biotite 0.39.0__cp311-cp311-macosx_11_0_arm64.whl → 0.40.0__cp311-cp311-macosx_11_0_arm64.whl

biotite/structure/io/mmtf/file.py

@@ -12,6 +12,7 @@ import struct
 import copy
 import numpy as np
 import msgpack
+import warnings
 from ....file import File, is_binary, is_open_compatible
 from ...error import BadStructureError
 from .decode import decode_array
@@ -21,7 +22,7 @@ from .encode import encode_array
 class MMTFFile(File, MutableMapping):
     """
     This class represents a MMTF file.
-    
+
     When reading a file, the *MessagePack* unpacker is used to create
     a dictionary of the file content.
     This dictionary is accessed by indexing the :class:`MMTFFile`
@@ -29,10 +30,13 @@ class MMTFFile(File, MutableMapping):
     If the dictionary value is an encoded array, the value automatically
     decoded.
     Decoded arrays are always returned as :class:`ndarray` instances.
-    
+
+    DEPRECATED: Use :class:`biotite.structure.io.pdbx.BinaryCIFFile`
+    instead.
+
     Examples
     --------
-    
+
     >>> import os.path
     >>> mmtf_file = MMTFFile.read(os.path.join(path_to_structures, "1l2y.mmtf"))
     >>> print(mmtf_file["title"])
@@ -42,24 +46,28 @@ class MMTFFile(File, MutableMapping):
      'A' 'A' 'A' 'A' 'A' 'A' 'A' 'A' 'A' 'A' 'A' 'A' 'A' 'A' 'A' 'A' 'A' 'A'
      'A' 'A']
     """
-    
+
     def __init__(self):
+        warnings.warn(
+            "'MMTFFile' is deprecated, use 'BinaryCIFFile' instead",
+            DeprecationWarning
+        )
         super().__init__()
         self._content = {}
         self._content["mmtfVersion"] = "1.0.0"
         self._content["mmtfProducer"] = "UNKNOWN"
-    
+
     @classmethod
     def read(self, file):
         """
         Read a MMTF file.
-        
+
         Parameters
         ----------
         file : file-like object or str
             The file to be read.
             Alternatively a file path can be supplied.
-        
+
         Returns
         -------
         file_object : MMTFFile
@@ -80,11 +88,11 @@ class MMTFFile(File, MutableMapping):
                 file.read(), use_list=True, raw=False
             )
         return mmtf_file
-    
+
     def write(self, file):
         """
         Write contents into a MMTF file.
-        
+
         Parameters
         ----------
         file : file-like object or str
@@ -101,20 +109,20 @@ class MMTFFile(File, MutableMapping):
             if not is_binary(file):
                 raise TypeError("A file opened in 'binary' mode is required")
             file.write(packed_bytes)
-    
+
     def __copy_fill__(self, clone):
         super().__copy_fill__(clone)
         clone._content = copy.deepcopy(self._content)
-    
+
     def get_codec(self, key):
         """
         Obtain the codec ID of an MMTF encoded value.
-        
+
         Parameters
         ----------
         key : str
             The key for the potentially encoded value.
-        
+
         Returns
         -------
         codec : int or None
@@ -126,16 +134,16 @@ class MMTFFile(File, MutableMapping):
             return codec
         else:
             return None
-    
+
     def get_length(self, key):
         """
         Obtain the length of an MMTF encoded value.
-        
+
         Parameters
         ----------
         key : str
             The key for the potentially encoded value.
-        
+
         Returns
         -------
         codec : int or None
@@ -148,16 +156,16 @@ class MMTFFile(File, MutableMapping):
             return length
         else:
             return None
-    
+
     def get_param(self, key):
         """
         Obtain the parameter of an MMTF encoded value.
-        
+
         Parameters
         ----------
         key : str
             The key for the potentially encoded value.
-        
+
         Returns
         -------
         codec : int or None
@@ -170,7 +178,7 @@ class MMTFFile(File, MutableMapping):
             return param
         else:
             return None
-    
+
     def set_array(self, key, array, codec, param=0):
         length = len(array)
         raw_bytes = encode_array(array, codec, param)
@@ -179,7 +187,7 @@ class MMTFFile(File, MutableMapping):
              + struct.pack(">i", param) \
              + raw_bytes
         self._content[key] = data
-    
+
     def __getitem__(self, key):
         data = self._content[key]
         if isinstance(data, bytes) and data[0] == 0:
@@ -191,22 +199,22 @@ class MMTFFile(File, MutableMapping):
             return decode_array(codec, raw_bytes, param)
         else:
             return data
-    
+
     def __setitem__(self, key, item):
         if isinstance(item, np.ndarray):
             raise TypeError("Arrays that need to be encoded must be addeed "
                             "via 'set_array()'")
         self._content[key] = item
-    
+
     def __delitem__(self, key):
         del self._content[key]
-    
+
     def __iter__(self):
         return self._content.__iter__()
-    
+
     def __len__(self):
         return len(self._content)
-    
+
     def __contains__(self, item):
         return item in self._content
 

