refresh package; fix #23; fix #24; fix #25

rapidsurveys · Dec 18, 2024 · 3d08d78 · 3d08d78
1 parent 87ae575
commit 3d08d78
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Showing 9 changed files with 46 additions and 32 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -8,3 +8,4 @@
 ^appveyor\.yml$
 ^codecov\.yml$
 ^_pkgdown\.yml$
+^README\.html$
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -4,9 +4,10 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
 
-name: R-CMD-check
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -4,12 +4,13 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
   release:
     types: [published]
   workflow_dispatch:
 
-name: pkgdown
+name: pkgdown.yaml
+
+permissions: read-all
 
 jobs:
   pkgdown:

diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -4,9 +4,10 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
 
-name: test-coverage
+name: test-coverage.yaml
+
+permissions: read-all
 
 jobs:
   test-coverage:
@@ -23,18 +24,28 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::covr
+          extra-packages: any::covr, any::xml2
           needs: coverage
 
       - name: Test coverage
         run: |
-          covr::codecov(
+          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 if error if not on PR, or if on PR and token is given
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
       - name: Show testthat output
         if: always()
         run: |

diff --git a/.gitignore b/.gitignore
@@ -2,4 +2,9 @@
 .Rhistory
 .RData
 .Ruserdata
+
+
 docs
+README.html
+
+
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -26,7 +26,7 @@ Suggests:
 Encoding: UTF-8
 Language: en-GB
 LazyData: true
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Roxygeon: list(markdown = TRUE)
 URL: https://rapidsurveys.io/okapi/,https://github.com/rapidsurveys/okapi
 BugReports: https://github.com/rapidsurveys/okapi/issues
diff --git a/README.Rmd b/README.Rmd
@@ -30,9 +30,9 @@ Data collection using computer-assisted personal interviewing or CAPI tools is n
 
 ## The ODK ecosystem
 
-## What does `okapi` do?
+## What does the package do?
 
-Currently, `okapi` provides functions to interface with two ODK-based systems: [ONA](https://getodk.org) and [KoboToolbox](https://kobotoolbox.org) via their respective APIs. The current set of functions perform the following tasks:
+Currently, `{okapi}` provides functions to interface with two ODK-based systems: [ONA](https://getodk.org) and [KoboToolbox](https://kobotoolbox.org) via their respective APIs. The current set of functions perform the following tasks:
 
 1. Authenticate with the respective servers using either an account password or an API token;
 
@@ -42,7 +42,7 @@ Currently, `okapi` provides functions to interface with two ODK-based systems: [
 
 ## Installation
 
-`okapi` is not yet available on [CRAN](https://cran.r-project.org).
+`{okapi}` is not yet available on [CRAN](https://cran.r-project.org).
 
 You can install `okapi` from the [RapidSurveys R Universe](https://rapidsurveys.r-universe.dev) with:
 
@@ -60,7 +60,7 @@ install.packages(
 
 ## Citation
 
-If you find the `okapi` package useful, please cite using the suggested citation provided by a call to the `citation` function as follows:
+If you use `{okapi}` in your work, please cite using the suggested citation provided by a call to the `citation` function as follows:
 
 ```{r cite}
 citation("okapi")

diff --git a/README.md b/README.md
@@ -28,9 +28,9 @@ Data Kit or ODK](https://getodk.org) technology.
 
 ## The ODK ecosystem
 
-## What does `okapi` do?
+## What does the package do?
 
-Currently, `okapi` provides functions to interface with two ODK-based
+Currently, `{okapi}` provides functions to interface with two ODK-based
 systems: [ONA](https://getodk.org) and
 [KoboToolbox](https://kobotoolbox.org) via their respective APIs. The
 current set of functions perform the following tasks:
@@ -45,7 +45,7 @@ current set of functions perform the following tasks:
 
 ## Installation
 
-`okapi` is not yet available on [CRAN](https://cran.r-project.org).
+`{okapi}` is not yet available on [CRAN](https://cran.r-project.org).
 
 You can install `okapi` from the [RapidSurveys R
 Universe](https://rapidsurveys.r-universe.dev) with:
@@ -64,16 +64,16 @@ install.packages(
 
 ## Citation
 
-If you find the `okapi` package useful, please cite using the suggested
+If you use `{okapi}` in your work, please cite using the suggested
 citation provided by a call to the `citation` function as follows:
 
 ``` r
 citation("okapi")
 #> To cite okapi in publications use:
 #> 
 #>   Ernest Guevarra (2023). okapi: Open Data Kit (ODK)-based
-#>   Computer-assisted Personal Interview (CAPI) Tools R package version
-#>   0.1.0.9000 URL https://rapidsurveys.io/okapi/
+#>   Computer-assisted Personal Interview (CAPI) Tools R package
+#>   version 0.1.0.9000 URL https://rapidsurveys.io/okapi/
 #> 
 #> A BibTeX entry for LaTeX users is
 #> 

diff --git a/pkgdown/_pkgdown.yml b/pkgdown/_pkgdown.yml
@@ -5,12 +5,11 @@ url: https://rapidsurveys.io/okapi
 template:
   bootstrap: 5
   bootswatch: united
-  theme: haddock
-  ganalytics:
+  theme: breeze-light
+  ganalytics: "G-VQQX28ZSBV"
 
 navbar:
-  bg: danger
-  type: light
+  bg: dark
   structure:
     left:  [home, intro, reference, articles, news]
     right: [mastodon, linkedin, github]
@@ -21,18 +20,14 @@ navbar:
     #   menu:
     #   - text: "Detecting haemoglobinaemia"
     #     href: articles/haemoglobinaemia.html
-    #   - text: "Detecting inflammation"
-    #     href: articles/inflammation.html
-    #   - text: "Detecting iron deficiency"
-    #     href: articles/iron-deficiency.html
-    #   - text: "Detecting iodine deficiency"
-    #     href: articles/iodine-deficiency.html
     mastodon:
       icon: "fab fa-mastodon fa-lg"
       href: https://fosstodon.org/@katilingban
+      aria-label: Mastodon
     linkedin:
       icon: "fab fa-linkedin fa-lg"
       href: https://www.linkedin.com/company/katilingban
+      aria-label: LinkedIn
 
 home:
   links:
@@ -61,15 +56,15 @@ reference:
 
   - title: ONA API - Forms
     contents:
-      - starts_with("ona_form")
+    - starts_with("ona_form")
 
   - title: ONA API - Projects
     contents:
-      - starts_with("ona_project")
+    - starts_with("ona_project")
 
   - title: ONA API - Organisations
     contents:
-      - starts_with("ona_org")
+    - starts_with("ona_org")
 
   - title: KoBo Toolbox API
     contents: