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refactor: clear the 22 pyrefly baseline entries in validation/compare.py #122

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Merged
michael-denyer merged 1 commit into from
Jul 26, 2026
Merged

refactor: clear the 22 pyrefly baseline entries in validation/compare.py #122

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264 changes: 0 additions & 264 deletions pyrefly-baseline.json
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Original file line number Diff line number Diff line change
Expand Up @@ -768,270 +768,6 @@
"concise_description": "`dict[Unknown, Unknown]` is not assignable to `PipelineTiming`",
"severity": "error"
},
{
"line": 299,
"column": 40,
"stop_line": 299,
"stop_column": 45,
"path": "src/jamma/validation/compare.py",
"code": -2,
"name": "bad-argument-type",
"description": "Unpacked keyword argument `float | int | str` is not assignable to parameter `chr` with type `str` in function `jamma.lmm.stats.AssocResult.__init__`",
"concise_description": "Unpacked keyword argument `float | int | str` is not assignable to parameter `chr` with type `str` in function `jamma.lmm.stats.AssocResult.__init__`",
"severity": "error"
},
{
"line": 299,
"column": 40,
"stop_line": 299,
"stop_column": 45,
"path": "src/jamma/validation/compare.py",
"code": -2,
"name": "bad-argument-type",
"description": "Unpacked keyword argument `float | int | str` is not assignable to parameter `rs` with type `str` in function `jamma.lmm.stats.AssocResult.__init__`",
"concise_description": "Unpacked keyword argument `float | int | str` is not assignable to parameter `rs` with type `str` in function `jamma.lmm.stats.AssocResult.__init__`",
"severity": "error"
},
{
"line": 299,
"column": 40,
"stop_line": 299,
"stop_column": 45,
"path": "src/jamma/validation/compare.py",
"code": -2,
"name": "bad-argument-type",
"description": "Unpacked keyword argument `float | int | str` is not assignable to parameter `ps` with type `int` in function `jamma.lmm.stats.AssocResult.__init__`",
"concise_description": "Unpacked keyword argument `float | int | str` is not assignable to parameter `ps` with type `int` in function `jamma.lmm.stats.AssocResult.__init__`",
"severity": "error"
},
{
"line": 299,
"column": 40,
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"path": "src/jamma/validation/compare.py",
"code": -2,
"name": "bad-argument-type",
"description": "Unpacked keyword argument `float | int | str` is not assignable to parameter `n_miss` with type `int` in function `jamma.lmm.stats.AssocResult.__init__`",
"concise_description": "Unpacked keyword argument `float | int | str` is not assignable to parameter `n_miss` with type `int` in function `jamma.lmm.stats.AssocResult.__init__`",
"severity": "error"
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{
"line": 299,
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"path": "src/jamma/validation/compare.py",
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"concise_description": "Unpacked keyword argument `float | int | str` is not assignable to parameter `allele1` with type `str` in function `jamma.lmm.stats.AssocResult.__init__`",
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{
"line": 299,
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"path": "src/jamma/validation/compare.py",
"code": -2,
"name": "bad-argument-type",
"description": "Unpacked keyword argument `float | int | str` is not assignable to parameter `allele0` with type `str` in function `jamma.lmm.stats.AssocResult.__init__`",
"concise_description": "Unpacked keyword argument `float | int | str` is not assignable to parameter `allele0` with type `str` in function `jamma.lmm.stats.AssocResult.__init__`",
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"description": "Unpacked keyword argument `float | int | str` is not assignable to parameter `af` with type `float` in function `jamma.lmm.stats.AssocResult.__init__`",
"concise_description": "Unpacked keyword argument `float | int | str` is not assignable to parameter `af` with type `float` in function `jamma.lmm.stats.AssocResult.__init__`",
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{
"line": 299,
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"path": "src/jamma/validation/compare.py",
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"name": "bad-argument-type",
"description": "Unpacked keyword argument `float | int | str` is not assignable to parameter `beta` with type `float` in function `jamma.lmm.stats.AssocResult.__init__`",
"concise_description": "Unpacked keyword argument `float | int | str` is not assignable to parameter `beta` with type `float` in function `jamma.lmm.stats.AssocResult.__init__`",
"severity": "error"
},
{
"line": 299,
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"path": "src/jamma/validation/compare.py",
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"name": "bad-argument-type",
"description": "Unpacked keyword argument `float | int | str` is not assignable to parameter `se` with type `float` in function `jamma.lmm.stats.AssocResult.__init__`",
"concise_description": "Unpacked keyword argument `float | int | str` is not assignable to parameter `se` with type `float` in function `jamma.lmm.stats.AssocResult.__init__`",
"severity": "error"
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{
"line": 299,
