Release v1.10.1

CHANGELOG.rst

@@ -2,6 +2,14 @@
 Changelog
 ==========
 
++++++++++
+v1.10.1 (14/01/2025)
++++++++++
+
+**Changed**
+
+- Coalesce null CTF values
+
 +++++++++
 v1.10.0 (10/12/2024)
 +++++++++

Dockerfile

@@ -3,7 +3,7 @@
 # The devcontainer should use the build target and run as root with podman
 # or docker with user namespaces.
 #
-FROM docker.io/library/python:3.12.7-slim-bookworm as build
+FROM docker.io/library/python:3.13.1-slim-bookworm as build
 
 # Add any system dependencies for the developer/build environment here
 RUN apt-get update && apt-get upgrade -y && \
@@ -40,7 +40,7 @@ RUN pip install --upgrade pip && \
     # and replace with a comment to avoid a zero length asset upload later
     sed -i '/file:/s/^/# Requirements for /' lockfiles/requirements.txt
 
-FROM docker.io/library/python:3.12.7-slim-bookworm as runtime
+FROM docker.io/library/python:3.13.1-slim-bookworm as runtime
 
 # Add apt-get system dependecies for runtime here if needed
 RUN apt-get update && apt-get install -y libmariadb-dev

pyproject.toml

@@ -24,7 +24,7 @@ dependencies = [
     "mysql-connector-python~=8.2.0",
     "pydantic~=2.9.2",
     "types-requests",
-    "lims-utils~=0.2.5"
+    "lims-utils~=0.2.6"
 ]
 dynamic = ["version"]
 license.file = "LICENSE"

src/pato/crud/autoproc.py

@@ -61,12 +61,13 @@ def get_motion_correction(limit: int, page: int, autoProcId: int) -> Paged[FullM
 
 
 def get_ctf(autoProcId: int):
+    # COALESCE strips out the column name
     data = db.session.execute(
         select(
-            CTF.estimatedResolution,
-            CTF.estimatedDefocus,
-            CTF.astigmatism,
-            ParticlePicker.numberOfParticles,
+            func.coalesce(CTF.estimatedResolution, 0).label("estimatedResolution"),
+            func.coalesce(CTF.estimatedDefocus, 0).label("estimatedDefocus"),
+            func.coalesce(CTF.astigmatism, 0).label("astigmatism"),
+            func.coalesce(ParticlePicker.numberOfParticles, 0).label("numberOfParticles"),
             MotionCorrection.imageNumber,
         )
         .filter(MotionCorrection.autoProcProgramId == autoProcId)

src/pato/crud/tomograms.py

@@ -10,7 +10,7 @@
     TiltImageAlignment,
     Tomogram,
 )
-from sqlalchemy import Column, literal_column, select
+from sqlalchemy import Column, func, literal_column, select
 from sqlalchemy import func as f
 
 from ..models.response import (
@@ -136,9 +136,9 @@ def get_motion_correction(
 def get_ctf(tomogramId: int):
     data = db.session.execute(
         select(
-            CTF.estimatedResolution,
-            CTF.estimatedDefocus,
-            CTF.astigmatism,
+            func.coalesce(CTF.estimatedResolution, 0).label("estimatedResolution"),
+            func.coalesce(CTF.estimatedDefocus, 0).label("estimatedDefocus"),
+            func.coalesce(CTF.astigmatism, 0).label("astigmatism"),
             TiltImageAlignment.refinedTiltAngle,
         )
         .filter(TiltImageAlignment.tomogramId == tomogramId)

tests/proposals/test_proposal.py

@@ -9,7 +9,7 @@
         pytest.param(mx_admin, 2, id="mx"),
         pytest.param(user, 1, id="user"),
         pytest.param(em_admin, 1, id="em"),
-        pytest.param(admin, 4, id="admin"),
+        pytest.param(admin, 5, id="admin"),
     ],
     indirect=["mock_user"],
 )