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", 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