mirror of
https://https.git.savannah.gnu.org/git/guix.git/
synced 2025-07-14 19:10:49 +02:00
db14ce5c4d
* gnu/packages/bioinformatics.scm (python-bed-reader): Fix build and enable tests.
[source]{snippet}: Delete bundled website-related javascript.
{patches}: Use the store-cached instead of pooch-cached samples.
[arguments]{tests?}: Enable them.
{cargo-test-flags}: Skip doc tests. Skip failing tests.
{cargo-inputs}: Improve style.
{cargo-development-inputs}: Improve style.
{phases}: Add phases 'set-data-path, 'patch-data-path to use
store-cached samples for library and tests. Rewrite phase
'prepare-python-module to rely more on the existing info in
pyproject.toml. Rewrite phase 'check-python entirely, and
marginaly rewrite phase 'install-python-library to match 'check-python
phase style.
{modules}: Adapt accordingly.
{propagated-inputs}: Remove python-pooch. Add python-scipy.
(bed-sample-files): Add origin, used in python-bed-reader.
* gnu/packages/patches/python-bed-reader-use-store-samples.patch: Add
patch.
* gnu/local.mk: Record patch.
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
147 lines
4.4 KiB
Diff
147 lines
4.4 KiB
Diff
From 7e6bcdfeed54500ca533d2f0eb12078248c43c77 Mon Sep 17 00:00:00 2001
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Message-ID: <7e6bcdfeed54500ca533d2f0eb12078248c43c77.1743682382.git.ngraves@ngraves.fr>
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From: Nicolas Graves <ngraves@ngraves.fr>
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Date: Thu, 3 Apr 2025 11:33:58 +0200
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Subject: [PATCH] samples: Use deterministic samples in Guix.
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---
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bed_reader/_sample_data.py | 86 +++++++++-----------------------------
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1 file changed, 19 insertions(+), 67 deletions(-)
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diff --git a/bed_reader/_sample_data.py b/bed_reader/_sample_data.py
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index 6ca4cc0..6a1146e 100644
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--- a/bed_reader/_sample_data.py
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+++ b/bed_reader/_sample_data.py
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@@ -1,33 +1,8 @@
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+import os
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import tempfile
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from pathlib import Path, PurePath
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from typing import Union
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-try:
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- import pooch
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-
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- """
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- Load sample data.
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- """
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-
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- POOCH = pooch.create(
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- # Use the default cache folder for the OS
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- path=pooch.os_cache("bed_reader"),
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- # The remote data is on Github
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- base_url="https://raw.githubusercontent.com/"
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- + "fastlmm/bed-sample-files/main/",
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- # If this is a development version, get the data from the master branch
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- version_dev="main",
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- # The registry specifies the files that can be fetched
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- env="BED_READER_DATA_DIR",
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- )
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-
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- # Get registry file from package_data
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- registry_file = Path(__file__).parent / "tests/registry.txt"
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- # Load this registry file
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- POOCH.load_registry(registry_file)
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-except ImportError:
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- pooch = None
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-
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def sample_file(filepath: Union[str, Path]) -> str:
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"""Retrieve a sample .bed file. (Also retrieves associated .fam and .bim files).
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@@ -40,50 +15,41 @@ def sample_file(filepath: Union[str, Path]) -> str:
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Returns
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-------
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str
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- Local name of sample .bed file.
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-
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-
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- .. note::
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- This function requires the :mod:`pooch` package. Install `pooch` with:
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-
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- .. code-block:: bash
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-
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- pip install --upgrade bed-reader[samples]
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-
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-
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- By default this function puts files under the user's cache directory.
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- Override this by setting
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- the `BED_READER_DATA_DIR` environment variable.
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+ Local path of sample .bed file.
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Example
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--------
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.. doctest::
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- >>> # pip install bed-reader[samples] # if needed
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>>> from bed_reader import sample_file
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>>>
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>>> file_name = sample_file("small.bed")
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>>> print(f"The local file name is '{file_name}'")
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The local file name is '...small.bed'
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-
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"""
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- if pooch is None:
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- raise ImportError(
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- "The function sample_file() requires pooch. "
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- + "Install it with 'pip install --upgrade bed-reader[samples]'.",
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+ filepath = Path(filepath)
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+ sample_dir = os.environ.get("BED_READER_DATA_DIR")
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+ if sample_dir is None:
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+ raise EnvironmentError(
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+ "BED_READER_DATA_DIR environment variable is not set. "
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+ "This should point to the directory containing the sample files."
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)
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- filepath = Path(filepath)
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- file_string = str(filepath)
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- if file_string.lower().endswith(".bed"):
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- POOCH.fetch(file_string[:-4] + ".fam")
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- POOCH.fetch(file_string[:-4] + ".bim")
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- return POOCH.fetch(file_string)
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+ file_path = Path(sample_dir) / filepath
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+
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+ # Check if file exists
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+ if not file_path.exists():
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+ raise FileNotFoundError(
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+ f"Sample file '{filepath}' not found in {sample_dir}. "
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+ f"Make sure you're using the latest samples in BED_READER_DATA_DIR."
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+ )
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+
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+ return str(file_path)
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def sample_url(filepath: Union[str, Path]) -> str:
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- """Retrieve a URL to a sample .bed file. (Also makes ready associated .fam and .bim files).
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+ """Retrieve a URL to a sample .bed file.
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Parameters
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----------
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@@ -95,25 +61,11 @@ def sample_url(filepath: Union[str, Path]) -> str:
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str
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URL to sample .bed file.
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-
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- .. note::
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- This function requires the :mod:`pooch` package. Install `pooch` with:
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-
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- .. code-block:: bash
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-
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- pip install --upgrade bed-reader[samples]
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-
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-
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- By default this function puts files under the user's cache directory.
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- Override this by setting
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- the `BED_READER_DATA_DIR` environment variable.
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-
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Example
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--------
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.. doctest::
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- >>> # pip install bed-reader[samples] # if needed
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>>> from bed_reader import sample_url
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>>>
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>>> url = sample_url("small.bed")
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--
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2.49.0
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