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(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")) From patchwork Fri Apr 4 19:16:36 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 41289 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id EAE7727BBED; Fri, 4 Apr 2025 20:19:38 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-7.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED,RCVD_IN_MSPIKE_H2, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS,URIBL_BLOCKED autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id A6C5627BBE2 for ; Fri, 4 Apr 2025 20:19:38 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1u0mYL-0006ce-4L; Fri, 04 Apr 2025 15:18:09 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1u0mYI-0006b6-7N for guix-patches@gnu.org; Fri, 04 Apr 2025 15:18:06 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1u0mYH-0007o8-Sj for guix-patches@gnu.org; Fri, 04 Apr 2025 15:18:05 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=FKlXzC6r0eYKiFWW+0Ds2RtLFfA0sKYzLGLS8sepJ5c=; b=EPNbf3vqoB+MDvt1RyZlVIqx/4qOn9BnMlPJYZ9Vt4bAwo/JQijrjDKkHkdFzC8DBRJrQuLIVb6biD2J8LaxCH+tMxPl2C0Z1GYnoW/tXEteVZXENJrVIuNGZoe6qauzYJMMctaEJ8hd/X7TrVBpQjTK6i6hZrgAkKE4/vPLi9/EMFOvg1/xotfkTNmgRdA/bUJiGfhjAWY1aA9fNvvPp1zC9eWP4Jg+d4SgiAcHGmYYn37gobgQcJXCTITUAc0VwuhCSsVgk6mRXec8QfsHWyXSx0tyb91PbDpj4WE8+Px8C5dfzzYhcs9EfXwvizyleksau5wRK71Y5yQEXVbHfA==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1u0mYG-0007Ki-Lq for guix-patches@gnu.org; Fri, 04 Apr 2025 15:18:04 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77541] [PATCH 04/38] gnu: autokey: Add missing native-inputs. 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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 From patchwork Fri Apr 4 19:16:39 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 41293 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 782B527BBE2; Fri, 4 Apr 2025 20:19:48 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-7.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED,RCVD_IN_MSPIKE_H2, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 589F927BBF1 for ; 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(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") From patchwork Fri Apr 4 19:16:40 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 41288 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 7AA5527BBEA; Fri, 4 Apr 2025 20:19:30 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-7.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED,RCVD_IN_MSPIKE_H2, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS,URIBL_BLOCKED autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id DDB2F27BBE2 for ; Fri, 4 Apr 2025 20:19:29 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1u0mYO-0006hi-Tc; Fri, 04 Apr 2025 15:18:12 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1u0mYJ-0006bo-2a for guix-patches@gnu.org; Fri, 04 Apr 2025 15:18:07 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1u0mYI-0007oW-Lb for guix-patches@gnu.org; Fri, 04 Apr 2025 15:18:06 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=pWmUJcn+pDxzrmhUDElIva61tu1JUjT4UFBsL/bCOkY=; b=MqBZt8eTxlNA8ZaswM92M1V1AsGGcdyMW/qMuZd9FyG9S9TCzg89AQJrr1eTBikjglhhbPdr8lCfI9Xu6/o8WjnXIs9eJm4qEZCKLCo11pULodc/Or5fxU5ZKQ+vV4uWsPs+CA23SAE+BtUJbXNXL1b1Eg4cDwu0BS4D1TwSePTbOuwbAuFNcA4HyL/W5wOcOQJIlW/71LmFn2UHlARf+lSiHZftyqiWkqeWSJZIkLw4lW87cJU9R7+N9A1UqolakSLL0shsXa2k1muG7dSItRXR+2j76b8WFh4xXGXtFg86DqbI0QjLyRiQq8Byz+tzAzf5QsCryZwnFvZQiDwLQw==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1u0mYI-0007LE-En for guix-patches@gnu.org; Fri, 04 Apr 2025 15:18:06 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77541] [PATCH 08/38] gnu: python-pytensor: Update to 2.30.1. 