pheval 0.5.1__py3-none-any.whl → 0.5.2__py3-none-any.whl

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Files changed (6) hide show
  1. pheval/analyse/benchmark.py +37 -17
  2. {pheval-0.5.1.dist-info → pheval-0.5.2.dist-info}/METADATA +4 -4
  3. {pheval-0.5.1.dist-info → pheval-0.5.2.dist-info}/RECORD +6 -6
  4. {pheval-0.5.1.dist-info → pheval-0.5.2.dist-info}/LICENSE +0 -0
  5. {pheval-0.5.1.dist-info → pheval-0.5.2.dist-info}/WHEEL +0 -0
  6. {pheval-0.5.1.dist-info → pheval-0.5.2.dist-info}/entry_points.txt +0 -0
pheval/analyse/benchmark.py CHANGED
@@ -23,27 +23,32 @@ def scan_directory(run: RunConfig, benchmark_type: BenchmarkOutputType) -> pl.La
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  run (RunConfig): RunConfig object.
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  benchmark_type (BenchmarkOutputTypeEnum): Benchmark output type.
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  Returns:
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- pl.LazyFrame: LazyFrame object containing all the results in the directory..
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+ pl.LazyFrame: LazyFrame object containing all the results in the directory.
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  """
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  logger = get_logger()
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  logger.info(f"Analysing results in {run.results_dir.joinpath(benchmark_type.result_directory)}")
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  return (
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- pl.scan_parquet(
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- run.results_dir.joinpath(benchmark_type.result_directory),
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- include_file_paths="file_path",
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- ).with_columns(
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- pl.col("rank").cast(pl.Int64),
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- pl.col("file_path").str.extract(r"([^/\\]+)$").alias("result_file"),
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- pl.col("true_positive").fill_null(False),
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- )
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- ).filter(
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  (
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- pl.col("score") >= run.threshold
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- if run.score_order.lower() == "descending"
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- else pl.col("score") <= run.threshold
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+ pl.scan_parquet(
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+ run.results_dir.joinpath(benchmark_type.result_directory),
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+ include_file_paths="file_path",
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+ ).with_columns(
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+ pl.col("rank").cast(pl.Int64),
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+ pl.col("file_path").str.extract(r"([^/\\]+)$").alias("result_file"),
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+ pl.col("true_positive").fill_null(False),
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+ )
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+ )
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+ .filter(
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+ (
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+ pl.col("score") >= run.threshold
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+ if run.score_order.lower() == "descending"
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+ else pl.col("score") <= run.threshold
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+ )
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+ if run.threshold is not None
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+ else True
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  )
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- if run.threshold is not None
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- else True
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+ .sort("rank")
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+ .unique(subset=["file_path", *benchmark_type.columns], keep="first")
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  )
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@@ -68,14 +73,29 @@ def process_stats(
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  )
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  curve_results.append(compute_curves(run.run_identifier, result_scan))
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  true_positive_cases.append(
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- result_scan.filter(pl.col("true_positive")).select(
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+ result_scan.filter(pl.col("true_positive"))
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+ .select(
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  ["result_file", *benchmark_type.columns, pl.col("rank").alias(run.run_identifier)]
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  )
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+ .sort(["result_file", *benchmark_type.columns])
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  )
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  return (
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  pl.concat(stats, how="vertical").collect(),
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  pl.concat(curve_results, how="vertical").collect(),
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- pl.concat(true_positive_cases, how="align_inner").collect(),
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+ pl.concat(
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+ [true_positive_cases[0]]
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+ + [
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+ df.select(
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+ [
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+ col
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+ for col in df.collect_schema().keys()
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+ if col not in ["result_file", *benchmark_type.columns]
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+ ]
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+ )
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+ for df in true_positive_cases[1:]
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+ ],
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+ how="horizontal",
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+ ).collect(),
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  )
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{pheval-0.5.1.dist-info → pheval-0.5.2.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.3
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  Name: pheval
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- Version: 0.5.1
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+ Version: 0.5.2
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  Summary:
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  Author: Yasemin Bridges
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  Author-email: y.bridges@qmul.ac.uk
@@ -32,10 +32,10 @@ Description-Content-Type: text/markdown
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  # PhEval - Phenotypic Inference Evaluation Framework
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- ![PyPI](https://img.shields.io/pypi/v/pheval)
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+ [![PyPI](https://img.shields.io/pypi/v/pheval)](https://pypi.org/project/pheval/)
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  ![Build Status](https://img.shields.io/github/actions/workflow/status/monarch-initiative/pheval/pypi-publish.yml?branch=main)
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  ![License](https://img.shields.io/github/license/monarch-initiative/pheval)
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- ![Python Version](https://img.shields.io/badge/python-3.8%2B-blue)
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+ ![Python Version](https://img.shields.io/badge/python-3.10%2B-blue)
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  ![Issues](https://img.shields.io/github/issues/monarch-initiative/pheval)
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  ## Overview
@@ -53,7 +53,7 @@ For more information please see the full [documentation](https://monarch-initiat
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  ## Download and Installation
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- 1. Ensure you have Python 3.8 or greater installed.
