Merge pull request carriedaymont#118 from carriedaymont/main

Bring upd-v3 up to date

.Rbuildignore

@@ -17,3 +17,4 @@ Dockerfile
 cran-comments.md
 ^LICENSE\.md$
 ^vignettes$
+.DS_Store

.github/dependabot.yml

@@ -0,0 +1,11 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"

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

@@ -23,7 +23,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-pandoc@v2
 

.github/workflows/build-and-publish-image-latest.yml

@@ -0,0 +1,26 @@
+# Adapted from:
+# https://github.com/VaultVulp/gp-docker-action#complete-workflow-example
+name: Build and publish latest
+
+on:
+  push:
+    branches:
+      - "main"
+  pull_request:
+    branches:
+      - "main"
+
+jobs:
+  build-and-publish-image:
+    if: github.repository == 'mitre/growthcleanr'
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Build and publish Docker image
+        uses: VaultVulp/[email protected]
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          image-name: gcr-image
+          image-tag: latest

.github/workflows/build-and-publish-image-tag.yml

@@ -0,0 +1,23 @@
+# Adapted from:
+# https://github.com/VaultVulp/gp-docker-action#complete-workflow-example
+name: Build and publish tag
+
+on:
+  push:
+    tags:
+    - "*"
+
+jobs:
+  build-and-publish-image:
+    if: github.repository == 'mitre/growthcleanr'
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Build and publish Docker image
+        uses: VaultVulp/[email protected]
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          image-name: gcr-image
+          extract-git-tag: true

.github/workflows/pkgdown.yaml

@@ -21,7 +21,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -40,7 +40,7 @@ jobs:
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/[email protected].4
+        uses: JamesIves/github-pages-deploy-action@v4.4.1
         with:
           clean: false
           branch: gh-pages

DESCRIPTION

@@ -1,23 +1,24 @@
 Package: growthcleanr
 Type: Package
 Title: Data Cleaner for Anthropometric Measurements
-Version: 2.0.2
+Version: 2.1.1
 Authors@R: c(
-    person("Daymont","Carrie", email = "[email protected]", role = "aut"),
-    person("Grundmeier","Robert", role = "aut"),
-    person("Miller","Jeffrey", role = "aut"),
-    person("Campos","Diego", role = "aut"),
-    person("Chudnov","Dan", role = "ctb"),
-    person("De los Santos","Hannah", email = "[email protected]", role = c("ctb","cre")),
-    person("Cao","Lusha", role = "ctb"),
-    person("Silva","Steffani", role = "ctb"),
-    person("Zhang","Hanzhe", role = "ctb"),
-    person("Boyas","Matt", role = "ctb"),
-    person("Freedman","David", role = "ctb"),
-    person("Achilleos","Andreas", role = "ctb"),
-    person("Butts","Jessica", role = "ctb"),
-    person("Nguyen","Sheila", role = "ctb"),
-    person("Soleymani","Taraneh", role = "ctb")
+    person("Carrie", "Daymont", email = "[email protected]", role = c("ctb","cre")),
+    person("Robert", "Grundmeier", role = "aut"),
+    person("Jeffrey", "Miller", role = "aut"),
+    person("Diego", "Campos", role = "aut"),
+    person("Dan", "Chudnov", email = "[email protected]", role = "ctb"),
+    person("Hannah", "De los Santos", email = "[email protected]", role = c("ctb")),
+    person("Lusha", "Cao", role = "ctb"),
+    person("Steffani", "Silva", role = "ctb"),
+    person("Hanzhe", "Zhang", role = "ctb"),
+    person("Matt", "Boyas", role = "ctb"),
+    person("David", "Freedman", role = "ctb"),
+    person("Andreas", "Achilleos", role = "ctb"),
+    person("Jessica", "Butts", role = "ctb"),
+    person("Sheila", "Nguyen", role = "ctb"),
+    person("Taraneh", "Soleymani", role = "ctb"),
+    person("Max", "Olivier", role = "ctb")
   )
 Description: Identifies implausible anthropometric (e.g., height,
     weight) measurements in irregularly spaced longitudinal datasets, such as those from electronic health records.
@@ -45,4 +46,4 @@ Suggests:
     knitr (>= 1.29),
     rmarkdown (>= 2.3),
     testthat (>= 2.3.2)
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3

Dockerfile

@@ -1,4 +1,4 @@
-FROM rocker/tidyverse:latest
+FROM ghcr.io/rocker-org/tidyverse:latest
 
 LABEL maintainer="Daniel Chudnov <[email protected]>"
 
@@ -13,7 +13,7 @@ RUN mkdir /app/R_libs
 RUN echo "R_LIBS_USER=/app/R_libs" > /home/gcuser/.Renviron
 RUN echo ".libPaths(c('/app/R_libs', .libPaths()))" > /home/gcuser/.Rprofile
 
-RUN R -e "devtools::install_github('mitre/growthcleanr', dependencies = TRUE, ref = 'main', lib='/app/R_libs')"
+RUN R -e "devtools::install_github('mitre/growthcleanr', dependencies = TRUE, ref = 'main', lib = '/app/R_libs')"
 
 ADD exec/gcdriver.R /usr/local/bin/
 RUN chmod ugo+rx /usr/local/bin/gcdriver.R

NEWS.md

@@ -1,3 +1,38 @@
+# growthcleanr 2.1.1 - 2023-03-01
+
+## Changed
+
+- Fixed missing adult measurements to be labeled "Missing" in output (#119)
+- Added tests for missingness in adult output
+- Fixed missing "-RV" codes in adult output
+- Corrected contributor names in DESCRIPTION (#120)
+- Added email for Dan Chudnov in DESCRIPTION (#95)
+
+# growthcleanr 2.1.0 - 2023-02-03
+
+## Added
+
+- Use dependabot to update GitHub workflow action versions (#94)
+- Use GitHub action to build and publish container image (#101)
+
+## Changed
+
+- Updated `ext_bmiz()` to match Dec 2022 NCHS guidelines (#98)
+- New options to keep dates, columns, unmatched rows in `longwide()` (#71)
+- Updated CITATION to match new CRAN requirements
+- Updated Dockerfile to build from repo, not CRAN
+
+# growthcleanr 2.0.3 - 2022-11-01
+
+## Added
+
+- CRAN release checklist now added under Developer Guidelines vignette (#99)
+
+## Changed
+
+- All possible levels for `cleangrowth()` output factor now enumerated
+- Updated maintainer to Carrie Daymont
+
 # growthcleanr 2.0.2 - 2022-09-13
 
 ## Added