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[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 From patchwork Fri Apr 4 19:16:41 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 41296 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 97BC827BBE2; Fri, 4 Apr 2025 20:19:50 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-7.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED,RCVD_IN_MSPIKE_H2, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id A2B8627BBF5 for ; Fri, 4 Apr 2025 20:19:46 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1u0mYL-0006dx-J8; Fri, 04 Apr 2025 15:18:09 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1u0mYJ-0006c8-Ml for guix-patches@gnu.org; Fri, 04 Apr 2025 15:18:07 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1u0mYJ-0007oh-B7 for guix-patches@gnu.org; Fri, 04 Apr 2025 15:18:07 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=66Sgzt2DmnR0I5i4pPLNsv3WZIJZVZcEGZYlAI2tSl0=; b=bvuiltbxB2HHqDD0fM3sFiOo6Wb7jECvQ/S0fTjFxd9evmIoPhxbzS4lNONKLSvnsLw1sGntEZUzOX8SPU34dy+sDbjuVodCfNYGRqZRqWi22sJ3vd+kRoecGIbLx3WnvS7GFLPxRf3RxU5EQaRW2yPKPqXwI6ggY7PDp3RvJNt8jfvpHlpBnVXc8g8to1QjW8mUpDutDNOqYWjdfEc/2Co1cy28kHQFwtmLJCCdbB03q8XLd9YMMS+x1Y+p2VVXTTtdvRzqDZXjxJ9lHoManoA4tobbljJtS18stZ0fxRJ56Ij5J+tb3+4il+bhNVMxTEi8qKkz4/EmCWLAPy6wlA==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1u0mYJ-0007LL-03 for guix-patches@gnu.org; Fri, 04 Apr 2025 15:18:07 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77541] [PATCH 09/38] gnu: python-vaex-core: Update to 4.17.1. 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i < nmaps; i++) { + string_arrays.emplace_back(std::make_shared()); + StringList64 *strings = string_arrays[i].get(); +- // equal_to& eq = this->maps[i].key_eq(); +- this->maps[i].m_ht.strings_equals = strings; +- this->maps[i].m_ht.strings_hash = strings; ++ equal_to eq; ++ eq.strings_equals = strings; ++ hash 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, T, T, V> { + template + static ordered_set *create(std::shared_ptr 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 eq; ++ eq.strings_equals = keys.get(); ++ hash 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, T, T, V> { + // string_arrays_overflow.emplace_back(std::make_shared()); + // for each key in overflow, it should be present in the main string array + StringList64 *strings = this->string_arrays[i].get(); +- // equal_to& eq = this->maps[i].key_eq(); +- overflows[i].m_ht.strings_equals = strings; +- overflows[i].m_ht.strings_hash = strings; ++ equal_to eq; ++ eq.strings_equals = strings; ++ hash 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 From patchwork Fri Apr 4 19:16:45 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 41290 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 97EAB27BBED; Fri, 4 Apr 2025 20:19:39 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-7.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED,RCVD_IN_MSPIKE_H2, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS,URIBL_BLOCKED autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id ADE1E27BBEA for ; Fri, 4 Apr 2025 20:19:38 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1u0mYR-0006io-9F; Fri, 04 Apr 2025 15:18:15 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1u0mYL-0006dw-Hi for guix-patches@gnu.org; Fri, 04 Apr 2025 15:18:09 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1u0mYL-0007pA-77 for guix-patches@gnu.org; Fri, 04 Apr 2025 15:18:09 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=tVwwadcVt5QtE/iwQljtuL12OeWdy8jZn/0xKIUhBLA=; b=RJWZRVlmOW+LIOC5Uu5QcExvOL7XlSEkyV9dYMrZOkyh9JAFblxu8x3x6zG+TMp96la3GiUsbbWvF/9OdpXbDy+6fhy1pkI+IHaEdA5PQewrBvHpTk17DfLmGlku3FDBj02RsZBgifACVdm6h7PnlIX/P8m4DanzvarBvopotawg5ZhBp4R8YbJ0QSAUqgR9H/GGx0hZ3GVra+ZKEvFXolOZhsmsz3nu0bMubfgjrSXBJ1nz9RcJlDviTqrQslzqjhXL34EB0WwCINnYwn6OJl4vfJFPGelyw4UxqdtY0I3uW/LJ88YmypQBme9He1mwq2bKgg7z/W6GECnQVMxxEQ==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1u0mYK-0007Lj-QC for guix-patches@gnu.org; Fri, 04 Apr 2025 15:18:08 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77541] [PATCH 13/38] gnu: python-serpent: Update to 1.41. 