Package: guix-patches;
Reported by: Nicolas Graves <ngraves <at> ngraves.fr>
Date: Fri, 4 Apr 2025 19:11:01 UTC
Severity: normal
Tags: patch
Done: Nicolas Graves <ngraves <at> ngraves.fr>
Bug is archived. No further changes may be made.
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guix-patches <at> gnu.org:bug#77541; Package guix-patches.
(Fri, 04 Apr 2025 19:11:01 GMT) Full text and rfc822 format available.Nicolas Graves <ngraves <at> ngraves.fr>:guix-patches <at> gnu.org.
(Fri, 04 Apr 2025 19:11:02 GMT) Full text and rfc822 format available.Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: guix-patches <at> gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 01/38] gnu: Add clipper2. Date: Fri, 4 Apr 2025 21:06:57 +0200
* gnu/packages/cpp.scm (clipper2): New variable.
---
gnu/packages/cpp.scm | 36 +++++++++++++++++++++++++++++++++++-
1 file changed, 35 insertions(+), 1 deletion(-)
diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
index a102a5d468..946484d325 100644
--- a/gnu/packages/cpp.scm
+++ b/gnu/packages/cpp.scm
@@ -44,7 +44,7 @@
;;; Copyright © 2024 Jakob Kirsch <jakob.kirsch <at> web.de>
;;; Copyright © 2025 Sharlatan Hellseher <sharlatanus <at> gmail.com>
;;; Copyright © 2025 Sergio Pastor Pérez <sergio.pastorperez <at> gmail.com>
-;;;
+;;; Copyright © 2025 Nicolas Graves <ngraves <at> ngraves.fr>
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
@@ -2620,6 +2620,40 @@ (define-public clipper
The library is based on Vatti's clipping algorithm.")
(license license:boost1.0)))
+(define-public clipper2
+ (package
+ (inherit clipper)
+ (name "clipper2")
+ (version "1.5.2")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/AngusJohnson/Clipper2")
+ (commit (string-append "Clipper2_" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1w8cmx712k45cb8gh9dakmbmybiwdx8c0b45mwpcldywx2lwxi2j"))
+ (modules '((guix build utils)))
+ (snippet #~(for-each
+ delete-file-recursively
+ '("CSharp" "DLL" "Delphi")))))
+ (build-system cmake-build-system)
+ (arguments
+ (list
+ #:configure-flags
+ #~(list "-DUSE_EXTERNAL_GTEST=ON"
+ "-DCLIPPER2_EXAMPLES=OFF")
+ #:phases #~(modify-phases %standard-phases
+ (add-after 'unpack 'chdir
+ (lambda _
+ (chdir "CPP"))))))
+ (native-inputs (list googletest))
+ (home-page "https://github.com/AngusJohnson/Clipper2")
+ (description
+ (string-append (package-description clipper) "\
+Note: This package is a major update of the original clipper library."))))
+
(define-public pcg-cpp
(let ((commit "ffd522e7188bef30a00c74dc7eb9de5faff90092")
(revision "2"))
--
2.49.0
Nicolas Graves <ngraves <at> ngraves.fr>
to control <at> debbugs.gnu.org.
(Fri, 04 Apr 2025 19:16:02 GMT) Full text and rfc822 format available.guix-patches <at> gnu.org:bug#77541; Package guix-patches.
(Fri, 04 Apr 2025 19:18:03 GMT) Full text and rfc822 format available.Message #10 received at 77541 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77541 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 01/38] gnu: Add clipper2. Date: Fri, 4 Apr 2025 21:16:33 +0200
* gnu/packages/cpp.scm (clipper2): New variable.
---
gnu/packages/cpp.scm | 35 +++++++++++++++++++++++++++++++++++
1 file changed, 35 insertions(+)
diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
index a102a5d468..4c645f0f9d 100644
--- a/gnu/packages/cpp.scm
+++ b/gnu/packages/cpp.scm
@@ -44,6 +44,7 @@
;;; Copyright © 2024 Jakob Kirsch <jakob.kirsch <at> web.de>
;;; Copyright © 2025 Sharlatan Hellseher <sharlatanus <at> gmail.com>
;;; Copyright © 2025 Sergio Pastor Pérez <sergio.pastorperez <at> gmail.com>
+;;; Copyright © 2025 Nicolas Graves <ngraves <at> ngraves.fr>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -2620,6 +2621,40 @@ (define-public clipper
The library is based on Vatti's clipping algorithm.")
(license license:boost1.0)))
+(define-public clipper2
+ (package
+ (inherit clipper)
+ (name "clipper2")
+ (version "1.5.2")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/AngusJohnson/Clipper2")
+ (commit (string-append "Clipper2_" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1w8cmx712k45cb8gh9dakmbmybiwdx8c0b45mwpcldywx2lwxi2j"))
+ (modules '((guix build utils)))
+ (snippet #~(for-each
+ delete-file-recursively
+ '("CSharp" "DLL" "Delphi")))))
+ (build-system cmake-build-system)
+ (arguments
+ (list
+ #:configure-flags
+ #~(list "-DUSE_EXTERNAL_GTEST=ON"
+ "-DCLIPPER2_EXAMPLES=OFF")
+ #:phases #~(modify-phases %standard-phases
+ (add-after 'unpack 'chdir
+ (lambda _
+ (chdir "CPP"))))))
+ (native-inputs (list googletest))
+ (home-page "https://github.com/AngusJohnson/Clipper2")
+ (description
+ (string-append (package-description clipper) "\
+Note: This package is a major update of the original clipper library."))))
+
(define-public pcg-cpp
(let ((commit "ffd522e7188bef30a00c74dc7eb9de5faff90092")
(revision "2"))
--
2.49.0
guix-patches <at> gnu.org:bug#77541; Package guix-patches.
(Fri, 04 Apr 2025 19:18:03 GMT) Full text and rfc822 format available.Message #13 received at 77541 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77541 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 02/38] gnu: labelme: Add missing native-inputs. Date: Fri, 4 Apr 2025 21:16:34 +0200
* gnu/packages/image-processing.scm (labelme)[native-inputs]: Add
python-wheel.
---
gnu/packages/image-processing.scm | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/gnu/packages/image-processing.scm b/gnu/packages/image-processing.scm
index 296dec738a..5a3e6f69ef 100644
--- a/gnu/packages/image-processing.scm
+++ b/gnu/packages/image-processing.scm
@@ -1845,7 +1845,8 @@ (define-public labelme
(native-inputs
(list python-pytest
python-pytest-qt
- xorg-server-for-tests))
+ xorg-server-for-tests
+ python-wheel))
(propagated-inputs
(list python-imgviz
python-matplotlib
--
2.49.0
guix-patches <at> gnu.org:bug#77541; Package guix-patches.
(Fri, 04 Apr 2025 19:18:04 GMT) Full text and rfc822 format available.Message #16 received at 77541 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77541 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 03/38] gnu: scregseg: Add missing native-inputs. Date: Fri, 4 Apr 2025 21:16:35 +0200
* gnu/packages/bioinformatics.scm (scregseg)[native-inputs]: Add
python-wheel.
---
gnu/packages/bioinformatics.scm | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e7685faf02..804cf057e2 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -24241,7 +24241,8 @@ (define-public scregseg
(substitute* "setup.py"
(("'sklearn',") "")))))))
(native-inputs
- (list python-cython))
+ (list python-cython
+ python-wheel))
(propagated-inputs
(list python-scikit-learn
python-scipy
--
2.49.0
guix-patches <at> gnu.org:bug#77541; Package guix-patches.
(Fri, 04 Apr 2025 19:18:04 GMT) Full text and rfc822 format available.Message #19 received at 77541 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77541 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 04/38] gnu: autokey: Add missing native-inputs. Date: Fri, 4 Apr 2025 21:16:36 +0200
* gnu/packages/python-xyz.scm (autokey)[native-inputs]: Add
python-wheel.
---
gnu/packages/python-xyz.scm | 6 +++++-
1 file changed, 5 insertions(+), 1 deletion(-)
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 12d6800a1c..4abe04007d 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -7938,7 +7938,11 @@ (define-public autokey
(setenv "LANG" "")
;; required for tests/test_configmanager.py
(setenv "HOME" "/tmp"))))))
- (native-inputs (list python-pytest python-pytest-cov python-pyhamcrest))
+ (native-inputs
+ (list python-pytest
+ python-pytest-cov
+ python-pyhamcrest
+ python-wheel))
(inputs
(list bash-minimal ; for wrap-program
gtksourceview-3
--
2.49.0
guix-patches <at> gnu.org:bug#77541; Package guix-patches.
(Fri, 04 Apr 2025 19:18:05 GMT) Full text and rfc822 format available.Message #22 received at 77541 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77541 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 05/38] gnu: mageck: Add missing native-inputs. Date: Fri, 4 Apr 2025 21:16:37 +0200
* gnu/packages/bioinformatics.scm (mageck)[native-inputs]: Add
python-wheel.
---
gnu/packages/bioinformatics.scm | 2 ++
1 file changed, 2 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 804cf057e2..4dbedc09f9 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9975,6 +9975,8 @@ (define-public mageck
(with-directory-excursion (string-append "demo/" dir)
(invoke "bash" script))))
tests))))))))
+ (native-inputs
+ (list python-wheel))
(inputs
(list python-numpy
python-scipy
--
2.49.0
guix-patches <at> gnu.org:bug#77541; Package guix-patches.
(Fri, 04 Apr 2025 19:18:05 GMT) Full text and rfc822 format available.Message #25 received at 77541 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77541 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 06/38] gnu: python-pytroch-geometric: Skip failing tests. Date: Fri, 4 Apr 2025 21:16:38 +0200
* gnu/packages/machine-learning.scm (python-pytroch-geometric):
[arguments]{test-flags}: Skip test_type_repr failing test.
---
gnu/packages/machine-learning.scm | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index e7923bd503..fb1d5d2eed 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -5399,7 +5399,10 @@ (define-public python-pytorch-geometric
;; These refuse to be run on CPU and really want a GPU
" and not test_add_random_walk_pe"
" and not test_asap"
- " and not test_two_hop"))
+ " and not test_two_hop"
+ ;; Failed when switched to python <at> 3.11
+ ;; typing module internals
+ " and not test_type_repr"))
#:phases
'(modify-phases %standard-phases
(add-after 'unpack 'delete-top-level-directories
--
2.49.0
guix-patches <at> gnu.org:bug#77541; Package guix-patches.
(Fri, 04 Apr 2025 19:18:05 GMT) Full text and rfc822 format available.Message #28 received at 77541 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77541 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 07/38] gnu: Add string-view-lite. Date: Fri, 4 Apr 2025 21:16:39 +0200
* gnu/packages/cpp.scm (string-view-lite): New variable.
---
gnu/packages/cpp.scm | 20 ++++++++++++++++++++
1 file changed, 20 insertions(+)
diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
index 4c645f0f9d..7d0135044a 100644
--- a/gnu/packages/cpp.scm
+++ b/gnu/packages/cpp.scm
@@ -3795,6 +3795,26 @@ (define-public nativefiledialog-extended
\"source files\" or \"image files\") where supported.")