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"path": "src/jamma/validation/compare.py",
"code": -2,
"name": "bad-argument-type",
"description": "Unpacked keyword argument `float | int | str` is not assignable to parameter `logl_H1` with type `float | None` in function `jamma.lmm.stats.AssocResult.__init__`",
"concise_description": "Unpacked keyword argument `float | int | str` is not assignable to parameter `logl_H1` with type `float | None` in function `jamma.lmm.stats.AssocResult.__init__`",
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{
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"name": "bad-argument-type",
"description": "Unpacked keyword argument `float | int | str` is not assignable to parameter `l_remle` with type `float | None` in function `jamma.lmm.stats.AssocResult.__init__`",
"concise_description": "Unpacked keyword argument `float | int | str` is not assignable to parameter `l_remle` with type `float | None` in function `jamma.lmm.stats.AssocResult.__init__`",
"severity": "error"
},
{
"line": 299,
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"stop_line": 299,
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"path": "src/jamma/validation/compare.py",
"code": -2,
"name": "bad-argument-type",
"description": "Unpacked keyword argument `float | int | str` is not assignable to parameter `p_wald` with type `float | None` in function `jamma.lmm.stats.AssocResult.__init__`",
"concise_description": "Unpacked keyword argument `float | int | str` is not assignable to parameter `p_wald` with type `float | None` in function `jamma.lmm.stats.AssocResult.__init__`",
"severity": "error"
},
{
"line": 299,
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"stop_line": 299,
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"path": "src/jamma/validation/compare.py",
"code": -2,
"name": "bad-argument-type",
"description": "Unpacked keyword argument `float | int | str` is not assignable to parameter `p_score` with type `float | None` in function `jamma.lmm.stats.AssocResult.__init__`",
"concise_description": "Unpacked keyword argument `float | int | str` is not assignable to parameter `p_score` with type `float | None` in function `jamma.lmm.stats.AssocResult.__init__`",
"severity": "error"
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{
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"path": "src/jamma/validation/compare.py",
"code": -2,
"name": "bad-argument-type",
"description": "Unpacked keyword argument `float | int | str` is not assignable to parameter `l_mle` with type `float | None` in function `jamma.lmm.stats.AssocResult.__init__`",
"concise_description": "Unpacked keyword argument `float | int | str` is not assignable to parameter `l_mle` with type `float | None` in function `jamma.lmm.stats.AssocResult.__init__`",
"severity": "error"
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{
"line": 299,
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"path": "src/jamma/validation/compare.py",
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"name": "bad-argument-type",
"description": "Unpacked keyword argument `float | int | str` is not assignable to parameter `p_lrt` with type `float | None` in function `jamma.lmm.stats.AssocResult.__init__`",
"concise_description": "Unpacked keyword argument `float | int | str` is not assignable to parameter `p_lrt` with type `float | None` in function `jamma.lmm.stats.AssocResult.__init__`",
"severity": "error"
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{
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{
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"path": "src/jamma/validation/compare.py",
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"name": "missing-attribute",
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{
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{
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"stop_column": 36,
"path": "src/jamma/validation/compare.py",
"code": -2,
"name": "missing-attribute",
"description": "Object of class `NoneType` has no attribute `passed`",
"concise_description": "Object of class `NoneType` has no attribute `passed`",
"severity": "error"
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{
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"path": "src/jamma/validation/compare.py",
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"name": "missing-attribute",
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{
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"path": "src/jamma/validation/compare.py",
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"name": "missing-attribute",
"description": "Object of class `NoneType` has no attribute `passed`",
"concise_description": "Object of class `NoneType` has no attribute `passed`",
"severity": "error"
},
{
"line": 619,
"column": 16,
"stop_line": 619,
"stop_column": 26,
"path": "src/jamma/validation/compare.py",
"code": -2,
"name": "bad-argument-type",
"description": "Argument `builtins.bool | numpy.bool | Unknown` is not assignable to parameter `passed` with type `builtins.bool` in function `AssocComparisonResult.__init__`",
"concise_description": "Argument `builtins.bool | numpy.bool | Unknown` is not assignable to parameter `passed` with type `builtins.bool` in function `AssocComparisonResult.__init__`",
"severity": "error"
},
{
"line": 192,
"column": 40,
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