From c962fa9b953405b2707e7f73ebc4b29a46a0aba0 Mon Sep 17 00:00:00 2001
From: Tim Dudgeon <tdudgeon@informaticsmatters.com>
Date: Wed, 5 Aug 2026 13:40:11 +0100
Subject: [PATCH] fix: bump im-data-manager-job-utilities to 1.3.0

im-rdkit-utilities==1.0.0 hard-pins im-data-manager-job-utilities==1.3.0,
which conflicted with these Dockerfiles' older pins (1.1.1/1.0.1) and
broke the build entirely (ResolutionImpossible) - not caught in #21
because the images weren't rebuilt locally at review time.

Verified: mordred, moldb and oddt images now build and pass their jote
suites end-to-end (mordred: 2/2, moldb's non-nextflow jobs, plus a
direct check of updateChargeFlagInAtomBlock). prep's image build is
separately blocked by an unrelated, pre-existing issue: its apt-get
step pulls packages from bullseye-security that have since been pruned
from the Debian mirror - confirmed this also fails identically on the
pre-migration Dockerfile-prep, so it's not something this change
introduced. Verified prep's pip resolution (the part this change
actually touches) succeeds cleanly in isolation.

Part of #18.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
---
 Dockerfile-jaqpot  | 2 +-
 Dockerfile-moldb   | 2 +-
 Dockerfile-mordred | 2 +-
 Dockerfile-oddt    | 2 +-
 Dockerfile-prep    | 2 +-
 5 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/Dockerfile-jaqpot b/Dockerfile-jaqpot
index e41f936..44d5010 100644
--- a/Dockerfile-jaqpot
+++ b/Dockerfile-jaqpot
@@ -4,7 +4,7 @@ RUN apt-get -y update &&\
   apt-get -y install procps &&\
   apt-get clean
 
-RUN pip install im-data-manager-job-utilities==1.0.1 im-rdkit-utilities==1.0.0
+RUN pip install im-data-manager-job-utilities==1.3.0 im-rdkit-utilities==1.0.0
 
 ENV HOME=/code
 WORKDIR ${HOME}
diff --git a/Dockerfile-moldb b/Dockerfile-moldb
index e6ede82..74ef9ed 100644
--- a/Dockerfile-moldb
+++ b/Dockerfile-moldb
@@ -17,7 +17,7 @@ RUN apt-get update && apt-get install -y gcc libpq-dev &&\
 RUN pip install sqlalchemy==1.4.49\
     psycopg2-binary==2.9.6\
     im-standardize-molecule==0.1.0\
-    im-data-manager-job-utilities==1.0.1\
+    im-data-manager-job-utilities==1.3.0\
     im-rdkit-utilities==1.0.0
 
 COPY *.py site_substructures.smarts ./
diff --git a/Dockerfile-mordred b/Dockerfile-mordred
index cd74f72..9270260 100644
--- a/Dockerfile-mordred
+++ b/Dockerfile-mordred
@@ -13,7 +13,7 @@ WORKDIR ${HOME}
 # install our requirements. RDKit is present in base container
 RUN pip install mordredcommunity==2.0.4 \
   im-standardize-molecule==0.1.0 \
-  im-data-manager-job-utilities==1.1.1 \
+  im-data-manager-job-utilities==1.3.0 \
   im-rdkit-utilities==1.0.0
 
 COPY im_mordred/descriptor_generator.py ./im_mordred/
diff --git a/Dockerfile-oddt b/Dockerfile-oddt
index 74440a5..75aa54a 100644
--- a/Dockerfile-oddt
+++ b/Dockerfile-oddt
@@ -15,7 +15,7 @@ ENV HOME=/code
 WORKDIR ${HOME}
 
 RUN pip install wheel six &&\
-  pip install im-data-manager-job-utilities==1.1.1\
+  pip install im-data-manager-job-utilities==1.3.0\
   im-rdkit-utilities==1.0.0\
   git+https://github.com/oddt/oddt.git@master
 
diff --git a/Dockerfile-prep b/Dockerfile-prep
index 43154b3..e47064f 100644
--- a/Dockerfile-prep
+++ b/Dockerfile-prep
@@ -19,7 +19,7 @@ WORKDIR ${HOME}
 RUN pip install scikit-learn==1.2.2\
   pdb2pqr==3.6.1\
   im-standardize-molecule==0.1.0\
-  im-data-manager-job-utilities==1.1.1\
+  im-data-manager-job-utilities==1.3.0\
   im-rdkit-utilities==1.0.0\
   sigfig==1.3.19