Package: python3-pynndescent
Version: 0.5.7-1
Severity: serious
Dear Debian Python Team,
in the python3 or ipython3 interpreter, the Python statement
import pynndescent.sparse as sparse
fails and the output in ipython3 is
```
---------------------------------------------------------------------------
TypingError Traceback (most recent call last)
Cell In [1], line 1
----> 1 import pynndescent.sparse as sparse
File /usr/lib/python3/dist-packages/pynndescent/__init__.py:3
1 import pkg_resources
2 import numba
----> 3 from .pynndescent_ import NNDescent, PyNNDescentTransformer
5 # Workaround: https://github.com/numba/numba/issues/3341
6 if numba.config.THREADING_LAYER == "omp":
File /usr/lib/python3/dist-packages/pynndescent/pynndescent_.py:16
12 from scipy.sparse import csr_matrix, coo_matrix, isspmatrix_csr, vstack
as sparse_vstack, issparse
14 import heapq
---> 16 import pynndescent.sparse as sparse
17 import pynndescent.sparse_nndescent as sparse_nnd
18 import pynndescent.distances as pynnd_dist
File /usr/lib/python3/dist-packages/pynndescent/sparse.py:381
377 result += aux_data[i] ** 2
378 return np.sqrt(result)
--> 381 @numba.njit(
382 [
383 "f4(i4[::1],f4[::1],i4[::1],f4[::1])",
384 numba.types.float32(
385 numba.types.Array(numba.types.int32, 1, "C", readonly=True),
386 numba.types.Array(numba.types.float32, 1, "C",
readonly=True),
387 numba.types.Array(numba.types.int32, 1, "C", readonly=True),
388 numba.types.Array(numba.types.float32, 1, "C",
readonly=True),
389 ),
390 ],
391 fastmath=True,
392 locals={
393 "aux_data": numba.types.float32[::1],
394 "result": numba.types.float32,
395 "diff": numba.types.float32,
396 "dim": numba.types.intp,
397 "i": numba.types.uint16,
398 },
399 )
400 def sparse_squared_euclidean(ind1, data1, ind2, data2):
401 _, aux_data = sparse_diff(ind1, data1, ind2, data2)
402 result = 0.0
File /usr/lib/python3/dist-packages/numba/core/decorators.py:219, in
_jit.<locals>.wrapper(func)
217 with typeinfer.register_dispatcher(disp):
218 for sig in sigs:
--> 219 disp.compile(sig)
220 disp.disable_compile()
221 return disp
File /usr/lib/python3/dist-packages/numba/core/dispatcher.py:965, in
Dispatcher.compile(self, sig)
963 with ev.trigger_event("numba:compile", data=ev_details):
964 try:
--> 965 cres = self._compiler.compile(args, return_type)
966 except errors.ForceLiteralArg as e:
967 def folded(args, kws):
File /usr/lib/python3/dist-packages/numba/core/dispatcher.py:129, in
_FunctionCompiler.compile(self, args, return_type)
127 return retval
128 else:
--> 129 raise retval
File /usr/lib/python3/dist-packages/numba/core/dispatcher.py:139, in
_FunctionCompiler._compile_cached(self, args, return_type)
136 pass
138 try:
--> 139 retval = self._compile_core(args, return_type)
140 except errors.TypingError as e:
141 self._failed_cache[key] = e
File /usr/lib/python3/dist-packages/numba/core/dispatcher.py:152, in
_FunctionCompiler._compile_core(self, args, return_type)
149 flags = self._customize_flags(flags)
151 impl = self._get_implementation(args, {})
--> 152 cres = compiler.compile_extra(self.targetdescr.typing_context,
153 self.targetdescr.target_context,
154 impl,
155 args=args, return_type=return_type,
156 flags=flags, locals=self.locals,
157 pipeline_class=self.pipeline_class)
158 # Check typing error if object mode is used
159 if cres.typing_error is not None and not flags.enable_pyobject:
File /usr/lib/python3/dist-packages/numba/core/compiler.py:716, in
compile_extra(typingctx, targetctx, func, args, return_type, flags, locals,
library, pipeline_class)
692 """Compiler entry point
693
694 Parameter
(...)