(license license:zlib)))
+(define-public string-view-lite
+ (package
+ (name "string-view-lite")
+ (version "1.8.0")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/martinmoene/string-view-lite")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1mfp3lmqx7ac0545akxd2v05rrapa3byz8q4gb9rqy94pcqbfyc5"))))
+ (build-system cmake-build-system)
+ (home-page "https://github.com/martinmoene/string-view-lite")
+ (synopsis "C++17 string-view for older C++")
+ (description "This package provides a compatibility header-only library
+for C++17 string-view.")
+ (license license:boost1.0)))
+
(define-public tsl-hopscotch-map
(package
(name "tsl-hopscotch-map")
--
2.49.0
guix-patches <at> gnu.org:bug#77541; Package guix-patches.
(Fri, 04 Apr 2025 19:18:06 GMT) Full text and rfc822 format available.Message #31 received at 77541 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77541 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 08/38] gnu: python-pytensor: Update to 2.30.1. Date: Fri, 4 Apr 2025 21:16:40 +0200
* gnu/packages/python-science.scm (python-pytensor): Update to 2.30.1.
[arguments]{test-flags}: Use field.
{phases}: Remove 'check phase replacement. Add phase 'pre-check.
---
gnu/packages/python-science.scm | 43 +++++++++++++++++----------------
1 file changed, 22 insertions(+), 21 deletions(-)
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 49e46f7ff3..3bf266582d 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -2465,7 +2465,7 @@ (define-public python-xarray-schema
(define-public python-pytensor
(package
(name "python-pytensor")
- (version "2.18.1")
+ (version "2.30.1")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -2474,10 +2474,28 @@ (define-public python-pytensor
(file-name (git-file-name name version))
(sha256
(base32
- "0qa0y13xfm6w7ry7gp0lv84c8blyg34a9ns7ynwqyhf9majq08s5"))))
+ "008ivcrab9j256mcrfrcd1xlkq5qicsx97wqaxaxwk1ynnmxdqbn"))))
(build-system pyproject-build-system)
(arguments
(list
+ #:test-flags
+ #~(list ;; test_tensor_basic.py file requires JAX.
+ "--ignore" "tests/link/jax/test_tensor_basic.py"
+ ;; No module named 'pytensor.scan.scan_perform'
+ "--ignore" "pytensor/scan/scan_perform_ext.py"
+ ;; Skip benchmark tests.
+ "-k" (string-append
+ "not test_elemwise_speed"
+ " and not test_logsumexp_benchmark"
+ " and not test_fused_elemwise_benchmark"
+ " and not test_scan_multiple_output"
+ " and not test_vector_taps_benchmark"
+ " and not test_cython_performance")
+ ;; Skip computationally intensive tests.
+ "--ignore" "tests/scan/"
+ "--ignore" "tests/tensor/"
+ "--ignore" "tests/sandbox/"
+ "--ignore" "tests/sparse/sandbox/")
#:phases
#~(modify-phases %standard-phases
;; Replace version manually because pytensor uses
@@ -2499,27 +2517,10 @@ (define-public python-pytensor
(substitute* "setup.py"
(("versioneer.get_version\\(\\)")
(string-append "\"" #$version "\"")))))
- (replace 'check
+ (add-before 'check 'pre-check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
- (setenv "HOME" "/tmp") ; required for most tests
- ;; Test discovery fails, have to call pytest by hand.
- ;; test_tensor_basic.py file requires JAX.
- (invoke "python" "-m" "pytest" "-vv"
- "--ignore" "tests/link/jax/test_tensor_basic.py"
- ;; Skip benchmark tests.
- "-k" (string-append
- "not test_elemwise_speed"
- " and not test_logsumexp_benchmark"
- " and not test_fused_elemwise_benchmark"
- " and not test_scan_multiple_output"
- " and not test_vector_taps_benchmark"
- " and not test_cython_performance")
- ;; Skip computationally intensive tests.
- "--ignore" "tests/scan/"
- "--ignore" "tests/tensor/"
- "--ignore" "tests/sandbox/"
- "--ignore" "tests/sparse/sandbox/")))))))
+ (setenv "HOME" "/tmp"))))))) ; required for most tests
(native-inputs (list python-cython
python-pytest
python-pytest-mock
--
2.49.0
guix-patches <at> gnu.org:bug#77541; Package guix-patches.
(Fri, 04 Apr 2025 19:18:06 GMT) Full text and rfc822 format available.Message #34 received at 77541 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77541 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 09/38] gnu: python-vaex-core: Update to 4.17.1. Date: Fri, 4 Apr 2025 21:16:41 +0200
* gnu/packages/python-science.scm (python-vaex-core): Update to 4.17.1.
* gnu/packages/patches/python-vaex-core-fix-tsl-use.patch: Add patch.
* gnu/local.mk: Record patch.
---
gnu/local.mk | 1 +
.../python-vaex-core-fix-tsl-use.patch | 67 +++++++++++++++++++
gnu/packages/python-science.scm | 44 ++++++++----
3 files changed, 100 insertions(+), 12 deletions(-)
create mode 100644 gnu/packages/patches/python-vaex-core-fix-tsl-use.patch
diff --git a/gnu/local.mk b/gnu/local.mk
index 18ba0073fc..93f346481d 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -2142,6 +2142,7 @@ dist_patch_DATA = \
%D%/packages/patches/python-robotframework-sshlibrary-rf5-compat.patch \
%D%/packages/patches/python-unittest2-python3-compat.patch \
%D%/packages/patches/python-unittest2-remove-argparse.patch \
+ %D%/packages/patches/python-vaex-core-fix-tsl-use.patch \
%D%/packages/patches/python-vega-datasets-remove-la-riots-code.patch \
%D%/packages/patches/python-versioneer-guix-support.patch \
%D%/packages/patches/python-werkzeug-tests.patch \
diff --git a/gnu/packages/patches/python-vaex-core-fix-tsl-use.patch b/gnu/packages/patches/python-vaex-core-fix-tsl-use.patch
new file mode 100644
index 0000000000..f4f6fc1c48
--- /dev/null
+++ b/gnu/packages/patches/python-vaex-core-fix-tsl-use.patch
@@ -0,0 +1,67 @@
+From 8cb8808b3ceccf4ab3ac542739ef490abe7e76b3 Mon Sep 17 00:00:00 2001
+Message-ID: <8cb8808b3ceccf4ab3ac542739ef490abe7e76b3.1743597010.git.ngraves <at> ngraves.fr>
+From: Nicolas Graves <ngraves <at> ngraves.fr>
+Date: Wed, 2 Apr 2025 14:29:40 +0200
+Subject: [PATCH] Fix tsl map use
+
+---
+ packages/vaex-core/src/hash_string.hpp | 25 ++++++++++++++++---------
+ 1 file changed, 16 insertions(+), 9 deletions(-)
+
+diff --git a/packages/vaex-core/src/hash_string.hpp b/packages/vaex-core/src/hash_string.hpp
+index d3b60199..0ed69d1c 100644
+--- a/packages/vaex-core/src/hash_string.hpp
++++ b/packages/vaex-core/src/hash_string.hpp
+@@ -39,13 +39,15 @@ class hash_base : public hash_common<Derived, T, hashmap<T, int64_t>> {
+ for (int i = 0; i < nmaps; i++) {
+ string_arrays.emplace_back(std::make_shared<StringList64>());
+ StringList64 *strings = string_arrays[i].get();
+- // equal_to<string_ref>& eq = this->maps[i].key_eq();
+- this->maps[i].m_ht.strings_equals = strings;
+- this->maps[i].m_ht.strings_hash = strings;
++ equal_to<key_type> eq;
++ eq.strings_equals = strings;
++ hash<key_type> h;
++ h.strings_hash = strings;
++ this->maps[i] = hashmap_type(8, h, eq);
+ }
+ };
+
+- virtual std::string _get(hashmap_type &map, typename hashmap_type::key_type key) override { return map.m_ht.strings_equals->get(key.index); };
++ virtual std::string _get(hashmap_type &map, typename hashmap_type::key_type key) override { return string_arrays[0]->get(key.index); };
+
+ size_t bytes_used() const {
+ int64_t buffer_size = 0; // collect buffer size
+@@ -391,9 +393,12 @@ class ordered_set : public hash_base<ordered_set<T>, T, T, V> {
+ template <class SL>
+ static ordered_set *create(std::shared_ptr<SL> keys, int64_t null_value, int64_t nan_count, int64_t null_count, std::string *fingerprint) {
+ ordered_set *set = new ordered_set(1);
+- set->maps[0].m_ht.strings_equals = keys.get();
+- set->maps[0].m_ht.strings_hash = keys.get();
+ set->string_arrays[0] = keys;
++ equal_to<key_type> eq;
++ eq.strings_equals = keys.get();
++ hash<key_type> h;
++ h.strings_hash = keys.get();
++ set->maps[0] = hashmap_type(keys->length, h, eq);
+ {
+ size_t size = keys->length;
+ set->maps[0].reserve(size);
+@@ -701,9 +706,11 @@ class index_hash : public hash_base<index_hash<T>, T, T, V> {
+ // string_arrays_overflow.emplace_back(std::make_shared<StringList64>());
+ // for each key in overflow, it should be present in the main string array
+ StringList64 *strings = this->string_arrays[i].get();
+- // equal_to<string_ref>& eq = this->maps[i].key_eq();
+- overflows[i].m_ht.strings_equals = strings;
+- overflows[i].m_ht.strings_hash = strings;
++ equal_to<key_type> eq;
++ eq.strings_equals = strings;
++ hash<key_type> h;
++ h.strings_hash = strings;
++ overflows[i] = overflow_type(8, h, eq);
+ }
+ }
+
+--
+2.49.0
+
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 3bf266582d..73e08fccbe 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -4097,24 +4097,44 @@ (define-public python-opt-einsum
(define-public python-vaex-core
(package
(name "python-vaex-core")
- (version "4.17.1")
+ (version "4.18.1")
(source
(origin
- (method url-fetch)
- (uri (pypi-uri "vaex-core" version))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://www.github.com/maartenbreddels/vaex")
+ (commit (string-append "core-v" version))))
+ (file-name (git-file-name name version))
(sha256
- (base32 "1rzx5px3fwi5mh1z8y91brvffk7dkhj287lnmqp8zp6836kkqhya"))
- (modules '((guix build utils)))
+ (base32 "1sp096msbzgjlwi8c1ink2bp4pjff9pvikqz1y1li8d3in4gpgdr"))
+ (patches
+ (search-patches "python-vaex-core-fix-tsl-use.patch"))
+ (modules '((guix build utils)
+ (ice-9 ftw)))
(snippet
- ;; Remove bundled libraries
- '(for-each delete-file-recursively
- (list "vendor/boost"
- "vendor/pcre"
- "vendor/pybind11")))))
+ #~(begin
+ ;; Delete everything except for vaex-core itself:
+ (define (delete-except exception)
+ (lambda (file)
+ (unless (member file `("." ".." ,exception))
+ (delete-file-recursively file))))
+ (for-each (delete-except "packages") (scandir "."))
