run error in older server, with updated python v3.13

[ruysan]

minion@wlwminion01:~/flui-1.0.2$ flui --ref ../gisaid_v3.fa --run /data/Output_test/Minion_2024_06_26_W24_01587_AIV/no_sample/20240626_0914_MN37062_FAY40802_410a091d/fastq_pass
Traceback (most recent call last):
File "/home/minion/.local/share/uv/tools/flui/lib/python3.13/site-packages/scipy/init.py", line 86, in
from scipy._lib._ccallback import LowLevelCallable
File "/home/minion/.local/share/uv/tools/flui/lib/python3.13/site-packages/scipy/_lib/_ccallback.py", line 1, in
from . import _ccallback_c
File "_ccallback_c.pyx", line 205, in init scipy._lib._ccallback_c
File "/usr/local/lib/python3.13/ctypes/init.py", line 8, in
from _ctypes import Union, Structure, Array
ModuleNotFoundError: No module named '_ctypes'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/home/minion/.local/bin/flui", line 5, in
from flui import cli
File "/home/minion/.local/share/uv/tools/flui/lib/python3.13/site-packages/flui/cli.py", line 14, in
from .app import FluiApp
File "/home/minion/.local/share/uv/tools/flui/lib/python3.13/site-packages/flui/app.py", line 17, in
from flui.subtype import Barcode, BarcodeProcessor, BarcodeSet, BarcodeUpdateKind
File "/home/minion/.local/share/uv/tools/flui/lib/python3.13/site-packages/flui/subtype/init.py", line 2, in
from .data import Barcode, BarcodeSet, Reads
File "/home/minion/.local/share/uv/tools/flui/lib/python3.13/site-packages/flui/subtype/data.py", line 14, in
from .kmer_index import KmerIndexFlu, SegmentMatch
File "/home/minion/.local/share/uv/tools/flui/lib/python3.13/site-packages/flui/subtype/kmer_index.py", line 14, in
from .kmer_set import KmerSet
File "/home/minion/.local/share/uv/tools/flui/lib/python3.13/site-packages/flui/subtype/kmer_set.py", line 6, in
from scipy.spatial.distance import jensenshannon
File "/home/minion/.local/share/uv/tools/flui/lib/python3.13/site-packages/scipy/init.py", line 91, in
raise ImportError(msg) from e
ImportError: The scipy install you are using seems to be broken, (extension modules cannot be imported), please try reinstalling.

[brettc]

Hi @ruysan. Ha, nice catch. It looks like you found a bug in uv. I can see it will be fixed soon. For now, just do this (I'll add it to the help).

uv tool install --from /path/to/zipfile/flui-x.x.x.zip flui --python 3.11 --native-tls

You might need to uv tool uninstall flui first...

[brettc]

Adding this here for references: astral-sh/uv#7827

[ruysan]

Had to say:
minion@wlwminion01:~$ uv tool install --from ./flui-1.0.2.zip flui --python 3.11 --native-tls --trusted-host files.pythonhosted.org --trusted-host pypi.org --trusted-host pypi.python.org
#it works