Fix #242: expose annotation versions on Gene/Transcript/Exon/Protein

[iskandr]

Summary

Closes #242 by surfacing the Ensembl annotation version columns (already loaded into the sqlite DB) on Gene, Transcript, Exon, and a new Protein view object accessed via Transcript.protein.

Each type has a prefixed canonical accessor plus a generic alias:

Entity	Canonical	Alias
Gene	gene_version, versioned_gene_id	version, versioned_id
Transcript	transcript_version, versioned_transcript_id	version, versioned_id
Exon	exon_version, versioned_exon_id	version, versioned_id
Protein (via t.protein)	protein_id, protein_version, versioned_protein_id	id, version, versioned_id

Example:

t = ensembl.transcript_by_id("ENSMUST00000103109")
t.transcript_version       # 3
t.versioned_transcript_id  # "ENSMUST00000103109.3"
t.version                  # 3  (alias)
t.versioned_id             # "ENSMUST00000103109.3"  (alias)
t.protein.id               # "ENSMUSP00000099398"
t.protein.versioned_id     # "ENSMUSP00000099398.3"

When the GTF omits version attributes (e.g. TAIR), every *_version returns None and versioned_* falls back to the unversioned id.

Compatibility

• Exon.__init__ gains a keyword-only exon_version=None (default preserves the old signature for positional callers).
• Transcript.protein_id and Transcript.protein_sequence stay; the new Transcript.protein is purely additive.
• Pyensembl's existing .N-stripping of FASTA IDs is unchanged — those strips are needed for sequence lookup and are orthogonal to surfacing the version on the metadata objects.
• Bumps version to 2.7.0 (additive features, no breakage).

Test plan

• tests/test_versions.py covers Gene/Transcript/Exon/Protein versions on mouse Ensembl 81 partial data (versions present) and on TAIR partial data (versions absent)
• pytest tests/test_versions.py tests/test_mouse.py tests/test_tair10_complete.py tests/test_serialization.py tests/test_missing_genome_sources.py tests/test_exon_object.py tests/test_locus.py tests/test_shell.py
• ./lint.sh
• CI on PR

[coveralls]

coverage: 84.129% (+0.6%) from 83.547% — fix-242-version-and-versioned-id into main