+ (with-directory-excursion "packages"
+ (for-each (delete-except "vaex-core") (scandir ".")))
+ (for-each (lambda (file)
+ (unless (member file '("." ".."))
+ (rename-file
+ (string-append "packages/vaex-core/" file)
+ file)))
+ (scandir "packages/vaex-core"))
+ (delete-file-recursively "packages")
+ (delete-file-recursively "vendor")))))
(build-system pyproject-build-system)
- (arguments (list #:tests? #false)) ;require vaex.server and others, which require vaex-core.
+ (arguments
+ ;; require vaex.server and others, which require vaex-core.
+ (list #:tests? #false))
(inputs
- (list boost pcre pybind11-2.3))
+ (list boost pcre pybind11 string-view-lite tsl-hopscotch-map))
(propagated-inputs
(list python-aplus
python-blake3
--
2.49.0
guix-patches <at> gnu.org:bug#77541; Package guix-patches.
(Fri, 04 Apr 2025 19:18:07 GMT) Full text and rfc822 format available.Message #37 received at 77541 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77541 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 10/38] gnu: Remove pybind11-2.3. Date: Fri, 4 Apr 2025 21:16:42 +0200
This package is now a leaf package that fails to build.
* gnu/packages/python-xyz.scm (pybind11-2.3): Delete variable.
---
gnu/packages/python-xyz.scm | 20 --------------------
1 file changed, 20 deletions(-)
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 4abe04007d..46efd10292 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -29832,26 +29832,6 @@ (define-public pybind11-2.10
"0rbcfvl7y472sykzdq3vrkw83kar0lpzhk3wq9yj9cdydl8cpfcz"))
(file-name (git-file-name name version))))))
-;; This is needed for python-vaex-core.
-(define-public pybind11-2.3
- (package
- (inherit pybind11)
- (name "pybind11")
- (version "2.3.0")
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/pybind/pybind11")
- (commit (string-append "v" version))))
- (sha256
- (base32
- "11b6dniri8m05spfd2a19irz82shf4sdca73566bniggrf3zclnf"))
- (file-name (git-file-name name version))))
- (arguments
- (substitute-keyword-arguments (package-arguments pybind11)
- ((#:tests? tests? #false)
- #false)))))
-
(define-public python-pooch
(package
(name "python-pooch")
--
2.49.0
guix-patches <at> gnu.org:bug#77541; Package guix-patches.
(Fri, 04 Apr 2025 19:18:08 GMT) Full text and rfc822 format available.Message #40 received at 77541 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77541 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 11/38] gnu: python-property-cached: Fix build. Date: Fri, 4 Apr 2025 21:16:43 +0200
* gnu/packages/python-xyz.scm (python-property-cached): Fix build.
* gnu/packages/patches/python-property-cached-asyncio-3_11.patch: Add
patch.
* gnu/local.mk: Record patch.
---
gnu/local.mk | 1 +
.../python-property-cached-asyncio-3_11.patch | 201 ++++++++++++++++++
gnu/packages/python-xyz.scm | 4 +-
3 files changed, 205 insertions(+), 1 deletion(-)
create mode 100644 gnu/packages/patches/python-property-cached-asyncio-3_11.patch
diff --git a/gnu/local.mk b/gnu/local.mk
index 93f346481d..1bf8f8deba 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -2129,6 +2129,7 @@ dist_patch_DATA = \
%D%/packages/patches/python-memcached-syntax-warnings.patch \
%D%/packages/patches/python-mox3-python3.6-compat.patch \
%D%/packages/patches/python-packaging-test-arch.patch \
+ %D%/packages/patches/python-property-cached-asyncio-3_11.patch \
%D%/packages/patches/python-pyan3-fix-absolute-path-bug.patch \
%D%/packages/patches/python-pyan3-fix-positional-arguments.patch \
%D%/packages/patches/python-pytorch-fix-codegen.patch \
diff --git a/gnu/packages/patches/python-property-cached-asyncio-3_11.patch b/gnu/packages/patches/python-property-cached-asyncio-3_11.patch
new file mode 100644
index 0000000000..21c176947e
--- /dev/null
+++ b/gnu/packages/patches/python-property-cached-asyncio-3_11.patch
@@ -0,0 +1,201 @@
+From d89186b47dc25c5ef5907c146edf3f792d50774b Mon Sep 17 00:00:00 2001
+Message-ID: <d89186b47dc25c5ef5907c146edf3f792d50774b.1743608515.git.ngraves <at> ngraves.fr>
+From: Nicolas Graves <ngraves <at> ngraves.fr>
+Date: Wed, 2 Apr 2025 17:29:45 +0200
+Subject: [PATCH] Update to python 3.11
+
+---
+ property_cached/__init__.py | 21 +++-------
+ tests/test_async_cached_property.py | 3 +-
+ tests/test_coroutine_cached_property.py | 51 ++++++++++---------------
+ 3 files changed, 27 insertions(+), 48 deletions(-)
+
+diff --git a/property_cached/__init__.py b/property_cached/__init__.py
+index 3353048..c033542 100644
+--- a/property_cached/__init__.py
++++ b/property_cached/__init__.py
+@@ -3,6 +3,7 @@ import functools
+ import pkg_resources
+ import threading
+ import weakref
++from inspect import iscoroutinefunction
+ from time import time
+
+
+@@ -31,12 +32,12 @@ class cached_property(property):
+ if obj is None:
+ return self
+
+- if asyncio and asyncio.iscoroutinefunction(self.func):
+- return self._wrap_in_coroutine(obj)
+-
+ value = self.cache.get(obj, self._sentinel)
+ if value is self._sentinel:
+- value = self.cache[obj] = self.func(obj)
++ if iscoroutinefunction(self.func):
++ self.cache[obj] = value = asyncio.ensure_future(self.func(obj))
++ else:
++ self.cache[obj] = value = self.func(obj)
+
+ return value
+
+@@ -49,18 +50,6 @@ class cached_property(property):
+ def __delete__(self, obj):
+ del self.cache[obj]
+
+- def _wrap_in_coroutine(self, obj):
+-
+- @functools.wraps(obj)
+- @asyncio.coroutine
+- def wrapper():
+- value = self.cache.get(obj, self._sentinel)
+- if value is self._sentinel:
+- self.cache[obj] = value = asyncio.ensure_future(self.func(obj))
+- return value
+-
+- return wrapper()
+-
+
+ class threaded_cached_property(cached_property):
+ """
+diff --git a/tests/test_async_cached_property.py b/tests/test_async_cached_property.py
+index 1af139d..32b3410 100644
+--- a/tests/test_async_cached_property.py
++++ b/tests/test_async_cached_property.py
+@@ -9,8 +9,7 @@ import property_cached as cached_property
+
+ def unittest_run_loop(f):
+ def wrapper(*args, **kwargs):
+- coro = asyncio.coroutine(f)
+- future = coro(*args, **kwargs)
++ future = f(*args, **kwargs)
+ loop = asyncio.get_event_loop()
+ loop.run_until_complete(future)
+
+diff --git a/tests/test_coroutine_cached_property.py b/tests/test_coroutine_cached_property.py
+index 40e443b..5864301 100644
+--- a/tests/test_coroutine_cached_property.py
++++ b/tests/test_coroutine_cached_property.py
+@@ -14,8 +14,7 @@ import property_cached as cached_property
+
+ def unittest_run_loop(f):
+ def wrapper(*args, **kwargs):
+- coro = asyncio.coroutine(f)
+- future = coro(*args, **kwargs)
++ future = f(*args, **kwargs)
+ loop = asyncio.get_event_loop()
+ loop.run_until_complete(future)
+
+@@ -33,14 +32,12 @@ def CheckFactory(cached_property_decorator):
+ self.control_total = 0
+ self.cached_total = 0
+
+- @asyncio.coroutine
+- def add_control(self):
++ async def add_control(self):
+ self.control_total += 1
+ return self.control_total
+
+ @cached_property_decorator
+- @asyncio.coroutine
+- def add_cached(self):
++ async def add_cached(self):
+ self.cached_total += 1
+ return self.cached_total
+
+@@ -52,74 +49,68 @@ class TestCachedProperty(unittest.TestCase):
+
+ cached_property_factory = cached_property.cached_property
+
+- @asyncio.coroutine
+- def assert_control(self, check, expected):
++ async def assert_control(self, check, expected):
+ """
+ Assert that both `add_control` and 'control_total` equal `expected`
+ """
+- value = yield from check.add_control()
++ value = await check.add_control()
+ self.assertEqual(value, expected)
+ self.assertEqual(check.control_total, expected)
+
+- @asyncio.coroutine
+- def assert_cached(self, check, expected):
++ async def assert_cached(self, check, expected):
+ """
+ Assert that both `add_cached` and 'cached_total` equal `expected`
+ """
+ print("assert_cached", check.add_cached)
+- value = yield from check.add_cached
++ value = await check.add_cached
+ self.assertEqual(value, expected)
+ self.assertEqual(check.cached_total, expected)
+
+ @unittest_run_loop
+- @asyncio.coroutine
+- def test_cached_property(self):
++ async def test_cached_property(self):
+ Check = CheckFactory(self.cached_property_factory)
+ check = Check()
+
+ # The control shows that we can continue to add 1
+- yield from self.assert_control(check, 1)
+- yield from self.assert_control(check, 2)
++ await self.assert_control(check, 1)
++ await self.assert_control(check, 2)
+
+ # The cached version demonstrates how nothing is added after the first
+- yield from self.assert_cached(check, 1)
+- yield from self.assert_cached(check, 1)
++ await self.assert_cached(check, 1)
++ await self.assert_cached(check, 1)
+
+ # The cache does not expire
+ with freeze_time("9999-01-01"):
+- yield from self.assert_cached(check, 1)
++ await self.assert_cached(check, 1)
+
+ # Typically descriptors return themselves if accessed though the class
+ # rather than through an instance.
+ self.assertTrue(isinstance(Check.add_cached, self.cached_property_factory))
+
+ @unittest_run_loop
+- @asyncio.coroutine
+- def test_reset_cached_property(self):
++ async def test_reset_cached_property(self):
+ Check = CheckFactory(self.cached_property_factory)
+ check = Check()
+
+ # Run standard cache assertion
+- yield from self.assert_cached(check, 1)
+- yield from self.assert_cached(check, 1)
++ await self.assert_cached(check, 1)
++ await self.assert_cached(check, 1)
+
+ # Clear the cache
+ del check.add_cached
+
+ # Value is cached again after the next access
+- yield from self.assert_cached(check, 2)
+- yield from self.assert_cached(check, 2)
++ await self.assert_cached(check, 2)
++ await self.assert_cached(check, 2)
+
+ @unittest_run_loop
+- @asyncio.coroutine
+- def test_none_cached_property(self):
++ async def test_none_cached_property(self):
+ class Check(object):
+ def __init__(self):
+ self.cached_total = None
+
+ @self.cached_property_factory
+- @asyncio.coroutine
+- def add_cached(self):
++ async def add_cached(self):
+ return self.cached_total
+
+- yield from self.assert_cached(Check(), None)
++ await self.assert_cached(Check(), None)
+--
+2.49.0
+
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 46efd10292..01dfc0799f 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -11700,7 +11700,9 @@ (define-public python-property-cached
(method url-fetch)
(uri (pypi-uri "property-cached" version ".zip"))
(sha256
- (base32 "0wxv5sdx1p7ils36j6j6hfscz8v2vzbq212i8y8r0lrnxpqlx71y"))))
+ (base32 "0wxv5sdx1p7ils36j6j6hfscz8v2vzbq212i8y8r0lrnxpqlx71y"))
+ (patches
+ (search-patches "python-property-cached-asyncio-3_11.patch"))))
(build-system pyproject-build-system)
(arguments
(list
--
2.49.0
guix-patches <at> gnu.org:bug#77541; Package guix-patches.