biotite/structure/io/npz/__init__.py

@@ -9,6 +9,9 @@ format is used to store `NumPy` arrays. Since atom arrays and stacks are
 completely built on `NumPy` arrays, this format is preferable for
 Biotite internal usage due to fast I/O operations and preservation
 of all atom annotation arrays.
+
+DEPRECATED: Pickle data directly or use
+:class:`biotite.structure.io.pdbx.BinaryCIFFile` instead.
 """
 
 __name__ = "biotite.structure.io.npz"

biotite/structure/io/npz/file.py

@@ -15,19 +15,22 @@ from ....file import File, is_binary
 class NpzFile(File):
     r"""
     This class represents a NPZ file, the preferable format for
-    Biotite internal structure storage. 
-    
+    Biotite internal structure storage.
+
     Internally the this class writes/reads all attribute arrays of an
     :class:`AtomArray` or :class:`AtomArrayStack` using the *NumPy*
     :func:`save()`/:func:`load()`
     method. This format offers the fastest I/O operations and completely
     preserves the content all atom annotation arrays.
-    
+
+    DEPRECATED: Pickle data directly or use
+    :class:`biotite.structure.io.pdbx.BinaryCIFFile` instead.
+
     Examples
     --------
     Load a \\*.npz file, modify the structure and save the new
     structure into a new file:
-    
+
     >>> import os.path
     >>> file = NpzFile.read(os.path.join(path_to_structures, "1l2y.npz"))
     >>> array_stack = file.get_structure()
@@ -35,30 +38,30 @@ class NpzFile(File):
     >>> file = NpzFile()
     >>> file.set_structure(array_stack_mod)
     >>> file.write(os.path.join(path_to_directory, "1l2y_mod.npz"))
-    
+
     """
-    
+
     def __init__(self):
         super().__init__()
         self._data_dict = None
-    
+
     def __copy_fill__(self, clone):
         super().__copy_fill__(clone)
         if self._data_dict is not None:
             for key, value in self._data_dict.items():
                 clone._data_dict[key] = np.copy(value)
-    
+
     @classmethod
     def read(cls, file):
         """
         Read a NPZ file.
-        
+
         Parameters
         ----------
         file : file-like object or str
             The file to be read.
             Alternatively a file path can be supplied.
-        
+
         Returns
         -------
         file_object : NPZFile
@@ -75,11 +78,11 @@ class NpzFile(File):
                 raise TypeError("A file opened in 'binary' mode is required")
             npz_file._data_dict = dict(np.load(file, allow_pickle=False))
         return npz_file
-                
+
     def write(self, file):
         """
         Write a NPZ file.
-        
+
         Parameters
         ----------
         file : file-like object or str
@@ -93,15 +96,15 @@ class NpzFile(File):
             if not is_binary(file):
                 raise TypeError("A file opened in 'binary' mode is required")
             np.savez(file, **self._data_dict)
-    
+
     def get_structure(self):
         """
         Get an :class:`AtomArray` or :class:`AtomArrayStack` from the
         file.
-        
+
         If this method returns an array or stack depends on which type
         of object was used when the file was written.
-        
+
         Returns
         -------
         array : AtomArray or AtomArrayStack
@@ -117,7 +120,7 @@ class NpzFile(File):
             array = AtomArrayStack(coord.shape[0], coord.shape[1])
         else:
             array = AtomArray(coord.shape[0])
-        
+
         for key, value in self._data_dict.items():
             if key == "coord":
                 array.coord = value
@@ -128,12 +131,12 @@ class NpzFile(File):
             else:
                 array.set_annotation(key, value)
         return array
-        
+
     def set_structure(self, array):
         """
         Set the :class:`AtomArray` or :class:`AtomArrayStack` for the
         file.
-        
+
         Parameters
         ----------
         array : AtomArray or AtomArrayStack