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[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 From patchwork Fri Apr 4 19:16:46 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 41291 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 08DD727BBEA; Fri, 4 Apr 2025 20:19:45 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-7.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED,RCVD_IN_MSPIKE_H2, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS,URIBL_BLOCKED autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 3C83D27BBE9 for ; Fri, 4 Apr 2025 20:19:44 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1u0mYQ-0006if-NJ; Fri, 04 Apr 2025 15:18:15 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1u0mYO-0006h2-9R for guix-patches@gnu.org; Fri, 04 Apr 2025 15:18:12 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1u0mYN-0007pQ-Vf for guix-patches@gnu.org; Fri, 04 Apr 2025 15:18:12 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=encm68WVVEs/0f3y5e6o5Q7lbmLA+jhw1kWxRVuYZYQ=; b=kCTbGMDPTDtpmueOtgE1VKmugKJ2neex12E9Gqqa/XBgkMotMWKCuFB2/4zC8AsUXAs2a4MxyxLso4SfoymZYtdwGJ0sS1vuJPIAkUj/cEb9zmE/tE/TeBnIEe004LzueoenkbUQo6VtzbID06rrx6zPLoYUhn9ly2nL6RIh2VvB4TAmi+2qYJtBuCnDVBJGcyF1HGypsxRVDkEkt/MYUVS7msryPAVPCv4cKeyiMUDOvq14scuXJxmP0Ty7JlNefQDXMhycus/MH0HOwMhPcrn0bja8vvb9JyAF4w0ojVYKCFvedhL3+s0lwryWO6sQvfdzHlVwEGY09aEChvC4cg==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1u0mYL-0007Lz-O2 for guix-patches@gnu.org; Fri, 04 Apr 2025 15:18:09 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77541] [PATCH 14/38] gnu: python-pyro4: Update to 4.82. 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[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") From patchwork Fri Apr 4 19:16:47 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 41311 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id D849427BBEA; Fri, 4 Apr 2025 20:20:18 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-7.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED,RCVD_IN_MSPIKE_H2, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id E58BD27BBEB for ; Fri, 4 Apr 2025 20:20:17 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1u0mYT-0006jC-1x; Fri, 04 Apr 2025 15:18:17 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1u0mYM-0006f9-Qq for guix-patches@gnu.org; Fri, 04 Apr 2025 15:18:11 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1u0mYM-0007pT-Ga for guix-patches@gnu.org; Fri, 04 Apr 2025 15:18:10 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=bZQsf9J+FDLcWNLK48sSVQyRpw3Le1LTj4YrPJAOP/w=; b=N8ZTiY0bFxKH2ImDxtOR2mmFVhxIWmvcx+ZPGJUR9lmz1ky9fxivIX4sQg1kDYcRssoLS96wwPfN64tdU4q5Da3KJIfTA9cfXgptRiGPdLWKQXHv88H2eERDRtQUZaPIF+lUjoi2loOS8QSmesLF3nt0STbD2ujLvu50/+cysY7UCqoOEbGk8S1ha7BIzVsSLFLY0yanrd9COozpRmwWng1z0HxvHWSC0ARU8e5NdDLWR9fo0E2goyqDY3nKGc+5lxY1Hcgse77UPPrC48XhHh4PwrjA3M7pnNeg5+r1nuLB+HAIr/bDsoRkVHwsqhjYoQSZ+v91kD/JXHEYBK2cng==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1u0mYM-0007M7-6o for guix-patches@gnu.org; Fri, 04 Apr 2025 15:18:10 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77541] [PATCH 15/38] gnu: python-lcapy: Add missing native-inputs. 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[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 From patchwork Fri Apr 4 19:16:50 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 41304 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 22B1627BBEA; Fri, 4 Apr 2025 20:20:06 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-7.