Potential package compatibility issues

[abiedermann]

• worms version: 0.1.26
• Python version: 3.8
• Operating System: macOS Catalina 10.15.7

Description

Hey, I was really interested in the WORMs work you've been doing so I tried to install and run some of the examples in the recent Science paper. I found there were some potential compatibility issues that can arise between the current versions of worms, Python, numba, and numpy.

Numba 0.54.0 (or similar) results in a jit error when the import worms command is called. This can be fixed by reverting numba to 0.47.0, as this earlier version doesn't have the issue and is compatible with Python 3.8 (which seems to be required by the current worms release due to the flake8 package). (Sorry, I failed to capture the error message for this one).

I also ran into a somewhat odd error when running the CLI for the first time. Apparently, there was an ABI change in numpy 1.20 which causes a dtype error message to be thrown during CLI execution. More details in this thread below:
numba/numba#6041

Error message below (error is thrown by one of the debugging lines I added, but it's representative of the one that occurs on line 159)

================== start job 0 ======================
output_prefix: ./worms
criteria: <worms.criteria.bounded.AxesIntersect object at 0x7fbe601257f0>
bbspec: [BBDir(bblockspec='fc_binder', direction='_C'), BBDir(bblockspec='connector', direction='NC'), BBDir(bblockspec='C3_N', direction='N_')]
precaching splices
reading pdb /Users/biedermann/test/antibody_cage_data/fc_binders/protein_a.pdb
reading pdb /Users/biedermann/test/antibody_cage_data/fc_binders/dhr79.pdb
reading pdb /Users/biedermann/test/antibody_cage_data/connectors/EXT6-DHR10.pdb
reading pdb /Users/biedermann/test/antibody_cage_data/connectors/EXT6-DHR14.pdb
reading pdb /Users/biedermann/test/antibody_cage_data/connectors/EXT6-DHR15.pdb
reading pdb /Users/biedermann/test/antibody_cage_data/connectors/EXT6-DHR18.pdb
reading pdb /Users/biedermann/test/antibody_cage_data/connectors/EXT6-DHR1.pdb
reading pdb /Users/biedermann/test/antibody_cage_data/connectors/EXT6-DHR20.pdb
reading pdb /Users/biedermann/test/antibody_cage_data/connectors/EXT6-DHR21.pdb
reading pdb /Users/biedermann/test/antibody_cage_data/connectors/EXT6-DHR23.pdb
reading pdb /Users/biedermann/test/antibody_cage_data/connectors/EXT6-DHR24.pdb
reading pdb /Users/biedermann/test/antibody_cage_data/connectors/EXT6-DHR26.pdb
reading pdb /Users/biedermann/test/antibody_cage_data/connectors/EXT6-DHR27.pdb
reading pdb /Users/biedermann/test/antibody_cage_data/connectors/EXT6-DHR31.pdb
reading pdb /Users/biedermann/test/antibody_cage_data/connectors/EXT6-DHR32.pdb
reading pdb /Users/biedermann/test/antibody_cage_data/connectors/EXT6-DHR36.pdb
reading pdb /Users/biedermann/test/antibody_cage_data/connectors/EXT6-DHR39.pdb
reading pdb /Users/biedermann/test/antibody_cage_data/connectors/EXT6-DHR3.pdb
reading pdb /Users/biedermann/test/antibody_cage_data/connectors/EXT6-DHR46.pdb
reading pdb /Users/biedermann/test/antibody_cage_data/connectors/EXT6-DHR47.pdb
reading pdb /Users/biedermann/test/antibody_cage_data/connectors/EXT6-DHR49.pdb
reading pdb /Users/biedermann/test/antibody_cage_data/connectors/EXT6-DHR4.pdb