biotite/structure/io/pdb/__init__.py

@@ -6,11 +6,11 @@
 This subpackage is used for reading and writing an :class:`AtomArray` or
 :class:`AtomArrayStack` using the popular PDB format.
 Since this format has some limitations, it will be completely replaced
-someday by the modern PDBx/mmCIF format.
+someday by the modern PDBx format.
 Therefore this subpackage should only be used, if usage of the
-PDBx/mmCIF format is not suitable (e.g. when interfacing
+PDBx (CIF or BinaryCIF) format is not suitable (e.g. when interfacing
 other software).
-In all other cases, usage of the ``pdbx`` subpackage is encouraged.
+In all other cases, usage of the :mod:`pdbx` subpackage is encouraged.
 """
 
 __name__ = "biotite.structure.io.pdb"

biotite/structure/io/pdb/file.py

@@ -53,7 +53,8 @@ class PDBFile(TextFile):
     r"""
     This class represents a PDB file.
 
-    The usage of PDBxFile is encouraged in favor of this class.
+    The usage of :mod:`biotite.structure.io.pdbx` is encouraged in favor
+    of this class.
 
     This class only provides support for reading/writing the pure atom
     information (*ATOM*, *HETATM*, *MODEL* and *ENDMDL* records). *TER*
@@ -62,7 +63,8 @@ class PDBFile(TextFile):
 
     See also
     --------
-    PDBxFile
+    CIFFile
+    BinaryCIFFile
 
     Examples
     --------
@@ -510,7 +512,7 @@ class PDBFile(TextFile):
                     warnings.warn(
                         "File contains invalid 'CRYST1' record, box is ignored"
                     )
-                    box = None
+                    break
 
                 if isinstance(array, AtomArray):
                     array.box = box

biotite/structure/io/pdb/hybrid36.c

@@ -1,4 +1,4 @@
-/* Generated by Cython 3.0.7 */
+/* Generated by Cython 3.0.10 */
 
