Add tximport-style transcript-length normalization and pytximport support

[gitbenlewis]

Reference Issue or PRs

Closes #305.
Closes #359.
Related to #412.

What does your PR implement? Be specific.

This PR adds DESeq2-style transcript-length
normalization and direct compatibility
with AnnData objects produced by
[pytximport](https://github.com/complextissue/
pytximport).

The generic API remains available:

dds = DeseqDataSet(
    counts=estimated_counts,
    metadata=metadata,
    transcript_lengths=average_transcript_lengths,
    design="~condition",
)

Compatible pytximport objects can also be passed
directly:

dds = DeseqDataSet(adata=txi, design="~condition")

The implementation:

• Rounds unscaled estimated counts, matching
  DESeq2.
• Stores average transcript lengths in
  layers["avg_tx_length"].
• Constructs sample-by-gene normalization factors
  containing both transcript-length
  and relative library-size components.
• Stores the final factors in
  layers["normalization_factors"].
• Uses the factor matrix throughout dispersion
  fitting, LFC fitting, Wald tests,
  shrinkage, Cook's outlier replacement/refitting,
  and VST.
• Supports the ratio and poscounts size-factor
  methods.
• Preserves sparse CSR and CSC counts through
  inference boundaries.
• Does not add pytximport as a runtime
  dependency.

Length-source precedence is deterministic:

1. Explicit transcript_lengths
2. adata.layers["avg_tx_length"]
3. Compatible pytximport fields

For pytximport input, only unscaled estimated
counts with
adata.uns["counts_from_abundance"] is None are
accepted. Abundance-scaled modes
are rejected to prevent applying transcript-length
correction twice.

Validation

Local verification completed successfully:

• Full test suite: 104 passed
• Dense-versus-CSR/CSC parity through dispersion
  fitting, LFCs, Wald tests,
  shrinkage, VST, Cook's distances, replacement,
  and refitting
• AnnData 0.11.4 compatibility checks passed
• Ruff, formatting, mypy, pre-commit, and Sphinx
  warnings-as-errors passed

Current limitations

• Direct pytximport normalization requires an in-
  memory AnnData object.
• Pytximport's current obsm["length"] matrix has
  no gene-axis labels, so it must
  remain synchronized when genes are subset or
  reordered.
• Iterative size-factor fitting is not supported
  with transcript-length offsets.
• VST transformation of an external count matrix
  with separate transcript lengths
  is not currently supported.

Related work and acknowledgements

This implementation began independently with the
generic transcript_lengths
API and was extended with direct pytximport
compatibility following discussion in
#412.

Thank you to @maltekuehl for the earlier draft
implementation and design work in
#412, and to @Zethson for encouraging this work to
be taken forward. The original
tximport, DESeq2, and pytximport work is credited
in the documentation.