[dajiaohuang]

Problem

The installation page's mytest.py and the README's Python example still use Python 2 print statements. Copying either example into Python 3 fails with SyntaxError before the example can run. The installation page also names the Ubuntu package build-essentials (the package is build-essential) and instructs users to run condatest.sh, which is no longer in the repository.

The design guide additionally calls a nonexistent BedTool.intersectBed method and uses merge rather than the BEDTools mergeBed alias in its shell pipeline. Its statement that every BedTool must point to a file contradicts the documented stream=True interface.

Changes

• Use print(...) in the two runnable onboarding examples.
• Correct the Ubuntu package name and remove the obsolete condatest.sh subsection, retaining the existing unit/doctest instructions.
• Correct the intersect method and merge executable names, and distinguish default file-backed results from streaming results.

No runtime code or generated documentation is changed.

Validation

• Built and installed the source at efb8534c11ca6b45a6cd173ff3b3d1bf754e34a1 in an isolated Python 3.12.3 environment on Ubuntu 24.04, using Cython 3.3.0 and bedtools 2.31.1.
• Confirmed both original Python examples fail to compile; the corrected installation quick test runs and produces exactly the documented three intersection rows using the bundled a.bed/b.bed fixtures.
• Ran the corrected README pipeline with tiny synthetic local interval files, including an intergenic interval, and checked the printed names.
• Checked synthetic public BedTool construction, coordinate/strand mutation, intersect/sort/merge, streaming/iterator consumption, saving and isolated temporary-file cleanup against real bedtools. The corrected shell pipeline matches the chained Python API result.
• Confirmed Ubuntu package metadata contains build-essential, and the repository tree has no condatest.sh.
• git diff --check passed.

The complete test suite, Sphinx site build and older Python/bedtools version matrix were not run. No external genomic data or chromosome-size downloads were used.