add workflows

.github/workflows/pkgdown.yaml

@@ -0,0 +1,33 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+    tags: ['*']
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - uses: r-lib/actions/setup-r@v1
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v1
+        with:
+          extra-packages: pkgdown
+          needs: website
+
+      - name: Deploy package
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'

.github/workflows/render-rmarkdown.yaml

@@ -0,0 +1,36 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    paths: ['**.Rmd']
+
+name: render-rmarkdown
+
+jobs:
+  render-rmarkdown:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - uses: r-lib/actions/setup-r@v1
+
+      - uses: r-lib/actions/setup-renv@v1
+
+      - name: Render Rmarkdown files
+        run: |
+          RMD_PATH=($(git diff --name-only ${{ github.event.before }} ${{ github.sha }} | grep '[.]Rmd$'))
+          Rscript -e 'for (f in commandArgs(TRUE)) if (file.exists(f)) rmarkdown::render(f)' ${RMD_PATH[*]}
+
+      - name: Commit results
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+          git commit ${RMD_PATH[*]/.Rmd/.md} -m 'Re-build Rmarkdown files' || echo "No changes to commit"
+          git push origin || echo "No changes to commit"

.github/workflows/test-coverage.yaml

@@ -0,0 +1,30 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v1
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v1
+        with:
+          extra-packages: covr
+
+      - name: Test coverage
+        run: covr::codecov()
+        shell: Rscript {0}

README.Rmd

@@ -22,27 +22,35 @@ knitr::opts_chunk$set(
 
 # Overview
 
-activAnalyzer is a shinny app that was developed to analyse ActiGraph accelerometer data (.agd files) recorded at the hip in adults. Once analysis is completed, the app allows to export results to .csv files and to generate a report of the measurement (.pdf file). All the configured inputs relevant for interpreting the results are recorded in the report. Be sure that the inputs that are configured when generating the report correspond to the analysis that was actually performed (in other words, avoid modifying the inputs after generating satisfactory results). Please read the user's guide for details about how the app works.
+activAnalyzer is a shinny app that was developed to analyse ActiGraph accelerometer data (.agd files) recorded at the hip in adults. Once analysis is completed, the app allows to export results to .csv files and to generate a report of the measurement (.pdf file). All the configured inputs relevant for interpreting the results are recorded in the report. Be sure that the inputs that are configured when generating the report correspond to the analysis that was actually performed (in other words, avoid modifying the inputs after generating satisfactory results). Please read the [user's guide](https://github.com/pydemull/activAnalyzer/blob/master/inst/guide/user_guide_en.pdf) for details about how the app works.
 
-## Installation
+# Usage
+
+For now, this app can be used following two different ways: (i) on the web via a [shinyapps.io plateform] (pydemull.shinyapps.io/activanalyzer); (ii) on PC after installing R software and the activAnalyzer package.
+
+## Installation for using with R
 
 You can install the development version from [GitHub](https://github.com/) with:
 
 ``` r
 # install.packages("devtools")
 devtools::install_github("pydemull/activAnalyzer")
 ```
+
 ## Example
 
-To launch the app:
+To launch the app using R:
 
 ```{r example, eval=FALSE}
 library(activAnalyzer)
-run_app()
+activAnalyzer::run_app()
 ```
 
 
 ```{r, include=FALSE, eval=FALSE}
-You'll still need to render `README.Rmd` regularly, to keep `README.md` up-to-date. `devtools::build_readme()` is handy for this. You could also use GitHub Actions to re-render `README.Rmd` every time you push. An example workflow can be found here: <https://github.com/r-lib/actions/tree/master/examples>.
+You'll still need to render `README.Rmd` regularly, to keep `README.md` up-to-date:
+devtools::build_readme()
+
+You could also use GitHub Actions to re-render `README.Rmd` every time you push. An example workflow can be found here: <https://github.com/r-lib/actions/tree/master/examples>.
 ```
 

README.md

@@ -20,10 +20,18 @@ configured inputs relevant for interpreting the results are recorded in
 the report. Be sure that the inputs that are configured when generating
 the report correspond to the analysis that was actually performed (in
 other words, avoid modifying the inputs after generating satisfactory
-results). Please read the user’s guide for details about how the app
-works.
+results). Please read the [user’s
+guide](https://github.com/pydemull/activAnalyzer/blob/master/inst/guide/user_guide_en.pdf)
+for details about how the app works.
 
-## Installation
+# Usage
+
+For now, this app can be used following two different ways: (i) on the
+web via a \[shinyapps.io plateform\]
+(pydemull.shinyapps.io/activanalyzer); (ii) on PC after installing R
+software and the activAnalyzer package.
+
+## Installation for using with R
 
 You can install the development version from
 [GitHub](https://github.com/) with:
@@ -35,9 +43,9 @@ devtools::install_github("pydemull/activAnalyzer")
 
 ## Example
 
-To launch the app:
+To launch the app using R:
 
 ``` r
 library(activAnalyzer)
-run_app()
+activAnalyzer::run_app()
 ```

codecov.yml

@@ -0,0 +1,14 @@
+comment: false
+
+coverage:
+  status:
+    project:
+      default:
+        target: auto
+        threshold: 1%
+        informational: true
+    patch:
+      default:
+        target: auto
+        threshold: 1%
+        informational: true