 /* BEGIN: Cython Metadata
 {
@@ -36,10 +36,10 @@ END: Cython Metadata */
 #else
 #define __PYX_EXTRA_ABI_MODULE_NAME ""
 #endif
-#define CYTHON_ABI "3_0_7" __PYX_EXTRA_ABI_MODULE_NAME
+#define CYTHON_ABI "3_0_10" __PYX_EXTRA_ABI_MODULE_NAME
 #define __PYX_ABI_MODULE_NAME "_cython_" CYTHON_ABI
 #define __PYX_TYPE_MODULE_PREFIX __PYX_ABI_MODULE_NAME "."
-#define CYTHON_HEX_VERSION 0x030007F0
+#define CYTHON_HEX_VERSION 0x03000AF0
 #define CYTHON_FUTURE_DIVISION 1
 #include <stddef.h>
 #ifndef offsetof
@@ -131,6 +131,8 @@ END: Cython Metadata */
   #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC
     #define CYTHON_UPDATE_DESCRIPTOR_DOC 0
   #endif
+  #undef CYTHON_USE_FREELISTS
+  #define CYTHON_USE_FREELISTS 0
 #elif defined(PYPY_VERSION)
   #define CYTHON_COMPILING_IN_PYPY 1
   #define CYTHON_COMPILING_IN_CPYTHON 0
@@ -192,6 +194,8 @@ END: Cython Metadata */
   #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC
     #define CYTHON_UPDATE_DESCRIPTOR_DOC 0
   #endif
+  #undef CYTHON_USE_FREELISTS
+  #define CYTHON_USE_FREELISTS 0
 #elif defined(CYTHON_LIMITED_API)
   #ifdef Py_LIMITED_API
     #undef __PYX_LIMITED_VERSION_HEX
@@ -253,6 +257,8 @@ END: Cython Metadata */
   #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC
     #define CYTHON_UPDATE_DESCRIPTOR_DOC 0
   #endif
+  #undef CYTHON_USE_FREELISTS
+  #define CYTHON_USE_FREELISTS 0
 #elif defined(Py_GIL_DISABLED) || defined(Py_NOGIL)
   #define CYTHON_COMPILING_IN_PYPY 0
   #define CYTHON_COMPILING_IN_CPYTHON 0
@@ -262,11 +268,17 @@ END: Cython Metadata */
   #ifndef CYTHON_USE_TYPE_SLOTS
     #define CYTHON_USE_TYPE_SLOTS 1
   #endif
+  #ifndef CYTHON_USE_TYPE_SPECS
+    #define CYTHON_USE_TYPE_SPECS 0
+  #endif
   #undef CYTHON_USE_PYTYPE_LOOKUP
   #define CYTHON_USE_PYTYPE_LOOKUP 0
   #ifndef CYTHON_USE_ASYNC_SLOTS
     #define CYTHON_USE_ASYNC_SLOTS 1
   #endif
+  #ifndef CYTHON_USE_PYLONG_INTERNALS
+    #define CYTHON_USE_PYLONG_INTERNALS 0
+  #endif
   #undef CYTHON_USE_PYLIST_INTERNALS
   #define CYTHON_USE_PYLIST_INTERNALS 0
   #ifndef CYTHON_USE_UNICODE_INTERNALS
@@ -274,8 +286,6 @@ END: Cython Metadata */
   #endif
   #undef CYTHON_USE_UNICODE_WRITER
   #define CYTHON_USE_UNICODE_WRITER 0
-  #undef CYTHON_USE_PYLONG_INTERNALS
-  #define CYTHON_USE_PYLONG_INTERNALS 0
   #ifndef CYTHON_AVOID_BORROWED_REFS
     #define CYTHON_AVOID_BORROWED_REFS 0
   #endif
@@ -287,11 +297,22 @@ END: Cython Metadata */
   #endif
   #undef CYTHON_FAST_THREAD_STATE
   #define CYTHON_FAST_THREAD_STATE 0
+  #undef CYTHON_FAST_GIL
+  #define CYTHON_FAST_GIL 0
+  #ifndef CYTHON_METH_FASTCALL
+    #define CYTHON_METH_FASTCALL 1
+  #endif
   #undef CYTHON_FAST_PYCALL
   #define CYTHON_FAST_PYCALL 0
+  #ifndef CYTHON_PEP487_INIT_SUBCLASS
+    #define CYTHON_PEP487_INIT_SUBCLASS 1
+  #endif
   #ifndef CYTHON_PEP489_MULTI_PHASE_INIT
     #define CYTHON_PEP489_MULTI_PHASE_INIT 1
   #endif
+  #ifndef CYTHON_USE_MODULE_STATE
+    #define CYTHON_USE_MODULE_STATE 0
+  #endif
   #ifndef CYTHON_USE_TP_FINALIZE
     #define CYTHON_USE_TP_FINALIZE 1
   #endif
@@ -299,6 +320,12 @@ END: Cython Metadata */
   #define CYTHON_USE_DICT_VERSIONS 0
   #undef CYTHON_USE_EXC_INFO_STACK
   #define CYTHON_USE_EXC_INFO_STACK 0
+  #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC
