Add Flex GEX support, release tooling, and docs updates

[rob-p]

Summary

This branch adds end-to-end support for 10x Flex Gene Expression quantification, extends the chemistry registry/schema to describe Flex-specific resources, adds a release helper script for crate version bumps and publishing, and updates the documentation/tooling to cover the new command and build cleanly with a current Sphinx toolchain.

What changed

1. New flex-quant command for 10x Flex GEX

• Added a new top-level CLI subcommand, simpleaf flex-quant, and wired it into command dispatch.
• Implemented the Flex pipeline in src/simpleaf_commands/flex_quant.rs.
• The command now handles the full Flex workflow:
  • chemistry lookup from the registry
  • automatic probe-set selection by organism
  • probe CSV to FASTA conversion
  • automatic probe_t2g.tsv generation
  • probe index construction with piscem build
  • cached resource reuse when probe indices or downloaded assets already exist
  • cell barcode whitelist resolution
  • sample barcode list resolution
  • mapping with piscem map-scrna
  • multi-barcode permit-list generation with alevin-fry generate-permit-list
  • alevin-fry collate
  • alevin-fry quant
  • writing run metadata to simpleaf_flex_quant_info.json

2. Chemistry schema and registry support for Flex protocols

• Extended src/utils/chem_utils.rs with new schema types used by Flex chemistries:
  • Organism
  • ProtocolType
  • SampleBcListInfo
  • ProbeSetInfo
• Extended CustomChemistry with new optional Flex-related fields:
  • sample_bc_list
  • probe_sets
• Added helpers to interpret chemistry metadata:
  • protocol_type()
  • is_flex_gex()
• Updated serde handling so the registry’s remote_url field maps correctly to the chemistry permit-list URL field.
• Updated chemistry creation code so newly-added custom chemistries initialize the new optional Flex fields to None.
• Registered two Flex chemistries in resources/chemistries.json:
  • 10x-flexv1-gex-3p
  • 10x-flexv2-gex-3p
• Those registry entries include:
  • geometry strings
  • expected orientation
  • permit-list metadata
  • sample barcode list metadata
  • organism-specific probe set metadata for human and mouse
  • protocol metadata identifying the chemistry as flex_gex

3. Flex- and geometry-related behavior fixes

• Updated geometry validation in src/utils/af_utils.rs to skip seq_geom_parser validation for piscem-only extensions such as s[N] and numbered barcode tags like b0[N], deferring validation to piscem where appropriate.
• Corrected the Flex mapping path to use piscem map-scrna.
• Ensured probe CSV conversion keeps all probes, including those marked excluded, in the generated FASTA and t2g mapping so quantification has a complete reference-to-gene mapping.
• Kept structural constraints opt-in rather than forcing them on.

4. Release tooling

• Added bump_and_publish.sh.
• The script now supports a safer release workflow that:
  • validates the requested version as SemVer
  • requires the new version to be greater than the current crate version
  • updates both Cargo.toml and the simpleaf package entry in Cargo.lock
  • performs preflight and post-bump cargo check / cargo package
  • creates the release commit and tag
  • pushes the branch and tag
  • separates dry-run behavior from actual crates.io publishing with --dry-run and --publish

5. Clippy / compile cleanup

• Cleaned up lints introduced by the new Flex work so the branch builds cleanly and passes strict clippy.
• Changes include:
  • boxing the large Chemistry::Custom enum variant
  • deriving Default for ProtocolType
  • replacing manual prefix stripping with strip_prefix

6. Documentation updates

• Added a dedicated documentation page for the new flex-quant command.
• Linked the new page from the main docs index.
• Added a pointer in the standard quant docs directing Flex users to flex-quant.
• Updated workflow and chemistry docs formatting so the docs build cleanly under modern Sphinx.
• Updated docs/requirements.txt to install sphinx explicitly instead of relying on whatever global version happens to be present.

7. Documentation toolchain modernization

• Verified docs builds against a current Sphinx/Furo environment.
• The docs now build cleanly with:
  • sphinx 9.1.0
  • furo 2025.12.19

8. Other repository updates

• Added local generated/test data paths and a helper script path to .gitignore.
• Updated the top-level CLI help snapshot to include flex-quant.
• The committed branch state includes the crate version reflected in Cargo.lock as 0.20.0.

Verification

• cargo build
• cargo clippy --all-targets --all-features -- -D warnings
• /tmp/simpleaf-docs-venv/bin/python -m sphinx -b html docs/source /tmp/simpleaf-docs-html

Notes

• The local uncommitted edits currently present in Cargo.toml and Cargo.lock were not included in this PR; this PR describes the committed main..dev diff only.