darribas
Numba needs NumPy 2.0
Description
PySAL requires Numba, and Numba needs NumPy<=2.0. Thus, Conda installs NumPy 1.26.4. However, Simplification needs NumPy>=2.0. Since Simplification is installed afterwards by Pip, which can't check the Numba constraint, Pip installs NumPy 2.2, released on 2024-12-08.
Collecting numpy>=2.0.0 (from simplification->-r ~/repos/gds_env/env/condaenv.ae1m7tzg.requirements.txt (line 7))
Downloading numpy-2.2.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (62 kB)
Installing collected packages: pymorton, polars-h3, polars, numpy, coverage, simplification, pytest-tornasync, watermark, pytest-cov, matplotlib-scalebar, urbangrammar-graphics
Attempting uninstall: numpy
Found existing installation: numpy 1.26.4
Uninstalling numpy-1.26.4:
Successfully uninstalled numpy-1.26.4
Successfully installed coverage-7.6.10 matplotlib-scalebar-0.9.0 numpy-2.2.2 polars-1.21.0 polars-h3-0.5.1 pymorton-1.0.5 pytest-cov-6.0.0 pytest-tornasync-0.6.0.post2 simplification-0.7.13 urbangrammar-graphics-1.2.3 watermark-2.5.0
That results in an error when importing the esda library.
$ python
Python 3.12.8 | packaged by conda-forge | (main, Dec 5 2024, 14:24:40) [GCC 13.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from pysal.explore import esda
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "~/miniforge3/envs/gds/lib/python3.12/site-packages/pysal/explore/__init__.py", line 1, in <module>
import esda
File "~/miniforge3/envs/gds/lib/python3.12/site-packages/esda/__init__.py", line 10, in <module>
from . import adbscan, shape # noqa F401
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "~/miniforge3/envs/gds/lib/python3.12/site-packages/esda/adbscan.py", line 12, in <module>
from libpysal.cg.alpha_shapes import alpha_shape_auto
File "~/miniforge3/envs/gds/lib/python3.12/site-packages/libpysal/__init__.py", line 27, in <module>
from . import cg, examples, graph, io, weights
File "~/miniforge3/envs/gds/lib/python3.12/site-packages/libpysal/examples/__init__.py", line 13, in <module>
from .base import Example, example_manager
File "~/miniforge3/envs/gds/lib/python3.12/site-packages/libpysal/examples/base.py", line 19, in <module>
from ..io import open as ps_open
File "~/miniforge3/envs/gds/lib/python3.12/site-packages/libpysal/io/__init__.py", line 2, in <module>
from .iohandlers import *
File "~/miniforge3/envs/gds/lib/python3.12/site-packages/libpysal/io/iohandlers/__init__.py", line 3, in <module>
from . import (
File "~/miniforge3/envs/gds/lib/python3.12/site-packages/libpysal/io/iohandlers/arcgis_dbf.py", line 3, in <module>
from ...weights.util import remap_ids
File "~/miniforge3/envs/gds/lib/python3.12/site-packages/libpysal/weights/__init__.py", line 10, in <module>
from .gabriel import Gabriel, Delaunay, Relative_Neighborhood
File "~/miniforge3/envs/gds/lib/python3.12/site-packages/libpysal/weights/gabriel.py", line 11, in <module>
from numba import njit
File "~/miniforge3/envs/gds/lib/python3.12/site-packages/numba/__init__.py", line 59, in <module>
_ensure_critical_deps()
File "~/miniforge3/envs/gds/lib/python3.12/site-packages/numba/__init__.py", line 45, in _ensure_critical_deps
raise ImportError(msg)
ImportError: Numba needs NumPy 2.0 or less. Got NumPy 2.2.
Solution
Add a constraint to Pip to install NumPy 2.0 in the yml environment specification.
- pip:
- numpy==2.0
Installing collected packages: pymorton, polars-h3, polars, numpy, coverage, simplification, pytest-tornasync, watermark, pytest-cov, matplotlib-scalebar, urbangrammar-graphics
Attempting uninstall: numpy
Found existing installation: numpy 1.26.4
Uninstalling numpy-1.26.4:
Successfully uninstalled numpy-1.26.4
Successfully installed coverage-7.6.10 matplotlib-scalebar-0.9.0 numpy-2.0.0 polars-1.21.0 polars-h3-0.5.1 pymorton-1.0.5 pytest-cov-6.0.0 pytest-tornasync-0.6.0.post2 simplification-0.7.13 urbangrammar-graphics-1.2.3 watermark-2.5.0
The esda library now loads correctly.
$ python
Python 3.12.8 | packaged by conda-forge | (main, Dec 5 2024, 14:24:40) [GCC 13.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from pysal.explore import esda
>>>
I totally missed this one, sorry!
I can confirm this is an issue still, although it's shifted from 2.0 to 2.1. I pressed a new image over the weekend and if I try to import esda, I get a similar error, but now pointing to numpy 2.1 required.
As a general rule, I don't like pinning to specific versions because I tend to forget that's there and then it gets stuck in old versions. But I think in this case it makes sense to do it while the issue gets resolved.
Can you change it to pin 2.1 instead? I'll merge then. Thanks very much for opening this.
Actually, hold on, I'm noticing simplification now is on conda-forge so I'll move from pip. This should allow for mamba/conda to do the arithmetic you've done in here dynamically and not force us to pin to any specific version. Let me check if that works and I'll report back!