feat(18): drop the local utils.py

Dockerfile-dmpk

@@ -18,7 +18,6 @@ WORKDIR ${HOME}
 
 # numpy is pinned below 2 because this matplotlib release predates
 # NumPy 2.0 and its compiled extensions are not ABI-compatible with it
-RUN pip install "numpy<2" matplotlib==3.7.1 im-data-manager-job-utilities==1.0.1
+RUN pip install "numpy<2" matplotlib==3.7.1 sigfig "im-data-manager-job-utilities>=1.4.0"
 
-COPY utils.py ./
 COPY dmpk/*.py ./dmpk/

Dockerfile-fns

@@ -14,7 +14,7 @@ WORKDIR ${HOME}
 RUN pip install \
   neo4j-driver==4.4.11 \
   im-standardize-molecule==0.1.0 \
-  im-data-manager-job-utilities==1.1.1
+  "im-data-manager-job-utilities>=1.4.0"
 
-COPY fn_*.py utils.py ./
+COPY fn_*.py ./
 

Dockerfile-jaqpot

@@ -4,9 +4,9 @@ RUN apt-get -y update &&\
   apt-get -y install procps &&\
   apt-get clean
 
-RUN pip install im-data-manager-job-utilities==1.3.0 im-rdkit-utilities==1.0.0
+RUN pip install "im-data-manager-job-utilities>=1.4.0" "im-rdkit-utilities>=1.1.2"
 
 ENV HOME=/code
 WORKDIR ${HOME}
 
-COPY utils.py jaqpot*.py ./
+COPY jaqpot*.py ./

Dockerfile-moldb

@@ -17,8 +17,8 @@ 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==1.3.0\
-    im-rdkit-utilities==1.0.0
+    "im-data-manager-job-utilities>=1.4.0"\
+    "im-rdkit-utilities>=1.1.2"
 
 COPY *.py site_substructures.smarts ./
 COPY moldb/* ./moldb/

Dockerfile-mordred

@@ -13,8 +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>=1.4.0 \
-  im-rdkit-utilities>=1.1.2
+  "im-data-manager-job-utilities>=1.4.0" \
+  "im-rdkit-utilities>=1.1.2"
 
 COPY im_mordred/descriptor_generator.py ./im_mordred/
-COPY utils.py ./

Dockerfile-oddt

@@ -15,8 +15,8 @@ ENV HOME=/code
 WORKDIR ${HOME}
 
 RUN pip install wheel six &&\
-  pip install im-data-manager-job-utilities==1.3.0\
-  im-rdkit-utilities==1.0.0\
+  pip install "im-data-manager-job-utilities>=1.4.0"\
+  "im-rdkit-utilities>=1.1.2"\
   git+https://github.com/oddt/oddt.git@master
 
 COPY *.py ./

Dockerfile-plants

@@ -13,7 +13,7 @@ RUN apt-get update &&\
     python3-openbabel &&\
   apt-get clean
 
-COPY pharmacophore.py utils.py /code/
+COPY pharmacophore.py /code/
 
 RUN chmod a+x /code/*.py &&\
-    pip install im-data-manager-job-utilities==1.1.1
+    pip install "im-data-manager-job-utilities>=1.4.0"

Dockerfile-prep

@@ -23,8 +23,8 @@ 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>=1.4.0\
-  im-rdkit-utilities>=1.1.2\
+  "im-data-manager-job-utilities>=1.4.0"\
+  "im-rdkit-utilities>=1.1.2"\
   sigfig==1.3.19
 
 COPY *.py fpscores.pkl.gz site_substructures.smarts ./

align_mol.py

@@ -21,7 +21,7 @@
 from rdkit.Chem import rdMolAlign
 from rdkit.Chem import rdFMCS
 
-import utils
+from dm_job_utilities import utils
 
 
 def align(query_mol, inputs_sdf, outputs_sdf, query_atoms=None, keep_all=False, mcs_params={}, interval=None):

assemble_conformers.py

@@ -24,7 +24,9 @@
 """
 
 import argparse, os, time, gzip
-import utils, rdkit_utils
+import rdkit_utils
+from dm_job_utilities import utils
+from digest_utils import get_path_from_digest
 from dm_job_utilities.dm_log import DmLog
 
 from rdkit import Chem
@@ -66,7 +68,7 @@ def execute(input, output, data_dir, mode,
                 uid = tokens[1]
                 digest = tokens[2]
                 parts = [data_dir]
-                parts.extend(utils.get_path_from_digest(digest))
+                parts.extend(get_path_from_digest(digest))
                 path = os.path.join(*parts)
                 if not os.path.isdir(path):
                     utils.log('WARNING, path', path, 'not found')

cluster_butina.py

@@ -20,7 +20,7 @@
 from rdkit.Chem import AllChem, MACCSkeys
 from rdkit.ML.Cluster import Butina
 
