[BUG] python3.9 compile failure with oxpy

[supers1x]

Describe the bug
For the latest oxDNA-3.3, fail to compile oxpy with python3.9(Anaconda3).
The old version 'oxDNA-analysis-tools-1.0.15' works just fine on my system.

To Reproduce
Steps to reproduce the behavior:

1. cmake .. -DCUDA=ON -DPython=ON -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DOxpySystemInstall=On
2. make
3. make install

Processing ./oxpy/python/oxpy
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'error'
  error: subprocess-exited-with-error
  
  × python setup.py egg_info did not run successfully.
  │ exit code: 1
  ╰─> [30 lines of output]
      Traceback (most recent call last):
        File "<string>", line 2, in <module>
        File "<pip-setuptools-caller>", line 34, in <module>
        File "/fsa/home/user/apps/oxDNA-3.3/build2/oxpy/python/oxpy/setup.py", line 7, in <module>
          setup(
        File "/fsa/home/user/apps/anaconda3/lib/python3.9/site-packages/setuptools/__init__.py", line 86, in setup
          _install_setup_requires(attrs)
        File "/fsa/home/user/apps/anaconda3/lib/python3.9/site-packages/setuptools/__init__.py", line 75, in _install_setup_requires
          dist = MinimalDistribution(attrs)
        File "/fsa/home/user/apps/anaconda3/lib/python3.9/site-packages/setuptools/__init__.py", line 57, in __init__
          super().__init__(filtered)
        File "/fsa/home/user/apps/anaconda3/lib/python3.9/site-packages/setuptools/dist.py", line 460, in __init__
          for ep in metadata.entry_points(group='distutils.setup_keywords'):
        File "/fsa/home/user/apps/anaconda3/lib/python3.9/site-packages/setuptools/_vendor/importlib_metadata/__init__.py", line 999, in entry_points
          return SelectableGroups.load(eps).select(**params)
        File "/fsa/home/user/apps/anaconda3/lib/python3.9/site-packages/setuptools/_vendor/importlib_metadata/__init__.py", line 449, in load
          ordered = sorted(eps, key=by_group)
        File "/fsa/home/user/apps/anaconda3/lib/python3.9/site-packages/setuptools/_vendor/importlib_metadata/__init__.py", line 996, in <genexpr>
          eps = itertools.chain.from_iterable(
        File "/fsa/home/user/apps/anaconda3/lib/python3.9/site-packages/setuptools/_vendor/importlib_metadata/_itertools.py", line 16, in unique_everseen
          k = key(element)
        File "/fsa/home/user/apps/anaconda3/lib/python3.9/site-packages/setuptools/_vendor/importlib_metadata/__init__.py", line 931, in _normalized_name
          return self._name_from_stem(stem) or super()._normalized_name
        File "/fsa/home/user/apps/anaconda3/lib/python3.9/site-packages/setuptools/_vendor/importlib_metadata/__init__.py", line 600, in _normalized_name
          return Prepared.normalize(self.name)
        File "/fsa/home/user/apps/anaconda3/lib/python3.9/site-packages/setuptools/_vendor/importlib_metadata/__init__.py", line 855, in normalize
          return re.sub(r"[-_.]+", "-", name).lower().replace('-', '_')
        File "/fsa/home/user/apps/anaconda3/lib/python3.9/re.py", line 210, in sub
          return _compile(pattern, flags).sub(repl, string, count)
      TypeError: expected string or bytes-like object
      [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.

[lorenzo-rovigatti]

Hi! It looks like compilation succeeds, but installation fails.

Can you copy&paste the content of the /fsa/home/user/apps/oxDNA-3.3/build2/oxpy/python/oxpy/setup.py file?

[supers1x]

Thanks for the rapid response. Here are the contents of the document /fsa/home/user/apps/oxDNA-3.3/build2/oxpy/python/oxpy/setup.py

from setuptools import setup

import sys
if sys.version_info < (3,0):
    sys.exit('Error, Python < 3.0 is not supported')

setup(
    name = 'oxpy',
    use_scm_version = {
        "root": "/fsa/home/user/apps/oxDNA-3.3",
        "fallback_version": "",
        },
    setup_requires = ['setuptools_scm'],
    packages = [ 'oxpy' ],
    package_dir = {
        'oxpy': '/fsa/home/user/apps/oxDNA-3.3/build2/oxpy/python/oxpy'
    },
    package_data = {
        'oxpy': ['core.so']
    }
)

[lorenzo-rovigatti]

That looks fine. Can you copy&paste the output of the cmake command? You can make a new folder (e.g. build2) and call it from there.

[supers1x]

Sorry, I do not quite understand how to call a file within a folder in GitHub. But I managed to pack the build2 folder with a file cmake_command_output.txt containing the shell output of CMake. The src folder was deleted for a smaller file size.
build2.zip

[lorenzo-rovigatti]

Sorry, that was badly worded. I just needed you to post the output of the cmake command. Your zip file contains it so that's all I needed.
Everything looks fine. The behaviour you see seems to be related to what other people are experiencing in different (but similar) contexts (see here or here).

There are a few things you can try (and get back to me if any of them works!):

1. Call pip install . from within the oxDNA root folder
2. Edit the oxpy/make_install_setup.py and change the "fallback_version": "${fallback_release}", line to "fallback_version": "3.3",
3. If that doesn't work add a version=3.3, line after name = oxpy,, like this:

setup(
    name = 'oxpy',
    version='3.3',
    use_scm_version = {
        "root": "${CMAKE_SOURCE_DIR}",
        "fallback_version": "3.3",
        },
    setup_requires = ['setuptools_scm'],
    packages = [ 'oxpy' ],
    package_dir = {
        'oxpy': '${OXPY_OUTPUT_DIR}'
    },
    package_data = {
        'oxpy': ['core.so']
    }
)

let me know how it goes!

[supers1x]

Hi! I have tried your suggestions and they did not go well(python3.9.12). Then I switched to an older python version(3.8.13) using conda create -n python38 python=3.8, and make install run smoothly alone with oat config.

[lorenzo-rovigatti]

Thanks, that's good to know. I'll try to reproduce the issue on my machine so that I can find a way of solving it!

[ErikPoppleton]

Just a warning that there are a couple oat scripts that don't work with Python <3.9 because of updates to the typing library (Lorenzo, if you would rather I make it more permissive, I can remove those type checks which would make it compatible with everything >3.7). I would suggest installing it in a clean environment with a newer version of Python (I've seen reports that python 3.11 is significantly faster, but I haven't had time to test yet.)

I have installed the both oxpy and oat on fresh conda environments from 3.8 - 3.10 and all have worked for me, so it's possible that this error is coming from a conflict with something else in your environment.

That being said, doing some Googling turned up a couple possible reasons for this error:
This one and a couple others suggested that it's because of a bad .egg-info file. It might be worth looking around in your installed packages to see if you have older versions of either oxpy or oxDNA-analysis-tools floating around that you can remove.
This one suggests that it could be a problem with an OS-provided version of pip or a missplaced copy of setuptools (though this might be specific to Arch Linux and it looks like you're on a mac)

[supers1x]

Hello ErikPoppleton, removing files relate to oxpy or oxDNA-analysis-tools under my Anaconda folder did help my installation.
For the record, my system is CentOS Linux release 7.3.1611.

[lorenzo-rovigatti]

@supers1x thank you for for the feedback! I'll add this issue and its solution to our docs.