M gnu/local.mk => gnu/local.mk +1 -0
@@ 2009,6 2009,7 @@ dist_patch_DATA = \
%D%/packages/patches/python-3.12-fix-tests.patch \
%D%/packages/patches/python-accupy-use-matplotx.patch \
%D%/packages/patches/python-accupy-fix-use-of-perfplot.patch \
+ %D%/packages/patches/python-bed-reader-use-store-samples.patch \
%D%/packages/patches/python-chai-drop-python2.patch \
%D%/packages/patches/python-clarabel-blas.patch \
%D%/packages/patches/python-docrepr-fix-tests.patch \
M gnu/packages/bioinformatics.scm => gnu/packages/bioinformatics.scm +136 -59
@@ 2185,6 2185,20 @@ Format (GFF) with Biopython integration.")
(modify-inputs (package-propagated-inputs python-bcbio-gff)
(replace "python-biopython" python-biopython-1.73))))))
+(define bed-sample-files
+ (let* ((name "bed-sample-files")
+ (commit "a06dc0450e484090f15656ffd5d317813a5e1e01")
+ (revision "0")
+ (version (git-version "0.0.0" revision commit)))
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/fastlmm/bed-sample-files")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1ldr2lvgbcykxa9i2s2298mhfh0sz96aaxs5dx217aipa9vsrjwk")))))
+
(define-public python-bed-reader
(package
(name "python-bed-reader")
@@ 2194,80 2208,124 @@ Format (GFF) with Biopython integration.")
(method url-fetch)
(uri (pypi-uri "bed_reader" version))
(sha256
- (base32 "1c8ibwvz3b069w7ffh9aasz16lfkmx4z0249c2v909a21mrkkd6n"))))
+ (base32 "1c8ibwvz3b069w7ffh9aasz16lfkmx4z0249c2v909a21mrkkd6n"))
+ (modules '((guix build utils)))
+ ;; Bundled unused javascript & co.
+ (snippet #~(delete-file-recursively "_static"))
+ (patches
+ (search-patches "python-bed-reader-use-store-samples.patch"))))
(build-system cargo-build-system)
(arguments
(list
- ;; Many of the tests (both the Rust tests and the Python tests) require
- ;; Internet access to fetch samples.
- #:tests? #false
#:install-source? #false
#:features '(list "extension-module")
- #:cargo-test-flags '(list "--features=extension-module")
+ #:cargo-test-flags
+ '(list "--features=extension-module"
+ ;; Skip doc tests.
+ "--lib" "--bins" "--tests" "--"
+ ;; This test is the only one not matched by our regexp.
+ "--skip=http_one"
+ ;; These test require a 84 GB file.
+ "--skip=http_two"
+ "--skip=http_cloud_urls_md_3")
#:cargo-inputs
- `(("rust-anyinput" ,rust-anyinput-0.1)
- ("rust-bytecount" ,rust-bytecount-0.6)
- ("rust-byteorder" ,rust-byteorder-1)
- ("rust-bytes" ,rust-bytes-1)
- ("rust-cloud-file" ,rust-cloud-file-0.2)
- ("rust-derive-builder" ,rust-derive-builder-0.20)
- ("rust-dpc-pariter" ,rust-dpc-pariter-0.4)
- ("rust-fetch-data" ,rust-fetch-data-0.2)
- ("rust-futures-util" ,rust-futures-util-0.3)
- ("rust-itertools" ,rust-itertools-0.13)
- ("rust-ndarray" ,rust-ndarray-0.16)
- ("rust-ndarray-npy" ,rust-ndarray-npy-0.9)
- ("rust-num-traits" ,rust-num-traits-0.2)
- ("rust-numpy" ,rust-numpy-0.22)
- ("rust-pyo3" ,rust-pyo3-0.22)
- ("rust-pyo3-build-config" ,rust-pyo3-build-config-0.22)
- ("rust-rayon" ,rust-rayon-1)
- ("rust-statrs" ,rust-statrs-0.17)
- ("rust-thiserror" ,rust-thiserror-1)
- ("rust-tokio" ,rust-tokio-1))
+ (list rust-anyinput-0.1
+ rust-bytecount-0.6
+ rust-byteorder-1
+ rust-bytes-1
+ rust-cloud-file-0.2
+ rust-derive-builder-0.20
+ rust-dpc-pariter-0.4
+ rust-fetch-data-0.2
+ rust-futures-util-0.3
+ rust-itertools-0.13
+ rust-ndarray-0.16
+ rust-ndarray-npy-0.9
+ rust-num-traits-0.2
+ rust-numpy-0.22
+ rust-pyo3-0.22
+ rust-pyo3-build-config-0.22
+ rust-rayon-1
+ rust-statrs-0.17
+ rust-thiserror-1
+ rust-tokio-1)
#:cargo-development-inputs
- `(("rust-anyhow" ,rust-anyhow-1)
- ("rust-ndarray-rand" ,rust-ndarray-rand-0.15)
- ("rust-rusoto-credential" ,rust-rusoto-credential-0.48)
- ("rust-temp-testdir" ,rust-temp-testdir-0.2)
- ("rust-thousands" ,rust-thousands-0.2))
+ (list rust-anyhow-1
+ rust-ndarray-rand-0.15
+ rust-rusoto-credential-0.48
+ rust-temp-testdir-0.2
+ rust-thousands-0.2)
#:imported-modules
(append %cargo-build-system-modules
%pyproject-build-system-modules)
#:modules
'((guix build cargo-build-system)
((guix build pyproject-build-system) #:prefix py:)
- (guix build utils))
+ (guix build utils)
+ (ice-9 match)
+ (ice-9 rdelim))
#:phases
#~(modify-phases %standard-phases
+ (add-after 'configure 'set-data-path
+ (lambda _
+ ;; This var is still necessary despite the patch-data-path phase.
