From 9856cebd9acfe6e467357bcc234f6b1a98018d81 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Wed, 11 Mar 2026 08:53:38 +0000 Subject: [PATCH 1/2] Update dependency numpy to v2 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 0e02281c..41492d14 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -58,7 +58,7 @@ server = [ "ispyb>=10.2.4", # Responsible for setting requirements for SQLAlchemy and mysql-connector-python; "jinja2", "mrcfile", - "numpy<2", + "numpy<3", "packaging", "passlib", "pillow", From 3b2fdff2cb7d124c05aa080e3dedfa99e63b4aca Mon Sep 17 00:00:00 2001 From: Eu Pin Tien Date: Thu, 12 Mar 2026 07:52:21 +0000 Subject: [PATCH 2/2] Added explicit conversion to built-in 'float' for calculations performed using NumPy --- src/murfey/workflows/spa/picking.py | 2 +- src/murfey/workflows/tomo/tomo_metadata.py | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/murfey/workflows/spa/picking.py b/src/murfey/workflows/spa/picking.py index 8d44645e..d07563ec 100644 --- a/src/murfey/workflows/spa/picking.py +++ b/src/murfey/workflows/spa/picking.py @@ -113,7 +113,7 @@ def _register_picked_particles_use_diameter(message: dict, _db: Session): picking_db = _db.exec( select(ParticleSizes.particle_size).where(ParticleSizes.pj_id == pj_id) ).all() - particle_diameter = np.quantile(list(picking_db), 0.75) + particle_diameter = float(np.quantile(list(picking_db), 0.75)) relion_params.particle_diameter = particle_diameter _db.add(relion_params) _db.commit() diff --git a/src/murfey/workflows/tomo/tomo_metadata.py b/src/murfey/workflows/tomo/tomo_metadata.py index da22252a..c9f3ff2d 100644 --- a/src/murfey/workflows/tomo/tomo_metadata.py +++ b/src/murfey/workflows/tomo/tomo_metadata.py @@ -351,7 +351,7 @@ def register_batch_position_in_database( search_map.width / 2, search_map.height / 2, ] - tilt_series.x_location = ( + tilt_series.x_location = float( ( centre_batch_pixel[0] - batch_parameters.x_beamshift / search_map.pixel_size @@ -359,7 +359,7 @@ def register_batch_position_in_database( * 512 / search_map.width ) - tilt_series.y_location = ( + tilt_series.y_location = float( ( centre_batch_pixel[1] + batch_parameters.y_beamshift / search_map.pixel_size