Compatibility with Numpy > 2.0

[BernalFA]

Dear all,

I successfully installed umap using conda. The environment already had the latest version of numpy (2.2.3) but upon installation of umap, numpy was downgraded (2.1.3). Unfortunately, when I tried to import umap, I got an Attribute error due to use of np.infty, which was deprecated already some time ago in numpy 2.0. Is umap not compatible with newer version of numpy? Is there any workaround this? Is the only way possible to use a second environment just for umap? Does anyone has experience on this?

Best,

Freddy

---

Here my import statements:

import numpy as np
import pandas as pd
import umap
from rdkit.Chem import AllChem

from database_access import search_compounds

and the output:

AttributeError                            Traceback (most recent call last)
Cell In[2], line 5
      3 import numpy as np
      4 import pandas as pd
----> 5 import umap
      6 from rdkit.Chem import AllChem
      8 from database_access import search_compounds

File ~/miniconda3/envs/ythdf2/lib/python3.12/site-packages/umap/__init__.py:2
      1 from warnings import warn, catch_warnings, simplefilter
----> 2 from .umap_ import UMAP
      4 try:
      5     with catch_warnings():

File ~/miniconda3/envs/ythdf2/lib/python3.12/site-packages/umap/umap_.py:48
     41 from umap.spectral import spectral_layout, tswspectral_layout
     42 from umap.layouts import (
     43     optimize_layout_euclidean,
     44     optimize_layout_generic,
     45     optimize_layout_inverse,
     46 )
---> 48 from pynndescent import NNDescent
     49 from pynndescent.distances import named_distances as pynn_named_distances
     50 from pynndescent.sparse import sparse_named_distances as pynn_sparse_named_distances

File ~/miniconda3/envs/ythdf2/lib/python3.12/site-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 ~/miniconda3/envs/ythdf2/lib/python3.12/site-packages/pynndescent/pynndescent_.py:17
     14 import heapq
     16 import pynndescent.sparse as sparse
---> 17 import pynndescent.sparse_nndescent as sparse_nnd
     18 import pynndescent.distances as pynnd_dist
     20 from pynndescent.utils import (
     21     tau_rand_int,
     22     tau_rand,
   (...)     35     sparse_initalize_heap_from_graph_indices,
     36 )

File ~/miniconda3/envs/ythdf2/lib/python3.12/site-packages/pynndescent/sparse_nndescent.py:24
     20 from pynndescent.sparse import sparse_euclidean
     22 locale.setlocale(locale.LC_NUMERIC, "C")
---> 24 EMPTY_GRAPH = make_heap(1, 1)
     27 @numba.njit(parallel=True, cache=True)
     28 def generate_leaf_updates(leaf_block, dist_thresholds, inds, indptr, data, dist):
     30     updates = [[(-1, -1, np.inf)] for i in range(leaf_block.shape[0])]

File ~/miniconda3/envs/ythdf2/lib/python3.12/site-packages/numba/core/dispatcher.py:443, in _DispatcherBase._compile_for_args(self, *args, **kws)
    441             e.patch_message('\n'.join((str(e).rstrip(), help_msg)))
    442     # ignore the FULL_TRACEBACKS config, this needs reporting!
--> 443     raise e
    444 finally:
    445     self._types_active_call.clear()

File ~/miniconda3/envs/ythdf2/lib/python3.12/site-packages/numba/core/dispatcher.py:376, in _DispatcherBase._compile_for_args(self, *args, **kws)
    374 return_val = None
    375 try:
--> 376     return_val = self.compile(tuple(argtypes))
    377 except errors.ForceLiteralArg as e:
    378     # Received request for compiler re-entry with the list of arguments
    379     # indicated by e.requested_args.
    380     # First, check if any of these args are already Literal-ized
    381     already_lit_pos = [i for i in e.requested_args
    382                        if isinstance(args[i], types.Literal)]

File ~/miniconda3/envs/ythdf2/lib/python3.12/site-packages/numba/core/dispatcher.py:904, in Dispatcher.compile(self, sig)
    902 with ev.trigger_event("numba:compile", data=ev_details):
    903     try:
--> 904         cres = self._compiler.compile(args, return_type)
    905     except errors.ForceLiteralArg as e:
    906         def folded(args, kws):

File ~/miniconda3/envs/ythdf2/lib/python3.12/site-packages/numba/core/dispatcher.py:80, in _FunctionCompiler.compile(self, args, return_type)
     79 def compile(self, args, return_type):
---> 80     status, retval = self._compile_cached(args, return_type)
     81     if status:
     82         return retval

File ~/miniconda3/envs/ythdf2/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 ~/miniconda3/envs/ythdf2/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 ~/miniconda3/envs/ythdf2/lib/python3.12/site-packages/numba/core/compiler.py:739, in compile_extra(typingctx, targetctx, func, args, return_type, flags, locals, library, pipeline_class)
    715 """Compiler entry point
    716 
    717 Parameter
   (...)    735     compiler pipeline
    736 """
    737 pipeline = pipeline_class(typingctx, targetctx, library,
    738                           args, return_type, flags, locals)
--> 739 return pipeline.compile_extra(func)

