Merge pull request #145 from atorus-research/devel

Add back code coverage workflow

.github/workflows/test-coverage.yaml

@@ -0,0 +1,50 @@
+# 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
+
+jobs:
+ test-coverage:
+ runs-on: ubuntu-latest
+ env:
+ GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+ steps:
+ - uses: actions/checkout@v3
+
+ - 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
+ needs: coverage
+
+ - name: Test coverage
+ run: |
+ covr::codecov(
+ quiet = FALSE,
+ clean = FALSE,
+ install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+ )
+ shell: Rscript {0}
+
+ - 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@v3
+ with:
+ name: coverage-test-failures
+ path: ${{ runner.temp }}/package

DESCRIPTION

@@ -46,7 +46,7 @@ Imports:
  tidyselect (>= 1.1.0),
  tibble (>= 3.0.1),
  lifecycle,
- forcats (>= 0.4.0)
+ forcats (>= 1.0.0)
 Suggests: 
  testthat (>= 2.1.0),
  haven (>= 2.2.0),

NAMESPACE

@@ -135,6 +135,7 @@ importFrom(dplyr,between)
 importFrom(dplyr,bind_cols)
 importFrom(dplyr,bind_rows)
 importFrom(dplyr,case_when)
+importFrom(dplyr,cur_column)
 importFrom(dplyr,cur_group)
 importFrom(dplyr,distinct)
 importFrom(dplyr,do)
@@ -146,6 +147,7 @@ importFrom(dplyr,group_keys)
 importFrom(dplyr,if_else)
 importFrom(dplyr,lag)
 importFrom(dplyr,left_join)
+importFrom(dplyr,matches)
 importFrom(dplyr,mutate)
 importFrom(dplyr,mutate_all)
 importFrom(dplyr,mutate_at)
@@ -164,7 +166,7 @@ importFrom(dplyr,vars)
 importFrom(forcats,fct_collapse)
 importFrom(forcats,fct_drop)
 importFrom(forcats,fct_expand)
-importFrom(forcats,fct_explicit_na)
+importFrom(forcats,fct_na_value_to_level)
 importFrom(lifecycle,deprecate_soft)
 importFrom(lifecycle,deprecate_stop)
 importFrom(magrittr,"%>%")
@@ -257,6 +259,7 @@ importFrom(tibble,add_column)
 importFrom(tibble,rownames_to_column)
 importFrom(tibble,tibble)
 importFrom(tidyr,complete)
+importFrom(tidyr,fill)
 importFrom(tidyr,nesting)
 importFrom(tidyr,pivot_longer)
 importFrom(tidyr,pivot_wider)

R/call_standardise.R

@@ -0,0 +1,56 @@
+# # MIT License
+#
+# Copyright (c) 2020 rlang authors
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+#' rlang deprecated call_standardise, but this is necessary for
+#' the `modify_nested_call()` function. The capability isn't
+#' matched by the `call_match()` function.
+#'
+#' In modify nested call, this is used to restructure the function call
+#' to have all named arguments. Since all the functions called inside
+#' `call_standardise()` are exported and currently stable within rlang,
+#' I'm porting the function here.
+#'
+#' @param call
+#'
+#' @return call
+#' @noRd
+tplyr_call_standardise <- function(call, env= rlang::caller_env()) {
+
+ expr <- rlang::get_expr(call)
+
+ if (!rlang::is_call(expr)) {
+ stop("call_standardise error")
+ }
+
+ # The call name might be a literal, not necessarily a symbol
+ env <- rlang::get_env(call, env)
+ fn <- rlang::eval_bare(rlang::node_car(expr), env)
+
+ if (rlang::is_primitive(fn)) {
+ call
+ } else {
+ matched <- match.call(fn, expr)
+ rlang::set_expr(call, matched)
+ }
+
+}
+