Covariates implementation and interface #209
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| @@ -11,4 +11,5 @@ twine==3.2.0 | |||
| # varspark dependencies | |||
| pandas==1.1.4 | |||
| typedecorator==0.0.5 | |||
| Jinja2==3.0.3 | |||
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Also update python/requirements.txt with this dependency
dev/py-test.sh
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| @@ -11,4 +11,5 @@ cd "$FWDIR" | |||
| pushd python | |||
| pytest -s -m spark | |||
| pytest -s -m hail | |||
| pytest -s -m covariates | |||
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There is not need to separate covariates into a new test category - they are in essence 'hail' tests.
Let's add them to hail tests.
dev/py-test.sh
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| @@ -11,4 +11,5 @@ cd "$FWDIR" | |||
| pushd python | |||
| pytest -s -m spark | |||
| pytest -s -m hail | |||
| pytest -s -m covariates | |||
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There is not need to separate covariates into a new test category - they are in essence 'hail' tests.
Let's add them to hail tests.
| row_exprs=dict(), | ||
| col_key=[], | ||
| entry_exprs=dict(e=x)) | ||
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This doc string should be moved to the top of the function (it's being used to generate automatic documentation).
Also the description of ':param covariates' needs to be updated.
| row_exprs=dict(), | ||
| col_key=[], | ||
| entry_exprs=dict(e=x)) | ||
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This doc string should be moved to the top of the function (it's being used to generate automatic documentation).
Also the description of ':param covariates' needs to be updated.
| # self.assertTrue(top_five_ranking) | ||
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| if __name__ == '__main__': | ||
| unittest.main(verbosity=2) |
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Do just one test (on data/chr22_1000_full_pheno.csv) and move it to test_hail.py
Note that setupClass has special function in the test and should normally be only used to initialise resources common for all the tests.
| } | ||
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| it.filter(tf => !tf.label.contains("cov__")) | ||
| .map { tf => |
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extract "cov__" to a static constants.
| } | ||
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| it.filter(tf => !tf.label.contains("cov__")) | ||
| .map { tf => |
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extract "cov__" to a static constants.
| val splitCount = brSplitCount.value | ||
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| it.filter { tf => tf.label.contains("cov__") } | ||
| .map { tf => |
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Strictly speaking it should be tf.label.startsWith
| val splitCount = brSplitCount.value | ||
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| it.filter { tf => tf.label.contains("cov__") } | ||
| .map { tf => |
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Strictly speaking it should be tf.label.startsWith
Implements the interface and usage by the model of the covariates.
Resolves #193.