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED,RCVD_IN_MSPIKE_H2, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS,URIBL_BLOCKED autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id B5B0227BBE2 for ; Fri, 4 Apr 2025 20:20:05 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1u0mYX-0006lq-9D; Fri, 04 Apr 2025 15:18:21 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1u0mYN-0006gN-Ps for guix-patches@gnu.org; Fri, 04 Apr 2025 15:18:12 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1u0mYN-0007pa-Fk for guix-patches@gnu.org; Fri, 04 Apr 2025 15:18:11 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=B4nAPwAOrdlctNBI+lNmNr4GMVKAz8bPfUS3s97fP6w=; b=IcwN/usI3dTEaeHl2eozPJ/l+Fg1/CBwLo7gJe8gBoXe/CkDIpLn2aQGbifK5jRRbLrhuKHip/0IDmE2dAJhOjKZPrnBrclkGP+c4oeTi92OZ+mKmjTx7QKtsqWaMI7WR5mMUeKUSpSs+Rq7ByI80A4eC7QwY8BeKpzXsrD4HKYGKNsjhMHjpH2WKLpaokWaB8XhrHa46lOIA024i5fwR4ZKIoV/vfA4XYvc8W666Nggrr7r0uqxzy3p8IzxE/4k/Rb7Yu5nfICr3y282PayZtUIkjkaR14a1OdbmyFbMRLm7+j7qeMGWFlqXfl9ysyoSYrHrANnfBTJSgNN7MWW1w==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1u0mYN-0007MN-8K for guix-patches@gnu.org; Fri, 04 Apr 2025 15:18:11 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77541] [PATCH 18/38] gnu: python-botorch: Add missing native-inputs. 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[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 From patchwork Fri Apr 4 19:16:52 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 41287 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 5F05627BBE9; Fri, 4 Apr 2025 20:19:26 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-7.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED,RCVD_IN_MSPIKE_H2, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 3E25B27BBE2 for ; Fri, 4 Apr 2025 20:19:26 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1u0mZS-0007Tk-Uk; Fri, 04 Apr 2025 15:19:19 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1u0mZM-0007Hc-81 for guix-patches@gnu.org; Fri, 04 Apr 2025 15:19:12 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1u0mZK-0007zX-Rv for guix-patches@gnu.org; Fri, 04 Apr 2025 15:19:10 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=NPbHHNyUuaITq8dbhueS1O/EhGcQb82gXSwFANmw258=; b=n2VxMNh9r0cTwmcWtSnAwhXFKzP8RPe+Np5yjuJugBskK2BZNM0rOvUpI3t8+O4I+g00aZKJdthOfmMJo3wBivq50B3qTmF5UYlO2YmRVhKaFS5PgR7Z97i5AA0UHWcDgsKm6HNHl8/YAjnqIzriSJsAx4uGzWNHeH/d46/0ytfD5I1PkvhmmC5gzrDssYLsSdhvAh16z4UW5omM9K6cRKj6aKFlx9kLON+PiRD7LlPMV/7ru0la8eL8xcKGcpeyxlfoNu7P/dH26+NvNc7832pRWHC7EFS0RbB1ie85jWNNQ/x/TP/rs5jvMJMJElILX/UuJKhjlCUSGiokGAQTPA==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1u0mZK-0007Si-HJ for guix-patches@gnu.org; Fri, 04 Apr 2025 15:19:10 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77541] [PATCH 20/38] gnu: python-botorch: Update to 0.13.0. 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[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 From patchwork Fri Apr 4 19:16:55 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 41294 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 8EE9F27BBE2; Fri, 4 Apr 2025 20:19:49 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-7.3 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED,RCVD_IN_MSPIKE_H2, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS,URIBL_BLOCKED,URIBL_SBL_A autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id BB72727BBE9 for ; Fri, 4 Apr 2025 20:19:45 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1u0mZL-0007G5-Px; Fri, 04 Apr 2025 15:19:12 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1u0mZI-0007CL-79 for guix-patches@gnu.org; Fri, 04 Apr 2025 15:19:08 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1u0mZG-0007xJ-Ay for guix-patches@gnu.org; Fri, 04 Apr 2025 15:19:07 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=Wr5mop/Npb6Aqxtnm/2tqbUqsZ19LUU5F21s83YH39s=; b=LeuPmX6aU3XLpqdDj4HAv+mrk1BMidyoU4bmISy54ECJnEoItO/HHt8XXanQ0vKmboAmPXXtChNJ0ce6FvShfKXzdkdIEpZTxsstwtwSzmO85oImvIiPWsx1Z/xljU+X3TflrBlXMrd31BkgiSizV5zOoQtQ+rSGf9ab2agbb0fQh95GRg8c5kB/srUnPZJdIlaGn6aSpCEW2nbmb2LwT9HxVvi7zhtanUE1MQGYar26upNVjLUsqfXnMTYI6c9Jozz+nk2xW0aDs/QExelCKe5QIR6hEeNnoGQwjMCh9At9/y2v4pm10wfSiW0YBJIPtmZaCnxx5kr7Atggrdlj8g==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1u0mZG-0007RZ-40 for guix-patches@gnu.org; Fri, 04 Apr 2025 15:19:06 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77541] [PATCH 23/38] gnu: python-bed-reader: Fix build and enable tests. 