pheval 0.6.4__py3-none-any.whl → 0.6.6__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.
Potentially problematic release.
This version of pheval might be problematic. Click here for more details.
- pheval/analyse/benchmark.py +2 -2
- pheval/analyse/benchmark_output_type.py +9 -0
- pheval/analyse/generate_rank_comparisons.py +1 -1
- {pheval-0.6.4.dist-info → pheval-0.6.6.dist-info}/METADATA +4 -2
- {pheval-0.6.4.dist-info → pheval-0.6.6.dist-info}/RECORD +8 -8
- {pheval-0.6.4.dist-info → pheval-0.6.6.dist-info}/WHEEL +1 -1
- {pheval-0.6.4.dist-info → pheval-0.6.6.dist-info}/entry_points.txt +0 -0
- {pheval-0.6.4.dist-info → pheval-0.6.6.dist-info/licenses}/LICENSE +0 -0
pheval/analyse/benchmark.py
CHANGED
|
@@ -6,7 +6,7 @@ import duckdb
|
|
|
6
6
|
import polars as pl
|
|
7
7
|
|
|
8
8
|
from pheval.analyse.benchmark_db_manager import write_table
|
|
9
|
-
from pheval.analyse.benchmark_output_type import BenchmarkOutputType, BenchmarkOutputTypeEnum
|
|
9
|
+
from pheval.analyse.benchmark_output_type import BenchmarkOutputType, BenchmarkOutputTypeEnum, _get_unique_subset
|
|
10
10
|
from pheval.analyse.binary_classification_curves import compute_curves
|
|
11
11
|
from pheval.analyse.binary_classification_stats import compute_confusion_matrix
|
|
12
12
|
from pheval.analyse.generate_plots import generate_plots
|
|
@@ -48,7 +48,7 @@ def scan_directory(run: RunConfig, benchmark_type: BenchmarkOutputType) -> pl.La
|
|
|
48
48
|
else True
|
|
49
49
|
)
|
|
50
50
|
.sort("rank")
|
|
51
|
-
.unique(subset=
|
|
51
|
+
.unique(subset=_get_unique_subset(benchmark_type), keep="first")
|
|
52
52
|
)
|
|
53
53
|
|
|
54
54
|
|
|
@@ -42,3 +42,12 @@ class BenchmarkOutputTypeEnum(Enum):
|
|
|
42
42
|
["disease_identifier", "mondo_identifier"],
|
|
43
43
|
"pheval_disease_results",
|
|
44
44
|
)
|
|
45
|
+
|
|
46
|
+
|
|
47
|
+
def _get_unique_subset(benchmark_type: BenchmarkOutputType) -> list[str]:
|
|
48
|
+
"""
|
|
49
|
+
Determine which columns to use for uniqueness in benchmarking results.
|
|
50
|
+
"""
|
|
51
|
+
if benchmark_type.prioritisation_type_string == "disease":
|
|
52
|
+
return ["file_path", "mondo_identifier"]
|
|
53
|
+
return ["file_path", *benchmark_type.columns]
|
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
from itertools import combinations
|
|
2
2
|
|
|
3
3
|
import polars as pl
|
|
4
|
-
from duckdb
|
|
4
|
+
from duckdb import DuckDBPyConnection
|
|
5
5
|
|
|
6
6
|
from pheval.analyse.benchmark_db_manager import write_table
|
|
7
7
|
from pheval.analyse.benchmark_output_type import BenchmarkOutputType
|
|
@@ -1,7 +1,8 @@
|
|
|
1
|
-
Metadata-Version: 2.
|
|
1
|
+
Metadata-Version: 2.4
|
|
2
2
|
Name: pheval
|
|
3
|
-
Version: 0.6.
