refactor(entry_points): Removing legacy entry points #985
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As a step towards #517 this commit removes the legacy entry points and their associated tests.
ns-rse
requested review from
SylviaWhittle,
MaxGamill-Sheffield and
llwiggins
The release of [skan-0.12.0]() introduced the below error where the type is wrong when `nbgraph()` uses `numba`.
For now we pin `skan==0.11.1`
```
tests/tracing/test_disordered_tracing.py:1265:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
topostats/tracing/disordered_tracing.py:660: in disordered_trace_grain
"branch_types": get_skan_image(
topostats/tracing/disordered_tracing.py:697: in get_skan_image
skan_skeleton = skan.Skeleton(skeleton_image, spacing=1e-9, value_is_height=True)
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/skan/csr.py:532: in __init__
self.nbgraph = csr_to_nbgraph(graph, self.pixel_values)
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/skan/csr.py:205: in csr_to_nbgraph
return NBGraph(
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/experimental/jitclass/base.py:124: in __call__
return cls._ctor(*bind.args[1:], **bind.kwargs)
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/dispatcher.py:442: in _compile_for_args
raise e
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/dispatcher.py:375: in _compile_for_args
return_val = self.compile(tuple(argtypes))
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/dispatcher.py:905: in compile
cres = self._compiler.compile(args, return_type)
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/dispatcher.py:80: in compile
status, retval = self._compile_cached(args, return_type)
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/dispatcher.py:94: in _compile_cached
retval = self._compile_core(args, return_type)
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/dispatcher.py:107: in _compile_core
cres = compiler.compile_extra(self.targetdescr.typing_context,
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/compiler.py:744: in compile_extra
return pipeline.compile_extra(func)
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/compiler.py:438: in compile_extra
return self._compile_bytecode()
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/compiler.py:506: in _compile_bytecode
return self._compile_core()
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/compiler.py:481: in _compile_core
raise e
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/compiler.py:472: in _compile_core
pm.run(self.state)
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/compiler_machinery.py:364: in run
raise e
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/compiler_machinery.py:356: in run
self._runPass(idx, pass_inst, state)
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/compiler_lock.py:35: in _acquire_compile_lock
return func(*args, **kwargs)
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/compiler_machinery.py:311: in _runPass
mutated |= check(pss.run_pass, internal_state)
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/compiler_machinery.py:273: in check
mangled = func(compiler_state)
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/typed_passes.py:112: in run_pass
typemap, return_type, calltypes, errs = type_inference_stage(
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/typed_passes.py:93: in type_inference_stage
errs = infer.propagate(raise_errors=raise_errors)
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/typeinfer.py:1083: in propagate
errors = self.constraints.propagate(self)
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/typeinfer.py:182: in propagate
raise e
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/typeinfer.py:160: in propagate
constraint(typeinfer)
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/typeinfer.py:583: in __call__
self.resolve(typeinfer, typevars, fnty)
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/typeinfer.py:606: in resolve
sig = typeinfer.resolve_call(fnty, pos_args, kw_args)
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/typeinfer.py:1577: in resolve_call
return self.context.resolve_function_type(fnty, pos_args, kw_args)
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/typing/context.py:196: in resolve_function_type
res = self._resolve_user_function_type(func, args, kws)
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/typing/context.py:248: in _resolve_user_function_type
return func.get_call_type(self, args, kws)
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/types/misc.py:441: in get_call_type
return self.ctor_template(context).apply(args, kws)
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/typing/templates.py:350: in apply
sig = generic(args, kws)
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/experimental/jitclass/base.py:269: in generic
sig = disp_type.get_call_type(self.context, boundargs, kws)
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/types/functions.py:541: in get_call_type
self.dispatcher.get_call_template(args, kws)
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/dispatcher.py:318: in get_call_template
self.compile(tuple(args))
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/dispatcher.py:905: in compile
cres = self._compiler.compile(args, return_type)
