Update crate versions

Cargo.toml

@@ -4,12 +4,12 @@ version = "0.0.0"
 edition = "2018"
 
 [dependencies]
-numpy = "0.25"
-ndarray = "0.16"
+numpy = "0.27"
+ndarray = "0.17"
 num-traits = "0.2"
 
 [dependencies.pyo3]
-version = "0.25"
+version = "0.27"
 features = ["extension-module"]
 
 [lib]

src/biotite/structure/atoms.py

@@ -1364,6 +1364,11 @@ def concatenate(atoms):
     has_bonds = False
     for element in atoms:
         if element_type is None:
+            if not isinstance(element, (AtomArray, AtomArrayStack)):
+                raise TypeError(
+                    "Expected 'AtomArray' or 'AtomArrayStack', "
+                    f"but got '{type(element).__name__}'"
+                )
             element_type = type(element)
         else:
             if not isinstance(element, element_type):
@@ -1384,9 +1389,9 @@ def concatenate(atoms):
         if element.bonds is not None:
             has_bonds = True
 
-    if element_type == AtomArray:
+    if issubclass(element_type, AtomArray):
         concat_atoms = AtomArray(length)
-    elif element_type == AtomArrayStack:
+    else:
         concat_atoms = AtomArrayStack(depth, length)
     concat_atoms.coord = np.concatenate([element.coord for element in atoms], axis=-2)
     for category in common_categories:

src/biotite/structure/filter.py

@@ -522,7 +522,7 @@ def filter_first_altloc(atoms, altloc_ids):
     # And filter all atoms for each residue with the first altloc ID
     residue_starts = get_residue_starts(atoms, add_exclusive_stop=True)
     for start, stop in zip(residue_starts[:-1], residue_starts[1:]):
-        letter_altloc_ids = [loc for loc in altloc_ids[start:stop] if loc.isalpha()]
+        letter_altloc_ids = [loc for loc in altloc_ids[start:stop] if loc.isalnum()]
         if len(letter_altloc_ids) > 0:
             first_id = letter_altloc_ids[0]
             altloc_filter[start:stop] |= altloc_ids[start:stop] == first_id
@@ -603,7 +603,7 @@ def filter_highest_occupancy_altloc(atoms, altloc_ids, occupancies):
         occupancies_in_res = occupancies[start:stop]
         altloc_ids_in_res = altloc_ids[start:stop]
 
-        letter_altloc_ids = [loc for loc in altloc_ids_in_res if loc.isalpha()]
+        letter_altloc_ids = [loc for loc in altloc_ids_in_res if loc.isalnum()]
 
         if len(letter_altloc_ids) > 0:
             highest = -1.0

src/rust/lib.rs

@@ -11,7 +11,7 @@ fn add_subpackage(
 ) -> PyResult<()> {
     module.add_submodule(submodule)?;
     let sys = PyModule::import(module.py(), "sys")?;
-    let sys_modules: Bound<'_, PyDict> = sys.getattr("modules")?.downcast_into()?;
+    let sys_modules: Bound<'_, PyDict> = sys.getattr("modules")?.cast_into()?;
     submodule.setattr("__name__", submodule_name)?;
     submodule.setattr("__package__", submodule_name)?;
     sys_modules.set_item(submodule_name, submodule)?;

src/rust/structure/io/mod.rs

@@ -4,7 +4,7 @@ use pyo3::prelude::*;
 mod pdb;
 
 pub fn module<'py>(parent_module: &Bound<'py, PyModule>) -> PyResult<Bound<'py, PyModule>> {
-    let module = PyModule::new(parent_module.py(), "structure")?;
+    let module = PyModule::new(parent_module.py(), "io")?;
     add_subpackage(
         &module,
         &pdb::module(&module)?,

src/rust/structure/io/pdb/file.rs

@@ -1,7 +1,7 @@
 //! Low-level PDB file parsing and writing.
 
-use ndarray::Axis;
 use num_traits::{Float, FloatConst};
+use numpy::ndarray::Axis;
 use numpy::ndarray::{
     Array, Array1, Array2, ArrayView1, ArrayView3, ArrayViewD, ArrayViewMut1, Ix3,
 };
@@ -109,7 +109,7 @@ impl PDBFile {
     #[classmethod]
     fn read<'py>(cls: &Bound<'py, PyType>, file: Bound<'py, PyAny>) -> PyResult<Bound<'py, PyAny>> {
         let contents;
-        if let Ok(file_path) = file.downcast::<PyString>() {
+        if let Ok(file_path) = file.cast::<PyString>() {
             // String path
             contents = fs::read_to_string(file_path.extract::<String>()?).map_err(|_| {
                 exceptions::PyOSError::new_err(format!("'{}' cannot be read", file_path))
@@ -135,7 +135,7 @@ impl PDBFile {
 
     fn write(&self, file: Bound<'_, PyAny>) -> PyResult<()> {
         let content = self.lines.join("\n");
-        if let Ok(file_path) = file.downcast::<PyString>() {
+        if let Ok(file_path) = file.cast::<PyString>() {
             // String path
             fs::write(file_path.extract::<String>()?, content).map_err(|_| {
                 exceptions::PyOSError::new_err(format!("'{}' cannot be written", file_path))
@@ -1177,7 +1177,8 @@ fn get_annotation_as_type<'py, T: numpy::Element>(
     atoms
         .getattr(annotation)?
         .call_method("astype", (), Some(&kwargs))?
-        .extract()
+        .cast_into()
+        .map_err(|e| e.into())
 }
 
 // Get an `AtomArray` annotation as a `Vec` of strings.

src/rust/structure/io/pdb/mod.rs

@@ -7,7 +7,7 @@ use file::*;
 use hybrid36::*;
 
 pub fn module<'py>(parent_module: &Bound<'py, PyModule>) -> PyResult<Bound<'py, PyModule>> {
-    let module = PyModule::new(parent_module.py(), "structure")?;
+    let module = PyModule::new(parent_module.py(), "pdb")?;
     module.add_class::<PDBFile>()?;
     module.add_function(wrap_pyfunction!(encode_hybrid36, &module)?)?;
     module.add_function(wrap_pyfunction!(decode_hybrid36, &module)?)?;

tests/database/test_rcsb.py

@@ -344,8 +344,7 @@ def test_search_content_types():
                     ("2VB1_1",),
                     ("7VOS_1", "3A38_1", "5D8V_1"),
                     ("1UCS_1",),
-                    ("3NIR_1", "1EJG_1"),
-                    ("9EWK_1",),
+                    ("3NIR_1", "9EWK_1", "1EJG_1"),
                 ]
             ),
         ),