+ ;; Otherwise more tests fail with a read-only filesystem error.
+ (setenv "BED_READER_DATA_DIR" #+bed-sample-files)))
+ (add-after 'unpack 'patch-data-path
+ (lambda _
+ ;; If BED_READER_DATA_DIR is unset, default to bed-sample-files.
+ (substitute* "bed_reader/_sample_data.py"
+ (("os\\.environ\\.get\\(\"BED_READER_DATA_DIR\"" all)
+ (format #f "~a, ~s" all #+bed-sample-files)))
+ ;; XXX: More work is necessary to use another
+ ;; version of sample files with BED_READER_DATA_DIR
+ ;; Currently, only the hardcoded Guix version is working.
+ (substitute* '("bed_reader/tests/test_open_bed_cloud.py"
+ "src/bed_cloud.rs"
+ "src/lib.rs"
+ "src/supplemental_documents/cloud_urls_etc.md"
+ "tests/tests_api_cloud.rs")
+ (("\
+https://raw\\.githubusercontent\\.com/fastlmm/bed-sample-files/main")
+ (string-append "file://" #+bed-sample-files)))
+ (substitute* "src/tests.rs"
+ (("bed_reader/tests/data")
+ #+bed-sample-files))))
(add-after 'install 'prepare-python-module
(lambda _
- ;; We don't use maturin.
- (delete-file "pyproject.toml")
- (call-with-output-file "pyproject.toml"
- (lambda (port)
- (format port "\
+ ;; We don't use maturin. Conveniently, what we want to drop
+ ;; from pyproject.toml is at the end of the file.
+ (rename-file "pyproject.toml" "pyproject.toml.bak")
+ (call-with-input-file "pyproject.toml.bak"
+ (lambda (in)
+ (call-with-output-file "pyproject.toml"
+ (lambda (out)
+ (let loop ()
+ (match (read-line in)
+ ((? eof-object? eof)
+ eof)
+ ("[build-system]"
+ (and (format out "\
[build-system]
build-backend = 'setuptools.build_meta'
requires = ['setuptools']
-")))
- (call-with-output-file "setup.cfg"
- (lambda (port)
- (format port "\
-[metadata]
-name = bed-reader
-version = ~a
-[options]
-packages = find:
-
-[options.packages.find]
-exclude =
- src
- docs
- tests
- Cargo.toml
-" #$version)))))
+[tool.setuptools.packages.find]
+where = [\".\"]
+exclude = [\"src\", \"docs\", \"tests\", \"Cargo.toml\"]
+")))
+ ("samples = [\"pooch>=1.5.0\"]"
+ (and (format out "samples = []~%")
+ (loop)))
+ ("[project]"
+ (and (format out "\
+[project]
+version = ~s
+" #$version)
+ (loop)))
+ (line
+ (and (format out "~a~%" line)
+ (loop)))))))))))
(add-after 'prepare-python-module 'enable-bytecode-determinism
(assoc-ref py:%standard-phases 'enable-bytecode-determinism))
(add-after 'enable-bytecode-determinism 'build-python-module
@@ 2279,16 2337,35 @@ exclude =
(let ((site (string-append #$output "/lib/python"
#$(version-major+minor
(package-version python))
- "/site-packages")))
- (mkdir-p site)
+ "/site-packages/")))
+ (mkdir-p (string-append site "bed_reader"))
(copy-file "target/release/libbed_reader.so"
- (string-append site "/bed_reader/bed_reader.so")))))
+ (string-append site "bed_reader/bed_reader.so")))))
(add-after 'install-python-library 'add-install-to-pythonpath
(assoc-ref py:%standard-phases 'add-install-to-pythonpath))
(add-after 'add-install-to-pythonpath 'check-python
- (lambda* (#:key tests? test-flags #:allow-other-keys)
+ (lambda* (#:key tests? #:allow-other-keys)
(when tests?
- (apply invoke "pytest" "-v" #$output test-flags)))))))
+ (let ((site (string-append #$output "/lib/python"
+ #$(version-major+minor
+ (package-version python))
+ "/site-packages/"))
+ (data-dir "bed_reader/tests/data"))
+ (symlink (canonicalize-path data-dir)
+ (string-append site data-dir))
+ (invoke "pytest" "-v" #$output
+ ;; These test require a 84 GB file.
+ "-k" (string-join
+ (list "not test_http_two"
+ "test_http_cloud_urls_rst_3"
+ "test_http_cloud_urls_rst_4"
+ ;; XXX: python-pooch dependency removed
+ "test_optional_dependencies")
+ " and not "))
+ (delete-file-recursively
+ (string-append site "bed_reader/tests"))
+ (delete-file-recursively
+ (string-append #$output "/.pytest_cache")))))))))
(native-inputs (list python-pytest
python-pytest-cov
python-pytest-datadir
@@ 2296,7 2373,7 @@ exclude =
python-recommonmark
python-sphinx))
(inputs (list python-wrapper))
- (propagated-inputs (list python-numpy python-pandas python-pooch))
+ (propagated-inputs (list python-numpy python-pandas python-scipy))
(home-page "https://fastlmm.github.io/")
(synopsis "Read and write the PLINK BED format, simply and efficiently")
(description
A gnu/packages/patches/python-bed-reader-use-store-samples.patch => gnu/packages/patches/python-bed-reader-use-store-samples.patch +147 -0
@@ 0,0 1,147 @@
+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
+