0.0.9000

.Rbuildignore

@@ -4,3 +4,10 @@
 ^\.Rproj\.user$
 ^\.positai$
 ^\.claude$
+^LICENSE\.md$
+^README\.Rmd$
+^\.github$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^README.html$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

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

@@ -0,0 +1,75 @@
+# 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, develop]
+  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: 'release'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+
+      - name: Install Linux system libraries
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y \
+            libcairo2-dev \
+            libfribidi-dev \
+            libfontconfig1-dev \
+            libfreetype6-dev \
+            libharfbuzz-dev \
+            libjpeg-dev \
+            libpng-dev \
+            libtiff5-dev \
+            libwebp-dev \
+            pkg-config
+
+      - name: Configure Linux Makevars for gdtools
+        if: runner.os == 'Linux'
+        run: |
+          mkdir -p ~/.R
+          cat <<EOF >> ~/.R/Makevars
+          CPPFLAGS=$(pkg-config --cflags cairo freetype2 fontconfig)
+          LDFLAGS=$(pkg-config --libs-only-L cairo freetype2 fontconfig)
+          LDLIBS=$(pkg-config --libs-only-l cairo freetype2 fontconfig)
+          EOF
+
+      - 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
+          error-on: '"error"'
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/pkgdown.yaml

@@ -0,0 +1,47 @@
+# 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, develop]
+  pull_request:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown.yaml
+
+permissions: read-all
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v6
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@d92aa235d04922e8f08b40ce78cc5442fcfbfa2f # v4.8.0
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.gitignore

@@ -4,3 +4,5 @@
 .Ruserdata
 .positai
 .DS_Store
+docs
+README.html

DESCRIPTION

@@ -1,24 +1,43 @@
-Package: StudyToolBelt
+Package: studyGenerics
 Type: Package
-Title: What the Package Does (Title Case)
-Version: 0.1.0
+Title: A centralised repository of tested and frequently used methods for OMOP-CDM studies
+Version: 0.0.0.9000
 Authors@R: c(
     person(
-      "Jane", "Doe",
-      email = "jane@example.com",
+      "Cesar", "Barboza",
+      email = "c.barboza@mi-erasmusmc.nl",
       role = c("aut", "cre")
+    ),
+    person(
+      "Cristiana", "Di Tullio",
+      email = "a.alamshahi@mi-erasmusmc.nl",
+      role = c("aut")
+    ),
+    person(
+      "Arianna", "Alamshahi",
+      email = "a.alamshahi@mi-erasmusmc.nl",
+      role = c("aut")
     )
   )
-Description: More about what it does (maybe more than one line).
-    Continuation lines should be indented.
-License: What license is it under?
+Description: This set of generic functions wraps routine and basic functions required to run an OMOP-CDM study. 
+  But besides testing this recurrent methods, studyGenerics aims to centralise colaboration to speed-up development of this type of projects. 
+License: Apache License (>= 2)
 Encoding: UTF-8
 LazyData: true
 Imports: 
     cli,
     httr,
-    renv
+    renv,
+    ParallelLogger,
+    checkmate,
+    glue,
+    stringr,
+    zip,
+    here,
+    fs,
+    usethis
 Config/roxygen2/version: 8.0.0
 Suggests: 
     testthat (>= 3.0.0)
 Config/testthat/edition: 3
+URL: https://mi-erasmusmc.github.io/studyGenerics/

LICENSE.md

@@ -0,0 +1,194 @@
+Apache License
+==============
+
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+
+### Terms and Conditions for use, reproduction, and distribution
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