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spacetx / starfish

starfish: unified pipelines for image-based transcriptomics
https://spacetx-starfish.readthedocs.io/en/latest/
MIT License
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versioneeer.py breaks on installation #2011

Open johnfmarkham opened 7 months ago

johnfmarkham commented 7 months ago

Description

Problem is described here: https://github.com/EJEP/datapoint-python/issues/183 configparser.SafeConfigParser() and parser.readfp() have been removed.

Steps/Code to Reproduce

Expected Results

Actual Results

Versions

import platform; print(platform.platform()) Linux-5.14.0-362.18.1.el9_3.x86_64-x86_64-with-glibc2.34 import sys; print("Python", sys.version) Python 3.12.2 | packaged by Anaconda, Inc. | (main, Feb 27 2024, 17:35:02) [GCC 11.2.0] import numpy; print("NumPy", numpy.version) NumPy 1.26.4 import scipy; print("SciPy", scipy.version) SciPy 1.11.4 import skimage; print("scikit-image", skimage.version) scikit-image 0.22.0 import pandas; print("pandas", pandas.version) pandas 2.2.1 import sklearn; print("sklearn", sklearn.version) sklearn 1.4.1.post1 import xarray; print("xarray", xarray.version) xarray 2024.2.0 import sympy; print("sympy", sympy.version) sympy 1.12

berl commented 7 months ago

@johnfmarkham want to make a PR for this? looks like that same thread suggests a fix that might work even with the current repo here

johnfmarkham commented 7 months ago

@berl, please excuse my ignorance, what do you mean by "make a PR"?

berl commented 7 months ago

@johnfmarkham no problem! it's easy:

  1. fork the repo
  2. make a new branch on your fork, maybe something like 2011-fix-versioneer
  3. fix the problem, maybe using the suggestion from that thread
  4. save the changes, make a commit on your new branch and and push (to your fork). now your changes should be in a new branch on your fork of the repo on github.
  5. make a pull request from your fork to master on this repo

I'm happy to help more and there are also lots of tutorials around for this kind of workflow

shachafl commented 3 months ago

@berl @johnfmarkham I have looked into it (forked and fixed versioneer) but Starfish can't support python 3.12 because of dependency issues (numba, etc). Once all the main dependencies support python 3.12, we can test.