- Expand README with installation, usage examples, and module reference table
- Replace seqlib/__init__.py SHRiMP pipeline stub with proper package docstring
  and __all__ export list; add __version__
- Expand qpcr/__init__.py to expose all submodules (abi, MinerMethod,
  qpcrAnalysis, util); add __version__
- Add tests/ with smoke tests for all qpcr and seqlib public modules
- Add .github/workflows/ci.yml: lint (ruff) + test matrix (Python 3.12/3.13)
- Add .pre-commit-config.yaml with ruff and pre-commit-hooks
- Add ruff, pytest, and coverage config sections to pyproject.toml
- Pin dependency upper bounds in requirements.txt; add ruff/pre-commit as dev deps
- Add CHANGELOG.md and CONTRIBUTING.md with development guidelines
- Remove dead rasmus try/except imports from seqlib/util.py
- Wrap pygr imports in genomelib.py and pygrlib.py with try/except ImportError
- Fix bare `import sequencelib` → relative import in genomelib.py
- Remove executable-at-import code from pygrlib.py (was a scratch script)

https://claude.ai/code/session_01CVzyi7WGAKyTJzbmnSNF6r

- Switch build-backend from setuptools.backends.legacy to setuptools.build_meta
  (legacy backend requires newer pip not available in all CI environments)
- Move rpy2 to optional [r] extra; add pandas as core dependency
- Add pytest.importorskip("rpy2") guards for seqstats, RIPDiff, JensenShannon,
  mySam, Chip, continuousData tests (these modules import rpy2 at module level)
- Fix remaining Python 2 syntax in sequencelib.py:
  - raise "string", arg → raise ValueError(...)
  - print "%d" % x → print("%d" % x)
  - import prob → from . import prob (bare sibling import)
- Fix remaining Python 2 syntax in solid.py:
  - import misc → from . import misc
  - print >>outhand, ... → outhand.write(...)
  - print "...", / print "" → print(...)
  - dict.has_key() → in operator
- Fix invalid regex escape sequence in util.py (\$ → r-string)
- Update requirements.txt to comment out rpy2 (now optional)
- Add ruff to dev dependencies in pyproject.toml

All 21 tests now pass (6 skipped without rpy2/R installed).

https://claude.ai/code/session_01CVzyi7WGAKyTJzbmnSNF6r

https://claude.ai/code/session_01CVzyi7WGAKyTJzbmnSNF6r

…ruff errors

- Run 2to3 print fixer on smRNA, lincClonelib, lincName, lincRNAs, dbConn,
  go, gibson, genomelib, primer3lib (print >>stream, expr → print(..., file=...))
- Fix remaining Python 2 except A, B: syntax → except A as B: in
  gibson.py, lincClonelib.py, lincName.py
- Fix backtick repr expressions (`expr` → repr(expr)) in myDataTypes.py
- Fix <> operator remaining in shrimp.py
- Fix raise 'string', arg → raise error('arg') in myDataTypes.py
- Fix bare import sequencelib → from . import sequencelib in smRNA.py
- Fix E731: convert lambda assignment to def in algorithms.py
- Fix E702: split semicolon-separated statements in util.py
- Fix F507: wrong number of % format args in primer3lib.py
- Fix F823: rename loop variable 'next' → 'nxt' in mySam.py (was shadowing builtin)
- Fix E402 in smRNA.py: merge dangling docstring into module docstring
- Add noqa: E402 to misc.py late import (intentional for code organization)
- Expand ruff ignore list: add E101, E402, E731 suppressed for legacy code
- Remove .bak files left by lib2to3 (via .gitignore)

ruff check src/ now passes with 0 errors.
pytest: 21 passed, 6 skipped (rpy2 not installed).

https://claude.ai/code/session_01CVzyi7WGAKyTJzbmnSNF6r

https://claude.ai/code/session_01CVzyi7WGAKyTJzbmnSNF6r