals):

``` r
install.packages("hubEvals", 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 hubEvals from
[GitHub](https://github.com/) with:

``` r
# install.packages("remotes")
remotes::install_github("Infectious-Disease-Modeling-Hubs/hubEvals")
remotes::install_github("hubverse-org/hubEvals")
```

## Example
Expand All @@ -48,5 +61,5 @@ 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 hubEvals package](.github/CONTRIBUTING.md).
Community](https://hubverse.io/en/latest/overview/contribute.html) or
[how to contribute to the hubEvals package](.github/CONTRIBUTING.md).
3 changes: 3 additions & 0 deletions _pkgdown.yml
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@@ -1,3 +1,6 @@
url: https://infectious-disease-modeling-hubs.github.io/hubEvals/
template:
package: hubStyle
development:
mode: auto

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