Migrate ldsc from Python 2.7 to Python 3.6+ (based on bulik/ldsc#360)

[Copilot]

Migrates the codebase from Python 2.7 to Python 3.6+ following bulik/ldsc#360, while preserving fork-specific enhancements from commit 1698c1b (--ref-ld-cts support, enhanced make_annot.py, and str match bug fix).

Core Changes

Python 3 Compatibility:

• Removed from __future__ import division
• xrange → range
• print statements → print() functions
• Pandas .ix → .iloc/.loc
• pd.set_option('precision') → pd.set_option('display.precision')
• Added functools.reduce import
• Updated ldscore module to relative imports (import jackknife → from . import jackknife)
• Added rcond=None to np.linalg.lstsq calls
• map() → list(map()) where needed

Configuration:

• requirements.txt: Updated dependencies, replaced nose with pytest
• environment.yml: Python 2.7 → Python >=3.6
• README.md: Updated version to 2.0.0

Code Quality:

• Converted all tabs to 4-space indentation
• Fixed indentation in munge_sumstats.py daner_n block
• Fixed test assertions and pytest.raises usage

Example

Before (Python 2):

for i in xrange(n_blocks):
    print >>log_fh, msg
    ref_ld = ref_ld.ix[ii, :]

After (Python 3):

for i in range(n_blocks):
    print(msg, file=log_fh)
    ref_ld = ref_ld.loc[ii, :]

Verification

• All scripts import successfully with Python 3.12
• CodeQL security scan: 0 alerts

Original prompt

this is a forked repo from the original ldsc package. Some one created a pull request in the original repo bulik#360 that migrate the code base from python 2 to python 3. review this pull request throughly, and create a separate pull request to my fork. note that I have commits that are ahead of bulik:master, review these commits first and make sure the pull request to be created correctly align with my commits

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