Closed mortunco closed 1 year ago
I try to remove that line np.warnings.filterwarnings('ignore')
from uniport/function.py and build it from the source but couldnt figure it out.
Is there a way to pip install uniprot from my own fork?
Code below didnt work.
(uniport-5) $ pip install git+https://github.com/mortunco/uniPort@main
Collecting git+https://github.com/mortunco/uniPort@main
Cloning https://github.com/mortunco/uniPort (to revision main) to /tmp/pip-req-build-8bruelni
Running command git clone --filter=blob:none --quiet https://github.com/mortunco/uniPort /tmp/pip-req-build-8bruelni
Resolved https://github.com/mortunco/uniPort to commit 06f58d8128d1a2fcdb18120c71a098d444e4755d
Installing build dependencies ... done
Getting requirements to build wheel ... error
error: subprocess-exited-with-error
× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> [15 lines of output]
Traceback (most recent call last):
File "/opt/conda/envs/uniport-5/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
main()
File "/opt/conda/envs/uniport-5/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/uniport-5/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 118, in get_requires_for_build_wheel
return hook(config_settings)
^^^^^^^^^^^^^^^^^^^^^
File "/tmp/pip-build-env-4ddh56s0/overlay/lib/python3.11/site-packages/flit_core/buildapi.py", line 31, in get_requires_for_build_wheel
module = Module(info.module, Path.cwd())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/tmp/pip-build-env-4ddh56s0/overlay/lib/python3.11/site-packages/flit_core/common.py", line 59, in __init__
raise ValueError("No file/folder found for module {}".format(name))
ValueError: No file/folder found for module uniPort
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error
× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> See above for output.
note: This error originates from a subprocess, and is likely not a problem with pip.
Hi, thanks for your interest! Could you please downgrade your numpy version, e.g., numpy 1.23.0? I tried this version and it works.
Hi. Thank you very much for your swift response. Your suggestion worked! I am leaving this here for future in case anyone else has the issue.
$ conda create --name uniport-env
$ conda activate uniport-env
$ pip install uniport numpy==1.23.0
$ python
Python 3.11.4 | packaged by conda-forge | (main, Jun 10 2023, 18:08:17) [GCC 12.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import uniport as up
>>>
quick addition:
If you are trying to follow the MERFISH Impute Genes tutorial. You will need sciVi.
In that case, numpy==1.23.3
solved the dependency conflict.
Hello.
I am having problems importing uniport. Basically, I created a fresh conda environment with pip and followed installation procedure. Here is the output.
Here is the relavent packages with their version.
I think this is a numpy version problem. To solve this, I also created a fresh conda env and tried pip install -r requirements in the repo. Same problem. I also tried installing without "=>" and made the versions exact. Pip install failed during the installation.
I would appreciate if could help me with this. We loved the tool, we loved the paper. Would like to implement to our work.
Best regards,
T.