TypingError Decoupler Import #34
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jvogenstahl
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deeenes
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Hi @jvogenstahl Unfortunately, this looks like a dependency issue with GoogleColab, could you try to redo the enviroment without upgrading numba? So basically: |
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Hi Pau, Thanks for your help ! Best, Jo |
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HI @jvogenstahl , The second one is about I also saw that you are using python 3.7, maybe update it to 3.10 just in case. @pablormier, did you encounter any of this issues? |
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I think The numba compilation error is independent and will stay around regardless. I would also highly recommend trying a more up-to-date Python, 3.10 or 3.11, and making sure all packages are up-to-date. |
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Is this problem resolved? as @deeenes said, pypath-omnipath is not required. It is also recommended to install the dependencies using the right version of each tool, as in the original notebook. The issue seems to be related to incompatible versions between packages. |
2 tasks
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nudge to devs, that this issue is still happening, at least to me. ---------------------------------------------------------------------------
TypingError Traceback (most recent call last)
Cell In[18], line 1
----> 1 import decoupler
File ~/Jose_BI/4_Projects/P26_BCCN/P26E18_ProteomicAnalysis/.pixi/envs/default/lib/python3.12/site-packages/decoupler/__init__.py:17
15 from .method_udt import run_udt # noqa: F401
16 from .method_ora import run_ora, test1r, get_ora_df # noqa: F401
---> 17 from .method_gsva import run_gsva # noqa: F401
18 from .method_gsea import run_gsea, get_gsea_df # noqa: F401
19 from .method_viper import run_viper # noqa: F401
File ~/Jose_BI/4_Projects/P26_BCCN/P26E18_ProteomicAnalysis/.pixi/envs/default/lib/python3.12/site-packages/decoupler/method_gsva.py:83
79 mat = mat_ecdf(mat)
80 return mat
---> 83 @nb.njit(nb.types.Tuple((nb.f4[:, :], nb.i8[:, :]))(nb.f4[:, :]), parallel=True, cache=True)
84 def nb_get_D_I(mat):
85 n = mat.shape[1]
86 rev_idx = np.abs(np.arange(start=n, stop=0, step=-1, dtype=nb.f4) - n / 2)
File ~/Jose_BI/4_Projects/P26_BCCN/P26E18_ProteomicAnalysis/.pixi/envs/default/lib/python3.12/site-packages/numba/core/decorators.py:232, in _jit.<locals>.wrapper(func)
230 with typeinfer.register_dispatcher(disp):
231 for sig in sigs:
--> 232 disp.compile(sig)
233 disp.disable_compile()
234 return disp
File ~/Jose_BI/4_Projects/P26_BCCN/P26E18_ProteomicAnalysis/.pixi/envs/default/lib/python3.12/site-packages/numba/core/dispatcher.py:905, in Dispatcher.compile(self, sig)
903 with ev.trigger_event("numba:compile", data=ev_details):
904 try:
--> 905 cres = self._compiler.compile(args, return_type)
906 except errors.ForceLiteralArg as e:
907 def folded(args, kws):
File ~/Jose_BI/4_Projects/P26_BCCN/P26E18_ProteomicAnalysis/.pixi/envs/default/lib/python3.12/site-packages/numba/core/dispatcher.py:84, in _FunctionCompiler.compile(self, args, return_type)
82 return retval
83 else:
---> 84 raise retval
File ~/Jose_BI/4_Projects/P26_BCCN/P26E18_ProteomicAnalysis/.pixi/envs/default/lib/python3.12/site-packages/numba/core/dispatcher.py:94, in _FunctionCompiler._compile_cached(self, args, return_type)
91 pass
93 try:
---> 94 retval = self._compile_core(args, return_type)
95 except errors.TypingError as e:
96 self._failed_cache[key] = e
File ~/Jose_BI/4_Projects/P26_BCCN/P26E18_ProteomicAnalysis/.pixi/envs/default/lib/python3.12/site-packages/numba/core/dispatcher.py:107, in _FunctionCompiler._compile_core(self, args, return_type)
104 flags = self._customize_flags(flags)
106 impl = self._get_implementation(args, {})
--> 107 cres = compiler.compile_extra(self.targetdescr.typing_context,
108 self.targetdescr.target_context,
109 impl,
110 args=args, return_type=return_type,
111 flags=flags, locals=self.locals,
112 pipeline_class=self.pipeline_class)
113 # Check typing error if object mode is used
114 if cres.typing_error is not None and not flags.enable_pyobject:
File ~/Jose_BI/4_Projects/P26_BCCN/P26E18_ProteomicAnalysis/.pixi/envs/default/lib/python3.12/site-packages/numba/core/compiler.py:744, in compile_extra(typingctx, targetctx, func, args, return_type, flags, locals, library, pipeline_class)
720 """Compiler entry point
721
722 Parameter
(...)
