Merge branch 'devel' into renovate/actions-checkout-4.x

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.99.600
+current_version = 0.99.632
 commit = True
 commit_args = --no-verify
 tag = True

.github/workflows/create_github_release.yaml

@@ -0,0 +1,84 @@
+on:
+  push:
+    branches:
+      - devel
+      - RELEASE*
+      - ci/*
+
+name: Create Github Release
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  create-release:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    outputs:
+      tag_version: ${{ steps.create_release.outputs.tag_version }}
+    steps:
+      - name: Install Act dependencies
+        if: ${{ env.ACT }}
+        run: |
+          apt-get update && apt-get install gh
+      - name: Checkout
+        uses: actions/checkout@44c2b7a8a4ea60a981eaca3cf939b5f4305c123b # v4.1.5
+        with:
+          fetch-depth: 0
+      - name: Get most recent tag
+        id: get_tag
+        run: echo "TAG_VERSION=$(git describe --tags --abbrev=0)" >> "$GITHUB_ENV"
+      - name: Create Release
+        id: create_release
+        env:
+          GITHUB_TOKEN: ${{ github.token }}
+        run: |
+          echo "Creating release for tag $TAG_VERSION"
+          gh release create $TAG_VERSION --title "Release $TAG_VERSION" --notes "Release $TAG_VERSION" --target ${{ github.ref }}
+          echo "tag_version=$TAG_VERSION" >> "$GITHUB_OUTPUT"
+  create_release_artifacts:
+    needs: [create-release]
+    permissions:
+      contents: write
+    strategy:
+      fail-fast: false
+      matrix:
+        r_version: ['release', 'devel']
+    runs-on: ubuntu-latest
+    steps:
+      - name: Install Act dependencies
+        if: ${{ env.ACT }}
+        run: |
+          apt-get update && apt-get install gh
+      - name: Checkout
+        uses: actions/checkout@44c2b7a8a4ea60a981eaca3cf939b5f4305c123b # v4.1.5
+      - name: Install system dependencies
+        run: |
+          sudo apt-get install -y libxml2-dev \
+          libssl-dev libcurl4-openssl-dev \
+          libharfbuzz-dev libfribidi-dev \
+          pandoc
+      - name: Setup R
+        uses: r-lib/actions/setup-r@929c772977a3a13c8733b363bf5a2f685c25dd91 # v2.9.0
+        with:
+          r-version: ${{ matrix.r_version }}
+          use-public-rspm: true
+        id: r
+      - name: Install dependencies
+        uses: r-lib/actions/setup-renv@929c772977a3a13c8733b363bf5a2f685c25dd91 # v2.9.0
+      - name: Build Package
+        run: R CMD build .
+      - name: Rename Package
+        run: echo "NEWNAME=$(./utilities/rename-package.R *.tar.gz)" >> "$GITHUB_ENV"
+      - name: debug
+        run: |
+          echo "R version: ${{ steps.r.outputs.installed-r-version }}"
+          echo "Current Tag: ${{ needs.create-release.outputs.tag_version }}"
+          echo "Release File Name: ${{ env.NEWNAME }}"
+      - name: Upload Release Artifact
+        env:
+          RELEASE_TAG: ${{ needs.create-release.outputs.tag_version }}
+          GH_TOKEN: ${{ github.token }}
+        run: gh release upload ${{ env.RELEASE_TAG }} ${{ env.NEWNAME }}

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: drugfindR
 Title: Investigate iLINCS for candidate repurposable drugs
-Version: 0.99.600
+Version: 0.99.632
 Authors@R: c(
     person(given = c("Ali", "Sajid"),
            family = "Imami",

codemeta.json

@@ -7,7 +7,7 @@
   "codeRepository": "https://github.com/CogDisResLab/drugfindR",
   "issueTracker": "https://github.com/CogDisResLab/drugfindR/issues",
   "license": "https://spdx.org/licenses/GPL-3.0",
-  "version": "0.99.600",
+  "version": "0.99.632",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",

inst/WORDLIST

@@ -713,6 +713,7 @@ AURKBP
 AURKC
 Austricin
 aut
+automerge
 AUY
 Avagacestat
 Avanafil
@@ -3673,6 +3674,7 @@ GeneSymbol
 GeneTargets
 Genistein
 Genz
+geometricPrecision
 Geraniol
 Geranyl
 Geranylgeraniol
@@ -4484,6 +4486,7 @@ Imami
 Imatinib
 IMD
 IMEXON
+img
 imidazo
 imidazol
 imidazolidine
@@ -5375,6 +5378,7 @@ MASCRNA
 Masitinib
 MASP
 MASTL
+matchManagers
 MATK
 MATN
 MATR
@@ -6798,6 +6802,7 @@ PABPN
 pacakge
 PACC
 PACERR
+packageRules
 PACRG
 PACRGL
 PACS

renovate.json

@@ -18,6 +18,14 @@
   "pre-commit": {
     "enabled": true
   },
+  "packageRules": [
+    {
+        "automerge": true,
+        "matchManagers": [
+            "pre-commit"
+        ]
+    }
+],
   "platformCommit": true,
   "schedule": [
       "after 10pm and before 5am every weekday",

utilities/bump-version.sh

@@ -1,4 +1,5 @@
 #!/bin/bash
+set -euo pipefail
 
 # Get the commit message of the latest commit
 commit_message=$(git log -1 --pretty=%B)

utilities/rename-package.R

@@ -0,0 +1,39 @@
+#!/usr/bin/env -S Rscript --vanilla
+
+# This script takes in a name and renames it to include the current R
+# version and the current platform. It is intended to be used to rename
+# packages that are being uploaded to releases on GitHub.
+
+##  Parse the first argument as the package name + package version
+args <- commandArgs(trailingOnly = TRUE)
+if (length(args) != 1L) {
+    stop("Usage: rename-package.R <package-name>")
+}
+
+message("Received package name: ", args[[1L]])
+
+packageName <- strsplit(args, "_")[[1L]][[1L]]
+message("Package name: ", packageName)
+packageVersion <- strsplit(args, "_")[[1L]][[2L]]
+message("Package version: ", packageVersion)
+
+newName <- paste(
+    packageName, paste("R",
+        getRversion(),
+        sep = "-"
+    ),
+    paste0("v", packageVersion),
+    sep = "_"
+)
+
+message("Renaming package to: ", newName)
+
+value <- file.rename(args[[1L]], newName)
+
+if (value) {
+    message("Successfully renamed package to: ", newName)
+    cat(newName)
+} else {
+    stop("Failed to rename package to: ", newName)
+    cat("")
+}