singjc
commented
11 months ago This seems to be an issue on Windows ubuntu subsystem as well. It seems PyMSNumpress requires Cython to be installed prior to installing dependencies in the setup.py
$ pip install -e . Obtaining file:///mnt/f/Users/JustinS/github/massseer Preparing metadata (setup.py) ... done
Collecting Click (from MassSeer==0.1.0a0) Using cached click-8.1.7-py3-none-any.whl.metadata (3.0 kB)
Collecting streamlit (from MassSeer==0.1.0a0) Using cached streamlit-1.28.1-py2.py3-none-any.whl.metadata (8.1 kB)
Collecting numpy>=1.9.0 (from MassSeer==0.1.0a0) Using cached numpy-1.26.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (61 kB)
Collecting pandas>=0.17 (from MassSeer==0.1.0a0)
Using cached pandas-2.1.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (18 kB)
Collecting cython==0.29.32 (from MassSeer==0.1.0a0)
Using cached Cython-0.29.32-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl (2.0 MB)
Collecting scipy (from MassSeer==0.1.0a0)
Using cached scipy-1.11.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB)
Collecting pyopenms (from MassSeer==0.1.0a0)
Using cached pyopenms-3.1.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (1.9 kB)
Collecting PyMSNumpress==0.2.2 (from MassSeer==0.1.0a0)
Using cached PyMSNumpress-0.2.2.tar.gz (32 kB)
Preparing metadata (setup.py) ... error
error: subprocess-exited-with-error × python setup.py egg_info did not run successfully. │ exit code: 1 ╰─> [6 lines of output]
Traceback (most recent call last): File "<string>", line 2, in <module> File "<pip-setuptools-caller>", line 34, in <module> File "/tmp/pip-install-5zplh61s/pymsnumpress_3ad6d8756c1944d389c4da6ebbf42a6d/setup.py", line 34, in <module> from Cython.Distutils import build_ext
ModuleNotFoundError: No module named 'Cython' [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. error: metadata-generation-failed × Encountered error while generating package metadata. ╰─> See above for output. note: This is an issue with the package mentioned above, not pip. hint: See above for details.I think to resolve this, we might have to try just switch over to using MSNumpress packaged with pyopenms.
If someone install this on a fresh environment, they will have troubles with these packages not being installed
Numpy Scipy
Also, cython for some reason is not installed properly when I used 'pip install -r requirements.txt' If someone calls 'pip install Cython', it will install a version that is not compatible with MSNumpress.