740 compiler pipeline
741 """
742 pipeline = pipeline_class(typingctx, targetctx, library,
743 args, return_type, flags, locals)
--> 744 return pipeline.compile_extra(func)
File ~/Jose_BI/4_Projects/P26_BCCN/P26E18_ProteomicAnalysis/.pixi/envs/default/lib/python3.12/site-packages/numba/core/compiler.py:438, in CompilerBase.compile_extra(self, func)
436 self.state.lifted = ()
437 self.state.lifted_from = None
--> 438 return self._compile_bytecode()
File ~/Jose_BI/4_Projects/P26_BCCN/P26E18_ProteomicAnalysis/.pixi/envs/default/lib/python3.12/site-packages/numba/core/compiler.py:506, in CompilerBase._compile_bytecode(self)
502 """
503 Populate and run pipeline for bytecode input
504 """
505 assert self.state.func_ir is None
--> 506 return self._compile_core()
File ~/Jose_BI/4_Projects/P26_BCCN/P26E18_ProteomicAnalysis/.pixi/envs/default/lib/python3.12/site-packages/numba/core/compiler.py:485, in CompilerBase._compile_core(self)
483 self.state.status.fail_reason = e
484 if is_final_pipeline:
--> 485 raise e
486 else:
487 raise CompilerError("All available pipelines exhausted")
File ~/Jose_BI/4_Projects/P26_BCCN/P26E18_ProteomicAnalysis/.pixi/envs/default/lib/python3.12/site-packages/numba/core/compiler.py:472, in CompilerBase._compile_core(self)
470 res = None
471 try:
--> 472 pm.run(self.state)
473 if self.state.cr is not None:
474 break
File ~/Jose_BI/4_Projects/P26_BCCN/P26E18_ProteomicAnalysis/.pixi/envs/default/lib/python3.12/site-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 ~/Jose_BI/4_Projects/P26_BCCN/P26E18_ProteomicAnalysis/.pixi/envs/default/lib/python3.12/site-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 ~/Jose_BI/4_Projects/P26_BCCN/P26E18_ProteomicAnalysis/.pixi/envs/default/lib/python3.12/site-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 ~/Jose_BI/4_Projects/P26_BCCN/P26E18_ProteomicAnalysis/.pixi/envs/default/lib/python3.12/site-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 ~/Jose_BI/4_Projects/P26_BCCN/P26E18_ProteomicAnalysis/.pixi/envs/default/lib/python3.12/site-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 ~/Jose_BI/4_Projects/P26_BCCN/P26E18_ProteomicAnalysis/.pixi/envs/default/lib/python3.12/site-packages/numba/core/typed_passes.py:112, in BaseTypeInference.run_pass(self, state)
106 """
107 Type inference and legalization
108 """
109 with fallback_context(state, 'Function "%s" failed type inference'
110 % (state.func_id.func_name,)):
111 # Type inference
--> 112 typemap, return_type, calltypes, errs = type_inference_stage(
113 state.typingctx,
114 state.targetctx,
115 state.func_ir,
116 state.args,
117 state.return_type,
118 state.locals,
119 raise_errors=self._raise_errors)
120 state.typemap = typemap
121 # save errors in case of partial typing
File ~/Jose_BI/4_Projects/P26_BCCN/P26E18_ProteomicAnalysis/.pixi/envs/default/lib/python3.12/site-packages/numba/core/typed_passes.py:93, in type_inference_stage(typingctx, targetctx, interp, args, return_type, locals, raise_errors)
91 infer.build_constraint()
92 # return errors in case of partial typing
---> 93 errs = infer.propagate(raise_errors=raise_errors)
94 typemap, restype, calltypes = infer.unify(raise_errors=raise_errors)
96 return _TypingResults(typemap, restype, calltypes, errs)
File ~/Jose_BI/4_Projects/P26_BCCN/P26E18_ProteomicAnalysis/.pixi/envs/default/lib/python3.12/site-packages/numba/core/typeinfer.py:1091, in TypeInferer.propagate(self, raise_errors)
1088 force_lit_args = [e for e in errors
1089 if isinstance(e, ForceLiteralArg)]
1090 if not force_lit_args:
-> 1091 raise errors[0]
1092 else:
1093 raise reduce(operator.or_, force_lit_args)
TypingError: Failed in nopython mode pipeline (step: nopython frontend)
No implementation of function Function(<built-in function arange>) found for signature:
>>> arange(start=int64, stop=Literal[int](0), step=Literal[int](-1), dtype=class(float32))
There are 2 candidate implementations:
- Of which 2 did not match due to:
Overload in function 'np_arange': File: numba/np/arrayobj.py: Line 4760.
With argument(s): '(start=int64, stop=int64, step=int64, dtype=class(float32))':
Rejected as the implementation raised a specific error:
TypingError: got some positional-only arguments passed as keyword arguments: 'start'
raised from /Users/jnimoca/Jose_BI/4_Projects/P26_BCCN/P26E18_ProteomicAnalysis/.pixi/envs/default/lib/python3.12/site-packages/numba/core/typing/templates.py:783
During: resolving callee type: Function(<built-in function arange>)
During: typing of call at /Users/jnimoca/Jose_BI/4_Projects/P26_BCCN/P26E18_ProteomicAnalysis/.pixi/envs/default/lib/python3.12/site-packages/decoupler/method_gsva.py (86)
File "../.pixi/envs/default/lib/python3.12/site-packages/decoupler/method_gsva.py", line 86:
def nb_get_D_I(mat):
<source elided>
n = mat.shape[1]
rev_idx = np.abs(np.arange(start=n, stop=0, step=-1, dtype=nb.f4) - n / 2)
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Dear Decoupler team,
I followed the PerMedCoE hands-on course on Tuesday and I'm trying to apply the analysis to my data (spatial transcriptomics) following the GoogleCollab file.
I managed to create the 'signalling' environment and I believe I managed to install all packages in Jupyter. However, I get a TypingError when importing decoupler in python and can't figure out what's wrong (see below).
Any assistance would be very welcome.
Have a great day,
Johanna
My code:
Error message:
The text was updated successfully, but these errors were encountered: