Modernize packaging, add test suite, remove shell-string system calls

[caleblareau]

Refactors the codebase in three steps, as requested.

Step 1 — Dependencies & packaging

• Replace setup.py/setup.cfg with a PEP 621 pyproject.toml. Fixes the distutils import (removed in Python 3.12+), de-duplicates biopython, drops the obsolete py2 universal wheel, sets requires-python >= 3.9, and moves pytest to a [test] extra.
• Replace deprecated pkg_resources.get_distribution with importlib.metadata via a new bap_version() helper; make @click.version_option() explicit.

Step 2 — Testing + documentation

• New pytest suite: test_helpers.py (pure functions + run_cmd), test_cli_smoke.py (hermetic CliRunner checks), and test_integration.py (end-to-end bap2 bam, auto-skips when samtools/bedtools/R/snakemake are absent).
• GitHub Actions CI across Python 3.9–3.12 (.github/workflows/ci.yml).
• Rewrote tests/README.md into a real testing guide; added a Testing section to the main README.

Step 3 — Refactor (no shell-string system calls)

• Added a run_cmd() subprocess wrapper (no shell). Replaced every os.system("..."), os.popen('ls ...'), and os.system("cp ...") in the active CLIs with run_cmd([...]), glob.glob, and shutil.copyfile; child scripts launch via sys.executable.
• Migrated YAML writing from the removed ruamel.yaml RoundTripDumper API to the modern YAML() API.
• Fixed latent bugs: Python-2 itertools.imap in string_hamming_distance, abs_file→abs_path, missing import subprocess, undefined macs2_genome_size/bs_genome, and import-time PyYAML dependency.

Out of scope (intentionally unchanged): the deprecated v1 bap command (cli_old_dontEdit.py) and the genuine shell pipelines inside the Snakemake run: blocks.

Verification

• pip install -e .[test] succeeds on modern Python; all console scripts report their version.
• pytest → 41 passed, 1 skipped (integration auto-skip). os.system/os.popen remain only in the legacy v1 CLI.

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