Update test-coverage.yaml

added uploaded action
          token: ${{ secrets.CODECOV_TOKEN }}

Update test-coverage.yaml

removed
          # token: ${{ secrets.CODECOV_TOKEN }}
to confirm that it is not useful

Update test-coverage.yaml

https://github.com/codecov/example-python/blob/main/.github/workflows/ci.yml

https://app.codecov.io/gh/JohnGavin/hellow/new

Update test-coverage.yaml

from r-lib/covr#430

Update test-coverage.yaml

v3 -> v4
        uses: actions/upload-artifact@v4

Update test-coverage.yaml

v4->v3 second try

Update test-coverage.yaml

trying again

Update test-coverage.yaml

v4 -> v3
      uses: actions/upload-artifact@v3

Update test-coverage.yaml

v4 to v3
codecov/codecov-action#1274

Add GitHub links to DESCRIPTION

Initial commit

.Rbuildignore

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+^hellow\.Rproj$
+^\.Rproj\.user$
+^LICENSE\.md$
+_quarto.yml
+about.qmd
+hellow.code-workspace
+index.qmd
+styles.css
+^\.github$
+^docker$

.github/.gitignore

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+*.html

.github/workflows/test-coverage.yaml

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+# 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.yaml
+
+permissions: read-all
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr, any::xml2
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          covr::codecov(token = "${{ secrets.CODECOV_TOKEN }}")
+          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}
+
+      - name: Upload coverage reports to Codecov
+        # uses: codecov/codecov-action@v4.0.1
+        uses: codecov/codecov-action@v4
+        with:
+          # token: ${{ secrets.CODECOV_TOKEN }}
+          verbose: true
+        env:
+          CODECOV_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
+          token: ${{ secrets.CODECOV_TOKEN }}
+

.gitignore

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+.Rproj.user
+.Rhistory
+.Rdata
+.httr-oauth
+.DS_Store
+.quarto

DESCRIPTION

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+Package: hellow
+Title: What the Package Does (One Line, Title Case)
+Version: 0.0.0.9001
+Authors@R: 
+    person("John", "Gavin", , "john.b.gavin@gmail.com", role = c("aut", "cre"))
+Description: What the package does (one paragraph).
+License: MIT + file LICENSE
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.2.9000
+Imports: 
+    praise
+Suggests: 
+    testthat (>= 3.0.0)
+Config/testthat/edition: 3
+URL: https://github.com/JohnGavin/hellow
+BugReports: https://github.com/JohnGavin/hellow/issues

LICENSE

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+YEAR: 2024
+COPYRIGHT HOLDER: john gavin

LICENSE.md

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+# MIT License
+
+Copyright (c) 2024 john gavin
+
+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.

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export(isay)

R/isay.R

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+# Cmd-Shift-D: Document with Roxygen
+
+#' say hellp
+#'
+#' @param size number of time to greet
+#' @param ... other args passed to [sample()].
+#'
+#' @return a greeting
+#' @export
+#'
+#' @examples
+#'
+
+
+isay <- function(size=1, ...) {
+  message(praise::praise())
+  h <- sample(c("Hello", "Hi", "Howdy", "What's up?"), size=size, ...)
+  return(h)
+}

_quarto.yml

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+project:
+  type: website
+
+website:
+  title: "new_project_hellow"
+  navbar:
+    left:
+      - href: index.qmd
+        text: Home
+      - about.qmd
+
+format:
+  html:
+    theme: cosmo
+    css: styles.css
+    toc: true
+
+
+

about.qmd

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+---
+title: "About"
+---
+
+About this site

docker/Dockerfile

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+
+# https://blog.stephenturner.us/p/r-package-development-in-positron
+# pak::pak('exactextractr')
+# pracpac::use_docker()
+# pracpac::use_docker(build = FALSE, use_case = "pipeline")
+# add the line to install a few additional system utilities using apt, and actually write this shell script. The pracpac package templated out everything else.
+# build local docker file with 'hellow' tag
+# docker build -t ttmmghmm/hellow:latest -t hellow:0.0.0.9000 ./docker
+# docker run --rm ttmmghmm/hellow:latest
+#   not docker build -f Dockerfile ./docker
+# https://stackoverflow.com/questions/34434231/docker-how-to-authenticate-for-docker-push
+# docker login --username=ttmmghmm
+#  not docker login -u="${DOCKER_USERNAME}" -p="${DOCKER_PASSWORD}"
+# docker push ttmmghmm/hellow:latest
+# docker pull ttmmghmm/hellow:latest
+
+
+# TODO: switch to rix
+
+FROM rocker/r-ver:latest
+
+## copy the renv.lock into the image
+COPY renv.lock /renv.lock
+
+## install renv
+RUN Rscript -e 'install.packages(c("renv"))'
+
+## set the renv path var to the renv lib
+ENV RENV_PATHS_LIBRARY renv/library
+
+## restore packages from renv.lock
+RUN Rscript -e 'renv::restore(lockfile="/renv.lock", repos=NULL)'
+
+## copy in built R package
+COPY hellow_0.0.0.9001.tar.gz /hellow_0.0.0.9001.tar.gz
+
+## run script to install built R package from source
+RUN Rscript -e 'install.packages("/hellow_0.0.0.9001.tar.gz", type="source", repos=NULL)'
+
+
+RUN apt-get update && apt-get install -y bsdmainutils translate-shell
+
+COPY assets/run.sh /run.sh
+COPY assets/pre.R /pre.R
+
+CMD ["bash", "/run.sh"]

