chore(deps): update dependency gemmi to >=0.5.5, <=0.7.0

reciprocalspaceship/utils/cell.py

@@ -29,7 +29,7 @@ def compute_dHKL(H, cell):
     if inverse.shape[-1] == 1:
         inverse = inverse.squeeze(-1)
 
-    F = np.array(cell.fractionalization_matrix.tolist()).astype(np.float64)
+    F = np.array(cell.frac.mat, dtype=np.float64)
     dhkls = np.reciprocal(np.linalg.norm((hkls @ F), 2, 1)).astype(np.float32)
     return dhkls[inverse]
 

reciprocalspaceship/utils/grid.py

@@ -50,6 +50,7 @@ def get_reciprocal_grid_size(cell, dmin, sample_rate=3.0, spacegroup=None):
 
     # Use gemmi.Mtz to find valid grid (FFT-friendly and obeys symmetry)
     m = gemmi.Mtz()
-    m.spacegroup = spacegroup
+    if spacegroup is not None:
+        m.spacegroup = spacegroup
 
     return m.get_size_for_hkl(min_size=min_size)

reciprocalspaceship/utils/structurefactors.py

@@ -131,4 +131,4 @@ def is_absent(H, spacegroup):
     absent : array
         Boolean array of length n. absent[i] == True if H[i] is systematically absent in sg.
     """
-    return spacegroup.operations().systematic_absences(H)
+    return spacegroup.operations().systematic_absences(np.array(H, dtype=np.int32))

setup.py

@@ -74,7 +74,7 @@ def getVersionNumber():
     project_urls=PROJECT_URLS,
     python_requires=">=3.9",
     install_requires=[
-        "gemmi>=0.5.5, <=0.6.7",
+        "gemmi>=0.7.0, <=0.7.0",
         "pandas>=2.2.2, <=2.2.3",
         "numpy",
         "scipy",
@@ -90,7 +90,7 @@ def getVersionNumber():
     entry_points={
         "console_scripts": [
             "rs.mtzdump=reciprocalspaceship.commandline.mtzdump:main",
-            "rs.cifdump=reciprocalspaceship.commandline.cifdump:main"
+            "rs.cifdump=reciprocalspaceship.commandline.cifdump:main",
         ]
     },
     classifiers=[

tests/test_dataset_grid.py

@@ -22,10 +22,10 @@ def test_to_reciprocal_grid_gemmi(mtz_by_spacegroup, sample_rate, p1, use_sf):
     grid_size = dataset.get_reciprocal_grid_size(sample_rate=sample_rate)
 
     if use_sf:
-        gemmigrid = gemmimtz.get_f_phi_on_grid("FMODEL", "PHIFMODEL", size=grid_size)
-        expected = np.array(gemmigrid, copy=False)
         dataset["sf"] = dataset.to_structurefactor("FMODEL", "PHIFMODEL")
         result = dataset.to_reciprocal_grid("sf", grid_size=grid_size)
+        gemmigrid = gemmimtz.get_f_phi_on_grid("FMODEL", "PHIFMODEL", size=grid_size)
+        expected = gemmigrid.array
 
         # Requires rtol due to truncations applied in gemmi
         assert np.allclose(result, expected, rtol=1e-4)