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[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@ngraves.fr> +From: Nicolas Graves +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 + From patchwork Fri Apr 4 19:16:56 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 41298 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id BE45327BBEA; Fri, 4 Apr 2025 20:19:52 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-7.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED,RCVD_IN_MSPIKE_H2, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS,URIBL_BLOCKED autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 22D4F27BBE2 for ; Fri, 4 Apr 2025 20:19:52 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1u0mZE-000779-98; Fri, 04 Apr 2025 15:19:04 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1u0mZD-00075O-31 for guix-patches@gnu.org; Fri, 04 Apr 2025 15:19:03 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1u0mZC-0007wB-Nk for guix-patches@gnu.org; Fri, 04 Apr 2025 15:19:02 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=3TkHtLDjxOYACiJqk8Wpz7yH+X5EdOKRVdzlXVs1/lg=; b=Fw+yhsfJ8FeXQ496+9HwlyaoUIt5vRpSNq4AhupVpENqPsbgJozz/Wg1XE1+ocK601D/DPObUs7aryCTAHhoI0skf0xAMv1Xk6SHBLAzOb05m1O4eyBzBHx9W2S5ma2rk/GJFYxC1Cuk6nmIeCmgR/IjOH2yKwdbkvGCxXQFAgohksXPTRhtIrlgh/CDg2nPd1QRJcV0wCPxVbGEJxzznywE2n6Rziu7cJ/efjr1aR4kazEIl9GmCmdl9XR5bNKeJpb1k5ct0DPY4f+JW/2R3u20Voiy7+szYRPPYd7fGgR4oUSTXLVdNP/HoOGORpGuNRun9RGp+87dcQIzjI8wrg==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1u0mZC-0007Qg-GM for guix-patches@gnu.org; Fri, 04 Apr 2025 15:19:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77541] [PATCH 24/38] gnu: python-pysnptools: Fix build and enable tests. 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[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 From patchwork Fri Apr 4 19:16:57 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 41303 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id B8B6727BBE2; Fri, 4 Apr 2025 20:20:02 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-7.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED,RCVD_IN_MSPIKE_H2, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 672A227BBEA for ; Fri, 4 Apr 2025 20:20:01 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1u0mZI-00079L-FL; Fri, 04 Apr 2025 15:19:08 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1u0mZE-00075q-I0 for guix-patches@gnu.org; Fri, 04 Apr 2025 15:19:04 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1u0mZD-0007wJ-6v for guix-patches@gnu.org; Fri, 04 Apr 2025 15:19:03 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=/HAxnahZy7GdztM5l3DvIvFXgWj6nPwY5XKwSwpzUMk=; b=Qv1y8ESU9U3QqolIG8WyYe3HIgkZbA1FuRQZTVAQKUw9h1+oeiDw9KvgqURQfqb3xDPkGVV30HkqzmsSp1wXj5D3/Qs4QpBumNZC6qHwn5Qz6qJQgH9yTAPDoizBjuRvl5IWRLTXuNRhN+WSAPbaIMZduY4kAlakJtgkiYdLgTMhIMJOmapHxKo0bgY3htVP2N5FkC3j56yoIxbAEsYzKzz4QQBMV0SUhlzQWgxxcHmTvLI2k8wiY5jBKBq2OBr7rsySj54rQFA/ZRoNYwSfrlMRdPrIiXGsRsqGBGdfougNyuAZ3tVH3nTbfO7qnyFMCdnFY4vJHzYjQTkaSGLbrQ==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1u0mZD-0007Qn-0D for guix-patches@gnu.org; Fri, 04 Apr 2025 15:19:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77541] [PATCH 25/38] gnu: Add python-poetry-core-next. 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(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 From patchwork Fri Apr 4 19:16:58 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 41312 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 4904127BBE2; Fri, 4 Apr 2025 20:20:19 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-7.