(Fri, 04 Apr 2025 19:18:08 GMT) Full text and rfc822 format available.Message #43 received at 77541 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77541 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 13/38] gnu: python-serpent: Update to 1.41. Date: Fri, 4 Apr 2025 21:16:45 +0200
* gnu/packages/python-xyz.scm (python-serpent): Update to 1.41.
[build-system]: Switch to pyproject-build-system.
[native-inputs]: Add python-setuptools, python-wheel.
---
gnu/packages/python-xyz.scm | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 8100b030c5..f36e5a3141 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -4368,16 +4368,16 @@ (define-public python-semantic-version
(define-public python-serpent
(package
(name "python-serpent")
- (version "1.28")
+ (version "1.41")
(source
(origin
(method url-fetch)
(uri (pypi-uri "serpent" version))
(sha256
- (base32 "1arnckykpkvv2qrp49l1k7q5mr5pisswl0rvdx98x8wsl1n361pk"))))
- (build-system python-build-system)
+ (base32 "15bhxpihxvbphsvp4wyh2kwfz7xasmki9zwcsj3l6r66wdgh61q4"))))
+ (build-system pyproject-build-system)
(native-inputs
- (list python-attrs python-pytz))
+ (list python-attrs python-pytz python-setuptools python-wheel))
(home-page "https://github.com/irmen/Serpent")
(synopsis "Serializer for literal Python expressions")
(description
--
2.49.0
guix-patches <at> gnu.org:bug#77541; Package guix-patches.
(Fri, 04 Apr 2025 19:18:09 GMT) Full text and rfc822 format available.Message #46 received at 77541 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77541 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 12/38] gnu: python-attr: Update to 0.3.2. Date: Fri, 4 Apr 2025 21:16:44 +0200
* gnu/packages/python-xyz.scm (python-attr): Update to 0.3.2.
---
gnu/packages/python-xyz.scm | 9 +++++----
1 file changed, 5 insertions(+), 4 deletions(-)
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 01dfc0799f..8100b030c5 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -31373,15 +31373,16 @@ (define-public python-doctest-ignore-unicode
(define-public python-attr
(package
(name "python-attr")
- (version "0.3.1")
+ (version "0.3.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "attr" version))
(sha256
- (base32
- "0pbpskvxp5hzdvcaf766ljwpckshir8sf7z6jqji6zyib20594ch"))))
- (build-system python-build-system)
+ (base32 "1x2627x0n2rxx8wib4cksbjjnncff8finq97k37dq70qd2kvrvhw"))))
+ (build-system pyproject-build-system)
+ (native-inputs
+ (list python-setuptools python-wheel))
(home-page "https://github.com/denis-ryzhkov/attr")
(synopsis "Decorator for attributes of target function or class")
(description "Simple decorator to set attributes of target function or
--
2.49.0
guix-patches <at> gnu.org:bug#77541; Package guix-patches.
(Fri, 04 Apr 2025 19:18:09 GMT) Full text and rfc822 format available.Message #49 received at 77541 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77541 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 14/38] gnu: python-pyro4: Update to 4.82. Date: Fri, 4 Apr 2025 21:16:46 +0200
* gnu/packages/python-xyz.scm (python-pyro4): Update to 4.82.
[build-system]: Switch to pyproject-build-system.
[arguments]{tests?}: Remove to enable tests.
{test-flags}: Skip missing tests.
{phases}: Add 'check phase replacement.
[native-inputs]: Add python-setuptools, python-wheel.
---
gnu/packages/python-xyz.scm | 45 ++++++++++++++++++++++++++++++++-----
1 file changed, 40 insertions(+), 5 deletions(-)
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index f36e5a3141..f262ccefcb 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -28438,18 +28438,53 @@ (define-public python-semver
(define-public python-pyro4
(package
(name "python-pyro4")
- (version "4.77")
+ (version "4.82")
(source
(origin
(method url-fetch)
(uri (pypi-uri "Pyro4" version))
(sha256
- (base32 "0gsjg869y4gpy265s1gj1f2qy6jn5iz8r2bwwnq78r1r5yi15zib"))))
- (build-system python-build-system)
+ (base32 "1yr1rv2afmq55wb14sx9qplzkqw7fya9rprsqdyxfbg90h45n7si"))))
+ (build-system pyproject-build-system)
(arguments
- '(#:tests? #f)) ;FIXME: Some tests require network access.
+ (list #:test-flags
+ #~(list "-k"
+ (string-join
+ ;; Those tests require network.
+ (list "testBCstart"
+ "testAutoClean"
+ "testDaemonPyroObj"
+ "testLookupAndRegister"
+ "testLookupInvalidHmac"
+ "testLookupUnixsockParsing"
+ "testMulti"
+ "testRefuseDottedNames"
+ "testResolve"
+ "testBCLookup0000"
+ "testPyroname"
+ "testResolveAsymmetricHmacUsage"
+ "testResolveWrongHmac"
+ "testStartNSfunc"
+ "testCustomDictClass"
+ "testDictClassFail"
+ "testBroadcast"
+ "testGetIP"
+ ;; XXX: Unclear why this test fails.
+ "testCustomClassFail")
+ " and not "))
+ #:phases
+ #~(modify-phases %standard-phases
+ (replace 'check
+ (lambda* (#:key tests? test-flags #:allow-other-keys)
+ (if tests?
+ (apply invoke "python" "-m" "unittest" test-flags)
+ (format #t "test suite not run.~%")))))))
(native-inputs
- (list python-cloudpickle python-dill python-msgpack))
+ (list python-cloudpickle
+ python-dill
+ python-msgpack
+ python-setuptools
+ python-wheel))
(propagated-inputs
(list python-serpent))
(home-page "https://pyro4.readthedocs.io")
--
2.49.0
guix-patches <at> gnu.org:bug#77541; Package guix-patches.
(Fri, 04 Apr 2025 19:18:10 GMT) Full text and rfc822 format available.Message #52 received at 77541 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77541 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 15/38] gnu: python-lcapy: Add missing native-inputs. Date: Fri, 4 Apr 2025 21:16:47 +0200
* gnu/packages/engineering.scm (python-lcapy)[native-inputs]: Add
python-setuptools, python-wheel.
---
gnu/packages/engineering.scm | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm
index ff268a1e08..e4aa046d3d 100644
--- a/gnu/packages/engineering.scm
+++ b/gnu/packages/engineering.scm
@@ -3138,7 +3138,9 @@ (define-public python-lcapy
python-scipy
python-sympy
python-wheel))
- (native-inputs (list python-pytest))
+ (native-inputs (list python-pytest
+ python-setuptools
+ python-wheel))
(home-page "https://github.com/mph-/lcapy")
(synopsis "Symbolic linear circuit analysis")
(description "Lcapy is a Python package for linear circuit analysis. It
--
2.49.0
guix-patches <at> gnu.org:bug#77541; Package guix-patches.
(Fri, 04 Apr 2025 19:18:10 GMT) Full text and rfc822 format available.Message #55 received at 77541 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77541 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 16/38] gnu: python-linear-operator: Update to 0.6. Date: Fri, 4 Apr 2025 21:16:48 +0200
* gnu/packages/machine-learning.scm (python-linear-operator): Update
to 0.6.
[propagated-inputs]: Remove python-typeguard. Add python-mpmath.
[native-inputs]: Remove python-flake8, python-flake8-print,
python-twine. Add python-typeguard, python-wheel.
---
gnu/packages/machine-learning.scm | 15 +++++++--------
1 file changed, 7 insertions(+), 8 deletions(-)
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index fb1d5d2eed..615768c492 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -6098,24 +6098,23 @@ (define-public python-pyro-ppl
(define-public python-linear-operator
(package
(name "python-linear-operator")
- (version "0.5.2")
+ (version "0.6")
(source (origin
(method url-fetch)
(uri (pypi-uri "linear_operator" version))
(sha256
(base32
- "03drb4hn9nn8jrqd9vbalihhahgpdm956hbs05bix7svradhknaw"))))
+ "0m56f3zrm8xh1bpwh4g7jfc79rf4j94g6zmz663b58pig4w6dqm9"))))
(build-system pyproject-build-system)
(propagated-inputs (list python-jaxtyping
+ python-mpmath
python-pytorch
- python-scipy
- python-typeguard))
- (native-inputs (list python-flake8
- python-flake8-print
- python-pytest
+ python-scipy))
+ (native-inputs (list python-pytest
python-setuptools
python-setuptools-scm
- python-twine))
+ python-typeguard
+ python-wheel))
(home-page "https://github.com/cornellius-gp/linear_operator/")
(synopsis "Linear operator implementation")
(description "LinearOperator is a PyTorch package for abstracting away the
--
2.49.0
guix-patches <at> gnu.org:bug#77541; Package guix-patches.
(Fri, 04 Apr 2025 19:18:11 GMT) Full text and rfc822 format available.Message #58 received at 77541 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77541 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 18/38] gnu: python-botorch: Add missing native-inputs. Date: Fri, 4 Apr 2025 21:16:50 +0200
* gnu/packages/machine-learning.scm (python-botorch)[native-inputs]:
Add python-setuptools, python-wheel.
---
gnu/packages/machine-learning.scm | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index dcebf89376..e5dd247c7d 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -6184,7 +6184,9 @@ (define-public python-botorch
python-scipy))
(native-inputs (list python-pytest
python-pytest-cov
- python-setuptools-scm))
+ python-setuptools
+ python-setuptools-scm
+ python-wheel))
(home-page "https://botorch.org")
(synopsis "Bayesian Optimization in PyTorch")
(description
--
2.49.0
guix-patches <at> gnu.org:bug#77541; Package guix-patches.
(Fri, 04 Apr 2025 19:18:11 GMT) Full text and rfc822 format available.Message #61 received at 77541 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77541 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 19/38] gnu: python-gpytorch: Update to 1.14. Date: Fri, 4 Apr 2025 21:16:51 +0200
* gnu/packages/machine-learning.scm (python-gpytorch): Update to 1.14.
[arguments]{test-flags}: Ignore additional failing test.
[propagated-inputs]: Add python-jaxtyping.
[native-inputs]: Add python-setuptools, python-wheel.
