Modify Renovate configuration for improved management

.github/renovate.json

@@ -1,21 +1,62 @@
 {
+  "$schema": "https://docs.renovatebot.com/renovate-schema.json",
   "extends": [
     "config:best-practices",
-    ":dependencyDashboard",
-    "group:monorepos",
-    "group:recommended"
+    "helpers:pinGitHubActionDigestsToSemver"
   ],
-  "enabledManagers": ["pep621", "github-actions"],
-  "pep621": {
-    "enabled": true
-  },
-  "rangeStrategy": "replace",
-  "schedule": ["* 8 * * 1-5"],
-  "labels": ["dependencies"],
+  "timezone": "Europe/London",
+  "schedule": ["after 9am and before 5pm every weekday"],
+  "dependencyDashboard": true,
+  "assignees": ["jimboid", "jkalayan"],
+  "minimumReleaseAge": "3 days",
   "packageRules": [
     {
-      "matchUpdateTypes": ["minor", "patch"],
-      "automerge": false
+      "matchManagers": ["github-actions"],
+      "groupName": "GitHub Actions",
+      "addLabels": ["ci", "dependencies"]
+    },
+    {
+      "matchManagers": ["pep621"],
+      "matchDepTypes": ["project.dependencies"],
+      "rangeStrategy": "widen",
+      "groupName": "Software Production Dependencies",
+      "addLabels": ["python", "production-deps"]
+    },
+    {
+      "matchManagers": ["pep621"],
+      "matchDepTypes": ["project.optional-dependencies", "build-system.requires"],
+      "rangeStrategy": "replace",
+      "groupName": "Python CI and Dev Tools",
+      "addLabels": ["python", "dev-dependencies"]
+    }
+  ],
+  "customManagers": [
+    {
+      "customType": "regex",
+      "managerFilePatterns": [
+        "/(^|/)Dockerfile[^/]*$/"
+      ],
+      "matchStringsStrategy": "recursive",
+      "matchStrings": [
+        "pip3? install[\\s\\S]*?(?<packages>(?:[\\w.-]+==[\\w.-]+[\\s\\\\]*)+)",
+        "(?<depName>[\\w.-]+)==(?<currentValue>[\\w.-]+)"
+      ],
+      "datasourceTemplate": "pypi",
+      "versioningTemplate": "pep440"
+    },
+    {
+      "customType": "regex",
+      "managerFilePatterns": [
+        "/(^|/)Dockerfile[^/]*$/"
+      ],
+      "matchStringsStrategy": "recursive",
+      "matchStrings": [
+        "(?:mamba|conda) install[\\s\\S]*?(?<packages>(?:(?:[\\w-]+::)?[\\w.-]+=[\\w.-]+[\\s\\\\]*)+)",
+        "(?:(?<channel>[\\w-]+)::)?(?<depName>[\\w.-]+)=(?<currentValue>[\\w.-]+)"
+      ],
+      "datasourceTemplate": "conda",
+      "registryUrlTemplate": "https://api.anaconda.org/package/{{#if channel}}{{channel}}{{else}}conda-forge{{/if}}/",
+      "versioningTemplate": "pep440"
     }
   ]
 }

docker/Dockerfile

@@ -42,9 +42,11 @@ COPY pyproject.toml README.md LICENSE ./
 COPY biosimdb_interface/ biosimdb_interface/
 
 # Install application and its dependencies into the venv
-RUN pip install --upgrade pip setuptools && \
-    pip install --no-cache-dir gunicorn .
-
+RUN pip install --upgrade pip
+RUN pip install --no-cache-dir \
+    setuptools==84.0.0 \
+    gunicorn==26.2.0
+    pip install --no-cache-dir .
 
 # Stage 3: Runtime
 FROM ubuntu:24.04