-import utils
+from dm_job_utilities import utils
 import rdkit_utils
 from dm_job_utilities.dm_log import DmLog
 

digest_utils.py

@@ -0,0 +1,40 @@
+# Copyright 2025 Informatics Matters Ltd.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""Mapping a molecule digest onto the sharded directory layout used by the
+enumeration/conformer pipeline.
+
+This lives here rather than in dm_job_utilities: the shared package
+deliberately dropped get_path_from_digest as obsolete, but the layout it
+describes is still what prepare_enum_conf_lists.py writes and
+assemble_conformers.py reads back.
+"""
+
+default_num_chars = 2
+default_num_levels = 2
+
+
+def get_path_from_digest(
+    digest, num_chars=default_num_chars, num_levels=default_num_levels
+):
+    """Split a digest into the directory components that locate its files,
+    e.g. 'abcdef...' -> ['ab', 'cd'] for the default 2 chars over 2 levels.
+    """
+    parts = []
+    start = 0
+    for _ in range(0, num_levels):
+        end = start + num_chars
+        parts.append(digest[start:end])
+        start = start + num_chars
+    return parts

dmpk/pk_tmax_cmax_sim.py

@@ -23,7 +23,15 @@
 matplotlib.use('Agg')
 import matplotlib.pyplot as plt
 
-import utils
+from dm_job_utilities import utils
+from sigfig import round as _sigfig_round
+
+
+def sigfig_round(value, sigfigs):
+    """Round to N significant figures. warn=False keeps sigfig quiet when a
+    value carries fewer significant figures than requested, which is common
+    here and was silent under the previous implementation."""
+    return _sigfig_round(value, sigfigs=sigfigs, warn=False)
 
 
 def generatePlot(t_hf, t_hf_a, D, AUC, tn, quiet=False, plot_height=4, plot_width=10, font_size=12, basename='output'):
@@ -37,11 +45,11 @@ def generatePlot(t_hf, t_hf_a, D, AUC, tn, quiet=False, plot_height=4, plot_widt
     V_F = D/kel/AUC
 
     outputs = collections.OrderedDict()
-    outputs['Tmax(hr)'] = utils.round_to_significant_number(Tmax, 3)
-    outputs['Cmax(mg/L)'] = utils.round_to_significant_number(Cmax, 3)
-    outputs['Kel(hr-1)'] = utils.round_to_significant_number(kel, 3)
-    outputs['Ka(hr-1)'] = utils.round_to_significant_number(ka, 3)
-    outputs['V/F(L)'] = utils.round_to_significant_number(V_F, 3)
+    outputs['Tmax(hr)'] = sigfig_round(Tmax, 3)
+    outputs['Cmax(mg/L)'] = sigfig_round(Cmax, 3)
+    outputs['Kel(hr-1)'] = sigfig_round(kel, 3)
+    outputs['Ka(hr-1)'] = sigfig_round(ka, 3)
+    outputs['V/F(L)'] = sigfig_round(V_F, 3)
 
     if not quiet:
         utils.log('------------------------------------------------------------------------------------------')

enumerate.py

@@ -26,7 +26,8 @@
 
 """
 import os, sys, argparse, traceback, uuid, gzip
-import utils, rdkit_utils
+import rdkit_utils
+from dm_job_utilities import utils
 from dm_job_utilities.cli import ProgressReporter, add_reporting_args
 from dm_job_utilities.dm_log import DmLog
 

fn_expand.py

@@ -25,7 +25,7 @@
 
 import os, argparse, time
 
-import utils
+from dm_job_utilities import utils
 from dm_job_utilities.dm_log import DmLog
 from standardize_molecule import standardize_to_noniso_smiles
 

fn_find_synthons.py

@@ -25,7 +25,7 @@
 
 import os, argparse, time
 
-import utils
+from dm_job_utilities import utils
 from dm_job_utilities.dm_log import DmLog
 from standardize_molecule import standardize_to_noniso_smiles
 

fn_synthon_expansion.py

@@ -55,7 +55,7 @@
 
 import os, argparse, time
 
-import utils
+from dm_job_utilities import utils
 from dm_job_utilities.dm_log import DmLog
 from standardize_molecule import standardize_to_noniso_smiles
 