---
gnu/packages/machine-learning.scm | 19 +++++++++++++------
1 file changed, 13 insertions(+), 6 deletions(-)
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index e5dd247c7d..4bf7442e09 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -6124,27 +6124,34 @@ (define-public python-linear-operator
(define-public python-gpytorch
(package
(name "python-gpytorch")
- (version "1.12")
+ (version "1.14")
(source (origin
(method url-fetch)
(uri (pypi-uri "gpytorch" version))
(sha256
(base32
- "1pwsccll1hrgkifdmlxzcn6cvnwvyq2cimqzbfgihr13yw51cb6w"))))
+ "13cs6dx8qa5j4ygji9w5xbmaqc68ihqyzz33fyyf9qa6d8gc2b03"))))
(build-system pyproject-build-system)
(arguments
(list #:test-flags
- ;; test_deprecated_methods fails with an AssertionError.
- #~(list "-k" (string-append "not test_deprecated_methods")
+ #~(list "-k" (string-append
+ ;; test_deprecated_methods fails with an AssertionError.
+ "not test_deprecated_methods"
+ ;; This test is flaky: Expects gradients of 0 exactly,
+ ;; can get negligible ones (e-10 to e-16).
+ " and not test_optimization_optimal_error")
;; Ignore lenghty tests of little relevance.
"--ignore=test/examples/")))
- (propagated-inputs (list python-linear-operator
+ (propagated-inputs (list python-jaxtyping
+ python-linear-operator
python-mpmath
python-scikit-learn
python-scipy))
(native-inputs (list python-nbval
python-pytest
- python-setuptools))
+ python-setuptools
+ python-setuptools-scm
+ python-wheel))
(home-page "https://gpytorch.ai")
(synopsis "Implementation of Gaussian Processes in PyTorch")
(description
--
2.49.0
guix-patches <at> gnu.org:bug#77541; Package guix-patches.
(Fri, 04 Apr 2025 19:18:12 GMT) Full text and rfc822 format available.Message #64 received at 77541 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77541 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 21/38] gnu: python-pgmpy: Update to 1.0.0. Date: Fri, 4 Apr 2025 21:16:53 +0200
* gnu/packages/statistics.scm (python-pgmpy): Update to 1.0.0.
[arguments]{test-flags}: Ignore failing tests.
[native-inputs]: Add python-pyro-ppl, python-setuptools, python-wheel,
python-xgboost.
---
gnu/packages/statistics.scm | 16 +++++++++++++---
1 file changed, 13 insertions(+), 3 deletions(-)
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 40991caab5..f883786f81 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -8312,7 +8312,7 @@ (define-public ruby-enumerable-statistics
(define-public python-pgmpy
(package
(name "python-pgmpy")
- (version "0.1.24")
+ (version "1.0.0")
(source
(origin
(method git-fetch) ;pypi package does not include test data
@@ -8322,8 +8322,14 @@ (define-public python-pgmpy
(file-name (git-file-name name version))
(sha256
(base32
- "0fvzh6v0yhgdryczamvzhfy2ymywkh0ssx4rl47xnfvi43hnij90"))))
+ "1hg6wrg3jcac71zn4gknni1wrn38wa86ka3sgp2bndz59mx6sr2s"))))
(build-system pyproject-build-system)
+ (arguments
+ (list #:test-flags
+ #~(list "-k" (string-append
+ "not test_pillai"
+ " and not test_estimate_with_cache_no_llm_calls"
+ " and not test_estimate_with_orientations"))))
(propagated-inputs (list python-daft
python-joblib
python-networkx
@@ -8337,7 +8343,11 @@ (define-public python-pgmpy
python-statsmodels
python-tqdm))
(native-inputs (list python-mock
- python-pytest))
+ python-pyro-ppl
+ python-pytest
+ python-setuptools
+ python-wheel
+ python-xgboost))
(home-page "https://github.com/pgmpy/pgmpy")
(synopsis "Probabilistic Graphical Models library")
(description "This package provides a library for Probabilistic
--
2.49.0
guix-patches <at> gnu.org:bug#77541; Package guix-patches.
(Fri, 04 Apr 2025 19:19:02 GMT) Full text and rfc822 format available.Message #67 received at 77541 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77541 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 17/38] gnu: gpytorch: Remove uneeded inputs. Date: Fri, 4 Apr 2025 21:16:49 +0200
* gnu/packages/machine-learning.scm (gpytorch): Remove uneeded inputs.
[arguments]{test-flags}: Ignore costly examples tests.
[native-inputs]: Remove python-coverage, python-flake8,
python-flake8-print, python-twine.
---
gnu/packages/machine-learning.scm | 12 +++++-------
1 file changed, 5 insertions(+), 7 deletions(-)
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 615768c492..dcebf89376 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -6135,18 +6135,16 @@ (define-public python-gpytorch
(arguments
(list #:test-flags
;; test_deprecated_methods fails with an AssertionError.
- #~(list "-k" (string-append "not test_deprecated_methods"))))
+ #~(list "-k" (string-append "not test_deprecated_methods")
+ ;; Ignore lenghty tests of little relevance.
+ "--ignore=test/examples/")))
(propagated-inputs (list python-linear-operator
python-mpmath
python-scikit-learn
python-scipy))
- (native-inputs (list python-coverage
- python-flake8
- python-flake8-print
- python-nbval
+ (native-inputs (list python-nbval
python-pytest
- python-setuptools
- python-twine))
+ python-setuptools))
(home-page "https://gpytorch.ai")
(synopsis "Implementation of Gaussian Processes in PyTorch")
(description
--
2.49.0
guix-patches <at> gnu.org:bug#77541; Package guix-patches.
(Fri, 04 Apr 2025 19:19:02 GMT) Full text and rfc822 format available.Message #70 received at 77541 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77541 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 24/38] gnu: python-pysnptools: Fix build and enable tests. Date: Fri, 4 Apr 2025 21:16:56 +0200
* gnu/packages/bioinformatics.scm (python-pysnptools): Fix build and enable
tests.
[arguments]{test-flags}: Ignore failing tests.
{phases}: Add 'patch-data-path and 'loosen-requirements phases.
(pysnptools-examples-files): Add origin.
(bgen-sample-files): Add origin.
---
gnu/packages/bioinformatics.scm | 80 ++++++++++++++++++++++++++++++---
1 file changed, 75 insertions(+), 5 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c5fe295f6c..3f612fd701 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3715,6 +3715,49 @@ (define-public python-pygam
familiar to anyone with experience of scikit-learn or scipy.")
(license license:asl2.0)))
+(define bgen-sample-files
+ (let* ((name "bgen-sample-files")
+ (commit "7b1bc74f58b326ca19606fa5f3c6093d48367993")
+ (revision "0")
+ (version (git-version "0.0.0" revision commit)))
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/fastlmm/bgen-sample-files")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1b8jkscccyspfr3y1b66xvwnljcha08r2i24v9d6hcm5zii0l54w")))))
+
+(define pynsptools-examples-files
+ (let* ((name "pysnptools-examples-files")
+ ;; taken from pysnptools/util/pysnptools.hashdown.json
+ (commit "ed14e050b2b75e7f4ddb73d512fbe928bbdb2b85")
+ (revision "0")
+ (version (git-version "0.0.0" revision commit)))
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/fastlmm/PySnpTools")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0hznpj15kx2sla16wlmcqz21n2vi2qb1493v30vz75hnm1m4iwm1"))
+ (modules '((guix build utils)
+ (ice-9 ftw)))
+ (snippet
+ #~(begin
+ ;; Delete everything except for examples directory:
+ (define (delete-except exceptions)
+ (lambda (file)
+ (unless (member file `("." ".." ,@exceptions))
+ (delete-file-recursively file))))
+ (for-each (delete-except '("pysnptools" "tests")) (scandir "."))
+ (with-directory-excursion "pysnptools"
+ (for-each (delete-except '("examples")) (scandir ".")))
+ (with-directory-excursion "tests"
+ (for-each (delete-except '("datasets")) (scandir "."))))))))
+
(define-public python-pysnptools
(package
(name "python-pysnptools")
@@ -3724,12 +3767,39 @@ (define-public python-pysnptools
(method url-fetch)
(uri (pypi-uri "pysnptools" version))
(sha256
- (base32
- "1babnyky5fk93as1ybdvpz9x3x5099gkgscxflngzfswin23mspk"))))
+ (base32 "1babnyky5fk93as1ybdvpz9x3x5099gkgscxflngzfswin23mspk"))))
(build-system pyproject-build-system)
- ;; Tests require test data from python-bed-reader, which fetches data with
- ;; python-pooch.
- (arguments (list #:tests? #f))
+ (arguments
+ (list
+ #:test-flags
+ #~(list
+ ;; These tests require the bgen feature and an additional input.
+ "--ignore" "pysnptools/distreader/bgen.py"
+ "--ignore" "pysnptools/distreader/test_bgen2.py"
+ "--ignore" "pysnptools/distreader/distreader.py"
+ "-k" "not pysnptools.distreader.distdata.DistData.val \
+and not pysnptools.distreader.disthdf5.DistHdf5.write \
+and not pysnptools.distreader.distmemmap.DistMemMap.write"
+ ;; These tests require network connection.
+ "--ignore" "pysnptools/util/_example_file.py"
+ "--ignore" "pysnptools/util/filecache/hashdown.py")
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'patch-data-path
+ (lambda _
+ (substitute* "pysnptools/util/pysnptools.hashdown.json"
+ (("https://github\\.com/fastlmm/PySnpTools/\
+raw/ed14e050b2b75e7f4ddb73d512fbe928bbdb2b85")
+ (string-append "file://" #+pynsptools-examples-files)))
+ (substitute* "pysnptools/util/bgen.hashdown.json"
+ (("https://raw\\.githubusercontent\\.com\
+/fastlmm/bgen-sample-files/7b1bc74f58b326ca19606fa5f3c6093d48367993")
+ (string-append "file://" #+bgen-sample-files)))))
+ (add-after 'unpack 'loosen-requirements
+ (lambda _
+ (substitute* "pyproject.toml"
+ (("(h5py|psutil|wheel)>=[0-9.]*" all target)
+ target)))))))
(propagated-inputs
(list python-bed-reader
python-cloudpickle
--
2.49.0
guix-patches <at> gnu.org:bug#77541; Package guix-patches.
(Fri, 04 Apr 2025 19:19:02 GMT) Full text and rfc822 format available.Message #73 received at 77541 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77541 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 25/38] gnu: Add python-poetry-core-next. Date: Fri, 4 Apr 2025 21:16:57 +0200
* gnu/packages/python-build.scm (python-poetry-core-next): New variable.
---
gnu/packages/python-build.scm | 10 ++++++++++
1 file changed, 10 insertions(+)
diff --git a/gnu/packages/python-build.scm b/gnu/packages/python-build.scm
index 6bea44fee6..9ac325094d 100644
--- a/gnu/packages/python-build.scm
+++ b/gnu/packages/python-build.scm
@@ -571,6 +571,16 @@ (define-public python-poetry-core
compatible build front-ends to build Poetry managed projects.")
(license license:expat)))
+(define-public python-poetry-core-next
+ (package/inherit python-poetry-core
+ (version "2.1.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "poetry_core" version))
+ (sha256
+ (base32 "015a0802radb2x5wsbywm4fggv4s1srh8zyml5v58xgrxg8bpnzr"))))))
+
;;; This package exists to bootstrap python-tomli.