docker/assets/pre.R

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+
+
+library(hellow)
+
+ isay()

docker/assets/run.sh

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+#!/bin/bash
+
+# https://blog.stephenturner.us/p/r-package-development-in-positron
+
+# get translation language from first arg: default is french
+TOLANG="${1:-:fr}"
+HELLO=$(Rscript /pre.R)
+
+trans "$HELLO" "$TOLANG"

docker/renv.lock

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+{
+  "R": {
+    "Version": "4.4.1",
+    "Repositories": [
+      {
+        "Name": "ropenscireviewtools",
+        "URL": "https://ropensci-review-tools.r-universe.dev"
+      },
+      {
+        "Name": "CRAN",
+        "URL": "https://cloud.r-project.org"
+      }
+    ]
+  },
+  "Packages": {
+    "praise": {
+      "Package": "praise",
+      "Version": "1.0.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "a555924add98c99d2f411e37e7d25e9f"
+    }
+  }
+}

hellow.Rproj

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+Version: 1.0
+
+RestoreWorkspace: No
+SaveWorkspace: No
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+Encoding: UTF-8
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+LineEndingConversion: Posix
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace

hellow.code-workspace

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+{
+	"folders": [
+		{
+			"path": "hellow"
+		},
+		{
+			"path": "."
+		}
+	],
+    "settings": {}
+}

index.qmd

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+---
+params:
+    source_url: "https://blog.stephenturner.us/p/r-package-development-in-positron"
+title: "r-package-development-in-positron"
+---
+
+This is a Quarto website.
+
+To learn more about Quarto websites visit <https://quarto.org/docs/websites>.
+
+# usethis
++ dependency management,
++ DESCRIPTION file manipulation,
++ .R and test file creation,
++ data-raw creation,
++ vignettes,
++ pkgdown,
++ GitHub actions ...
+
+```{r, eval = FALSE}
+usethis::create_packagesw("hellow")
+usethis::use_mit_license("john gavin")
+usethis::use_package("praise")
+#
+# Cmd-Shift-D: Document with Roxygen
+#
+devtools::document()
+# cmd-shift-E
+devtools::check()
+# RStudio keyboard shortcut cmd-shift-B
+devtools::build()
+pak::local_install()
+
+usethis::use_test("hello")
+# cmd-shift-T
+devtools::test()
+
+```
+
++ RStudio uses `R CMD INSTALL`
++ Positron uses `pak::local_install()`
+
+## covr
++ https://covr.r-lib.org/
+
+```{r}
+library(covr)
+report() # requries DT
+# or
+if (interactive()) {
+    # covr::report(covr::package_coverage())
+    usethis::use_github_action("test-coverage")
+}
+```
+
+## pracpac
++ R Packaging with Docker
+
+```{r}
+# pak::pak('pracpac')
+# add renv.lock file and a Dockerfile
+pracpac::use_docker() # analyzes package DESCRIPTION
+```
++ build renv lock file
+    + captures versions of dependent packages installed
+    + writes Dockerfile builds R package
++ install all dependencies from renv lock file
+    + guarantees dependent pkgs versions install in Docker image
++ templates out pre- and post-processing R scripts
++ shell script that will drive the analysis
+
+## workflow
++ https://www.tidyverse.org/blog/2017/12/workflow-vs-script/
+```{r}
+library(here)
+```

inst/qmd/symlink pins_download_local_board.qmd

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+/Users/johngavin/docs_gh/rix/inst/qmd/pins_download_local_board.qmd

inst/qmd/symlink rix.qmd

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+/Users/johngavin/docs_gh/rix/inst/qmd/rix.qmd

inst/qmd/symlink usethis_targets.qmd

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+/Users/johngavin/docs_gh/rix/inst/qmd/usethis_targets.qmd