From 7e6bcdfeed54500ca533d2f0eb12078248c43c77 Mon Sep 17 00:00:00 2001
Message-ID: <7e6bcdfeed54500ca533d2f0eb12078248c43c77.1743682382.git.ngraves@ngraves.fr>
From: Nicolas Graves <ngraves@ngraves.fr>
Date: Thu, 3 Apr 2025 11:33:58 +0200
Subject: [PATCH] samples: Use deterministic samples in Guix.
---
bed_reader/_sample_data.py | 86 +++++++++-----------------------------
1 file changed, 19 insertions(+), 67 deletions(-)
diff --git a/bed_reader/_sample_data.py b/bed_reader/_sample_data.py
index 6ca4cc0..6a1146e 100644
--- a/bed_reader/_sample_data.py
+++ b/bed_reader/_sample_data.py
@@ -1,33 +1,8 @@
+import os
import tempfile
from pathlib import Path, PurePath
from typing import Union
-try:
- import pooch
-
- """
- Load sample data.
- """
-
- POOCH = pooch.create(
- # Use the default cache folder for the OS
- path=pooch.os_cache("bed_reader"),
- # The remote data is on Github
- base_url="https://raw.githubusercontent.com/"
- + "fastlmm/bed-sample-files/main/",
- # If this is a development version, get the data from the master branch
- version_dev="main",
- # The registry specifies the files that can be fetched
- env="BED_READER_DATA_DIR",
- )
-
- # Get registry file from package_data
- registry_file = Path(__file__).parent / "tests/registry.txt"
- # Load this registry file
- POOCH.load_registry(registry_file)
-except ImportError:
- pooch = None
-
def sample_file(filepath: Union[str, Path]) -> str:
"""Retrieve a sample .bed file. (Also retrieves associated .fam and .bim files).
@@ -40,50 +15,41 @@ def sample_file(filepath: Union[str, Path]) -> str:
Returns
-------
str
- Local name of sample .bed file.
-
-
- .. note::
- This function requires the :mod:`pooch` package. Install `pooch` with:
-
- .. code-block:: bash
-
- pip install --upgrade bed-reader[samples]
-
-
- By default this function puts files under the user's cache directory.
- Override this by setting
- the `BED_READER_DATA_DIR` environment variable.
+ Local path of sample .bed file.
Example
--------
.. doctest::
- >>> # pip install bed-reader[samples] # if needed
>>> from bed_reader import sample_file
>>>
>>> file_name = sample_file("small.bed")
>>> print(f"The local file name is '{file_name}'")
The local file name is '...small.bed'
-
"""
- if pooch is None:
- raise ImportError(
- "The function sample_file() requires pooch. "
- + "Install it with 'pip install --upgrade bed-reader[samples]'.",
+ filepath = Path(filepath)
+ sample_dir = os.environ.get("BED_READER_DATA_DIR")
+ if sample_dir is None:
+ raise EnvironmentError(
+ "BED_READER_DATA_DIR environment variable is not set. "
+ "This should point to the directory containing the sample files."
)
- filepath = Path(filepath)
- file_string = str(filepath)
- if file_string.lower().endswith(".bed"):
- POOCH.fetch(file_string[:-4] + ".fam")
- POOCH.fetch(file_string[:-4] + ".bim")
- return POOCH.fetch(file_string)
+ file_path = Path(sample_dir) / filepath
+
+ # Check if file exists
+ if not file_path.exists():
+ raise FileNotFoundError(
+ f"Sample file '{filepath}' not found in {sample_dir}. "
+ f"Make sure you're using the latest samples in BED_READER_DATA_DIR."
+ )
+
+ return str(file_path)
def sample_url(filepath: Union[str, Path]) -> str:
- """Retrieve a URL to a sample .bed file. (Also makes ready associated .fam and .bim files).
+ """Retrieve a URL to a sample .bed file.
Parameters
----------
@@ -95,25 +61,11 @@ def sample_url(filepath: Union[str, Path]) -> str:
str
URL to sample .bed file.
-
- .. note::
- This function requires the :mod:`pooch` package. Install `pooch` with:
-
- .. code-block:: bash
-
- pip install --upgrade bed-reader[samples]
-
-
- By default this function puts files under the user's cache directory.
- Override this by setting
- the `BED_READER_DATA_DIR` environment variable.
-
Example
--------
.. doctest::
- >>> # pip install bed-reader[samples] # if needed
>>> from bed_reader import sample_url
>>>
>>> url = sample_url("small.bed")
--
2.49.0
