Cleanup issues AlphaGenes/AlphaImpute2#64

[XingerTang]

Related Issue

Closes #64
Closes #58
Closes #60

Relate to #59

What changed

• Add -version parser
• Modify files as suggested by Reassess Numba support for recent Python versions and Update test coverage #58
• Cannot update tinyhouse reference as the most recent version of tinyhousealso has the changes for metafounders and X chromosomes, which are incompatible with the current code of the AlphaImpute2.
  • The boilerplate printout mentioned in the Change the AlphaImpute2 help version string (defined in tinyhouse.print_boilerplate) #59 is therefore commented out as a temporary measure.

Why this change

Clean up issues

Notes / Risks

• The recent changes in tinyhouse is incompatible with current AlphaImpute2 code.

[XingerTang]

Error output with the up-to-date tinyhouse version:

TypeError: 'NoneType' object is not subscriptable
Traceback (most recent call last):
  File "/Users/xtang3/anaconda3/envs/phase/bin/AlphaImpute2", line 7, in <module>
    sys.exit(main())
             ^^^^^^
  File "/Users/xtang3/anaconda3/envs/phase/lib/python3.11/site-packages/alphaimpute2/tinyhouse/Utils.py", line 10, in timer
    values = func(*args, **kwargs)
             ^^^^^^^^^^^^^^^^^^^^^
  File "/Users/xtang3/anaconda3/envs/phase/lib/python3.11/site-packages/alphaimpute2/alphaimpute2.py", line 495, in main
    read_in_data(pedigree, args)
  File "/Users/xtang3/anaconda3/envs/phase/lib/python3.11/site-packages/alphaimpute2/tinyhouse/Utils.py", line 10, in timer
    values = func(*args, **kwargs)
             ^^^^^^^^^^^^^^^^^^^^^
  File "/Users/xtang3/anaconda3/envs/phase/lib/python3.11/site-packages/alphaimpute2/alphaimpute2.py", line 455, in read_in_data
    InputOutput.readInPedigreeFromInputs(pedigree, args, genotypes=True, haps=True)
  File "/Users/xtang3/anaconda3/envs/phase/lib/python3.11/site-packages/alphaimpute2/tinyhouse/InputOutput.py", line 376, in readInPedigreeFromInputs
    if pedigree.MainMetaFounder[:3] != "MF_":
       ~~~~~~~~~~~~~~~~~~~~~~~~^^^^
TypeError: 'NoneType' object is not subscriptable
___________________________________________________

[XingerTang]

All the tests are now tested on the three OSs: ubuntu-latest, Windows-latest, macos-latestand all Python versions 3.6 - 3.13.

The tests can be passed for all cases, but sometimes the accuracy report may fail to generate for the ubuntu system for population-based imputation for some unknown reason. I have added a warning if the accuracy report is only partial, and encourage the user to re-run the tests if that is the case.

[gregorgorjanc]

Looks good. Only left you a couple of minor bits to address.

[gregorgorjanc]

I looked at the changes, which look ok. Best to address the -help while we are at it in the other package too, so we have two use cases that are the same so we then follow this template.

All requests done!

[gregorgorjanc]

Time for squash and merge this PR @XingerTang;)