v1.8.0

MINOR release. Adds a new entry-point group research_os.adapter for pluggable
detectors + provenance extractors for the tools a project uses around its
code (HPC schedulers, workflow engines, analysis platforms, data systems).
Six adapters ship bundled with the core wheel. Also extends the tools.md
extractor from Python-only to multi-language with adapter-contributed
regex patterns, so a step's tools.md finally captures R libraries, HPC
modules, Snakemake rules, Nextflow processes, etc. Distinct from the
v1.7.0 research_os.protocol_pack group: packs add protocols; adapters
add provenance extractors. They share the loader pattern but have separate
registries.

Added — adapter framework

• src/research_os/adapters/__init__.py, base.py, loader.py, runner.py.
• AdapterRegistration dataclass + register_adapter() convenience constructor
  with namespace validation + regex compile-time check.
• Discovery via research_os.adapter entry-point group + in-tree bundled list.
• Per-adapter error isolation: bad adapters log to
  workspace/logs/adapter_errors.log and are skipped without blocking startup
  or other adapters.
• Three new core MCP tools: sys_adapters_installed (diagnostic),
  tool_adapter_extract (run one), tool_adapters_list (status of all),
  tool_adapters_run_all (run every detected).

Added — 6 bundled adapters

Adapter	Detects	Extracts
slurm	#SBATCH/#PBS directives + inline sbatch/qsub	partition, time, nodes, cpus, mem, GPU, dependencies, modules
snakemake	Snakefile / *.smk	rules: name, inputs, outputs, shell preview, conda, container, threads
nextflow	*.nf / nextflow.config / main.nf	process blocks, containers, resources, executor profiles
cytoscape	*.cys session archives	per-network: nodes, edges, attribute schemas, layout, visual styles
redcap	data-dictionary CSV OR exports with record_id + redcap_event_name	fields (name/type/validation/identifier), longitudinal vs cross-sectional, sample N, PHI warnings
synapse	.synapseConfig / synapseclient imports / synXXXXXXXX refs	referenced entity IDs with source script + line + nearby comment

Added — 8 adapter-contributed tools

tool_slurm_job_status, tool_slurm_estimate_cost,
tool_snakemake_dryrun, tool_snakemake_dag_render,
tool_nextflow_validate, tool_cytoscape_export_static,
tool_redcap_schema_describe, tool_synapse_entity_info.
All gracefully degrade when their optional system deps (snakemake,
nextflow, synapseclient, matplotlib, openpyxl) are absent — returning
a status='warning' envelope with an install hint instead of failing.

Added — multi-language tools.md extractor

src/research_os/tools/actions/state/extractors.py (new module). Per-language
extractors return (kind, name, version) tuples; a dispatcher routes by
file suffix; an adapter-pattern collector applies every registered adapter's
tools_md_patterns on top.

Languages covered: Python imports, R library() / require() / p_load() /
BiocManager::install(), R DESCRIPTION parsing, renv.lock,
Bash module load + conda activate + source venv,
Node package.json + JS/TS import / require,
Rust Cargo.toml + .rs use statements,
Julia Project.toml + .jl using / import.

src/research_os/tools/actions/state/path.py _render_tools_md_section now
delegates to extract_from_tree. Output format unchanged but vastly more
populated: a step's tools.md entry now reads like a full reproducibility
manifest ("R library: DESeq2", "HPC module: bwa/0.7.17", "Snakemake rule:
align").

Added — 3 reference projects

• slurm_snakemake — RNA-seq pipeline (Snakefile + sbatch wrapper, exercises
  slurm + snakemake adapters)
• nextflow_chipseq — ChIP-seq DSL2 pipeline (exercises nextflow adapter)
• redcap_longitudinal — 3-event observational cohort (exercises redcap adapter)

CI stress matrix: 8 → 11 projects × mock model on every PR.

Added — extras

pip install research-os[slurm], [snakemake], [nextflow], [cytoscape],
[redcap], [synapse] reserved as no-op extras (adapters ship bundled).
pip install research-os[all_adapters] installs all six.

Added — preflight + tests

Two new preflight checks: Bundled adapters discovered + Adapter regex
patterns compile. Preflight: 19/19 → 21/21 green.

43 new tests under tests/unit/test_v180_adapters_extractors.py covering:
framework validation, all 6 adapters detect + extract, optional tools
dispatch, multi-language extractor coverage, 3 new reference projects
stress-run at 100% success, adapter cross-detection on real fixtures.

Added — docs

• docs/ADAPTERS.md (new) — overview + write-your-own-adapter quickstart.

Bumped

• version 1.7.1 → 1.8.0 in pyproject.toml, src/research_os/__init__.py, CITATION.cff.
• Embeddings rebuilt (now 150 protocol docs + 201 tool docs).

Counts

• Adapters: 0 → 6 (slurm, snakemake, nextflow, cytoscape, redcap, synapse).
• Tools surface: 189 → 201 (+3 core adapter tools + 9 optional pack tools).
• Reference projects: 8 → 11 (+3 infra-focused).
• Preflight: 19 → 21 checks.
• Pytest: 685 → 728 passes.

Compatibility

No breaking changes. Every v1.6.x / v1.7.x tool name, protocol name, alias,
redirect stub, plugin API, stress-runner contract continues to work. The
adapter framework is a NEW namespace (research_os.adapter) separate from
the protocol-pack namespace (research_os.protocol_pack); they don't
cross-contaminate.

---