reading pdb /Users/biedermann/test/antibody_cage_data/connectors/EXT6-DHR53.pdb
reading pdb /Users/biedermann/test/antibody_cage_data/connectors/EXT6-DHR54.pdb
reading pdb /Users/biedermann/test/antibody_cage_data/connectors/EXT6-DHR55.pdb
reading pdb /Users/biedermann/test/antibody_cage_data/connectors/EXT6-DHR57.pdb
reading pdb /Users/biedermann/test/antibody_cage_data/connectors/EXT6-DHR58.pdb
reading pdb /Users/biedermann/test/antibody_cage_data/connectors/EXT6-DHR59.pdb
reading pdb /Users/biedermann/test/antibody_cage_data/connectors/EXT6-DHR62.pdb
reading pdb /Users/biedermann/test/antibody_cage_data/connectors/EXT6-DHR64.pdb
reading pdb /Users/biedermann/test/antibody_cage_data/connectors/EXT6-DHR68.pdb
reading pdb /Users/biedermann/test/antibody_cage_data/connectors/EXT6-DHR70.pdb
reading pdb /Users/biedermann/test/antibody_cage_data/connectors/EXT6-DHR71.pdb
reading pdb /Users/biedermann/test/antibody_cage_data/connectors/EXT6-DHR72.pdb
reading pdb /Users/biedermann/test/antibody_cage_data/connectors/EXT6-DHR76.pdb
reading pdb /Users/biedermann/test/antibody_cage_data/connectors/EXT6-DHR77.pdb
reading pdb /Users/biedermann/test/antibody_cage_data/connectors/EXT6-DHR78.pdb
reading pdb /Users/biedermann/test/antibody_cage_data/connectors/EXT6-DHR79.pdb
reading pdb /Users/biedermann/test/antibody_cage_data/connectors/EXT6-DHR7.pdb
reading pdb /Users/biedermann/test/antibody_cage_data/connectors/EXT6-DHR80.pdb
reading pdb /Users/biedermann/test/antibody_cage_data/connectors/EXT6-DHR81.pdb
reading pdb /Users/biedermann/test/antibody_cage_data/connectors/EXT6-DHR82.pdb
reading pdb /Users/biedermann/test/antibody_cage_data/connectors/EXT6-DHR8.pdb
reading pdb /Users/biedermann/test/antibody_cage_data/connectors/EXT6-DHR9.pdb
reading pdb /Users/biedermann/test/antibody_cage_data/cyclic_oligomers/tj04C3_int5v2.pdb
reading pdb /Users/biedermann/test/antibody_cage_data/cyclic_oligomers/tj18C3_V04.pdb
reading pdb /Users/biedermann/test/antibody_cage_data/cyclic_oligomers/2L6HC3_6_design.pdb
bblocks 0
<numba.jitclass.boxing._BBlock object at 0x7fbe507f4f70>
<class 'numba.jitclass.boxing._BBlock'>
Traceback (most recent call last):
  File "/Users/biedermann/miniconda3.8/envs/bar/lib/python3.8/runpy.py", line 192, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "/Users/biedermann/miniconda3.8/envs/bar/lib/python3.8/runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "/Users/biedermann/Dropbox (MIT)/01 Research/03 Code/worms/worms/__main__.py", line 7, in <module>
    worms_main(sys.argv[1:])
  File "/Users/biedermann/Dropbox (MIT)/01 Research/03 Code/worms/worms/app/main.py", line 43, in worms_main
    raise e
  File "/Users/biedermann/Dropbox (MIT)/01 Research/03 Code/worms/worms/app/main.py", line 39, in worms_main
    worms_main2(criteria_list, kw)
  File "/Users/biedermann/Dropbox (MIT)/01 Research/03 Code/worms/worms/app/main.py", line 65, in worms_main2
    kw["bbs"] = simple_search_dag(criteria, merge_bblock=None, precache_only=True, pbar=True,
  File "/Users/biedermann/Dropbox (MIT)/01 Research/03 Code/worms/worms/ssdag.py", line 162, in simple_search_dag
    print(b.file)
TypeError: expected dtype object, got 'numpy.dtype[int8]'

Anyways, just wanted to flag these issues in case anyone else runs into them. Thanks for sharing the awesome code!