File ~/miniconda3/envs/ythdf2/lib/python3.12/site-packages/numba/core/compiler.py:439, in CompilerBase.compile_extra(self, func)
    437 self.state.lifted = ()
    438 self.state.lifted_from = None
--> 439 return self._compile_bytecode()

File ~/miniconda3/envs/ythdf2/lib/python3.12/site-packages/numba/core/compiler.py:505, in CompilerBase._compile_bytecode(self)
    501 """
    502 Populate and run pipeline for bytecode input
    503 """
    504 assert self.state.func_ir is None
--> 505 return self._compile_core()

File ~/miniconda3/envs/ythdf2/lib/python3.12/site-packages/numba/core/compiler.py:481, in CompilerBase._compile_core(self)
    479 except Exception as e:
    480     if not isinstance(e, errors.NumbaError):
--> 481         raise e
    482     self.state.status.fail_reason = e
    483     if is_final_pipeline:

File ~/miniconda3/envs/ythdf2/lib/python3.12/site-packages/numba/core/compiler.py:473, in CompilerBase._compile_core(self)
    471 res = None
    472 try:
--> 473     pm.run(self.state)
    474     if self.state.cr is not None:
    475         break

File ~/miniconda3/envs/ythdf2/lib/python3.12/site-packages/numba/core/compiler_machinery.py:363, in PassManager.run(self, state)
    361 except Exception as e:
    362     if not isinstance(e, errors.NumbaError):
--> 363         raise e
    364     msg = "Failed in %s mode pipeline (step: %s)" % \
    365         (self.pipeline_name, pass_desc)
    366     patched_exception = self._patch_error(msg, e)

File ~/miniconda3/envs/ythdf2/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 ~/miniconda3/envs/ythdf2/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 ~/miniconda3/envs/ythdf2/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 ~/miniconda3/envs/ythdf2/lib/python3.12/site-packages/numba/core/compiler_machinery.py:272, in PassManager._runPass.<locals>.check(func, compiler_state)
    271 def check(func, compiler_state):
--> 272     mangled = func(compiler_state)
    273     if mangled not in (True, False):
    274         msg = ("CompilerPass implementations should return True/False. "
    275                "CompilerPass with name '%s' did not.")

File ~/miniconda3/envs/ythdf2/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 ~/miniconda3/envs/ythdf2/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 ~/miniconda3/envs/ythdf2/lib/python3.12/site-packages/numba/core/typeinfer.py:1066, in TypeInferer.propagate(self, raise_errors)
   1063 oldtoken = newtoken
   1064 # Errors can appear when the type set is incomplete; only
   1065 # raise them when there is no progress anymore.
-> 1066 errors = self.constraints.propagate(self)
   1067 newtoken = self.get_state_token()
   1068 self.debug.propagate_finished()

File ~/miniconda3/envs/ythdf2/lib/python3.12/site-packages/numba/core/typeinfer.py:160, in ConstraintNetwork.propagate(self, typeinfer)
    157 with typeinfer.warnings.catch_warnings(filename=loc.filename,
    158                                        lineno=loc.line):
    159     try:
--> 160         constraint(typeinfer)
    161     except ForceLiteralArg as e:
    162         errors.append(e)

File ~/miniconda3/envs/ythdf2/lib/python3.12/site-packages/numba/core/typeinfer.py:708, in GetAttrConstraint.__call__(self, typeinfer)
    706 valtys = typevars[self.value.name].get()
    707 for ty in valtys:
--> 708     attrty = typeinfer.context.resolve_getattr(ty, self.attr)
    709     if attrty is None:
    710         raise UntypedAttributeError(ty, self.attr,
    711                                     loc=self.inst.loc)

File ~/miniconda3/envs/ythdf2/lib/python3.12/site-packages/numba/core/typing/context.py:282, in BaseContext.resolve_getattr(self, typ, attr)
    279     return out
    281 if isinstance(typ, types.Module):
--> 282     attrty = self.resolve_module_constants(typ, attr)
    283     if attrty is not None:
    284         return attrty

File ~/miniconda3/envs/ythdf2/lib/python3.12/site-packages/numba/core/typing/context.py:347, in BaseContext.resolve_module_constants(self, typ, attr)
    342 """
    343 Resolve module-level global constants.
    344 Return None or the attribute type
    345 """
    346 assert isinstance(typ, types.Module)
--> 347 attrval = getattr(typ.pymod, attr)
    348 try:
    349     return self.resolve_value_type(attrval)

File ~/miniconda3/envs/ythdf2/lib/python3.12/site-packages/numpy/__init__.py:400, in __getattr__(attr)
    397     raise AttributeError(__former_attrs__[attr], name=None)
    399 if attr in __expired_attributes__:
--> 400     raise AttributeError(
    401         f"`np.{attr}` was removed in the NumPy 2.0 release. "
    402         f"{__expired_attributes__[attr]}",
    403         name=None
    404     )
    406 if attr == "chararray":
    407     warnings.warn(
    408         "`np.chararray` is deprecated and will be removed from "
    409         "the main namespace in the future. Use an array with a string "
    410         "or bytes dtype instead.", DeprecationWarning, stacklevel=2)

AttributeError: `np.infty` was removed in the NumPy 2.0 release. Use `np.inf` instead.