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+ 1. Ensure you have Python 3.10 or greater installed.
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  2. Install with `pip`:
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  ```bash
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  pip install pheval
{pheval-0.5.1.dist-info → pheval-0.5.2.dist-info}/RECORD RENAMED
@@ -1,6 +1,6 @@
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  pheval/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  pheval/analyse/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
3
- pheval/analyse/benchmark.py,sha256=1ysz1peGb21DhgNpEam9NgUOS5eGv7K0CI3RNjy0crQ,6275
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+ pheval/analyse/benchmark.py,sha256=sfjReLmodXwCT9ZyZDE6Oli0j1S5ygicJshb7n4-x4U,6916
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  pheval/analyse/benchmark_db_manager.py,sha256=zS1TI76YuV2_YXLipHLSyh-XDR5kTxyOwhRhHRFHfjQ,764
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  pheval/analyse/benchmark_output_type.py,sha256=bh-qQvV4AF7BHQyr_bdY8HTTzYZVe7KvoIoUF0D9k-g,1468
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  pheval/analyse/binary_classification_curves.py,sha256=Crb45rJWc5rxDdx82sgoHRvYHE2D5pus91fgl39FyRw,5007
@@ -46,8 +46,8 @@ pheval/utils/logger.py,sha256=5DZl5uMltUDQorhkvg_B7_ZhFwApAmEkWneFIOKfRGQ,1566
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  pheval/utils/phenopacket_utils.py,sha256=AfV_mWac6n5HCc5zjfH6CGP8T0qI0LR0VBrooaKmgdY,26978
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  pheval/utils/semsim_utils.py,sha256=s7ZCR2VfPYnOh7ApX6rv66eGoVSm9QJaVYOWBEhlXpo,6151
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  pheval/utils/utils.py,sha256=9V6vCT8l1g4O2-ZATYqsVyd7AYZdWGd-Ksy7_oIC3eE,2343
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- pheval-0.5.1.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
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- pheval-0.5.1.dist-info/METADATA,sha256=EsSCTQApiqCwO-40ZZX9sYf3ufyJTV9f2Z8nh0WeZZ4,6456
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- pheval-0.5.1.dist-info/WHEEL,sha256=XbeZDeTWKc1w7CSIyre5aMDU_-PohRwTQceYnisIYYY,88
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- pheval-0.5.1.dist-info/entry_points.txt,sha256=o9gSwDkvT4-lqKy4mlsftd1nzP9WUOXQCfnbqycURd0,81
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- pheval-0.5.1.dist-info/RECORD,,
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+ pheval-0.5.2.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
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+ pheval-0.5.2.dist-info/METADATA,sha256=do8ya_Tw3VD-md2rPf83DBmVTyytUrH7tEhQenjN-6o,6494
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+ pheval-0.5.2.dist-info/WHEEL,sha256=XbeZDeTWKc1w7CSIyre5aMDU_-PohRwTQceYnisIYYY,88
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+ pheval-0.5.2.dist-info/entry_points.txt,sha256=o9gSwDkvT4-lqKy4mlsftd1nzP9WUOXQCfnbqycURd0,81
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+ pheval-0.5.2.dist-info/RECORD,,
{pheval-0.5.1.dist-info → pheval-0.5.2.dist-info}/WHEEL RENAMED
File without changes