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Rplibs - #50
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Rplibs#50
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Pathway.__init__ calls set_target_id(None), which dispatches to rpPathway.set_target_id and then __build_intermediate_species, both of which read self.__species_groups. Since that attribute was assigned after the Pathway.__init__ call, every rpPathway construction raised AttributeError: 'rpPathway' object has no attribute '_rpPathway__species_groups'. This broke selenzy-wrapper's planemo tests (and any other caller building an rpPathway from an SBML file). Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
RDKit's rendered SVG markup for a molecule (attributes, styling) can change across RDKit versions even though the molecule itself is unchanged, and rdkit is unpinned in environment.yaml. Comparing it byte-for-byte against the golden tests/rpviz/outputs/network.json made test_dir_input/test_tar_input fail on every RDKit upgrade despite no actual regression. The 'svg' field is now excluded from the DeepDiff comparison; the rest of the generated network (structure, ids, etc.) is still verified. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Brings the codebase into compliance with ruff's default rule set and black formatting, ahead of a new .github/workflows/lint.yml CI job that enforces both. Highlights: - N999: rename 17 PascalCase modules to snake_case (Args.py -> args.py per package, rpPathway.py -> rp_pathway.py, rpSBML.py -> rp_sbml.py, etc.) plus their 7 mirrored test files, and update every internal import. No sibling repo imports these by file path (verified), only via the rptools.rplibs package, so this is not a breaking change for downstream consumers. - B008: move ~88 `logger: Logger = getLogger(__name__)` call-defaults out of signatures into `logger = logger or getLogger(__name__)` at the top of each function body (same effective default, no call at import/def time). - LOG015, F401, TRY203, RUF012, SIM102/113/114/117, PLC0206, E722, PLW0602, PLR1704, EXE001/EXE005: mechanical fixes (module loggers instead of the root logger, explicit __all__, dead try/except removal, ClassVar on mutable class defaults, collapsed nested ifs, dict.items() iteration, bare except narrowed, unused globals/locals removed, executable bit set on real shebangs). - BLE001, SIM115: narrowed the one `except BaseException` to `except Exception`; the remaining broad catches around network/ third-party calls (requests, libsbml, eQuilibrator, RDKit) and two file handles whose lifetime must outlive the function (an h5py Dataset and a csv.reader returned to the caller) are intentional and now carry a `# noqa` plus a one-line reason instead of being papered over with a guessed, possibly-incomplete exception type. - F811: rp_graph.py and rp_sbml.py each had a method defined twice (orderedRetroReactions; check_SBML_compartment; check_SBML_rxnid). Deleted the shadowed first definition in each pair and kept whatever Python was already executing (the second one), so this is a behavior-preserving dead-code removal, not a logic change. - black: reformatted the files it flagged. Verified: ruff check . and black --check . both pass; full test suite gives the same 29 pre-existing failures (all tests/rplibs/test_rp_pathway.py, tests/rpcompletion, tests/rpfba) as on a clean, unmodified checkout -- traced to the installed rr_cache 3.6.1 package, unrelated to this change. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
environment-dev.yaml gains black and ruff (needed by the new lint.yml CI job) and pytest-monitor. deepdiff moves to environment.yaml, where it's listed under the rpviz dependency group even though it's currently only imported by rpviz's own CLI tests (tests/rpviz/test_cli.py), not by rptools/rpviz itself. brs_utils is pinned to <1.26.0. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
deepdiff is only imported by rpviz's CLI tests (tests/rpviz/test_cli.py), not by rptools/rpviz itself, so it belongs with the other dev/test dependencies rather than the runtime environment. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Switches to the same ci-env + mamba setup pattern as the new lint.yml job, adds a build matrix (ubuntu/macos/windows), and triggers on pull_request in addition to pushes to main/master/stable. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
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