From 87c3afde193b78d41a61632f0a3e46c08aba46e5 Mon Sep 17 00:00:00 2001
From: James Gebbie-Rayet <james.gebbie@gmail.com>
Date: Wed, 16 Sep 2026 13:56:49 +0100
Subject: [PATCH 1/3] Update Renovate schedule and add custom managers

---
 .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 39e514524b69b6ef118f57a53fbee76f71bb58d6 Mon Sep 17 00:00:00 2001
From: James Gebbie-Rayet <james.gebbie@gmail.com>
Date: Wed, 16 Sep 2026 15:59:08 +0100
Subject: [PATCH 2/3] Refactor Dockerfile to install specific AiiDA versions

Updated dependencies for AiiDA and GROMACS in Dockerfile.
---
 docker/Dockerfile | 27 ++++-----------------------
 1 file changed, 4 insertions(+), 23 deletions(-)

diff --git a/docker/Dockerfile b/docker/Dockerfile
index 49de432..ac5109b 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -5,31 +5,14 @@ FROM ghcr.io/ccpbiosim/jupyterhub-base:$BASE_IMAGE
 LABEL maintainer="James Gebbie-Rayet <james.gebbie@stfc.ac.uk>"
 ARG TARGETPLATFORM
 
-USER root
-WORKDIR /opt/
-
-# Install RabbitMQ for Mac
-RUN apt-get update --yes && \
-    apt-get install --yes --no-install-recommends \
-    erlang  && \
-    apt-get clean && rm -rf /var/lib/apt/lists/* && \
-    wget -c --no-check-certificate https://github.com/rabbitmq/rabbitmq-server/releases/download/v3.10.14/rabbitmq-server-generic-unix-3.10.14.tar.xz && \
-    tar -xf rabbitmq-server-generic-unix-3.10.14.tar.xz && \
-    rm rabbitmq-server-generic-unix-3.10.14.tar.xz && \
-    ln -sf /opt/rabbitmq_server-3.10.14/sbin/* /usr/local/bin/ && \
-    fix-permissions /opt/rabbitmq_server-3.10.14
-
 USER $NB_USER
 WORKDIR $HOME
 
 # Dependencies for the workshop
-RUN mamba install -c conda-forge -y aiida-core
-RUN if [ "$TARGETPLATFORM" = "linux/amd64" ]; then \
-      mamba install conda-forge/linux-64::gromacs=2024.5=nompi_h5f56185_100 -y; \
-    elif [ "$TARGETPLATFORM" = "linux/arm64" ]; then \
-      mamba install conda-forge/linux-aarch64::gromacs=2024.5=nompi_h9afd374_100 -y; \
-    fi
-RUN pip3 install aiida-gromacs
+RUN conda install -y -c conda-forge \
+    conda-forge::aiida-core=2.9.2 \
+    conda-forge::aiida-gromacs=2.2.2 \
+    conda-forge::gromacs=2026.3=nompi_*
 
 RUN git clone https://github.com/PSDI-UK/aiida-gromacs.git && \
     mv aiida-gromacs/examples/lysozyme_files . && \
@@ -38,8 +21,6 @@ RUN git clone https://github.com/PSDI-UK/aiida-gromacs.git && \
 
 RUN echo "./aiida-start" >> ~/.bashrc
 COPY --chown=1000:100 docker/default-37a8.jupyterlab-workspace /home/jovyan/.jupyter/lab/workspaces/default-37a8.jupyterlab-workspace
-COPY --chown=1000:100 aiida-start /home/jovyan/
-COPY --chown=1000:100 aiida-stop /home/jovyan/
 
 # Always finish with non-root user as a precaution.
 USER $NB_USER

From a93daf46f5bc70580a08ee121c92ce83937da050 Mon Sep 17 00:00:00 2001
From: James Gebbie-Rayet <james.gebbie@gmail.com>
Date: Wed, 16 Sep 2026 16:06:50 +0100
Subject: [PATCH 3/3] Update Dockerfile to include ccpbiosim channel

---
 docker/Dockerfile | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docker/Dockerfile b/docker/Dockerfile
index ac5109b..eb18bb7 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -9,9 +9,9 @@ USER $NB_USER
 WORKDIR $HOME
 
 # Dependencies for the workshop
-RUN conda install -y -c conda-forge \
+RUN conda install -y -c conda-forge -c ccpbiosim \
     conda-forge::aiida-core=2.9.2 \
-    conda-forge::aiida-gromacs=2.2.2 \
+    ccpbiosim::aiida-gromacs=2.2.2 \
     conda-forge::gromacs=2026.3=nompi_*
 
 RUN git clone https://github.com/PSDI-UK/aiida-gromacs.git && \