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED,RCVD_IN_MSPIKE_H2, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS,URIBL_BLOCKED autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id CA3E827BBE9 for ; Fri, 4 Apr 2025 20:20:18 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1u0mZM-0007GM-1X; Fri, 04 Apr 2025 15:19:12 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1u0mZF-00078W-GJ for guix-patches@gnu.org; Fri, 04 Apr 2025 15:19:05 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1u0mZE-0007wh-7Z for guix-patches@gnu.org; Fri, 04 Apr 2025 15:19:05 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=uFSkaTv6DWHc306mZ++Hn+cB1Hn4I2HJHFFUVhXVOg4=; b=GNvXLE4PTwj/ONARZeuRxYKEs08v0j2colyioDI+SdGSQTr6Pa8TPp7kmHOorY1RvI4hLheHVPz5nnnEFbUV4DKfoWdgp8u1LvKYtc9LOs7aDsO1f77ZO5hvea/yWFnAFsy5pICB01iuWbjd7wj2WPZw4pawMbkOr/cPe+rekuvL8lrtdM1gPNbjUcvSVysyZpf8AVTsBBIk0cmu0Cs+Bukkge7rpBAk6cSUYkD0E+cFiewdWJ8m4RwJsKdRpxHGmdf4cN7wZJKVSAY2BMlaOo+5INMKzbq8pVpGBdRt3EMSwOV6QSdwtaAhlSPakgrTQSWRbUwVeY+PzKz7f6oT4A==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1u0mZE-0007R2-2H for guix-patches@gnu.org; Fri, 04 Apr 2025 15:19:04 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77541] [PATCH 26/38] gnu: python-duniterpy: Update to 1.2.1. 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[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 From patchwork Fri Apr 4 19:17:00 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 41308 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 05FCC27BBEA; Fri, 4 Apr 2025 20:20:14 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-7.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED,RCVD_IN_MSPIKE_H2, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS,URIBL_BLOCKED autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 9104B27BBE2 for ; Fri, 4 Apr 2025 20:20:13 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1u0mZM-0007IN-LP; Fri, 04 Apr 2025 15:19:12 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1u0mZI-0007CM-7y for guix-patches@gnu.org; Fri, 04 Apr 2025 15:19:08 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1u0mZG-0007ww-C9 for guix-patches@gnu.org; Fri, 04 Apr 2025 15:19:07 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=JHnb5nTIe+Bcn46BTqGgYSmnQ/0gvni3j7raluUYDX8=; b=ZHYBNq8fQk/ncCFbwkSJh1B4AhKfCoJ81ISRzu7k9Gl+KrJAt0I8kJ/+sTEm2r2Hls03KVDHb8fbIgwqbykAF9EKwFgJGUntOYU3F3FMYuQka0WpNlSVU+XMj1BUe99Ohl4lWIpp+GSPe10zAtaVdVUHFk+hYJNNC2cTiQU090hamd1A26QUReLBsYUQa7eYstHCY08EBtSBeSQRNsij7S1NM1Qq6RS0Uj33RAH9JqNTfO4hbbOsUXDE/0BZ28R/QLM9liyTHkIWgxzS5JynU5JS5/IB8GJm/sJy88HBa+mCFL6ryA32ZNwCI5Js3X0SC9ixKHUhYoaTT98Dp0PjGg==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1u0mZF-0007RH-2b for guix-patches@gnu.org; Fri, 04 Apr 2025 15:19:05 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77541] [PATCH 28/38] gnu: python-furl: Update to 2.1.4. 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[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 From patchwork Fri Apr 4 19:17:01 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 41306 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id E7B0527BBE2; Fri, 4 Apr 2025 20:20:10 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-7.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED,RCVD_IN_MSPIKE_H2, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id A50A627BBEB for ; Fri, 4 Apr 2025 20:20:09 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1u0mZN-0007Ih-8A; Fri, 04 Apr 2025 15:19:13 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1u0mZI-0007CK-6P for guix-patches@gnu.org; Fri, 04 Apr 2025 15:19:08 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1u0mZF-0007xI-S4 for guix-patches@gnu.org; Fri, 04 Apr 2025 15:19:07 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=KNKam4WCJemZAOyPnpur3+CCACUgjwph7Z3RcwK2xbc=; b=c3qfVbWS2FEpy0trpFd27vxkMNROEJk3btqX2QA4K+gjjns9dkmCgnRkWLxVUdc9BPtjhUh6Bj877+kRjG1d1msXAFXTOMViAUAy6iWqqFeE/Rovvwna8uMXyTfZOpKuLBRzW+WT5h3trdFS2gBmdi9KnLWONV16CQ6LkniFHYvNdkUJLLisM5wzdaq5sVJ12Mh48OGpWV6NJn/G2q+WZxdAWhFHAJAgvjYjzirV4KpPpe7qyK+s4AAxymY9TuDPcb10g9Tlg3XEISWfRzBRv/579EqurdaTsgJ3nrgOaf54llim/dPHsnRuK0Fo9K1pMJ3CpkK7GiXu2EeO+IMr1w==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1u0mZF-0007RS-LU for guix-patches@gnu.org; Fri, 04 Apr 2025 15:19:05 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77541] [PATCH 29/38] gnu: python-rq: Update to 2.3.1. 