feat: add ProbeParameters() to encapsulate settings for PickHybProbeOnly Primer3Task
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feat: add penalty weights for pick_hyb_probe task
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## em_feat_pick_hyb_probe #35 +/- ##
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- Coverage 97.39% 97.05% -0.35%
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Files 25 25
Lines 1614 1664 +50
Branches 303 317 +14
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+ Hits 1572 1615 +43
- Misses 23 26 +3
- Partials 19 23 +4 ☔ View full report in Codecov by Sentry. |
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| """Assembles necessary inputs for Primer3 to orchestrate primer, primer pair, and/or internal | ||
| probe design.""" |
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doc same comment as on #28 - make the summary one line, and add Attributes
| if self.primer_and_amplicon_params is not None and self.primer_weights is None: | ||
| object.__setattr__(self, "primer_weights", PrimerAndAmpliconWeights()) | ||
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| if self.probe_params is not None and self.probe_weights is None: | ||
| object.__setattr__(self, "probe_weights", ProbeWeights()) |
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suggestion I think it'd be appropriate to make each of these the default value for the attribute, and change the type of the attributes to not be Optional
| optional_attributes = { | ||
| field.name: getattr(self, field.name) | ||
| for field in fields(self) | ||
| if field.default is not MISSING |
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suggestion and if you make the above change, you can remove this check
| probe_tms: the min, optimal, and max probe melting temperatures | ||
| probe_gcs: the min and max GC content for individual probes | ||
| number_probes_return: the number of probes to return | ||
| probe_max_dinuc_bases: the max number of bases in a dinucleotide run in a probe |
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| probe_max_dinuc_bases: the max number of bases in a dinucleotide run in a probe | |
| probe_max_dinuc_bases: the max number of bases in a dinucleotide run in a probe |
| isinstance(self.probe_excluded_region, tuple) | ||
| and all(isinstance(param, int) for param in self.probe_excluded_region) |
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issue Also check that the length of the tuple is 2
| # we use `type: ignore` here to bypass mypy | ||
| replace( | ||
| valid_probe_params, | ||
| probe_sizes=MinOptMax(min=18.1, opt=22.1, max=30.1), # type: ignore |
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issue Add the ignore code, and a comment that the the mypy errors are deliberate in the context of this test - we are deliberately passing the wrong type to test our runtime checks
Primer3Parametersto now be calledPrimerAndAmpliconParametersDeprecationWarningtoPrimer3Parametersfor backwards compatibilityProbeParametersto encapsulate settings forPickHybProbeOnlyPrimer3Task, as well as apost_init()andto_input_tags()that maps each of the user-specified arguments to the correspondingPrimer3InputTag*_paramsand*_weightsboth optional input toPrimer3Input, use the__post_init()__to assign default weights when given the corresponding params