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Use stdlib JSON for NaN-tolerant report exports - #580
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simplejson was a Python 2 era backport of json (see #10). The stdlib encoder is faster and produces byte-identical output for everything serializable emits (checked against golden payloads, including numpy float64 / IntEnum / float-Enum values, -0.0, denormals, huge ints and non-ASCII strings). NaN handling is now explicit instead of depending on the installed simplejson version (>=3.19 rejects NaN by default, older versions accept it): - to_json raises ValueError for NaN/inf (allow_nan=False), matching simplejson>=3.19, so existing output and content hashes don't change. - from_json accepts NaN/Infinity, so files written with older simplejson versions can be read again. Drops the simplejson dependency. vaxrank imports simplejson without declaring it, so openvax/vaxrank#580 should be released first. Supersedes PR #10. Part of #15 (the typechecks and coveralls dependencies are left for a separate change). Claude-Session: https://claude.ai/code/session_01JRDMg3F5kNKmnjv5jvQBgr
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iskandr
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simplejson was a Python 2 era backport of json (see #10). The stdlib encoder is faster and produces byte-identical output for everything serializable emits (checked against golden payloads, including numpy float64 / IntEnum / float-Enum values, -0.0, denormals, huge ints and non-ASCII strings). NaN handling is now explicit instead of depending on the installed simplejson version (>=3.19 rejects NaN by default, older versions accept it): - to_json raises ValueError for NaN/inf (allow_nan=False), matching simplejson>=3.19, so existing output and content hashes don't change. - from_json accepts NaN/Infinity, so files written with older simplejson versions can be read again. Drops the simplejson dependency. vaxrank imports simplejson without declaring it, so openvax/vaxrank#580 should be released first. Supersedes PR #10. Part of #15 (the typechecks and coveralls dependencies are left for a separate change). Claude-Session: https://claude.ai/code/session_01JRDMg3F5kNKmnjv5jvQBgr
iskandr
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Oct 6, 2026
simplejson was a Python 2 era backport of json (see #10). The stdlib encoder is faster and produces byte-identical output for everything serializable emits (checked against golden payloads, including numpy float64 / IntEnum / float-Enum values, -0.0, denormals, huge ints and non-ASCII strings). NaN handling is now explicit instead of depending on the installed simplejson version (>=3.19 rejects NaN by default, older versions accept it): - to_json raises ValueError for NaN/inf (allow_nan=False), matching simplejson>=3.19, so existing output and content hashes don't change. - from_json accepts NaN/Infinity, so files written with older simplejson versions can be read again. Drops the simplejson dependency. vaxrank imports simplejson without declaring it, so openvax/vaxrank#580 should be released first. Supersedes PR #10. Part of #15 (the typechecks and coveralls dependencies are left for a separate change). Claude-Session: https://claude.ai/code/session_01JRDMg3F5kNKmnjv5jvQBgr
iskandr
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simplejson was a Python 2 era backport of json (see #10). The stdlib encoder is faster and produces byte-identical output for everything serializable emits (checked against golden payloads, including numpy float64 / IntEnum / float-Enum values, -0.0, denormals, huge ints and non-ASCII strings). NaN handling is now explicit instead of depending on the installed simplejson version (>=3.19 rejects NaN by default, older versions accept it): - to_json raises ValueError for NaN/inf (allow_nan=False), matching simplejson>=3.19, so existing output and content hashes don't change. - from_json accepts NaN/Infinity, so files written with older simplejson versions can be read again. Drops the simplejson dependency. vaxrank imports simplejson without declaring it, so openvax/vaxrank#580 should be released first. Supersedes PR #10. Part of #15 (the typechecks and coveralls dependencies are left for a separate change). Claude-Session: https://claude.ai/code/session_01JRDMg3F5kNKmnjv5jvQBgr
iskandr
added a commit
to openvax/serializable
that referenced
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Oct 6, 2026
simplejson was a Python 2 era backport of json (see #10). The stdlib encoder is faster and produces byte-identical output for everything serializable emits (checked against golden payloads, including numpy float64 / IntEnum / float-Enum values, -0.0, denormals, huge ints and non-ASCII strings). NaN handling is now explicit instead of depending on the installed simplejson version (>=3.19 rejects NaN by default, older versions accept it): - to_json raises ValueError for NaN/inf (allow_nan=False), matching simplejson>=3.19, so existing output and content hashes don't change. - from_json accepts NaN/Infinity, so files written with older simplejson versions can be read again. Drops the simplejson dependency. vaxrank imports simplejson without declaring it, so openvax/vaxrank#580 should be released first. Supersedes PR #10. Part of #15 (the typechecks and coveralls dependencies are left for a separate change). Claude-Session: https://claude.ai/code/session_01JRDMg3F5kNKmnjv5jvQBgr
iskandr
added a commit
to openvax/serializable
that referenced
this pull request
Oct 6, 2026
simplejson was a Python 2 era backport of json (see #10). The stdlib encoder is faster and produces byte-identical output for everything serializable emits (checked against golden payloads, including numpy float64 / IntEnum / float-Enum values, -0.0, denormals, huge ints and non-ASCII strings). NaN handling is now explicit instead of depending on the installed simplejson version (>=3.19 rejects NaN by default, older versions accept it): - to_json raises ValueError for NaN/inf (allow_nan=False), matching simplejson>=3.19, so existing output and content hashes don't change. - from_json accepts NaN/Infinity, so files written with older simplejson versions can be read again. Drops the simplejson dependency. vaxrank imports simplejson without declaring it, so openvax/vaxrank#580 should be released first. Supersedes PR #10. Part of #15 (the typechecks and coveralls dependencies are left for a separate change). Claude-Session: https://claude.ai/code/session_01JRDMg3F5kNKmnjv5jvQBgr
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The CLI JSON writer currently imports SimpleJSON for its
ignore_nan=Trueoption, which turns NaN and infinities into JSON null. Replace that call with stdlibjson.dumpsafter recursively normalizing non-finite floats into_serializable_repr's dict/list representation. Keepallow_nan=Falseso output remains strict JSON, and retain the report protection from #289.Remove the proposed direct SimpleJSON dependency. Regression checks cover nested NumPy float64 values, preserved tuple/set/object metadata, unchanged input values, exact output bytes for finite edge cases and non-ASCII text, and successful writing when SimpleJSON cannot be imported. Existing scalar/list NaN tests remain. Version: 3.38.2, rebased onto 3.38.1.
Validation: lint and all 2,160 tests pass. B16 VCF/BAM CLI export produces a strict JSON report and its peptide/mRNA reports; re-encoding the prior 60,571-byte B16 report is byte-identical. The built wheel and sdist pass strict Twine checks and metadata verification, including absence of a direct SimpleJSON dependency and preservation of the coordinated Osteosarc/Isovar/Topiary floors. All refreshed GitHub CI must pass before merge, followed immediately by clean-main deployment and public PyPI verification.
Related upstream context: openvax/serializable#10 and openvax/serializable#15.