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[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/") From patchwork Fri Apr 4 19:17:02 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 41302 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 61E6827BBE2; Fri, 4 Apr 2025 20:20:01 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-7.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED,RCVD_IN_MSPIKE_H2, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id A68F127BBE9 for ; Fri, 4 Apr 2025 20:20:00 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1u0mZN-0007Ir-Vo; Fri, 04 Apr 2025 15:19:14 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1u0mZI-0007CN-8h for guix-patches@gnu.org; Fri, 04 Apr 2025 15:19:08 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1u0mZG-0007xR-Po for guix-patches@gnu.org; Fri, 04 Apr 2025 15:19:07 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=lLtJ/xcCmMlwzsTs2JRUixO64Sa3B/eOdlEMAZBVek4=; b=cswyxVpzu2WSMIAy0GDFkRubyAc/0B/4/sk1LYDCpUD0tqxgEbqAMRZfT9CWlqxJ5JLEfmbIvqUrDby/HCDjACs22H1S+0gjPysLAt13nCxMmuMj5hkC7+/AFipaCKCVF367Wy/KroZXJZDR57oZE19/Iz5Re5HU/yPI8v26wRU5ajD2d7EKCKDPxr7q2Sux83BcmYROfKxHN5f4lCCPaGA7RFyABnuXprWMJ7kkyBT2gx+cEozw/bpjVcWPP0FHSQqHNMZf/RxRLcj5psSoPsqhQNUjTI4wpmBrUbLJFW/YzNrynS4iyT9FGT561CP/htjBciLt+KQBk31GT1MPzg==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1u0mZG-0007Rh-K7 for guix-patches@gnu.org; Fri, 04 Apr 2025 15:19:06 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77541] [PATCH 30/38] gnu: python-crontab: Update to 3.2.0. 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[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 From patchwork Fri Apr 4 19:17:03 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 41307 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 1EBC227BBEA; Fri, 4 Apr 2025 20:20:11 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-7.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED,RCVD_IN_MSPIKE_H2, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id A3AF527BBE9 for ; Fri, 4 Apr 2025 20:20:09 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1u0mZP-0007Mb-SY; Fri, 04 Apr 2025 15:19:15 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1u0mZJ-0007Em-78 for guix-patches@gnu.org; Fri, 04 Apr 2025 15:19:09 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1u0mZH-0007xS-7E for guix-patches@gnu.org; Fri, 04 Apr 2025 15:19:07 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=06JTOoaGWltD35Oh6/FyI/1N+vmpe0xMJNBo2zsOBQc=; b=anHrPlV3BfCE+hzjo2V5PgLMk+gUg6tZdRLSRcNi8X42B7ckLvCInfds4W3i6+zCciYxMjWudbw9HqgGF0LjlULOfpaXuh0ZhCymoVpYmw5i7dGc/WHs052qpCCyXkB6ZDCE26j/EiMwf2hrzQN5XqgP6e+Vt4iusl6hXGNYFULSYZ7zyriy0hiLMVcZtOHbMkcPLIkPxqivMTGp4NZewEVuDDErGYEM+zqLC1ohbaHfgsQCoDzg3QgtSdr4shrR/Rtazk6+Vq7P2xbrfwgKaBKsjNyBmzE2yAPGIjrMkLujt7o/X2kWRs0xg2Y9lHsBHFejxdXq5SALDOkv0TasNw==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1u0mZH-0007Rq-1T for guix-patches@gnu.org; Fri, 04 Apr 2025 15:19:07 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77541] [PATCH 31/38] gnu: python-stone: Update to 3.3.9. 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[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 From patchwork Fri Apr 4 19:17:04 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 41309 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 9BEBE27BBE9; Fri, 4 Apr 2025 20:20:16 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-7.