+    #define CYTHON_UPDATE_DESCRIPTOR_DOC 1
+  #endif
+  #ifndef CYTHON_USE_FREELISTS
+    #define CYTHON_USE_FREELISTS 0
+  #endif
 #else
   #define CYTHON_COMPILING_IN_PYPY 0
   #define CYTHON_COMPILING_IN_CPYTHON 1
@@ -389,6 +416,9 @@ END: Cython Metadata */
   #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC
     #define CYTHON_UPDATE_DESCRIPTOR_DOC 1
   #endif
+  #ifndef CYTHON_USE_FREELISTS
+    #define CYTHON_USE_FREELISTS 1
+  #endif
 #endif
 #if !defined(CYTHON_FAST_PYCCALL)
 #define CYTHON_FAST_PYCCALL  (CYTHON_FAST_PYCALL && PY_VERSION_HEX >= 0x030600B1)
@@ -581,14 +611,14 @@ END: Cython Metadata */
         PyObject *exception_table = NULL;
         PyObject *types_module=NULL, *code_type=NULL, *result=NULL;
         #if __PYX_LIMITED_VERSION_HEX < 0x030B0000
-        PyObject *version_info; // borrowed
+        PyObject *version_info;
         PyObject *py_minor_version = NULL;
         #endif
         long minor_version = 0;
         PyObject *type, *value, *traceback;
         PyErr_Fetch(&type, &value, &traceback);
         #if __PYX_LIMITED_VERSION_HEX >= 0x030B0000
-        minor_version = 11; // we don't yet need to distinguish between versions > 11
+        minor_version = 11;
         #else
         if (!(version_info = PySys_GetObject("version_info"))) goto end;
         if (!(py_minor_version = PySequence_GetItem(version_info, 1))) goto end;
@@ -646,7 +676,7 @@ END: Cython Metadata */
                                                     PyObject *fv, PyObject *cell, PyObject* fn,
                                                     PyObject *name, int fline, PyObject *lnos) {
     PyCodeObject *result;
-    PyObject *empty_bytes = PyBytes_FromStringAndSize("", 0);  // we don't have access to __pyx_empty_bytes here
+    PyObject *empty_bytes = PyBytes_FromStringAndSize("", 0);
     if (!empty_bytes) return NULL;
     result =
       #if PY_VERSION_HEX >= 0x030C0000
@@ -732,8 +762,13 @@ END: Cython Metadata */
   typedef PyObject *(*__Pyx_PyCFunctionFastWithKeywords) (PyObject *self, PyObject *const *args,
                                                           Py_ssize_t nargs, PyObject *kwnames);
 #else
-  #define __Pyx_PyCFunctionFast _PyCFunctionFast
-  #define __Pyx_PyCFunctionFastWithKeywords _PyCFunctionFastWithKeywords
+  #if PY_VERSION_HEX >= 0x030d00A4
+  #  define __Pyx_PyCFunctionFast PyCFunctionFast
+  #  define __Pyx_PyCFunctionFastWithKeywords PyCFunctionFastWithKeywords
+  #else
+  #  define __Pyx_PyCFunctionFast _PyCFunctionFast
+  #  define __Pyx_PyCFunctionFastWithKeywords _PyCFunctionFastWithKeywords
+  #endif
 #endif
 #if CYTHON_METH_FASTCALL
   #define __Pyx_METH_FASTCALL METH_FASTCALL
@@ -1085,7 +1120,7 @@ static CYTHON_INLINE PyObject * __Pyx_PyDict_GetItemStrWithError(PyObject *dict,
   #define __Pyx_PyBytes_GET_SIZE(o) PyBytes_Size(o)
   #define __Pyx_PyByteArray_GET_SIZE(o) PyByteArray_Size(o)
 #endif
-#if PY_VERSION_HEX >= 0x030d00A1
+#if __PYX_LIMITED_VERSION_HEX >= 0x030d00A1
   #define __Pyx_PyImport_AddModuleRef(name) PyImport_AddModuleRef(name)
 #else
   static CYTHON_INLINE PyObject *__Pyx_PyImport_AddModuleRef(const char *name) {
@@ -1172,7 +1207,7 @@ static CYTHON_INLINE float __PYX_NAN() {
 #endif
 
