Automate version check for Docker images

.github/version_check.sh

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+#!/bin/bash
+
+# Script to check API calls to GitHub and Pip packages and return list with existing version of Dockerimages
+
+get_current_version() {
+    local DOCKER=$1
+
+    VERSIONED_FILES=$(find "../${DOCKER}" -maxdepth 1 -type f -name 'Dockerfile_*' | grep -v 'Dockerfile_latest')
+    CURRENT_VERSION_FILE=$(echo "$VERSIONED_FILES" | grep -Eo 'Dockerfile_[0-9]+\.[0-9]+' | sort -V | tail -n 1)
+
+    if [ -z "$CURRENT_VERSION_FILE" ]; then
+        echo "No versioned Dockerfile found for ${DOCKER}."
+        return 1
+    fi
+
+    CURRENT_VERSION=$(echo "$CURRENT_VERSION_FILE" | grep -Eo '[0-9]+\.[0-9]+')
+    echo "$CURRENT_VERSION"
+}
+
+
+## Tools with Github API calls
+declare -A github_dict=(["samtools"]="samtools/samtools" ["bedtools"]="arq5x/bedtools2" ["bcftools"]="samtools/bcftools" ["bwa"]="lh3/bwa" ["picard"]="broadinstitute/picard" \
+                        ["star"]="alexdobin/STAR" ["umitools"]="CGATOxford/UMI-tools" ["rtorch"]="mlverse/torch")
+
+for DOCKER in "${!github_dict[@]}"
+do
+    LATEST_VERSION=$(curl --silent "https://api.github.com/repos/${github_dict[$DOCKER]}/releases/latest" | jq -r .tag_name)
+    CURRENT_VERSION=$(get_current_version "$DOCKER")
+    echo "${DOCKER}:${CURRENT_VERSION}:${LATEST_VERSION}" >> version_list.txt
+done
+
+## Tools with PyPi API calls
+declare -A pypi_dict=(["scanpy"]="scanpy" ["scvi-tools"]="scvi-tools")
+for DOCKER in "${!pypi_dict[@]}"
+do
+    LATEST_VERSION=$(curl --silent "https://pypi.org/pypi/${pypi_dict[$DOCKER]}/json" | jq -r '.info.version')
+    CURRENT_VERSION=$(get_current_version "$DOCKER")
+    echo "${DOCKER}:${CURRENT_VERSION}:${LATEST_VERSION}" >> version_list.txt
+done
+
+## GATK
+LATEST_VERSION=$(curl --silent "https://api.anaconda.org/package/bioconda/gatk4" | jq -r '.latest_version')
+CURRENT_VERSION=$(get_current_version "gatk")
+echo "gatk:${CURRENT_VERSION}:${LATEST_VERSION}" >> version_list.txt
+
+# ## sra-tools
+# TOOL="sra-tools"
+# LATEST_VERSION=$(curl --silent "https://api.github.com/repos/ncbi/${TOOL}/tags" | jq -r '.[0].name')
+# CURRENT_VERSION=$(get_current_version "$TOOL")
+# echo "${TOOL}:${CURRENT_VERSION}:${LATEST_VERSION}" >> version_list.txt
+
+{ echo Tool:Current_version: Latest_version; cat version_list.txt; } | csvlook  > version_table.txt
+
+rm version_list.txt

.github/workflows/docker-version-check.yml

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+name: Dockerfile Version Check
+
+
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - main
+      - automate_version_check
+  schedule:
+    - cron: "0 0 1 * *"     # Run every 1 month
+
+env:
+  GH_TOKEN: ${{ github.token }}
+
+
+jobs:
+  check-version:
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+    defaults:
+      run:
+        working-directory: ./.github
+    steps:
+      - name: Check out the repository to the runner
+        uses: actions/checkout@v4  
+      - name: Install jq, curl, csvkit
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y jq curl csvkit
+      - name: Make the script files executable
+        run: chmod +x version_check.sh
+      - name: Run the scripts
+        run: |
+          ./version_check.sh
+          gh issue create --repo getwilds/wilds-docker-library --title "$(date +%B): Docker version check" --body-file version_table.txt