Merge pull request #16 from tscnlab/dev_general

Dev general

.Rbuildignore

@@ -13,3 +13,4 @@
 
 ^app\.R$
 ^vignettes/articles$
+^\.gitlab-ci\.yml$

.github/workflows/test-coverage.yaml

@@ -1,13 +1,14 @@
 # Workflow derived from https://github.com/r-lib/actions/tree/v2/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
+name: test-coverage
+
+permissions: read-all
 
 jobs:
   test-coverage:
@@ -16,36 +17,45 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
       - 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_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
       - name: Show testthat output
         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
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: LightLogR
 Title: Work With Data from Wearable Light Loggers and Optical Radiation Dosimeters
-Version: 0.3.3
+Version: 0.3.4
 Authors@R: c(
     person("Johannes", "Zauner", 
       email = "[email protected]", role = c("aut", "cre"),
@@ -27,7 +27,8 @@ Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.1
 URL: https://github.com/tscnlab/LightLogR,
-    https://tscnlab.github.io/LightLogR/
+    https://tscnlab.github.io/LightLogR/,
+    https://zenodo.org/doi/10.5281/zenodo.11562600
 BugReports: https://github.com/tscnlab/LightLogR/issues
 Imports: 
     cowplot,
@@ -46,7 +47,6 @@ Imports:
     rlang,
     rsconnect,
     scales,
-    shiny,
     slider,
     stats,
     stringr,
@@ -57,6 +57,7 @@ Depends:
     R (>= 2.10)
 LazyData: true
 Suggests: 
+    covr,
     gt,
     knitr,
     patchwork,

NEWS.md

@@ -1,3 +1,7 @@
+# LightLogR 0.3.4
+
+* Backup to Zenodo, DOI and all
+
 # LightLogR 0.3.3
 
 * New and updated metric functions. LightLogR now contains 16 metric families with 60 sub-metrics.

R/aaa.r

@@ -1,4 +1,4 @@
-Time <- mEDI <- Time.data <- Datetime <- timestamp <- tz <- Day.data <- `DATE/TIME` <- n <- Datetime.rounded <- id <- sleep.colname.string <- file.name <- Interval <- original.datapoints.fleeting <- MEDI <- State.Brown <- Reference <- Reference.check <- Id <- Start.date.shift <- data <- Shift <- `MELANOPIC EDI` <- State <- group <- End <- Start <- Quant.x <- Quant.y <- is.implicit <- group.indices <- Id2 <- gap.id <- start <- end <- path <- auto.id <- n_max <- manual.id <- silent <- Light <- Day <- N <- is_missing <- Hour <- .change <- dst_start <- .dst <- .dst2 <- dst_adjustment <- auto.plot <- group.1 <- group.2 <- group.indices2 <-  NULL
+Time <- mEDI <- Time.data <- Datetime <- timestamp <- tz <- Day.data <- `DATE/TIME` <- n <- Datetime.rounded <- id <- sleep.colname.string <- file.name <- Interval <- original.datapoints.fleeting <- MEDI <- State.Brown <- Reference <- Reference.check <- Id <- Start.date.shift <- data <- Shift <- `MELANOPIC EDI` <- State <- group <- End <- Start <- Quant.x <- Quant.y <- is.implicit <- group.indices <- Id2 <- gap.id <- start <- end <- path <- auto.id <- n_max <- manual.id <- silent <- Light <- Day <- N <- is_missing <- Hour <- .change <- dst_start <- .dst <- .dst2 <- dst_adjustment <- auto.plot <- group.1 <- group.2 <- group.indices2 <- cluster_start <- cluster_end <- row_idx <- is_cluster <- cluster_idx <- is_pulse <- pulse_idx <- light <- time <- level <- duration <- mean_duration <- onset <- midpoint <- offset <- mean_onset <- mean_midpoint <- mean_offset <-  NULL
 
 empty_function <- function() {
   rsconnect::accountInfo()

R/data.r

@@ -38,7 +38,8 @@
 #' These expressions are used to import and prepare data from specific devices.
 #' The list is made explicit, so that a user, requiring slight changes to the
 #' import functions, (e.g., because a timestamp is formatted differently) can
-#' modify or add to the list. The list can be turned into a fully functional import function through `import_adjustment‚()`.
+#' modify or add to the list. The list can be turned into a fully functional 
+#' import function through `import_adjustment()`.
 #'
 #' @format `ll_import_expr` A list, with specific expressions for each supported device
 #' \describe{

README.Rmd

@@ -17,7 +17,7 @@ knitr::opts_chunk$set(
 
 <!-- badges: start -->
 [![R-CMD-check](https://github.com/tscnlab/LightLogR/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/tscnlab/LightLogR/actions/workflows/R-CMD-check.yaml)
-[![Test coverage](https://github.com/JZauner/LightLogR/actions/workflows/test-coverage.yaml/badge.svg)](https://github.com/JZauner/LightLogR/actions/workflows/test-coverage.yaml)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.11562600.svg)](https://doi.org/10.5281/zenodo.11562600)
 <!-- badges: end -->
 
 Personalized luminous exposure data is progressively gaining importance in various sectors, including research, occupational affairs, and fitness tracking. Data are collected through a proliferating selection of wearable loggers and dosimeters, varying in size, shape, functionality, and output format. Despite or maybe because of numerous use cases, the field lacks a unified framework for collecting, validating, and analyzing the accumulated data. This issue increases the time and expertise necessary to handle such data and also compromises the FAIRness (Findability, Accessibility, Interoperability, Reusability) of the results, especially in meta-analyses.

README.md

@@ -6,8 +6,7 @@
 <!-- badges: start -->
 
 [![R-CMD-check](https://github.com/tscnlab/LightLogR/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/tscnlab/LightLogR/actions/workflows/R-CMD-check.yaml)
-[![Test
-coverage](https://github.com/JZauner/LightLogR/actions/workflows/test-coverage.yaml/badge.svg)](https://github.com/JZauner/LightLogR/actions/workflows/test-coverage.yaml)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.11562600.svg)](https://doi.org/10.5281/zenodo.11562600)
 <!-- badges: end -->
 
 Personalized luminous exposure data is progressively gaining importance

inst/CITATION

@@ -10,7 +10,8 @@ bibentry(
   number   = "",
   pages    = "",
   url      = "https://github.com/tscnlab/LightLogR",
+  doi      = "10.5281/zenodo.11562600",
   textVersion = paste(
-  "Zauner, J.; Hartmeyer, S.L.; Spitschan, M. (2023): LightLogR: Working With Wearable Light Logger Data. R Package, Available on https://github.com/tscnlab/LightLogR"
+  "Zauner, J.; Hartmeyer, S.L.; Spitschan, M. (2023): LightLogR: Working With Wearable Light Logger Data. R Package, Available on https://github.com/tscnlab/LightLogR, doi:10.5281/zenodo.11562600"
   )
 )