im_mordred/descriptor_generator.py

@@ -20,7 +20,8 @@
 
 from rdkit import Chem
 
-import utils, rdkit_utils
+import rdkit_utils
+from dm_job_utilities import utils
 from dm_job_utilities.cli import ProgressReporter, add_reporting_args
 from dm_job_utilities.dm_log import DmLog
 

le_conformers.py

@@ -23,7 +23,8 @@
 """
 import os, sys, argparse, traceback, time, gzip
 
-import utils, rdkit_utils
+import rdkit_utils
+from dm_job_utilities import utils
 from dm_job_utilities.cli import ProgressReporter, add_reporting_args
 from dm_job_utilities.dm_log import DmLog
 

le_conformers_for_mol.py

@@ -16,7 +16,8 @@
 
 
 import time, argparse
-import utils, le_conformers
+import le_conformers
+from dm_job_utilities import utils
 from dm_job_utilities.dm_log import DmLog
 
 from rdkit import Chem

max_min_picker.py

@@ -16,7 +16,7 @@
 
 
 import argparse, time
-import utils
+from dm_job_utilities import utils
 from dm_job_utilities.dm_log import DmLog
 
 from rdkit import Chem, SimDivFilters

minimize.py

@@ -16,7 +16,7 @@
 
 
 import sys, argparse, time
-import utils
+from dm_job_utilities import utils
 from dm_job_utilities.dm_log import DmLog
 
 from rdkit import Chem

moldb/analyse.py

@@ -16,7 +16,7 @@
 
 import argparse, datetime, time
 
-import utils
+from dm_job_utilities import utils
 from . import models, filter, moldb_utils
 
 from dm_job_utilities.dm_log import DmLog

moldb/conformers.py

@@ -20,7 +20,7 @@
 same methodology that this module uses.
 """
 import os, argparse, traceback, time, gzip
-import utils
+from dm_job_utilities import utils
 from dm_job_utilities.dm_log import DmLog
 
 from rdkit import Chem

moldb/enumerate.py

@@ -26,7 +26,8 @@
 
 """
 import os, sys, argparse, traceback, logging
-import utils, rdkit_utils
+import rdkit_utils
+from dm_job_utilities import utils
 from dm_job_utilities.dm_log import DmLog
 
 from rdkit import Chem

moldb/extract_need_molprops.py

@@ -14,7 +14,7 @@
 
 import argparse, time, os, random, string, traceback
 
-import utils
+from dm_job_utilities import utils
 from . import models
 
 from sqlalchemy import text

moldb/filter.py

@@ -14,7 +14,7 @@
 
 
 import os, glob, argparse, time
-import utils
+from dm_job_utilities import utils
 
 from sqlalchemy import text
 from sqlalchemy.orm import Session

moldb/models.py

@@ -21,7 +21,7 @@
 
 import sqlalchemy
 
-import utils
+from dm_job_utilities import utils
 
 utils.log('sqlalchemy version:', sqlalchemy.__version__)
 

moldb/moldb_utils.py

@@ -12,7 +12,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-import utils
+from dm_job_utilities import utils
 
 def add_filter_args(parser):
     parser.add_argument('--min-hac', type=int, help="Min value for heavy atom count")

moldb/standardize.py

@@ -16,7 +16,7 @@
 
 
 import argparse, os, json, gzip, time, logging
-import utils
+from dm_job_utilities import utils
 from dm_job_utilities.dm_log import DmLog
 
 from rdkit import Chem, RDLogger

oddt_ifp.py

@@ -16,7 +16,7 @@
 
 
 import sys, argparse
-import utils
+from dm_job_utilities import utils
 from dm_job_utilities.dm_log import DmLog
 
 from oddt import toolkit, fingerprints

oddt_interactions.py

@@ -81,7 +81,8 @@
 import argparse, traceback
 import json, sys
 
-import utils, interact
+import interact
+from dm_job_utilities import utils
 from dm_job_utilities.dm_log import DmLog
 
 import oddt

open3dalign.py

@@ -19,7 +19,7 @@
 """
 
 import argparse, sys
-import utils
+from dm_job_utilities import utils
 from dm_job_utilities.dm_log import DmLog
 
 from rdkit import Chem

pharmacophore.py

@@ -14,7 +14,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-import utils
+from dm_job_utilities import utils
 from dm_job_utilities.dm_log import DmLog
 from openbabel import pybel, openbabel
 from jinja2 import Template