(define-public python-flit-core-bootstrap
(package
--
2.49.0
guix-patches <at> gnu.org:bug#77541; Package guix-patches.
(Fri, 04 Apr 2025 19:19:03 GMT) Full text and rfc822 format available.Message #76 received at 77541 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77541 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 22/38] gnu: python-qasync: Ignore failing test. Date: Fri, 4 Apr 2025 21:16:54 +0200
* gnu/packages/python-xyz.scm (python-qasync)[arguments]{test-flags}:
Ignore failing tests.
---
gnu/packages/python-xyz.scm | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index f262ccefcb..b526c6161a 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -21749,7 +21749,10 @@ (define-public python-qasync
(base32 "0j6ksfnq9qfjdfppbkdz7jh6w0gnslwnckhafmlgim29b25g0z51"))))
(build-system pyproject-build-system)
(arguments
- (list #:phases
+ (list #:test-flags
+ ;; XXX: Added with python <at> 3.11, not fixed upstream.
+ #~(list "-k" "not test_regression_bug13")
+ #:phases
#~(modify-phases %standard-phases
(add-before 'check 'set-qpa
(lambda _
--
2.49.0
guix-patches <at> gnu.org:bug#77541; Package guix-patches.
(Fri, 04 Apr 2025 19:19:04 GMT) Full text and rfc822 format available.Message #79 received at 77541 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77541 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 26/38] gnu: python-duniterpy: Update to 1.2.1. Date: Fri, 4 Apr 2025 21:16:58 +0200
* gnu/packages/finance.scm (python-duniterpy): Update to 1.2.1.
[source]: Switch to git-fetch to get tests.
[arguments]: Remove field.
[native-inputs]: Replace python-poetry-core by
python-poetry-core-next. Add python-pytest.
[propagated-inputs]: Remove python-attrs.
---
gnu/packages/finance.scm | 40 ++++++++++------------------------------
1 file changed, 10 insertions(+), 30 deletions(-)
diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm
index 69cee44386..680ebe467c 100644
--- a/gnu/packages/finance.scm
+++ b/gnu/packages/finance.scm
@@ -1412,42 +1412,22 @@ (define-public python-stdnum
(define-public python-duniterpy
(package
(name "python-duniterpy")
- (version "1.1.1")
+ (version "1.2.1")
(source
(origin
- (method url-fetch)
- (uri (pypi-uri "duniterpy" version))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://git.duniter.org/clients/python/duniterpy")
+ (commit version)))
+ (file-name (git-file-name name version))
(sha256
- (base32 "0h0fsawsrjd50lb1bkysb21ph39qlhmiymd3r5vs695qxvbwaqaa"))))
+ (base32 "1ysh9b5lzg053hv4iw3zbn7hid05qssiwmrl8sir8qlk958r8x60"))))
(build-system pyproject-build-system)
- (arguments
- ;; FIXME: Tests fail with: "TypeError: block_uid() missing 1 required
- ;; positional argument: 'value'".
- `(#:tests? #f
- #:phases (modify-phases %standard-phases
- (add-after 'unpack 'loosen-requirements
- (lambda _
- (substitute* "pyproject.toml"
- (("mnemonic = \"\\^0\\.19")
- "mnemonic = \">=0.19")
- (("jsonschema = \"\\^3\\.2")
- "jsonschema = \">=3.2"))))
- (add-after 'unpack 'adjust-for-new-libnacl
- (lambda _
- ;; Mimic upstream commit ad8f6a26e9e7067; remove
- ;; for newer versions of duniterpy.
- (substitute* "pyproject.toml"
- (("libnacl = \"1\\.8")
- "libnacl = \">=1.9"))
- (substitute* "duniterpy/key/ascii_armor.py"
- (("from libnacl\\.version import version as libnacl_version")
- "import importlib.metadata
-libnacl_version = importlib.metadata.version('libnacl')")))))))
(native-inputs
- (list python-poetry-core))
+ (list python-poetry-core-next
+ python-pytest))
(propagated-inputs
- (list python-attrs
- python-base58
+ (list python-base58
python-graphql-core
python-jsonschema
python-libnacl
--
2.49.0
guix-patches <at> gnu.org:bug#77541; Package guix-patches.
(Fri, 04 Apr 2025 19:19:04 GMT) Full text and rfc822 format available.Message #82 received at 77541 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77541 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 27/38] gnu: python-pgpy: Fix tests. Date: Fri, 4 Apr 2025 21:16:59 +0200
* gnu/packages/python-crypto.scm (python-pgpy): Fix tests.
[build-system]: Switch to pyproject.
[arguments]{phases}: Remove argument.
{test-flags}: Ignore failing tests.
[native-inputs]: Add python-setuptools.
---
gnu/packages/python-crypto.scm | 15 ++++++---------
1 file changed, 6 insertions(+), 9 deletions(-)
diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm
index 13ad37bca8..fc57afb862 100644
--- a/gnu/packages/python-crypto.scm
+++ b/gnu/packages/python-crypto.scm
@@ -1634,17 +1634,14 @@ (define-public python-pgpy
(uri (pypi-uri "PGPy" version))
(sha256
(base32 "10w3h934fi1ijx72ppn67a50yhkf8n1db6xx02gk2fjc7wsjx717"))))
- (build-system python-build-system)
+ (build-system pyproject-build-system)
(arguments
- `(#:phases
- (modify-phases %standard-phases
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- (invoke "pytest")))))))
+ (list #:test-flags
+ ;; All broken tests are in this file.
+ ;; They fail with ValueError: key_size must be at least 1024-bits.
+ #~(list "--ignore" "tests/test_10_exceptions.py")))
(native-inputs
- (list python-pytest
- python-wheel))
+ (list python-pytest python-setuptools python-wheel))
(propagated-inputs (list python-cryptography python-pyasn1))
(home-page "https://github.com/SecurityInnovation/PGPy")
(synopsis "Python implementation of OpenPGP")
--
2.49.0
guix-patches <at> gnu.org:bug#77541; Package guix-patches.
(Fri, 04 Apr 2025 19:19:05 GMT) Full text and rfc822 format available.Message #85 received at 77541 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77541 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 28/38] gnu: python-furl: Update to 2.1.4. Date: Fri, 4 Apr 2025 21:17:00 +0200
* gnu/packages/python-web.scm (python-furl): Update to 2.1.4.
[build-system]: Swtich to pyproject.
[arguments]{test-flags}: Ignore failing tests.
[propagated-inputs]: Sort.
[native-inputs]: Add python-pytest, python-setuptools, python-wheel.
---
gnu/packages/python-web.scm | 16 ++++++++++------
1 file changed, 10 insertions(+), 6 deletions(-)
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index bf379c3699..579386e5ab 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -1941,19 +1941,23 @@ (define-public python-falcon-cors
(define-public python-furl
(package
(name "python-furl")
- (version "2.1.3")
+ (version "2.1.4")
(source
(origin
(method url-fetch)
(uri (pypi-uri "furl" version))
(sha256
- (base32
- "0knc76pm8pzigs3bpx9fccfsfxqrgblqphar46hq9i364vz8hqas"))))
- (build-system python-build-system)
+ (base32 "05b058xisv8kghvcpaxvssml2jjkh1cmzyrrjwk2kjb62985fxl7"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list #:test-flags
+ #~(list "-k" (string-append "not test_hosts"
+ " and not test_netloc"
+ " and not test_odd_urls"))))
(propagated-inputs
- (list python-six python-orderedmultidict))
+ (list python-orderedmultidict python-six))
(native-inputs
- (list python-flake8))
+ (list python-flake8 python-pytest python-setuptools python-wheel))
(home-page "https://github.com/gruns/furl")
(synopsis "URL manipulation in Python")
(description "Furl provides an easy-to-use alternative to the
--
2.49.0
guix-patches <at> gnu.org:bug#77541; Package guix-patches.
(Fri, 04 Apr 2025 19:19:05 GMT) Full text and rfc822 format available.Message #88 received at 77541 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77541 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 29/38] gnu: python-rq: Update to 2.3.1. Date: Fri, 4 Apr 2025 21:17:01 +0200
* gnu/packages/databases.scm (python-rq): Update to 2.3.1.
[build-system]: Switch to pyproject.
[arguments]{phases}: Delete 'check phase replacement. Improve style.
[native-inputs]: Add python-hatchling.
---
gnu/packages/databases.scm | 30 +++++++++++++-----------------
1 file changed, 13 insertions(+), 17 deletions(-)
diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 097617e094..4ecf237115 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -4611,7 +4611,7 @@ (define-public python-aioredis
(define-public python-rq
(package
(name "python-rq")
- (version "1.11.1")
+ (version "2.3.1")
(source
(origin
(method git-fetch)
@@ -4620,24 +4620,20 @@ (define-public python-rq
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "0dnjm2s036l4j4ypq0h903vh132dp2wiwjrn8jicz1nw829dqpzf"))))
- (build-system python-build-system)
+ (base32 "1w9aqvbvh1mfpgng0mdcskxl5y3ybcqqai5dnwgvg18am0xxhya6"))))
+ (build-system pyproject-build-system)
(arguments
- '(#:phases (modify-phases %standard-phases
- (add-before 'check 'start-redis
- (lambda _
- (invoke "redis-server" "--daemonize" "yes")))
- (replace 'check
- (lambda* (#:key outputs #:allow-other-keys)
- (let ((out (assoc-ref outputs "out")))
- ;; Drop test that needs the SDK for Sentry.io.
- (delete-file "tests/test_sentry.py")
- ;; Ensure 'rq' and 'rqworker' ends up on PATH.
- (setenv "PATH" (string-append out "/bin:"
- (getenv "PATH")))
- (invoke "pytest" "-vv")))))))
+ (list
+ #:phases #~(modify-phases %standard-phases
+ (add-before 'check 'start-redis
+ (lambda _
+ (invoke "redis-server" "--daemonize" "yes"))))))
(native-inputs
- (list python-mock python-psutil python-pytest redis))
+ (list python-hatchling
+ python-mock
+ python-psutil
+ python-pytest
+ redis))
(propagated-inputs
(list python-click python-redis))
(home-page "https://python-rq.org/")
--
2.49.0
guix-patches <at> gnu.org:bug#77541; Package guix-patches.
(Fri, 04 Apr 2025 19:19:06 GMT) Full text and rfc822 format available.Message #91 received at 77541 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77541 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 23/38] gnu: python-bed-reader: Fix build and enable tests. Date: Fri, 4 Apr 2025 21:16:55 +0200
* 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.
