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Lower level unit tests for every QC criterion #21

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mirams opened this issue Aug 8, 2024 · 3 comments · Fixed by #23 · May be fixed by #25
Closed

Lower level unit tests for every QC criterion #21

mirams opened this issue Aug 8, 2024 · 3 comments · Fixed by #23 · May be fixed by #25
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@kwabenantim @frankiepe
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enhancement New feature or request good first issue Good for newcomers

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@mirams
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mirams commented Aug 8, 2024

We want an example of a trace to pass/fail each QC criterion, in the automated test suite.
@mirams mirams added enhancement New feature or request good first issue Good for newcomers labels Aug 8, 2024
@mirams
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mirams commented Aug 8, 2024

Based on CSV files so they don't depend on other libraries to export code etc.

@frankiepe frankiepe self-assigned this Aug 8, 2024
@kwabenantim
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kwabenantim commented Aug 8, 2024 •
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To Do

  • Review current tests
  • Double-check ranges/thresholds against paper (https://doi.org/10.1016/j.bpj.2019.07.029)
  • Output number that failed/passed as well as pass/fail result.
  • Add unit testing for each QC.
  • Change data input from loading json files to loading pickled Trace objects #25

@kwabenantim kwabenantim self-assigned this Aug 8, 2024
kwabenantim added a commit that referenced this issue Aug 8, 2024
@kwabenantim
#21 Fix qc_vals_after in herg qc test
264c697
@frankiepe
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We may need to separate the Trace class from syncropatch_export so we don't rely on syncropatch_export. In the meantime, we will pickle the Trace objects and load them in, but continue to rely on syncropatch_export to manipulate the Trace objects once loaded.

kwabenantim added a commit that referenced this issue Aug 8, 2024
@kwabenantim
#21 parameterise herg QC test
b9ebc16
@kwabenantim kwabenantim mentioned this issue Aug 8, 2024
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This was linked to pull requests Aug 8, 2024
Fine-grained tests for herg QC #23
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frankie_edits_pickled_data #25
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@kwabenantim kwabenantim mentioned this issue Aug 8, 2024
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8 tasks
kwabenantim added a commit that referenced this issue Aug 12, 2024
@kwabenantim
#21 simplify herg QC test parametrisation
3815c47
kwabenantim added a commit that referenced this issue Aug 12, 2024
@kwabenantim
#21 add itemised trace to hERG QC
d26d12e
kwabenantim added a commit that referenced this issue Aug 12, 2024
@kwabenantim
#21 Annotate converted QC units
2f56479
kwabenantim added a commit that referenced this issue Aug 12, 2024
@kwabenantim
#21 Update calls to hergQC methods
fa8644d
kwabenantim added a commit that referenced this issue Aug 12, 2024
@kwabenantim
#21 Add unit test for herg qc1
78e172e
kwabenantim added a commit that referenced this issue Aug 12, 2024
@kwabenantim
#21 Adjust tolerances for herg qc1 unit test
bfe9047
kwabenantim added a commit that referenced this issue Aug 13, 2024
@kwabenantim
#21 Add QCDict
e5cfda3
kwabenantim added a commit that referenced this issue Nov 18, 2024
@kwabenantim
#21 Add test_qc2
27a6a76
kwabenantim added a commit that referenced this issue Nov 18, 2024
@kwabenantim
#21 Add test_qc3
bed87c1
kwabenantim added a commit that referenced this issue Nov 18, 2024
@kwabenantim
#21 Add test_qc4
14fd052
kwabenantim added a commit that referenced this issue Nov 18, 2024
@kwabenantim
#21 Add test_qc5
0e9a781
kwabenantim added a commit that referenced this issue Nov 18, 2024
@kwabenantim
#21 Add test_qc5_1
69ba7ba
kwabenantim added a commit that referenced this issue Nov 18, 2024
@kwabenantim
#21 Update test_qc2
b976f5f
kwabenantim added a commit that referenced this issue Nov 19, 2024
@kwabenantim
#21 Update qc unit tests
1b273f6
kwabenantim added a commit that referenced this issue Nov 20, 2024
@kwabenantim
#21 Update test_qc6
de5602d
kwabenantim added a commit that referenced this issue Nov 20, 2024
@kwabenantim
#21 test_qc1 on test data
cca851b
kwabenantim added a commit that referenced this issue Nov 27, 2024
@kwabenantim
#21 Remove ghost export_staircase_data from branch
d615b8c
kwabenantim added a commit that referenced this issue Nov 27, 2024
@kwabenantim
#21 Run qc1 on all test data
64a90d8
kwabenantim added a commit that referenced this issue Nov 27, 2024
@kwabenantim
#21 Run qc2 on all test data
cf9aa1c
kwabenantim added a commit that referenced this issue Nov 27, 2024
@kwabenantim
#21 Run qc3 on all test data
fc70547
kwabenantim added a commit that referenced this issue Nov 28, 2024
@kwabenantim
#21 Run qc4 on all test data
356469c
kwabenantim added a commit that referenced this issue Nov 28, 2024
@kwabenantim
#21 Fix test_qc4 rseriess
8e1f008
kwabenantim added a commit that referenced this issue Nov 28, 2024
@kwabenantim
#21 Expand qc1 data tests
2b981dc
kwabenantim added a commit that referenced this issue Nov 28, 2024
@kwabenantim
#21 Run qc5 on all test data
6bf42de
kwabenantim added a commit that referenced this issue Nov 28, 2024
@kwabenantim
#21 Run qc5_1 on all test data
467fae2
kwabenantim added a commit that referenced this issue Nov 29, 2024
@kwabenantim
#21 Run qc6 on all test data
f2ac760
kwabenantim added a commit that referenced this issue Nov 29, 2024
@kwabenantim
#21 Add docstring for QCDict
884346b
kwabenantim added a commit that referenced this issue Nov 29, 2024
@kwabenantim
#21 Linter fixes
f40f8f3
kwabenantim added a commit that referenced this issue Nov 29, 2024
@kwabenantim
#21 Implement QCDict with UserDict
0bbfd44
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