metahq-core 0.1.2__py3-none-any.whl → 1.0.0rc2__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- metahq_core/__init__.py +1 -1
- metahq_core/curations/annotation_converter.py +5 -5
- metahq_core/curations/annotations.py +361 -151
- metahq_core/curations/index.py +104 -43
- metahq_core/curations/labels.py +259 -128
- metahq_core/curations/propagator.py +62 -85
- metahq_core/export/__init__.py +0 -0
- metahq_core/export/annotations.py +125 -59
- metahq_core/export/labels.py +128 -70
- metahq_core/logger.py +11 -18
- metahq_core/query.py +346 -241
- metahq_core/{ontology/loader.py → relations_loader.py} +2 -1
- metahq_core/search.py +37 -14
- metahq_core/util/io.py +109 -46
- metahq_core/util/supported.py +16 -5
- {metahq_core-0.1.2.dist-info → metahq_core-1.0.0rc2.dist-info}/METADATA +13 -6
- metahq_core-1.0.0rc2.dist-info/RECORD +30 -0
- {metahq_core-0.1.2.dist-info → metahq_core-1.0.0rc2.dist-info}/WHEEL +1 -1
- metahq_core-1.0.0rc2.dist-info/licenses/LICENSE +28 -0
- metahq_core/ontology/base.py +0 -376
- metahq_core/ontology/graph.py +0 -252
- metahq_core-0.1.2.dist-info/RECORD +0 -30
- /metahq_core/{ontology → curations}/__init__.py +0 -0
metahq_core/__init__.py
CHANGED
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@@ -1 +1 @@
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-
__version__ = "0.
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1
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__version__ = "1.0.0-rc.2"
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@@ -17,10 +17,10 @@ import polars as pl
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from metahq_core.curations.labels import Labels
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from metahq_core.curations.propagator import Propagator, propagate_controls
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from metahq_core.logger import setup_logger
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from metahq_core.
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from metahq_core.relations_loader import RelationsLoader
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from metahq_core.util.helpers import merge_list_values
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from metahq_core.util.progress import progress_wrapper
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from metahq_core.util.supported import get_ontology_families
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from metahq_core.util.supported import get_default_log_dir, get_ontology_families
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if TYPE_CHECKING:
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import logging
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@@ -69,7 +69,7 @@ class AnnotationsConverter:
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control_col="MONDO:0000000",
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logger=None,
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loglevel=20,
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logdir=
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logdir=get_default_log_dir(),
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verbose=False,
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):
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self.anno: Annotations = anno
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@@ -276,8 +276,8 @@ class AnnotationsConverter:
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relatives=["ancestors", "descendants"],
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verbose=self.verbose,
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)
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up_mat, cols, up_ids = propagator.propagate_up(
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down_mat, _, _ = propagator.propagate_down(
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up_mat, cols, up_ids = propagator.propagate_up()
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down_mat, _, _ = propagator.propagate_down()
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neg_mask = (up_mat == 0) & (down_mat == 0)
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up_mat[neg_mask] = -1
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