---
gnu/local.mk | 1 +
gnu/packages/bioinformatics.scm | 195 ++++++++++++------
.../python-bed-reader-use-store-samples.patch | 147 +++++++++++++
3 files changed, 284 insertions(+), 59 deletions(-)
create mode 100644 gnu/packages/patches/python-bed-reader-use-store-samples.patch
diff --git a/gnu/local.mk b/gnu/local.mk
index 1bf8f8deba..6c2466114d 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -2008,6 +2008,7 @@ 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 \
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4dbedc09f9..c5fe295f6c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2167,6 +2167,20 @@ (define-public python-bcbio-gff/biopython-1.73
(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")
@@ -2176,80 +2190,124 @@ (define-public python-bed-reader
(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']
+
+[tool.setuptools.packages.find]
+where = [\".\"]
+exclude = [\"src\", \"docs\", \"tests\", \"Cargo.toml\"]
")))
- (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)))))
+ ("samples = [\"pooch>=1.5.0\"]"
+ (and (format out "samples = []~%")
+ (loop)))
+ ("[project]"
+ (and (format out "\
+[project]
+version = ~s
+" #$version)
+ (loop)))
+ (line
+ (and (format out "~a~%" line)
+ (loop)))))))))))
(add-after 'prepare-python-module 'enable-bytecode-determinism
(assoc-ref py:%standard-phases 'enable-bytecode-determinism))
(add-after 'enable-bytecode-determinism 'build-python-module
@@ -2261,16 +2319,35 @@ (define-public python-bed-reader
(let ((site (string-append #$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
@@ -2278,7 +2355,7 @@ (define-public python-bed-reader
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
diff --git a/gnu/packages/patches/python-bed-reader-use-store-samples.patch b/gnu/packages/patches/python-bed-reader-use-store-samples.patch
new file mode 100644
index 0000000000..813f155225
--- /dev/null
+++ b/gnu/packages/patches/python-bed-reader-use-store-samples.patch
@@ -0,0 +1,147 @@
+From 7e6bcdfeed54500ca533d2f0eb12078248c43c77 Mon Sep 17 00:00:00 2001
+Message-ID: <7e6bcdfeed54500ca533d2f0eb12078248c43c77.1743682382.git.ngraves <at> ngraves.fr>
+From: Nicolas Graves <ngraves <at> 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
+
--
2.49.0
guix-patches <at> gnu.org:bug#77541; Package guix-patches.
(Fri, 04 Apr 2025 19:19:06 GMT) Full text and rfc822 format available.Message #94 received at 77541 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77541 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 30/38] gnu: python-crontab: Update to 3.2.0. Date: Fri, 4 Apr 2025 21:17:02 +0200
* gnu/packages/python-xyz.scm (python-crontab): Update to 3.2.0.
[build-system]: Switch to pyproject.
[arguments]{test-flags}: Ignore test.
{phases}: Remove phase 'disable-failing-tests. Add phase
default-to-mcron.
[inputs]: Add mcron.
[native-inputs]: Add python-pytest, python-setuptools, python-wheel.
---
gnu/packages/python-xyz.scm | 36 +++++++++++++++++-------------------
1 file changed, 17 insertions(+), 19 deletions(-)
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index b526c6161a..e63e41ba18 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -231,6 +231,7 @@ (define-module (gnu packages python-xyz)
#:use-module (gnu packages gsasl)
#:use-module (gnu packages gstreamer)
#:use-module (gnu packages gtk)
+ #:use-module (gnu packages guile-xyz)
#:use-module (gnu packages haskell-xyz)
#:use-module (gnu packages icu4c)
#:use-module (gnu packages image)
@@ -31789,32 +31790,29 @@ (define-public python-croniter
(define-public python-crontab
(package
(name "python-crontab")
- (version "3.0.0")
+ (version "3.2.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri name version))
(sha256
- (base32 "0yd3vdhl7z8lxa30czsry65srha51ppdcwnhjgxx9pwx0djp9yvr"))))
- (build-system python-build-system)
+ (base32 "0sy3qlki43n6qmhzzzyya4wcs50mcp3mg1ddn9h39plsscfps1j0"))))
+ (build-system pyproject-build-system)
(arguments
- (list
- #:phases
- #~(modify-phases %standard-phases
- (add-before 'check 'disable-failing-tests
- (lambda _
- (substitute* '("tests/test_compatibility.py"
- "tests/test_frequency.py")
- (("test_07_non_posix_shell")
- "__off_test_07_non_posix_shell")
- ;; Fails on leap years
- (("test_19_frequency_at_month")
- "__off_test_19_frequency_at_month")
- ;; AssertionError: 48 != 24
- (("test_20_frequency_at_year")
- "__off_test_20_frequency_at_year")))))))
+ (list #:test-flags
+ ;; This test is made for Windows.
+ #~(list "-k" "not test_07_non_posix_shell")
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'defaults-to-mcron
+ (lambda* (#:key inputs #:allow-other-keys)
+ (substitute* "crontab.py"
+ (("/usr/bin/crontab")
+ (search-input-file inputs "bin/crontab"))))))))
(inputs
- (list python-dateutil))
+ (list mcron python-dateutil))
+ (native-inputs
+ (list python-pytest python-setuptools python-wheel))
(home-page "https://gitlab.com/doctormo/python-crontab/")
(synopsis "Module for reading and writing crontab files")
(description "This Python module can read, write crontab files, and
--
2.49.0
guix-patches <at> gnu.org:bug#77541; Package guix-patches.
(Fri, 04 Apr 2025 19:19:07 GMT) Full text and rfc822 format available.Message #97 received at 77541 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77541 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 31/38] gnu: python-stone: Update to 3.3.9. Date: Fri, 4 Apr 2025 21:17:03 +0200
* gnu/packages/python-xyz.scm (python-stone): Update to 3.3.9.
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject.
[arguments]: Remove field.
[propagated-inputs]: Add python-jinja2, python-packaging.
[native-inputs]: Add python-setuptools, python-wheel. Remove
python-coverage, python-mock.
---
gnu/packages/python-xyz.scm | 41 +++++++++++--------------------------
1 file changed, 12 insertions(+), 29 deletions(-)
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index e63e41ba18..d18e4cfebd 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -29754,38 +29754,21 @@ (define-public python-userspacefs
(define-public python-stone
(package
(name "python-stone")
- (version "3.2.1")
+ (version "3.3.9")
(source
- (origin
- (method url-fetch)
- (uri (pypi-uri "stone" version))
- (sha256
- (base32
- "0xby5mpsms7b2rv8j6mvxzmzz5i9ii01brb9ylxz6kiv2i08piwv"))))
- (build-system python-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'change-version-requirements
- (lambda _
- ;; Match the requirement in test/requirements.txt
- (substitute* "setup.py"
- (("pytest < 5") "pytest < 7"))
- ;; We don't care about a coverage report.
- (substitute* "test/requirements.txt"
- (("coverage.*") "coverage\n"))))
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- ;; These tests don't import correctly.
- (delete-file "test/test_js_client.py")
- (delete-file "test/test_tsd_types.py")
- (delete-file "test/test_python_gen.py")
- (invoke "pytest")))))))
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/dropbox/stone")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1x0kj4jygssjn66lbkln95chhf85vzy1wnpziy9jvpf4kbc1bmfy"))))
+ (build-system pyproject-build-system)
(propagated-inputs
- (list python-ply python-six))
+ (list python-jinja2 python-packaging python-ply python-six))
(native-inputs
- (list python-coverage python-mock python-pytest python-pytest-runner))
+ (list python-pytest python-pytest-runner python-setuptools python-wheel))
(home-page "https://github.com/dropbox/stone")
(synopsis "Official Api Spec Language for Dropbox")
(description
--
2.49.0
guix-patches <at> gnu.org:bug#77541; Package guix-patches.
(Fri, 04 Apr 2025 19:19:07 GMT) Full text and rfc822 format available.Message #100 received at 77541 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77541 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 32/38] gnu: python-rq-scheduler: Update to 0.14. Date: Fri, 4 Apr 2025 21:17:04 +0200
* gnu/packages/databases.scm (python-rq-scheduler): Update to 0.14.
[build-system]: Switch to pyproject.
[arguments]{test-flags}: Ignore failing tests. They fail because of
mcron's requirements to be run with root when -u flag is used.
{phases}: Remove 'check phase replacement.
[native-inputs]: Add python-crontab, python-freezegun, python-pytest,
python-setuptools, python-wheel. Remove which.
---
gnu/packages/databases.scm | 37 +++++++++++++++++++++++--------------
1 file changed, 23 insertions(+), 14 deletions(-)
diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 4ecf237115..1aebf982ae 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -4647,7 +4647,7 @@ (define-public python-rq
(define-public python-rq-scheduler
(package
(name "python-rq-scheduler")
- (version "0.10.0")
+ (version "0.14")
(home-page "https://github.com/rq/rq-scheduler")
(source (origin
(method git-fetch)
@@ -4657,21 +4657,30 @@ (define-public python-rq-scheduler
(file-name (git-file-name name version))
(sha256
(base32
- "0xg6yazqs5kbr2ayvhvljs1h5vgx5k5dds613fmhswln7gglf9hk"))))
- (build-system python-build-system)
+ "09fh9m2vcl1jndq35xp1x0j8ih009r71qmhn2pkl93fykrqfavyn"))))
+ (build-system pyproject-build-system)
(arguments
- '(#:phases (modify-phases %standard-phases
- (add-before 'check 'start-redis
- (lambda _
- (invoke "redis-server" "--daemonize" "yes")))
- (replace 'check
- (lambda _
- (substitute* "run_tests.py"
- (("/usr/bin/env")
- (which "env")))
- (invoke "./run_tests.py"))))))
+ (list
+ #:test-flags
+ #~(list "-k" (string-append "not test_cron"
+ " and not test_job_creation_with"
+ " and not test_job_with_crontab"))
+ #:phases #~(modify-phases %standard-phases
+ (add-before 'check 'start-redis
+ (lambda _
+ (invoke "redis-server" "--daemonize" "yes")))
+ (add-after 'unpack 'loosen-requirements
+ (lambda _
+ (substitute* "setup.py"
+ (("crontab>=[0-9.]*")
+ "python-crontab")))))))
(native-inputs
- (list redis which))
+ (list python-crontab
+ python-freezegun
+ python-pytest
+ python-setuptools
+ python-wheel
+ redis))
(propagated-inputs
(list python-croniter python-rq))
(synopsis "Job scheduling capabilities for RQ (Redis Queue)")
--
2.49.0
guix-patches <at> gnu.org:bug#77541; Package guix-patches.
(Fri, 04 Apr 2025 19:19:08 GMT) Full text and rfc822 format available.Message #103 received at 77541 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77541 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 33/38] gnu: python-port-for: Update to 0.7.4. Date: Fri, 4 Apr 2025 21:17:05 +0200
* gnu/packages/python-web.scm (python-port-for): Update to 0.7.4.
[build-system]: Switch to pyproject.
[native-inputs]: Remove python-mock. Add python-setuptools,
python-wheel.
