meren
commented
8 months ago @Mild-High, that workaround should not have been necessary, since the anvi'o installed on my computer following the installation instructions word-by-word already has numpy 1.23.5. This is because the requirements.txt has the line numpy<=1.24 as a dependency. I'm not sure how you installed, but you shouldn't ever run into this. I'm glad it is resolved though!
Mild-High
Short description of the problem
When running anvi-get-metabolic-model-file "ImportError: Numba needs NumPy 1.25 or less" occurs.
anvi'o version
Anvi'o .......................................: marie (v8-dev) Python .......................................: 3.10.12
Profile database .............................: 38 Contigs database .............................: 22 Pan database .................................: 17 Genome data storage ..........................: 7 Auxiliary data storage .......................: 2 Structure database ...........................: 2 Metabolic modules database ...................: 4 tRNA-seq database ............................: 2
System info
Running through wsl on Windows
Files / commands to reproduce the issue
$ anvi-get-metabolic-model-file -c control/control-contigs.db -o control_fba.jsonTraceback (most recent call last): File "/home/chrysanthemyl/github/anvio/bin/anvi-get-metabolic-model-file", line 10, in
import anvio.biochemistry.reactionnetwork as reactionnetwork
File "/home/chrysanthemyl/github/anvio/anvio/biochemistry/reactionnetwork.py", line 26, in
import anvio.utils as utils
File "/home/chrysanthemyl/github/anvio/anvio/utils.py", line 31, in
from numba import jit
File "/home/chrysanthemyl/miniconda3/envs/anvio-dev/lib/python3.10/site-packages/numba/init.py", line 55, in
_ensure_critical_deps()
File "/home/chrysanthemyl/miniconda3/envs/anvio-dev/lib/python3.10/site-packages/numba/init.py", line 42, in _ensure_critical_deps
raise ImportError("Numba needs NumPy 1.25 or less")
ImportError: Numba needs NumPy 1.25 or less
Workaround
pip install --force-reinstall numpy==1.25(installed numpy-1.23.5 in my case)