guix_mirror_bot pushed a commit to branch master
in repository guix.
commit 898721e1749cbfd5357b02be6f5373e0a5888b12
Author: Sharlatan Hellseher <[email protected]>
AuthorDate: Thu Oct 30 09:49:54 2025 +0000
gnu: python-ega-download-client: Update to 5.2.1.
* gnu/packages/bioinformatics.scm (python-ega-download-client): Update to
5.2.1.
[arguments]: Use G-Expressions.
<test-flags>: Rework skipped tests and ignored tests files
generating very larg test files (up to 150GiB) which may affect the CI
or user's machine.
[native-inputs]: Remove python-coverage and python-wheel; add
nss-certs-for-test.
Change-Id: Ic91c65e548e27d6c57396000233b6e5f5949554c
---
gnu/packages/bioinformatics.scm | 63 +++++++++++++++++++++--------------------
1 file changed, 33 insertions(+), 30 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 81b46be02f..c0c0ae3200 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3912,54 +3912,57 @@ operators such as union, intersection, and difference.")
(define-public python-ega-download-client
(package
(name "python-ega-download-client")
- (version "5.1.0")
+ (version "5.2.1")
(source
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/EGA-archive/ega-download-client";)
- (commit (string-append "v" version))))
+ (url "https://github.com/EGA-archive/ega-download-client";)
+ (commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "0k9rfq2yyvfxs5sq9lsm8krp9ddx4s18hv85ikf3b37zv24kpwjk"))))
+ (base32 "0wz36ii6sb65nknh56vr5ss6b446zy9iibz7jv3irgfas955jlrc"))))
(build-system pyproject-build-system)
(arguments
(list
+ ;; tests: 78 passed, 2 deselected, 1 warning
#:test-flags
- '(list
- ;; These tests fail because they require internet access.
- "--ignore=tests/functional/test_download.py"
- "--ignore=tests/functional/test_htsget.py"
- "-k"
- (string-append "not test_error_5xx"
- " and not test_error_too_many_requests"
- ;; Something's wrong here. On some powerful machines
- ;; (but not on my laptop) these fail, and tests like
- ;;
test_file_is_saved_into_an_existing_directory_which_was_specified_by_the_user
- ;; take a *very* long time to complete.
- ;;
- ;; It looks like "dataset_in_fire.download" takes an
- ;; unusually long time on those machines. We disable
- ;; tests that fail under these conditions.
- " and not test_download_file"
- " and not
test_output_file_is_removed_if_md5_was_invalid"
- " and not test_post_stats_if_download_succeeded"))
+ ;; Test suite does a lot of fake os mocking and extensively hash
+ ;; checking on a large amount of generated files (up to 150GiB each)
+ ;; which would take some extra compute resources, therefor functional
+ ;; and some of unit tests are excluded to relax the load.
+ #~(list #$@(map (lambda (file) (string-append "--ignore="
+ "tests/"
+ file))
+ (list "functional/"
+ "unit/test_save_to_with_dataset.py"
+ "unit/test_save_to_with_file.py"
+ "unit/test_verify_output_dir.py"))
+ #$@(map (lambda (test) (string-append "--deselect="
+ "tests/unit/"
+ "test_commands.py::"
+ test))
+ ;; requests.exceptions.RetryError: None: Max retries
+ ;; exceeded with url:
+ ;; https://test.data.server/metadata/datasets (Caused by
+ ;; ResponseError('too many 503 error responses'))
+ (list "test_error_5xx"
+ "test_error_too_many_requests")))
#:phases
- '(modify-phases %standard-phases
- (add-after 'unpack 'relax-requirements
- (lambda _
- (substitute* "setup.py"
- (("==") ">=")))))))
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'relax-requirements
+ (lambda _
+ (substitute* "setup.py"
+ (("==") ">=")))))))
(propagated-inputs (list python-htsget python-psutil python-requests
python-tqdm python-urllib3))
(native-inputs
- (list python-coverage
+ (list nss-certs-for-test
python-mock
python-pyfakefs
python-pytest
python-responses
- python-setuptools
- python-wheel))
+ python-setuptools))
(home-page "https://github.com/EGA-archive/ega-download-client";)
(synopsis "EGA download client")
(description "PyEGA3 is a tool for viewing and downloading files from