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/dispatcher.py:80: in compile
status, retval = self._compile_cached(args, return_type)
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/dispatcher.py:94: in _compile_cached
retval = self._compile_core(args, return_type)
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/dispatcher.py:107: in _compile_core
cres = compiler.compile_extra(self.targetdescr.typing_context,
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/compiler.py:744: in compile_extra
return pipeline.compile_extra(func)
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/compiler.py:438: in compile_extra
return self._compile_bytecode()
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/compiler.py:506: in _compile_bytecode
return self._compile_core()
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/compiler.py:481: in _compile_core
raise e
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/compiler.py:472: in _compile_core
pm.run(self.state)
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/compiler_machinery.py:364: in run
raise e
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/compiler_machinery.py:356: in run
self._runPass(idx, pass_inst, state)
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/compiler_lock.py:35: in _acquire_compile_lock
return func(*args, **kwargs)
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/compiler_machinery.py:311: in _runPass
mutated |= check(pss.run_pass, internal_state)
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/compiler_machinery.py:273: in check
mangled = func(compiler_state)
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/typed_passes.py:468: in run_pass
lower.lower()
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/lowering.py:187: in lower
self.lower_normal_function(self.fndesc)
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/lowering.py:226: in lower_normal_function
entry_block_tail = self.lower_function_body()
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/lowering.py:256: in lower_function_body
self.lower_block(block)
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/lowering.py:270: in lower_block
self.lower_inst(inst)
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/lowering.py:564: in lower_inst
return impl(self.builder, (target, value))
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/base.py:627: in wrapped
return impl(self, builder, sig, args, attr)
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/imputils.py:166: in res
return real_impl(context, builder, sig, args, attr)
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/experimental/jitclass/base.py:505: in set_attr_impl
setattr(data, _mangle_attr(attr), val)
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/cgutils.py:164: in __setattr__
self[self._datamodel.get_field_position(field)] = value
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/cgutils.py:178: in __setitem__
value = self._cast_member_from_value(index, value)
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/cgutils.py:251: in _cast_member_from_value
return model.as_data(self._builder, val)
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/numba/core/datamodel/models.py:586: in as_data
struct = builder.insert_value(struct, el, [i])
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/llvmlite/ir/builder.py:983: in insert_value
instr = instructions.InsertValue(self.block, agg, value, idx, name=name)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <[AttributeError("'InsertValue' object has no attribute '_name'") raised in repr()] InsertValue object at 0x7ccfbd4f6b90>, parent = <ir.Block 'B0' of type 'label'>
agg = <ir.InsertValue '.258' of type '{i8*, i8*, i64, i64, double*, [1 x i64], [1 x i64]}', opname 'insertvalue', operands [...value=<llvmlite.ir.values._Undefined object at 0x7cd0142cda50>>, <ir.Argument 'arg.node_props.6.0' of type i64>]>]>]>]>
elem = <ir.ExtractValue 'extracted.data.22' of type 'float*', opname 'extractvalue', operands [<ir.InsertValue 'inserted.stri...' value=<llvmlite.ir.values._Undefined object at 0x7cd0142cda50>>, <ir.Argument 'arg.node_props.6.0' of type i64>]>]>]>
indices = [4], name = ''
def __init__(self, parent, agg, elem, indices, name=''):
typ = agg.type
try:
for i in indices:
typ = typ.elements[i]
except (AttributeError, IndexError):
raise TypeError("Can't index at %r in %s"
% (list(indices), agg.type))
if elem.type != typ:
> raise TypeError("Can only insert %s at %r in %s: got %s"
% (typ, list(indices), agg.type, elem.type))
E TypeError: Can only insert double* at [4] in {i8*, i8*, i64, i64, double*, [1 x i64], [1 x i64]}: got float*
/home/neil/.virtualenvs/topostats-311b/lib/python3.11/site-packages/llvmlite/ir/instructions.py:702: TypeError
__________________________________________________________________________________________ tests/test_run_topostats.py ___________________________________________________________________________________________
```
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SylviaWhittle
approved these changes
Oct 30, 2024
|
Thanks @SylviaWhittle merged so you're good to rebase onto |
This was referenced Nov 13, 2024
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As a step towards #517 this commit removes the legacy entry points and their associated tests.