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docs: remove cross-language and code-history commentary - #720
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Comments and docstrings across the codebase described the current implementation's behavior in comparison to the Python port (raven-toolbox/raven_python), cobrapy, or geckopy, and narrated how the code changed over time (issue/PR references, "used to" framing, before/after comparisons). Rewritten to describe only the current MATLAB behavior and its technical rationale; functionally necessary distinctions (e.g. between two supported file-format conventions) are kept but reworded without naming the other project.
Function test results304 tests 277 ✅ 1m 15s ⏱️ Results for commit 131082c. |
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Summary
Comments and docstrings across the codebase described current behavior in comparison to the Python port (raven-toolbox/raven_python), cobrapy, or geckopy, and narrated how the code changed over time (issue/PR references, "used to" framing, before/after comparisons). Rewritten to describe only the current MATLAB behavior and its rationale.
io/readYAMLmodel.m/io/writeYAMLmodel.m's two supported key/field conventions are still explained, just not attributed to a specific Python tool).% Mirrors _node_to_dnf in raven-toolbox manipulation/expand.py.).Untouched by design:
io/parseYAML.m's Python references (it genuinely bridges into a Python interpreter to parse YAML, a technical dependency of its own implementation, not a comparison to a sibling port); the MATLAB COBRA Toolbox references throughout (a different, MATLAB-native tool, not "the other language"); domain/algorithmic uses of words like "previously"/"no longer"/"legacy" that describe current data state or a still-supported option rather than code history.Test plan
testing/function_testssuite (local) — 289 passed, 10 failed, 14 incomplete, reproduced identically across two separate local runs of this branch. All 10 failures are solver-configuration errors (Unrecognized field name "mipgap") intAnalysis/tAssignCompartments/tGapfilling/tINIT-- none in a file this PR touches. On a pristine, unmodifieddevelop3checkout in the same local environment, these same test classes were instead skipped outright (Filtered by assumption, solver-availability gated) rather than attempted -- consistent with local solver-detection/configuration flakiness, not a regression from this change, but not a byte-for-byte reproduction either. Deferring to CI for the authoritative signal here.Filtered by assumption(missing optional deps: quadprog, Python/pyyaml, KEGG data files) -- pre-existing skips.