v0.30.7 - Modernize gget

• gget cellxgene: Added support for the three non-human primate species available in the CZ CELLxGENE Census LTS 2025-11-08: rhesus macaque (macaca_mulatta), common marmoset (callithrix_jacchus), and chimpanzee (pan_troglodytes).
  • The species argument (both Python and command line) now accepts all five supported organisms; the CLI choices, help text, and docstrings list them.
  • Added early validation of the species argument that raises a clear ValueError listing the supported species, instead of failing later inside the Census API call.
  • Note: the new primate species require census_version="2025-11-08" (LTS) or newer.
• Docs/README: updated gget repository and manual URLs from pachterlab to scverse (github.com/scverse/gget, scverse.org/gget) to reflect the project's move under the scverse organization. Links to separate resources (pachterlab/gget_examples, pachterlab/kvar, pachterlab/varseek, and the Pachter Lab homepage) were left unchanged. Resolves issue 217.
• gget g2p: New module to query the Genomics 2 Proteins (G2P) portal for residue-level protein structure/function annotations — per-residue features (AlphaFold pLDDT, UniProt sites, predicted pockets, PTMs), the gene–transcript–protein–isoform–structure map, and isoform alignments. Resolves issue 138.
• Deprecations:
  • gget alphafold and gget gpt are no longer actively maintained. Both now emit a warning when invoked, and a deprecation notice was added to the top of each module's docs.
• Bug fixes:
  • gget search: Missing values are now consistently returned as None instead of NaN, both in scalar cells and inside synonym lists ([None] rather than [nan] for genes with no synonyms). The previous output was an artifact of SQL LEFT JOINs surfacing as pandas NaNs; the JSON output was already null either way, so this only affects the DataFrame return path.
  • gget mutate: Fixed pyarrow.lib.ArrowNotImplementedError: Function 'binary_join_element_wise' has no kernel matching input types (large_string, null, large_string) when the input contained no substitutions (only deletions/insertions/delins/duplications/inversions). The substitution-only sequence-build branches now short-circuit on an empty selection instead of triggering an arrow-string kernel that older pyarrow versions don't implement.
  • gget muscle and gget diamond: When the bundled MUSCLE / DIAMOND binary fails because a system library is missing (most commonly libgomp / libomp on macOS without Homebrew gcc/libomp installed), gget now raises a clear RuntimeError naming the missing library and the exact brew install / apt install command to fix it — instead of the raw dyld / ld.so error spilling onto stderr.
  • gget muscle: When the MUSCLE binary fails, gget now exits with a non-zero status code instead of silently exiting 0. Pipelines and CI scripts can finally detect MUSCLE failures programmatically.
• Developer tooling / packaging:
  • Migrated packaging to a single pyproject.toml (the hatchling build backend); removed setup.py, setup.cfg, requirements.txt, dev-requirements.txt, and MANIFEST.in. Runtime dependencies and the test dependency group are now declared in pyproject.toml.
  • The minimum supported Python version is now 3.12; CI tests on 3.12, 3.13, and 3.14.
  • cellxgene-census is now declared as an optional extra (pip install gget[cellxgene]) because it has no wheels for Python 3.14 yet. Users who install it via gget setup cellxgene are unaffected.
  • Added a pre-commit configuration (lint + format via ruff, plus standard hygiene hooks). Run prek run --all-files (or pre-commit run --all-files) before opening a PR.
  • Added type annotations across the entire gget/ source tree (175 functions across all 28 source files) and wired mypy into the pre-commit config with a permissive baseline. IDE intellisense and downstream typed-code consumers benefit immediately; the type-error baseline can be tightened module-by-module over time.
  • Modernized the test CI to use uv and run on pull requests, and added package-build-check and PyPI trusted-publishing workflows.