From 80508f32882d5e412d830bc4c5c2588820d250ab Mon Sep 17 00:00:00 2001
From: James Gebbie-Rayet <james.gebbie@gmail.com>
Date: Wed, 16 Sep 2026 13:54:54 +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 e7570b1e821a1709ae63cab9185cf90b4a162986 Mon Sep 17 00:00:00 2001
From: James Gebbie-Rayet <james.gebbie@gmail.com>
Date: Wed, 16 Sep 2026 15:26:23 +0100
Subject: [PATCH 2/3] Update Dockerfile

---
 docker/Dockerfile | 15 ++++++++++++---
 1 file changed, 12 insertions(+), 3 deletions(-)

diff --git a/docker/Dockerfile b/docker/Dockerfile
index c2a533c..ad99c04 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -10,9 +10,18 @@ USER $NB_USER
 WORKDIR $HOME
 
 # Install workshop deps
-RUN mamba install oddt::oddt -y
-RUN pip install openbabel-wheel
-RUN mamba install termcolor numpy=2.3.5 matplotlib seaborn pandas vina
+RUN conda install -y -c conda-forge -c oddt \
+    conda-forge::matplotlib=3.11.1 \
+    conda-forge::numpy=2.5.3 \
+    conda-forge::pandas=3.0.5 \
+    conda-forge::seaborn=0.13.2 \
+    conda-forge::termcolor=3.3.0 \
+    conda-forge::vina=1.2.7 \
+    oddt::oddt=0.7
+RUN pip install --no-cache-dir \
+    openbabel-wheel==3.1.1.23
+
+RUN mamba install     
 
 # Get workshop files and move them to jovyan directory.
 COPY --chown=1000:100 . .

From 8ee514e2b3608224c9f50ee5a7d18c3c38661817 Mon Sep 17 00:00:00 2001
From: James Gebbie-Rayet <james.gebbie@gmail.com>
Date: Wed, 16 Sep 2026 15:36:50 +0100
Subject: [PATCH 3/3] Downgrade numpy version in Dockerfile

---
 docker/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docker/Dockerfile b/docker/Dockerfile
index ad99c04..178efe0 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -12,7 +12,7 @@ WORKDIR $HOME
 # Install workshop deps
 RUN conda install -y -c conda-forge -c oddt \
     conda-forge::matplotlib=3.11.1 \
-    conda-forge::numpy=2.5.3 \
+    conda-forge::numpy=2.3.5 \
     conda-forge::pandas=3.0.5 \
     conda-forge::seaborn=0.13.2 \
     conda-forge::termcolor=3.3.0 \