Update dependency numpy to v2 (#574)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Co-authored-by: Eu Pin Tien <eu-pin.tien@diamond.ac.uk>

Author: renovate[bot]

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",

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()

src/murfey/workflows/tomo/tomo_metadata.py

@@ -351,15 +351,15 @@ 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
             )
             * 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