CI/CD Updates

.Rbuildignore

@@ -0,0 +1,9 @@
+^\.github$
+^metadata\.yaml$
+^.*\.Rproj$
+^\.Rproj\.user$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^.*\.{jpeg,png,gif,tiff}$
+.cicd-env

.cicd-env

@@ -0,0 +1 @@
+VALIDATE_R="false"

.github/workflows/CICD-base.yaml

@@ -0,0 +1,21 @@
+---
+name: CICD-base
+
+on:
+  - push
+  - pull_request
+
+jobs:
+  CICD-base:
+    runs-on: ubuntu-latest
+
+    timeout-minutes: 15
+
+    steps:
+      # Checkout codebase
+      - name: Checkout
+        uses: actions/checkout@v2
+
+      # Run CICD-base
+      - name: CICD-base
+        uses: docker://ghcr.io/uclahs-cds/cicd-base:latest

.github/workflows/r-cmd-check.yaml

@@ -0,0 +1,23 @@
+---
+name: R-CMD-check (r-lib)
+'on':
+  workflow_dispatch:
+  pull_request:
+    branches:
+      - main
+  push:
+    branches:
+      - main
+  schedule:
+    - cron: '0 0 * * MON'
+jobs:
+  R-CMD-check:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: r-lib/actions/setup-tinytex@v2
+      - name: Install LaTeX packages
+        run: |
+          tlmgr install \
+          mathpazo \
+          pgf
+      - uses: uclahs-cds/tool-R-CMD-check-action@stable

.gitignore

@@ -0,0 +1,9 @@
+# System files
+*.DS_Store
+
+# R
+.Rhistory
+.Rapp.history
+.RData
+*.Rproj*
+.Rproj.user

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: iSubGen
 Title: Integrative Subtype Generation
-Version: 1.0.0
-Date: 2021-04-07
+Version: 1.0.2
+Date: 2023-11-06
 Author: Natalie Fox
 Maintainer: Natalie Fox <nfox@mednet.ucla.edu>
 Description: Multi-data type subtyping, which is data type agnostic and accepts missing data. Subtyping is performed using intermediary assessments created with autoencoders and similarity calculations.
@@ -10,3 +10,5 @@ Imports: ConsensusClusterPlus, cluster (>= 1.14.4), keras, tensorflow, philentro
 Suggests: knitr, rmarkdown
 VignetteBuilder: knitr
 License: GPL-2
+URL: https://github.com/uclahs-cds/package-iSubGen
+BugReports: https://github.com/uclahs-cds/package-iSubGen/issues

NEWS

@@ -0,0 +1,15 @@
+iSubGen 1.0.2 2023-11-06
+
+ADDED
+* CI/CD actions to test code style and run standard R package checks
+* Standard metadata files for development
+
+--------------------------------------------------------------------------
+iSubGen 1.0.1 2021-04-15
+
+
+--------------------------------------------------------------------------
+iSubGen 1.0.0 2021-04-07
+
+ADDED
+* Initial release

metadata.yaml

@@ -0,0 +1,8 @@
+---
+Category: 'tool'
+Description: 'Multi-data type subtyping, which is data type agnostic and accepts missing data. Subtyping is performed using intermediary assessments created with autoencoders and similarity calculations.'
+Maintainers: 'pboutros@mednet.ucla.edu'
+Contributors: ['Natalie Fox', 'Paul C. Boutros']
+Languages: 'R'
+Dependencies: ['ConsensusClusterPlus', 'cluster', 'keras', 'tensorflow', 'philentropy']
+References: ''