712 compiler pipeline
713 """
714 pipeline = pipeline_class(typingctx, targetctx, library,
715 args, return_type, flags, locals)
--> 716 return pipeline.compile_extra(func)
File /usr/lib/python3/dist-packages/numba/core/compiler.py:452, in
CompilerBase.compile_extra(self, func)
450 self.state.lifted = ()
451 self.state.lifted_from = None
--> 452 return self._compile_bytecode()
File /usr/lib/python3/dist-packages/numba/core/compiler.py:520, in
CompilerBase._compile_bytecode(self)
516 """
517 Populate and run pipeline for bytecode input
518 """
519 assert self.state.func_ir is None
--> 520 return self._compile_core()
File /usr/lib/python3/dist-packages/numba/core/compiler.py:499, in
CompilerBase._compile_core(self)
497 self.state.status.fail_reason = e
498 if is_final_pipeline:
--> 499 raise e
500 else:
501 raise CompilerError("All available pipelines exhausted")
File /usr/lib/python3/dist-packages/numba/core/compiler.py:486, in
CompilerBase._compile_core(self)
484 res = None
485 try:
--> 486 pm.run(self.state)
487 if self.state.cr is not None:
488 break
File /usr/lib/python3/dist-packages/numba/core/compiler_machinery.py:368, in
PassManager.run(self, state)
365 msg = "Failed in %s mode pipeline (step: %s)" % \
366 (self.pipeline_name, pass_desc)
367 patched_exception = self._patch_error(msg, e)
--> 368 raise patched_exception
File /usr/lib/python3/dist-packages/numba/core/compiler_machinery.py:356, in
PassManager.run(self, state)
354 pass_inst = _pass_registry.get(pss).pass_inst
355 if isinstance(pass_inst, CompilerPass):
--> 356 self._runPass(idx, pass_inst, state)
357 else:
358 raise BaseException("Legacy pass in use")
File /usr/lib/python3/dist-packages/numba/core/compiler_lock.py:35, in
_CompilerLock.__call__.<locals>._acquire_compile_lock(*args, **kwargs)
32 @functools.wraps(func)
33 def _acquire_compile_lock(*args, **kwargs):
34 with self:
---> 35 return func(*args, **kwargs)
File /usr/lib/python3/dist-packages/numba/core/compiler_machinery.py:311, in
PassManager._runPass(self, index, pss, internal_state)
309 mutated |= check(pss.run_initialization, internal_state)
310 with SimpleTimer() as pass_time:
--> 311 mutated |= check(pss.run_pass, internal_state)
312 with SimpleTimer() as finalize_time:
313 mutated |= check(pss.run_finalizer, internal_state)
File /usr/lib/python3/dist-packages/numba/core/compiler_machinery.py:273, in
PassManager._runPass.<locals>.check(func, compiler_state)
272 def check(func, compiler_state):
--> 273 mangled = func(compiler_state)
274 if mangled not in (True, False):
275 msg = ("CompilerPass implementations should return True/False. "
276 "CompilerPass with name '%s' did not.")
File /usr/lib/python3/dist-packages/numba/core/typed_passes.py:105, in
BaseTypeInference.run_pass(self, state)
99 """
100 Type inference and legalization
101 """
102 with fallback_context(state, 'Function "%s" failed type inference'
103 % (state.func_id.func_name,)):
104 # Type inference
--> 105 typemap, return_type, calltypes, errs = type_inference_stage(
106 state.typingctx,
107 state.targetctx,
108 state.func_ir,
109 state.args,
110 state.return_type,
111 state.locals,
112 raise_errors=self._raise_errors)
113 state.typemap = typemap
114 # save errors in case of partial typing
File /usr/lib/python3/dist-packages/numba/core/typed_passes.py:83, in
type_inference_stage(typingctx, targetctx, interp, args, return_type, locals,
raise_errors)
81 infer.build_constraint()
82 # return errors in case of partial typing
---> 83 errs = infer.propagate(raise_errors=raise_errors)
84 typemap, restype, calltypes = infer.unify(raise_errors=raise_errors)
86 # Output all Numba warnings
File /usr/lib/python3/dist-packages/numba/core/typeinfer.py:1086, in
TypeInferer.propagate(self, raise_errors)
1083 force_lit_args = [e for e in errors
1084 if isinstance(e, ForceLiteralArg)]
1085 if not force_lit_args:
-> 1086 raise errors[0]
1087 else:
1088 raise reduce(operator.or_, force_lit_args)
TypingError: Failed in nopython mode pipeline (step: nopython frontend)
Internal error at <numba.core.typeinfer.CallConstraint object at
0x7fa880d3f550>.
Failed in nopython mode pipeline (step: native lowering)
AST node line range (200, 1) is not valid
File "../../usr/lib/python3/dist-packages/pynndescent/sparse.py", line 202:
def sparse_diff(ind1, data1, ind2, data2):
return sparse_sum(ind1, data1, ind2, -data2)
^
During: lowering "$24unary_negative.6 = arrayexpr(expr=(<built-in function neg>,
[Var(data2, sparse.py:200)]), ty=array(float32, 1d, C))" at
/usr/lib/python3/dist-packages/pynndescent/sparse.py (202)
During: resolving callee type: type(CPUDispatcher(<function sparse_diff at
0x7fa881010680>))
During: typing of call at /usr/lib/python3/dist-packages/pynndescent/sparse.py
(401)
Enable logging at debug level for details.
File "../../usr/lib/python3/dist-packages/pynndescent/sparse.py", line 401:
def sparse_squared_euclidean(ind1, data1, ind2, data2):
_, aux_data = sparse_diff(ind1, data1, ind2, data2)
^
```
I'm not sure if the failure is due to this package or the package
python3-numba.
Or is this just a Python 3.11 transition outfall?
Any help appreciated.
Regards,
Jörg.
-- System Information:
Debian Release: bookworm/sid
APT prefers testing
APT policy: (600, 'testing'), (500, 'unstable'), (5, 'experimental')
Architecture: amd64 (x86_64)
Kernel: Linux 6.1.4 (SMP w/16 CPU threads; PREEMPT)
Locale: LANG=C.utf8, LC_CTYPE=C.utf8 (charmap=UTF-8), LANGUAGE not set
Shell: /bin/sh linked to /usr/bin/dash
Init: sysvinit (via /sbin/init)
Versions of packages python3-pynndescent depends on:
ii python3 3.11.1-1
ii python3-joblib 1.2.0-4
ii python3-llvmlite 0.39.1-2
ii python3-numba 0.56.4+dfsg-1
ii python3-scipy 1.8.1-20
ii python3-sklearn 1.1.2+dfsg-92
python3-pynndescent recommends no packages.
python3-pynndescent suggests no packages.
-- no debconf information
