From 3f3c793d4ae1486c7beb19552da76393082829d3 Mon Sep 17 00:00:00 2001
From: James Gebbie-Rayet <james.gebbie@gmail.com>
Date: Wed, 16 Sep 2026 13:58:12 +0100
Subject: [PATCH 1/2] 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 9aced30fb1ff6515b225d8965d907f0ac8853f7d Mon Sep 17 00:00:00 2001
From: James Gebbie-Rayet <james.gebbie@gmail.com>
Date: Wed, 16 Sep 2026 14:58:52 +0100
Subject: [PATCH 2/2] Refactor dependency installation in Dockerfile

Updated package installation commands for dependencies.
---
 docker/Dockerfile | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/docker/Dockerfile b/docker/Dockerfile
index c4cb954..32360bd 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -9,8 +9,12 @@ USER $NB_USER
 WORKDIR $HOME
 
 # Install workshop deps
-RUN mamba install matplotlib numpy ipywidgets -y
-RUN pip install mdtraj
+RUN conda install -y -c conda-forge \
+    conda-forge::matplotlib=3.11.1 \
+    conda-forge::numpy=2.5.3 \
+    conda-forge::ipywidgets=8.1.9
+RUN pip install --no-cache-dir \
+    mdtraj==1.11.1.post2
 
 COPY --chown=1000:100 . .
 RUN rm -rf AUTHORS LICENSE README.md docker .git .github && \