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Port vcfaz to Python 3 and remove legacy py27 directory#1

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Port vcfaz to Python 3 and remove legacy py27 directory#1
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copilot/port-vcfaz-to-python3

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Copilot AI commented Mar 6, 2026 •
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Completes the Python 3 (≥3.10) port of the vcfaz package, migrating from the legacy Python 2.7 conda package layout to a src/ layout, and removes the legacy directory entirely.

Python 3 compatibility fixes

src/vcfaz/model.py

  • class _AltRecord(object, metaclass=ABCMeta) replaces __metaclass__ = ABCMeta
  • basestring → str
  • Removed __cmp__ (Python 2 only)
  • Dropped legacy try/except ImportError fallbacks for Counter/OrderedDict

src/vcfaz/parser.py

  • All intra-package imports converted to explicit relative imports (from .model import ...)
  • itertools.izip → zip
  • dict.has_key() → in operator
  • dict.iteritems()/iterkeys()/itervalues() → .items()/.keys()/.values()
  • def next(self) renamed to def __next__(self) with next = __next__ alias for backwards compat
  • Gzip handling simplified — always wraps with codecs.getreader on Python 3
  • Invalid regex escape sequences fixed to raw strings

src/vcfaz/sample_filter.py

  • Relative import: from .parser import Reader, Writer
  • xrange → range

src/vcfaz/utils.py

  • readers[i].next() → next(readers[i])

src/vcfaz/__init__.py

  • All imports converted to explicit relative imports; exposes Reader, Writer, VCFReader, VCFWriter, Filter, SampleFilter, RESERVED_INFO, RESERVED_FORMAT

Removed

  • pyvcfaz-0.6.8-py27_0/ — entire legacy Python 2.7 directory deleted

Tests

Added tests/test_import.py with smoke tests covering imports and basic in-memory VCF parsing:

# Quick non-installed smoke test
PYTHONPATH=src python -c "import vcfaz; print(vcfaz.__file__)"

# Or run the full smoke test suite
PYTHONPATH=src python -m pytest tests/test_import.py -v
Original prompt

Goal

Create a PR in biofold/Py3VCF that completes the Python 3 (>=3.10) port of the legacy vcfaz package and removes the legacy Python 2 directory.

Background / Context

The repository currently contains a legacy, Python 2.7-era copy of the vcfaz package under:

  • pyvcfaz-0.6.8-py27_0/lib/python2.7/site-packages/vcfaz/

We want to:

  1. Port the package to a modern Python 3 codebase using a src/ layout.
  2. Place the Python 3 port under:
  • src/vcfaz/
  1. Delete the legacy directory:
  • pyvcfaz-0.6.8-py27_0/

Requirements

A. Add Python 3 package sources

Create the following files under src/vcfaz/ with Python 3-compatible code:

  • src/vcfaz/__init__.py
  • src/vcfaz/parser.py
  • src/vcfaz/model.py
  • src/vcfaz/utils.py
  • src/vcfaz/filters.py
  • src/vcfaz/sample_filter.py

Key compatibility fixes include (non-exhaustive):

  • Convert legacy intra-package imports to explicit relative imports (e.g. from .model import ...).
  • Replace Python 2-only APIs:
    • itertools.izip -> zip
    • dict.iteritems()/iterkeys()/itervalues() -> .items()/.keys()/.values()
    • xrange -> range
    • basestring -> str
    • has_key -> in
    • implement iterator protocol (__iter__ + __next__) for Reader.
  • Ensure gzipped VCF handling works correctly on Python 3 (decode bytes to text via codecs reader).
  • Maintain backwards-compatible aliases where present (e.g. VCFReader, VCFWriter) and export public API from src/vcfaz/__init__.py.

B. Remove legacy directory

Delete the entire directory:

  • pyvcfaz-0.6.8-py27_0/

C. Smoke tests / verification

Add minimal smoke tests (can be lightweight and not require external data) or at least include instructions in PR description. Preferably add tests/test_import.py that verifies:

  • import vcfaz works
  • from vcfaz.parser import Reader works

If tests are added, ensure they pass in CI or at least locally.

D. PR details

  • Base branch: main
  • Create a feature branch (suggested name: python3-port if available; otherwise python3-port-2).
  • PR title suggestion: Port vcfaz to Python 3 and remove legacy py27 directory
  • PR should include a clear summary and how to run a quick non-installed smoke test:
    • PYTHONPATH=src python -c "import vcfaz; print(vcfaz.__file__)"

Reference legacy sources

Legacy files to port (current commit context):

  • pyvcfaz-0.6.8-py27_0/lib/python2.7/site-packages/vcfaz/__init__.py
  • pyvcfaz-0.6.8-py27_0/lib/python2.7/site-packages/vcfaz/parser.py
  • pyvcfaz-0.6.8-py27_0/lib/python2.7/site-packages/vcfaz/model.py
  • pyvcfaz-0.6.8-py27_0/lib/python2.7/site-packages/vcfaz/utils.py
  • pyvcfaz-0.6.8-py27_0/lib/python2.7/site-packages/vcfaz/filters.py
  • pyvcfaz-0.6.8-py27_0/lib/python2.7/site-packages/vcfaz/sample_filter.py

Notes

  • Keep changes focused on the vcfaz package port and removal of the legacy directory.
  • If other packaging files (e.g. pyproject.toml) are required for tests/imports, add them as needed, but do not over-scope.

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Copilot AI and others added 2 commits March 6, 2026 16:44
@ecapriotti
Port vcfaz to Python 3 and remove legacy py27 directory
dc6f4e3 
Co-authored-by: ecapriotti <5848298+ecapriotti@users.noreply.github.com>
@ecapriotti
Add .gitignore and remove committed pycache files
fb47daa 
Co-authored-by: ecapriotti <5848298+ecapriotti@users.noreply.github.com>
Copilot AI changed the title [WIP] Complete Python 3 port of legacy vcfaz package Port vcfaz to Python 3 and remove legacy py27 directory Mar 6, 2026
@ecapriotti

ecapriotti commented Mar 6, 2026

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