0.3.1.9000 dev

.Rbuildignore

@@ -12,3 +12,4 @@
 ^README\.Rmd$
 ^CRAN-SUBMISSION$
 ^revdep$
+^codecov\.yml$

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,51 @@
+# 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:
+
+name: R-CMD-check.yaml
+
+permissions: read-all
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - 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
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/test-coverage.yaml

@@ -0,0 +1,62 @@
+# 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:
+
+name: test-coverage.yaml
+
+permissions: read-all
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - 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, any::xml2
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          print(cov)
+          covr::to_cobertura(cov)
+        shell: Rscript {0}
+
+      - uses: codecov/codecov-action@v5
+        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 }}
+          files: ./cobertura.xml
+          plugins: 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
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

NEWS.md

@@ -1,6 +1,12 @@
 # massProps (development version)
 
-* Covariance exposition for RoG uncertainty clarified (#43)
+* Invocation instructions in vignette cleaned up (#41).
+
+* Covariance exposition for RoG uncertainty clarified (#43).
+
+* Initialization in rollup_radii_of_gyration_unc() cleaned up (#44).
+
+* igraph loading fix for vignette (#48).
 
 # massProps 0.3.1
 

R/radii.R

@@ -71,7 +71,7 @@ rollup_radii_of_gyration_unc <- function(tree, df) {
               },
               sources
             ),
-            init <- c(0, 0, 0)
+            init = c(0, 0, 0)
           )
       ) / 2
       set_radii_of_gyration_unc(ds, target, amp)

README.Rmd

@@ -17,6 +17,9 @@ knitr::opts_chunk$set(
 # massProps
 
 <!-- badges: start -->
+[![CRAN status](https://www.r-pkg.org/badges/version/massProps)](https://CRAN.R-project.org/package=massProps)
+[![R-CMD-check](https://github.com/jsjuni/massProps/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/jsjuni/massProps/actions/workflows/R-CMD-check.yaml)
+[![Codecov test coverage](https://codecov.io/gh/jsjuni/massProps/graph/badge.svg)](https://app.codecov.io/gh/jsjuni/massProps)
 <!-- badges: end -->
 
 The `massProps` package extends `rollupTree` with functions to recursively calculate mass properties (and optionally, their uncertainties) for arbitrary composition trees. Formulas implemented are described in a technical paper published by the Society of Allied Weight Engineers [@zimmerman:05:sawe].

README.md

@@ -5,6 +5,11 @@
 
 <!-- badges: start -->
 
+[![CRAN
+status](https://www.r-pkg.org/badges/version/massProps)](https://CRAN.R-project.org/package=massProps)
+[![R-CMD-check](https://github.com/jsjuni/massProps/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/jsjuni/massProps/actions/workflows/R-CMD-check.yaml)
+[![Codecov test
+coverage](https://codecov.io/gh/jsjuni/massProps/graph/badge.svg)](https://app.codecov.io/gh/jsjuni/massProps)
 <!-- badges: end -->
 
 The `massProps` package extends `rollupTree` with functions to

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

vignettes/massProps.Rmd

@@ -141,9 +141,7 @@ The tree is an `igraph::graph` with vertices named by identifiers in the mass pr
 ## Invocation
 
 ```{r setup}
-library(rollupTree)
 library(massProps)
-suppressPackageStartupMessages({library(igraph)})
 ```
 
 Suppose we have the following mass properties table:
@@ -154,12 +152,16 @@ test_table
 
 Suppose we also have this tree:
 
+```{r echo = FALSE}
+suppressPackageStartupMessages({library(igraph)})
+```
 ```{r}
+library(igraph)
 test_tree
 ```
 
 ```{r echo = FALSE}
-plot(test_tree,layout=layout_as_tree(test_tree, 2, mode="in"), vertex.shape = 'none', edge.arrow.mode = 0)
+igraph::plot.igraph(test_tree,layout=igraph::layout_as_tree(test_tree, 2, mode="in"), vertex.shape = 'none', edge.arrow.mode = 0)
 ```
 
 Then we can compute mass properties for non-leaf elements by calling `rollup_mass_props()`:
@@ -189,7 +191,7 @@ na_mass_props_and_unc <- function(d, t, v) {
 na_mass_props_and_unc_update <- function(d, t, s) {
   update_mass_props_and_unc(d, t, s, override = na_mass_props_and_unc)
 }
-sawe_input <- rollup(sawe_tree, sawe_table, update = na_mass_props_and_unc_update, validate_ds = validate_mass_props_and_unc_table)
+sawe_input <- rollupTree::rollup(sawe_tree, sawe_table, update = na_mass_props_and_unc_update, validate_ds = validate_mass_props_and_unc_table)
 ```
 
 ```{r}
@@ -806,7 +808,7 @@ The corresponding R code is
               },
               sources
             ),
-            init <- c(0, 0, 0)
+            init = c(0, 0, 0)
           )
       ) / 2
  ```
@@ -1100,7 +1102,7 @@ The SAWE reference provides computed results for their example (excluding radii
 # Performance Evaluation
 
 ```{r echo = FALSE}
-mp_tree_depth <- max(dfs(mp_tree, 2, mode = "in", order=FALSE, dist=TRUE)$dist) + 1
+mp_tree_depth <- max(igraph::dfs(mp_tree, 2, mode = "in", order=FALSE, dist=TRUE)$dist) + 1
 nv <- length(igraph::V(mp_tree))
 ne <- length(igraph::E(mp_tree))
 nl <- length(which(igraph::degree(mp_tree, mode="in") == 0))