---
gnu/packages/python-web.scm | 18 +++++-------------
1 file changed, 5 insertions(+), 13 deletions(-)
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 579386e5ab..e82d59037c 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -7701,26 +7701,18 @@ (define-public grip
(define-public python-port-for
(package
(name "python-port-for")
- (version "0.4")
+ (version "0.7.4")
(source
(origin
(method url-fetch)
- (uri (pypi-uri "port-for" version))
+ (uri (pypi-uri "port_for" version))
(sha256
- (base32
- "1pncxlj25ggw99r0ijfbkq70gd7cbhqdx5ivsxy4jdp0z14cpda7"))))
- (build-system python-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'use-urllib3
- (lambda _
- (substitute* "port_for/_download_ranges.py"
- (("urllib2") "urllib3")))))))
+ (base32 "13826s2d4hzzmv69wws6a7ryhminclv2bqaw6cpl929gnbki6xzw"))))
+ (build-system pyproject-build-system)
(propagated-inputs
(list python-urllib3))
(native-inputs
- (list python-mock))
+ (list python-pytest python-setuptools python-wheel))
(home-page "https://github.com/kmike/port-for/")
(synopsis "TCP localhost port finder and association manager")
(description
--
2.49.0
guix-patches <at> gnu.org:bug#77541; Package guix-patches.
(Fri, 04 Apr 2025 19:19:08 GMT) Full text and rfc822 format available.Message #106 received at 77541 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77541 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 34/38] gnu: Remove python-cookies. Date: Fri, 4 Apr 2025 21:17:06 +0200
This is a leaf package in python, broken and undevelopped for 10 years.
* gnu/packages/python-web.scm (python-cookies): Delete variable.
---
gnu/packages/python-web.scm | 22 ----------------------
1 file changed, 22 deletions(-)
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index e82d59037c..8bb808b846 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -5496,28 +5496,6 @@ (define-public python-flask-multistatic
for overriding static files.")
(license license:gpl3+)))
-(define-public python-cookies
- (package
- (name "python-cookies")
- (version "2.2.1")
- (source (origin
- (method url-fetch)
- (uri (pypi-uri "cookies" version))
- (sha256
- (base32
- "13pfndz8vbk4p2a44cfbjsypjarkrall71pgc97glk5fiiw9idnn"))))
- (build-system python-build-system)
- (arguments
- `(;; test are broken: https://gitlab.com/sashahart/cookies/issues/3
- #:tests? #f))
- (native-inputs
- (list python-pytest))
- (synopsis "HTTP cookie parser and renderer")
- (description "A RFC 6265-compliant HTTP cookie parser and renderer in
-Python.")
- (home-page "https://gitlab.com/sashahart/cookies")
- (license license:expat)))
-
(define-public python-responses
(package
(name "python-responses")
--
2.49.0
guix-patches <at> gnu.org:bug#77541; Package guix-patches.
(Fri, 04 Apr 2025 19:19:09 GMT) Full text and rfc822 format available.Message #109 received at 77541 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77541 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 35/38] gnu: python-django-rq: Update to 3.0.0. Date: Fri, 4 Apr 2025 21:17:07 +0200
* gnu/packages/django.scm (python-django-rq): Update to 3.0.0.
[arguments]{test-flags}: Ignore failing tests.
{phases}: Replace 'check phase replacement by a simpler 'pre-check
configuration phase.
[native-inputs]: Add python-pytest, python-pytest-django.
[propagated-inputs]: Add python-redis, python-pyaml.
---
gnu/packages/django.scm | 28 +++++++++++++++-------------
1 file changed, 15 insertions(+), 13 deletions(-)
diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm
index cb9df0d2df..44d47b39ab 100644
--- a/gnu/packages/django.scm
+++ b/gnu/packages/django.scm
@@ -1055,39 +1055,41 @@ (define-public python-django-redis
(define-public python-django-rq
(package
(name "python-django-rq")
- (version "2.7.0")
+ (version "3.0.0")
(source (origin
(method url-fetch)
(uri (pypi-uri "django-rq" version))
(sha256
(base32
- "0aw0fi0lg80qgdp9fhjbnlhvfh2p09rgy1nj6hxpyhi37kihni2h"))))
+ "1b371w4cdjlz83i2sg4gpx0z3svl3bfrn6zfy661374hv62xpnkv"))))
(build-system pyproject-build-system)
(arguments
(list
+ #:test-flags
+ #~(list "-k" "not test_scheduled_jobs and not test_started_jobs")
#:phases
- '(modify-phases %standard-phases
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- (invoke "redis-server" "--daemonize" "yes")
- (invoke "django-admin" "test" "django_rq"
- "--settings=django_rq.tests.settings"
- "--pythonpath=.")))))))
+ #~(modify-phases %standard-phases
+ (add-before 'check 'pre-check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (invoke "redis-server" "--daemonize" "yes")
+ (setenv "DJANGO_SETTINGS_MODULE" "django_rq.tests.settings")
+ (setenv "PYTHONPATH" (getcwd))))))))
(native-inputs
(list python-django-redis
- python-mock
+ python-pytest
+ python-pytest-django
python-rq-scheduler
python-setuptools
python-wheel
redis
tzdata-for-tests))
(propagated-inputs
- (list python-django python-rq))
+ (list python-django python-redis python-rq python-pyaml))
(home-page "https://github.com/ui/django-rq")
(synopsis "Django integration with RQ")
(description
- "Django integration with RQ, a Redis based Python queuing library.
+ "Django integration with RQ, a Redis based Python queuing library.
Django-RQ is a simple app that allows you to configure your queues in django's
settings.py and easily use them in your project.")
(license license:expat)))
--
2.49.0
guix-patches <at> gnu.org:bug#77541; Package guix-patches.
(Fri, 04 Apr 2025 19:19:09 GMT) Full text and rfc822 format available.Message #112 received at 77541 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77541 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 36/38] gnu: python-flask-seasurf: Update to 2.0.0. Date: Fri, 4 Apr 2025 21:17:08 +0200
* gnu/packages/python-web.scm (python-flask-seasurf): Update to 2.0.0.
---
gnu/packages/python-web.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 8bb808b846..a740f9638b 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -5433,13 +5433,13 @@ (define-public python-flask-compress
(define-public python-flask-seasurf
(package
(name "python-flask-seasurf")
- (version "1.1.1")
+ (version "2.0.0")
(source (origin
(method url-fetch)
(uri (pypi-uri "Flask-SeaSurf" version))
(sha256
(base32
- "1aaib4n27q0f2alp87mhv3f79vg7qckp71rphbd0mb39qw470lsl"))))
+ "0g5dsm2ikv8q4qcrb2446pbs972l5wkxyfmxsriqdsl02nz06h4f"))))
(build-system pyproject-build-system)
(arguments
(list #:tests? #false)) ;there are none
--
2.49.0
guix-patches <at> gnu.org:bug#77541; Package guix-patches.
(Fri, 04 Apr 2025 19:19:10 GMT) Full text and rfc822 format available.Message #115 received at 77541 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77541 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 37/38] gnu: python-country-converter: Add missing native-input. Date: Fri, 4 Apr 2025 21:17:09 +0200
* gnu/packages/iso-codes.scm (python-country-converter)[native-inputs]:
Add python-wheel.
---
gnu/packages/iso-codes.scm | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/gnu/packages/iso-codes.scm b/gnu/packages/iso-codes.scm
index fd04d13a9f..ad9b90a564 100644
--- a/gnu/packages/iso-codes.scm
+++ b/gnu/packages/iso-codes.scm
@@ -122,7 +122,8 @@ (define-public python-country-converter
(build-system pyproject-build-system)
(native-inputs
(list python-pytest
- python-setuptools))
+ python-setuptools
+ python-wheel))
(propagated-inputs
(list python-pandas))
(home-page "https://github.com/IndEcol/country_converter")
--
2.49.0
guix-patches <at> gnu.org:bug#77541; Package guix-patches.
(Fri, 04 Apr 2025 19:19:10 GMT) Full text and rfc822 format available.Message #118 received at 77541 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77541 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 20/38] gnu: python-botorch: Update to 0.13.0. Date: Fri, 4 Apr 2025 21:16:52 +0200
* gnu/packages/machine-learning.scm (python-botorch): Update to
0.13.0.
[native-inputs]: Add python-pyre-extensions.
---
gnu/packages/machine-learning.scm | 7 ++++---
1 file changed, 4 insertions(+), 3 deletions(-)
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 4bf7442e09..e62535d890 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -6161,7 +6161,7 @@ (define-public python-gpytorch
(define-public python-botorch
(package
(name "python-botorch")
- (version "0.11.3")
+ (version "0.13.0")
(source (origin
(method git-fetch) ;no tests in PyPI
(uri (git-reference
@@ -6170,7 +6170,7 @@ (define-public python-botorch
(file-name (git-file-name name version))
(sha256
(base32
- "0nf9zrg1khvckb8kdpffqc3bnlhc0x03jd1560qmjamwl3j59m02"))))
+ "1sxgxdq892vg5xj30kb86003b9rwsipc95c7p1zdv865y4f38a8y"))))
(build-system pyproject-build-system)
(arguments
(list #:test-flags #~(list "-k" "not test_all_cases_covered")
@@ -6189,7 +6189,8 @@ (define-public python-botorch
python-pyro-ppl
python-pytorch
python-scipy))
- (native-inputs (list python-pytest
+ (native-inputs (list python-pyre-extensions
+ python-pytest
python-pytest-cov
python-setuptools
python-setuptools-scm
--
2.49.0
guix-patches <at> gnu.org:bug#77541; Package guix-patches.
(Fri, 04 Apr 2025 19:19:10 GMT) Full text and rfc822 format available.Message #121 received at 77541 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77541 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 38/38] gnu: python-itemloaders: Update to 1.3.2. Date: Fri, 4 Apr 2025 21:17:10 +0200
* gnu/packages/python-xyz.scm (python-itemloaders): Update to 1.3.2.
[native-inputs]: Add python-packaging.
[propagated-inputs]: Remove python-w3lib.
---
gnu/packages/python-xyz.scm | 12 ++++++++----
1 file changed, 8 insertions(+), 4 deletions(-)
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index d18e4cfebd..ceebb018d9 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -39158,17 +39158,21 @@ (define-public python-itemadapter
(define-public python-itemloaders
(package
(name "python-itemloaders")
- (version "1.1.0")
+ (version "1.3.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "itemloaders" version))
(sha256
- (base32 "0j2aw4ipalj208594x80blpgkh1i63gqqa4nb67b823av9hirn11"))))
+ (base32 "0w37g31n06x6v6b4w7cz3nbq4wl6cv7rrzg3fr203gw3pqx5pbsg"))))
(build-system pyproject-build-system)
- (native-inputs (list python-pytest python-setuptools python-wheel))
+ (native-inputs
+ (list python-packaging
+ python-pytest
+ python-setuptools
+ python-wheel))
(propagated-inputs
- (list python-itemadapter python-jmespath python-parsel python-w3lib))
+ (list python-itemadapter python-jmespath python-parsel))
(home-page "https://github.com/scrapy/itemloaders")
(synopsis "Base library for scrapy's ItemLoader")
(description "Itemloaders is a library that helps you collect data
--
2.49.0
Debbugs Internal Request <help-debbugs <at> gnu.org>
to internal_control <at> debbugs.gnu.org.
(Sat, 03 May 2025 11:24:15 GMT) Full text and rfc822 format available.
GNU bug tracking system
Copyright (C) 1999 Darren O. Benham,
1997,2003 nCipher Corporation Ltd,
1994-97 Ian Jackson.