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ENH: Added new type FeatureTable[Normalized] #340

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merged 3 commits into from
Jul 31, 2024
Merged

ENH: Added new type FeatureTable[Normalized] #340

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f5e1bac
added new type normalized
VinzentRisch Jul 19, 2024
8018da5
lint
VinzentRisch Jul 19, 2024
5b9bd51
Merge branch 'dev' into 339_featuretable_normalized
ebolyen Jul 31, 2024
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4 changes: 2 additions & 2 deletions q2_types/feature_table/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,9 +10,9 @@
BIOMV210DirFmt)
from ._types import (FeatureTable, Frequency, RelativeFrequency,
PresenceAbsence, Composition, Balance,
PercentileNormalized, Design)
PercentileNormalized, Design, Normalized)

__all__ = ['BIOMV100Format', 'BIOMV100DirFmt', 'FeatureTable', 'Frequency',
'RelativeFrequency', 'PresenceAbsence', 'BIOMV210Format',
'BIOMV210DirFmt', 'Composition', 'Balance', 'PercentileNormalized',
'Design']
'Design', 'Normalized']
9 changes: 7 additions & 2 deletions q2_types/feature_table/_deferred_setup/__init__.py
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Expand Up @@ -15,7 +15,7 @@
from .. import (BIOMV100Format, BIOMV210Format, BIOMV100DirFmt,
BIOMV210DirFmt, FeatureTable, Frequency, RelativeFrequency,
PresenceAbsence, Composition, Balance,
PercentileNormalized, Design)
PercentileNormalized, Design, Normalized)

from ...plugin_setup import plugin

Expand All @@ -27,7 +27,7 @@

plugin.register_semantic_types(FeatureTable, Frequency, RelativeFrequency,
PresenceAbsence, Balance, Composition,
PercentileNormalized, Design)
PercentileNormalized, Design, Normalized)

plugin.register_artifact_class(
FeatureTable[Frequency],
Expand Down Expand Up @@ -76,5 +76,10 @@
FeatureTable[Design],
directory_format=BIOMV210DirFmt
)
plugin.register_artifact_class(
FeatureTable[Normalized],
directory_format=BIOMV210DirFmt,
description="A feature table that was normalized."
)

importlib.import_module('._transformers', __name__)
3 changes: 3 additions & 0 deletions q2_types/feature_table/_types.py
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Expand Up @@ -31,3 +31,6 @@
# Design is the type of design matrices for linear regressions that have
# been transformed/coded.
Design = SemanticType('Design', variant_of=FeatureTable.field['content'])

Normalized = SemanticType('Normalized',
variant_of=FeatureTable.field['content'])
9 changes: 8 additions & 1 deletion q2_types/feature_table/tests/test_types.py
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Expand Up @@ -13,7 +13,8 @@
from q2_types.feature_table import (FeatureTable, Frequency,
RelativeFrequency, PercentileNormalized,
Composition, Balance,
PresenceAbsence, BIOMV210DirFmt, Design)
PresenceAbsence, BIOMV210DirFmt, Design,
Normalized)


class TestTypes(TestPluginBase):
Expand All @@ -37,6 +38,9 @@ def test_composition_semantic_type_registration(self):
def test_balance_semantic_type_registration(self):
self.assertRegisteredSemanticType(Balance)

def test_normalized_semantic_type_registration(self):
self.assertRegisteredSemanticType(Normalized)

def test_feature_table_semantic_type_to_v210_format_registration(self):
self.assertSemanticTypeRegisteredToFormat(
FeatureTable[Frequency],
Expand All @@ -59,6 +63,9 @@ def test_feature_table_semantic_type_to_v210_format_registration(self):
self.assertSemanticTypeRegisteredToFormat(
FeatureTable[Design],
BIOMV210DirFmt)
self.assertSemanticTypeRegisteredToFormat(
FeatureTable[Normalized],
BIOMV210DirFmt)


if __name__ == "__main__":
Expand Down
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