 #define __PYX_MARK_ERR_POS(f_index, lineno) \
-    { __pyx_filename = __pyx_f[f_index]; (void)__pyx_filename; __pyx_lineno = lineno; (void)__pyx_lineno; __pyx_clineno = __LINE__; (void)__pyx_clineno; }
+    { __pyx_filename = __pyx_f[f_index]; (void)__pyx_filename; __pyx_lineno = lineno; (void)__pyx_lineno; __pyx_clineno = __LINE__;  (void)__pyx_clineno; }
 #define __PYX_ERR(f_index, lineno, Ln_error) \
     { __PYX_MARK_ERR_POS(f_index, lineno) goto Ln_error; }
 
@@ -1278,24 +1313,7 @@ static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char*);
 #define __Pyx_PyByteArray_FromCString(s)   __Pyx_PyByteArray_FromString((const char*)s)
 #define __Pyx_PyStr_FromCString(s)     __Pyx_PyStr_FromString((const char*)s)
 #define __Pyx_PyUnicode_FromCString(s) __Pyx_PyUnicode_FromString((const char*)s)
-#if CYTHON_COMPILING_IN_LIMITED_API
-static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const wchar_t *u)
-{
-    const wchar_t *u_end = u;
-    while (*u_end++) ;
-    return (size_t)(u_end - u - 1);
-}
-#else
-static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u)
-{
-    const Py_UNICODE *u_end = u;
-    while (*u_end++) ;
-    return (size_t)(u_end - u - 1);
-}
-#endif
 #define __Pyx_PyUnicode_FromOrdinal(o)       PyUnicode_FromOrdinal((int)o)
-#define __Pyx_PyUnicode_FromUnicode(u)       PyUnicode_FromUnicode(u, __Pyx_Py_UNICODE_strlen(u))
-#define __Pyx_PyUnicode_FromUnicodeAndLength PyUnicode_FromUnicode
 #define __Pyx_PyUnicode_AsUnicode            PyUnicode_AsUnicode
 #define __Pyx_NewRef(obj) (Py_INCREF(obj), obj)
 #define __Pyx_Owned_Py_None(b) __Pyx_NewRef(Py_None)
@@ -1345,7 +1363,7 @@ static CYTHON_INLINE Py_hash_t __Pyx_PyIndex_AsHash_t(PyObject*);
   #endif
   typedef Py_ssize_t  __Pyx_compact_pylong;
   typedef size_t  __Pyx_compact_upylong;
-  #else  // Py < 3.12
+  #else
   #define __Pyx_PyLong_IsNeg(x)  (Py_SIZE(x) < 0)
   #define __Pyx_PyLong_IsNonNeg(x)  (Py_SIZE(x) >= 0)
   #define __Pyx_PyLong_IsZero(x)  (Py_SIZE(x) == 0)
@@ -1916,8 +1934,8 @@ static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int
     #define __Pyx_Arg_NewRef_VARARGS(arg) __Pyx_NewRef(arg)
     #define __Pyx_Arg_XDECREF_VARARGS(arg) Py_XDECREF(arg)
 #else
-    #define __Pyx_Arg_NewRef_VARARGS(arg) arg // no-op
-    #define __Pyx_Arg_XDECREF_VARARGS(arg) // no-op - arg is borrowed
+    #define __Pyx_Arg_NewRef_VARARGS(arg) arg
+    #define __Pyx_Arg_XDECREF_VARARGS(arg)
 #endif
 #define __Pyx_NumKwargs_VARARGS(kwds) PyDict_Size(kwds)
 #define __Pyx_KwValues_VARARGS(args, nargs) NULL
@@ -1933,8 +1951,9 @@ static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int
   #else
     #define __Pyx_KwargsAsDict_FASTCALL(kw, kwvalues) _PyStack_AsDict(kwvalues, kw)
   #endif
-    #define __Pyx_Arg_NewRef_FASTCALL(arg) arg // no-op, __Pyx_Arg_FASTCALL is direct and this needs
-    #define __Pyx_Arg_XDECREF_FASTCALL(arg)  // no-op - arg was returned from array
+    #define __Pyx_Arg_NewRef_FASTCALL(arg) arg  /* no-op, __Pyx_Arg_FASTCALL is direct and this needs
+                                                   to have the same reference counting */
+    #define __Pyx_Arg_XDECREF_FASTCALL(arg)
 #else
     #define __Pyx_Arg_FASTCALL __Pyx_Arg_VARARGS
     #define __Pyx_NumKwargs_FASTCALL __Pyx_NumKwargs_VARARGS
@@ -2571,7 +2590,7 @@ typedef struct {
 #endif
     void *defaults;
     int defaults_pyobjects;
-    size_t defaults_size;  // used by FusedFunction for copying defaults
+    size_t defaults_size;
     int flags;
     PyObject *defaults_tuple;
     PyObject *defaults_kwdict;
@@ -22004,11 +22023,11 @@ static CYTHON_INLINE PyObject * __Pyx_GetKwValue_FASTCALL(PyObject *kwnames, PyO
     {
         int eq = __Pyx_PyUnicode_Equals(s, PyTuple_GET_ITEM(kwnames, i), Py_EQ);
         if (unlikely(eq != 0)) {
-            if (unlikely(eq < 0)) return NULL;  // error
+            if (unlikely(eq < 0)) return NULL;
             return kwvalues[i];
         }
     }
-    return NULL;  // not found (no exception set)
+    return NULL;
 }
 #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030d0000
 CYTHON_UNUSED static PyObject *__Pyx_KwargsAsDict_FASTCALL(PyObject *kwnames, PyObject *const *kwvalues) {
@@ -22121,7 +22140,7 @@ static int __Pyx_ParseOptionalKeywords(
         if (*name) {
             values[name-argnames] = value;
 #if CYTHON_AVOID_BORROWED_REFS
-            Py_INCREF(value); // transfer ownership of value to values
+            Py_INCREF(value);
             Py_DECREF(key);
 #endif
             key = NULL;
@@ -22140,7 +22159,7 @@ static int __Pyx_ParseOptionalKeywords(
                         && _PyString_Eq(**name, key)) {
                     values[name-argnames] = value;
 #if CYTHON_AVOID_BORROWED_REFS
-                    value = NULL;  // ownership transferred to values
+                    value = NULL;
 #endif
                     break;
                 }
@@ -22172,7 +22191,7 @@ static int __Pyx_ParseOptionalKeywords(
                 if (cmp == 0) {
                     values[name-argnames] = value;
 #if CYTHON_AVOID_BORROWED_REFS
-                    value = NULL; // ownership transferred to values
+                    value = NULL;
 #endif
                     break;
                 }
@@ -24164,9 +24183,10 @@ static CYTHON_INLINE PyObject* __Pyx_decode_c_bytes(
 
