From d50eb9e726082222436d93a68d9a0c2133cd1481 Mon Sep 17 00:00:00 2001
From: James Gebbie-Rayet <james.gebbie@gmail.com>
Date: Wed, 16 Sep 2026 13:55:23 +0100
Subject: [PATCH 1/3] Modify Renovate schedule and add custom managers

Updated the schedule to allow Renovate to run after 5am and before 5pm on weekdays. Added custom managers for pip and conda in Dockerfiles.
---
 .github/renovate.json | 31 ++++++++++++++++++++++++++++++-
 1 file changed, 30 insertions(+), 1 deletion(-)

diff --git a/.github/renovate.json b/.github/renovate.json
index c54154b..0b3e5d8 100644
--- a/.github/renovate.json
+++ b/.github/renovate.json
@@ -5,7 +5,7 @@
     "helpers:pinGitHubActionDigestsToSemver"
   ],
   "timezone": "Europe/London",
-  "schedule": ["after 9am and before 5pm every weekday"],
+  "schedule": ["after 5am and before 5pm every weekday"],
   "dependencyDashboard": true,
   "assignees": ["jimboid"],
   "minimumReleaseAge": "3 days",
@@ -15,5 +15,34 @@
       "groupName": "GitHub Actions",
       "addLabels": ["ci", "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 ae2c09f8521aab8527f9bbb116ea1db09893b1b2 Mon Sep 17 00:00:00 2001
From: James Gebbie-Rayet <james.gebbie@gmail.com>
Date: Wed, 16 Sep 2026 15:35:03 +0100
Subject: [PATCH 2/3] Update dependencies in Dockerfile installation

---
 docker/Dockerfile | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/docker/Dockerfile b/docker/Dockerfile
index a031257..ceea56f 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -11,7 +11,13 @@ USER $NB_USER
 WORKDIR $HOME
 
 # Install workshop deps 
-RUN mamba install -c conda-forge bioconda::blast openmm numpy=2.2 matplotlib scipy ambertools=$AMBERTOOLS_VER
+RUN conda install -y -c conda-forge -c bioconda \
+    conda-forge::matplotlib=3.11.1 \
+    conda-forge::numpy=2.5.3 \
+    conda-forge::openmm=8.6.1 \
+    conda-forge::scipy=1.18.1 \
+    conda-forge::ambertools=$AMBERTOOLS_VER \
+    bioconda::blast=2.17.0
 RUN pip install git+https://github.com/CharlieLaughton/Alphafix.git
 
 RUN mkdir blastp

From 6382330a5c273606b6f3af7741ceb7dbd83c93f0 Mon Sep 17 00:00:00 2001
From: James Gebbie-Rayet <james.gebbie@gmail.com>
Date: Wed, 16 Sep 2026 15:41:10 +0100
Subject: [PATCH 3/3] Update build.yaml to exclude linux/arm64

Removed linux/arm64 from the build matrix.
---
 .github/workflows/build.yaml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml
index 0596bd1..7502327 100644
--- a/.github/workflows/build.yaml
+++ b/.github/workflows/build.yaml
@@ -13,7 +13,6 @@ jobs:
       matrix:
         platform:
           - linux/amd64
-          - linux/arm64
     runs-on: ${{ matrix.platform == 'linux/amd64' && 'ubuntu-24.04' || matrix.platform == 'linux/arm64' && 'ubuntu-24.04-arm' }}
     name: build ${{ matrix.platform }}
     outputs: