From 610152071792d9077649bee08e80c4c5e044904d Mon Sep 17 00:00:00 2001
From: James Gebbie-Rayet <james.gebbie@gmail.com>
Date: Thu, 17 Sep 2026 13:48:20 +0100
Subject: [PATCH 1/2] Enhance Renovate configuration for better management

Updated Renovate configuration with new settings for dependency management, including timezone, schedules, and custom managers.
---
 .github/renovate.json | 65 +++++++++++++++++++++++++++++++++++--------
 1 file changed, 53 insertions(+), 12 deletions(-)

diff --git a/.github/renovate.json b/.github/renovate.json
index 825ebdd..b1104d7 100644
--- a/.github/renovate.json
+++ b/.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"
     }
   ]
 }

From bae25c5cecc9dc8b8dfe6062c131d73b7d143018 Mon Sep 17 00:00:00 2001
From: James Gebbie-Rayet <james.gebbie@gmail.com>
Date: Thu, 17 Sep 2026 14:09:49 +0100
Subject: [PATCH 2/2] Refactor pip installation in Dockerfile

Updated pip installation commands to specify versions for setuptools and gunicorn.
---
 docker/Dockerfile | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/docker/Dockerfile b/docker/Dockerfile
index b0805c3..4a837a2 100644
--- a/docker/Dockerfile
+++ b/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