feat(reactome): add gget reactome module to query the Reactome pathway database (#114)

[Elarwei001]

Resolves #114

What this adds

A new gget reactome module that queries the Reactome pathway knowledgebase via its ContentService REST API, returning gget-ified data frames (or list-of-dicts with json=True). The query type is selected with the resource argument:

resource	Returns	query is
pathways (default)	the pathways an identifier participates in	an identifier (e.g. UniProt P04637)
search	full-text search of the knowledgebase	a search term (e.g. TP53)
entity	details for a Reactome stable ID	a stable ID (e.g. R-HSA-6804754)
interactors	molecular interactors (IntAct static)	a molecule accession
orthology	project a stable ID to another species	a stable ID (needs --species)
event-hierarchy	the full pathway/reaction hierarchy for a species	a species name or taxon ID

gget reactome P04637 --species "Homo sapiens"                 # pathways
gget reactome TP53 -r search -t Pathway                       # search
gget reactome R-HSA-6804754 -r entity                         # entity
gget reactome P04637 -r interactors                           # interactors
gget reactome R-HSA-6804754 -r orthology -sp "Mus musculus"   # orthology
gget reactome "Homo sapiens" -r event-hierarchy               # event hierarchy

• source selects the identifier database for pathways (UniProt default, Ensembl, ChEBI, NCBI); species / types filter where applicable.
• Names from the search endpoint have Reactome's HTML highlight tags stripped; the returned data frame carries the Reactome release in .attrs["reactome_release"] for reproducibility.
• CLI format follows gget's convention: JSON by default, --csv for CSV.

Robustness

http_json now raises HTTPStatusError (a RuntimeError subclass carrying .status_code), so reactome branches on the status code (e.g. 404 → empty result / clear ValueError) instead of string-matching the error message. Backward-compatible: existing except RuntimeError callers are unaffected.

Testing

• Network-free unit tests (TestReactomeOffline): parsing and error branches for every resource, HTML stripping, name/summation fallbacks, species resolution, and argument validation.
• Network tests (TestReactome) that assert structural invariants (columns, identifier shape, species honored, a stable well-known entry) rather than drift-prone exact lists, and skip when Reactome is unreachable. Includes a species-by-name case.

[codecov-commenter]

Codecov Report

❌ Patch coverage is 92.94118% with 12 lines in your changes missing coverage. Please review.
✅ Project coverage is 57.56%. Comparing base (e43a804) to head (5e3b536).
⚠️ Report is 2 commits behind head on dev.

Files with missing lines	Patch %	Lines
gget/gget_reactome.py	93.25%	11 Missing ⚠️
gget/utils.py	83.33%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##              dev     #236      +/-   ##
==========================================
+ Coverage   56.70%   57.56%   +0.85%     
==========================================
  Files          29       30       +1     
  Lines        9392     9560     +168     
==========================================
+ Hits         5326     5503     +177     
+ Misses       4066     4057       -9     

☔ View full report in Codecov by Harness.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[Elarwei001]

Hi @lauraluebbert — this adds the gget reactome module that querying Reactome's ContentService REST API.

Key points:

1. What it does — one module, six query types via resource (pathways/search/entity/interactors/orthology/event-hierarchy, same pattern as opentargets).

2. Scope & shape trade-offs — deliberately query/fetch only (left out Reactome's Analysis Service since that's enrichment, which gget enrichr covers); orthology takes a species name/taxon ID (resolved to Reactome's dbId); event-hierarchy is flattened to one row per event (a large table for human).

3. Robustness + reproducibility — http_json now raises a small HTTPStatusError (RuntimeError subclass with .status_code) so 404s branch on status, not string-matching (backward-compatible); data frames carry the Reactome release in .attrs["reactome_release"].

would appreciate a review whenever you have a moment. Thanks