 /* UnpackUnboundCMethod */
 static PyObject *__Pyx_SelflessCall(PyObject *method, PyObject *args, PyObject *kwargs) {
+    PyObject *result;
     PyObject *selfless_args = PyTuple_GetSlice(args, 1, PyTuple_Size(args));
     if (unlikely(!selfless_args)) return NULL;
-    PyObject *result = PyObject_Call(method, selfless_args, kwargs);
+    result = PyObject_Call(method, selfless_args, kwargs);
     Py_DECREF(selfless_args);
     return result;
 }
@@ -26131,7 +26151,7 @@ static PyObject * __Pyx_CyFunction_Vectorcall_FASTCALL_KEYWORDS(PyObject *func,
     default:
         return NULL;
     }
-    return ((_PyCFunctionFastWithKeywords)(void(*)(void))def->ml_meth)(self, args, nargs, kwnames);
+    return ((__Pyx_PyCFunctionFastWithKeywords)(void(*)(void))def->ml_meth)(self, args, nargs, kwnames);
 }
 static PyObject * __Pyx_CyFunction_Vectorcall_FASTCALL_KEYWORDS_METHOD(PyObject *func, PyObject *const *args, size_t nargsf, PyObject *kwnames)
 {
@@ -26590,7 +26610,7 @@ static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
     #else
     py_code = PyCode_NewEmpty(filename, funcname, py_line);
     #endif
-    Py_XDECREF(py_funcname);  // XDECREF since it's only set on Py3 if cline
+    Py_XDECREF(py_funcname);
     return py_code;
 bad:
     Py_XDECREF(py_funcname);