|
|
3
|
+
Version: 0.6.6
|
|
4
4
|
Summary:
|
|
5
|
+
License-File: LICENSE
|
|
5
6
|
Author: Yasemin Bridges
|
|
6
7
|
Author-email: y.bridges@qmul.ac.uk
|
|
7
8
|
Requires-Python: >=3.10,<4.0.0
|
|
@@ -10,6 +11,7 @@ Classifier: Programming Language :: Python :: 3.10
|
|
|
10
11
|
Classifier: Programming Language :: Python :: 3.11
|
|
11
12
|
Classifier: Programming Language :: Python :: 3.12
|
|
12
13
|
Classifier: Programming Language :: Python :: 3.13
|
|
14
|
+
Classifier: Programming Language :: Python :: 3.14
|
|
13
15
|
Requires-Dist: class-resolver (>=0.4.2)
|
|
14
16
|
Requires-Dist: click (>=8.1.3)
|
|
15
17
|
Requires-Dist: deprecation (>=2.1.0)
|
|
@@ -1,12 +1,12 @@
|
|
|
1
1
|
pheval/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
|
|
2
2
|
pheval/analyse/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
|
|
3
|
-
pheval/analyse/benchmark.py,sha256=
|
|
3
|
+
pheval/analyse/benchmark.py,sha256=Eiqwx0cJXkx4U3YOpt3LK55xyXyeF2MSYbu5o-O8Erk,6890
|
|
4
4
|
pheval/analyse/benchmark_db_manager.py,sha256=zS1TI76YuV2_YXLipHLSyh-XDR5kTxyOwhRhHRFHfjQ,764
|
|
5
|
-
pheval/analyse/benchmark_output_type.py,sha256=
|
|
5
|
+
pheval/analyse/benchmark_output_type.py,sha256=J92VJq_VkMdROOGBjR9TmdxKLP27xtWyWs3eBUNVYDU,1822
|
|
6
6
|
pheval/analyse/binary_classification_curves.py,sha256=b5YseLqv519DT7rsOweMRx7ElxYv9LcukXtLeAxflQE,4953
|
|
7
7
|
pheval/analyse/binary_classification_stats.py,sha256=oWkaj-A2-2MaUIsJjlehwLApx-wGLx-TQ49v9O4lMAs,6910
|
|
8
8
|
pheval/analyse/generate_plots.py,sha256=fyUMOgmbqYeYMPW843VR-CVArt3R75HgGbyq1i2XO7A,14489
|
|
9
|
-
pheval/analyse/generate_rank_comparisons.py,sha256=
|
|
9
|
+
pheval/analyse/generate_rank_comparisons.py,sha256=MURu5fs15vQVUpY35qZ7ugiZqc7oz3qa8tGkgqIjfOc,1653
|
|
10
10
|
pheval/analyse/rank_stats.py,sha256=io8UWTEUZfZQSnxXBjk2Z_1u6WWoxX0kSfEvxtpC-Kg,8241
|
|
11
11
|
pheval/analyse/run_data_parser.py,sha256=da8-J9sSwyOUow80A2ETKdVP7GUX-zuEiiBix-M18Mo,3601
|
|
12
12
|
pheval/cli.py,sha256=1kPhBYFSKjvPv9YcpknDj3Y7DZl5CA41ucqDRR7fAjk,1599
|
|
@@ -50,8 +50,8 @@ pheval/utils/logger.py,sha256=5DZl5uMltUDQorhkvg_B7_ZhFwApAmEkWneFIOKfRGQ,1566
|
|
|
50
50
|
pheval/utils/phenopacket_utils.py,sha256=qt816uYkJKAe2MATFoulqEr78zg0-Z2Z_FxfEO9iSFE,26740
|
|
51
51
|
pheval/utils/semsim_utils.py,sha256=tSDin3PwCdtMjtMXubIXTiGaCEFNz7iF4IngrjNHprI,6104
|
|
52
52
|
pheval/utils/utils.py,sha256=T9zzqMlzY2hrcYn9ObatYgOHtKWTpWbW5nU0tTTcYxI,4489
|
|
53
|
-
pheval-0.6.
|
|
54
|
-
pheval-0.6.
|
|
55
|
-
pheval-0.6.
|
|
56
|
-
pheval-0.6.
|
|
57
|
-
pheval-0.6.
|
|
53
|
+
pheval-0.6.6.dist-info/METADATA,sha256=fXDOIB49Qaran6fWjgwWy-xsmnL7bIjlyH9_3d74lg0,6567
|
|
54
|
+
pheval-0.6.6.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
|
|
55
|
+
pheval-0.6.6.dist-info/entry_points.txt,sha256=o9gSwDkvT4-lqKy4mlsftd1nzP9WUOXQCfnbqycURd0,81
|
|
56
|
+
pheval-0.6.6.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
|
|
57
|
+
pheval-0.6.6.dist-info/RECORD,,
|
|
File without changes
|
|
File without changes
|