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED,RCVD_IN_MSPIKE_H2, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS,URIBL_BLOCKED autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 348BB27BBE2 for ; Fri, 4 Apr 2025 20:20:16 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1u0mZO-0007Jr-Rb; Fri, 04 Apr 2025 15:19:14 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1u0mZI-0007CO-96 for guix-patches@gnu.org; Fri, 04 Apr 2025 15:19:08 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1u0mZH-0007xZ-Pk for guix-patches@gnu.org; Fri, 04 Apr 2025 15:19:07 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=SA+A6hy6T8OpCxqcJaJxpB3ESyUhRDVW0x0G0PhMnEk=; b=ddrjET+/ncnqJjoHbR7/qseslZeuv1Dopj0uoeQjqvZBjWyLuRR601gnzv0HuOUHVK9H4QDVBJ73eKABEM8GZloH/42H8wAe7X3Czd/9bQAbx7WNVJNUrcsXfNCOoD4KQHiWoKIIFau4dF6OYC/6jBz1eYbbE0HO0u6EYG+fD88Rh7ILcho71C5n3giLfGileNnrfK7aUH4/Mdr3Z6u0+YcXjp+yLrrfgOOjqlm5mmQg6TM1KT9aqNve9jDDaOiYEoxdx8LxPGgE5jFZr/Yi6FGqOz3jQQ4Gu3S3tUiGepA+jSt+FO0CreL20Kpqu69EEwy7f6j8VJk3pSECs3axSQ==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1u0mZH-0007Rx-Iq for guix-patches@gnu.org; Fri, 04 Apr 2025 15:19:07 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77541] [PATCH 32/38] gnu: python-rq-scheduler: Update to 0.14. 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[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)") From patchwork Fri Apr 4 19:17:05 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 41292 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 93D4827BBEB; Fri, 4 Apr 2025 20:19:47 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-7.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED,RCVD_IN_MSPIKE_H2, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 2766127BBE2 for ; Fri, 4 Apr 2025 20:19:46 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1u0mZN-0007Iq-UE; Fri, 04 Apr 2025 15:19:13 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1u0mZI-0007Db-Mh for guix-patches@gnu.org; Fri, 04 Apr 2025 15:19:08 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1u0mZI-0007ya-8A for guix-patches@gnu.org; Fri, 04 Apr 2025 15:19:08 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=A2CqAaRHw0fEJJTWN/aaeC7lg+bfK+ZL7gxW4tv+I0o=; b=GlDGRuI4IA4DJNKSyZsNhP/7iRZf1TrC4XihsL0fSfVVYPgFqvKOdiT+augt0qUrB5FAMBGXHI6GxmbNFz0Lw98D1NQ8miQH1xnsfxAnGXeP7Ugm5jiXJoOcrPog7DmdRceZNLSGAwJ4aGWvg/06t5z52kLSVeajiS49ljNY66VCo5DVBpjeB0Pttr+lDBiZFh4ihV21LwbYQl6nSvsu4+dNfDruOU2uvdMqI4XJuZNhvWIWC6N4UEJ0hQ0D+Tr33LiCohdcDBH3//1PFq0jGvk04ev1VOTI/Ad+DiDZ+1HLcJBwiOzKdN0PRpsrgYeRMh+c9ndbQVrkaaGbY7g1hw==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1u0mZI-0007S5-2e for guix-patches@gnu.org; Fri, 04 Apr 2025 15:19:08 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77541] [PATCH 33/38] gnu: python-port-for: Update to 0.7.4. 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[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 From patchwork Fri Apr 4 19:17:06 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 41305 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 6F36527BBEA; Fri, 4 Apr 2025 20:20:07 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-7.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED,RCVD_IN_MSPIKE_H2, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id EF60127BBE2 for ; Fri, 4 Apr 2025 20:20:06 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1u0mZQ-0007Ly-E8; Fri, 04 Apr 2025 15:19:16 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1u0mZJ-0007Ek-54 for guix-patches@gnu.org; Fri, 04 Apr 2025 15:19:09 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1u0mZI-0007yu-P4 for guix-patches@gnu.org; Fri, 04 Apr 2025 15:19:08 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=UymMTuymJrpNBEsapT3vUU1jdCsQwRsy7vX1aFUe+qk=; b=vWx8OzN/wvKfKyQaxGcOFTUachVnuJrATuRR2YnMQvHedZhr5be/611JHpi4VB+6OWrfuoVxJ2bZNxIVEbNoAV/3XdPhfvO0gQfvBcth0218SUzvXN+0sKile9aknFyYnqQyXqtPt46RMEs43oYWAtLdUp5tSQn5QtxpqKZaZ2QYsDsZbXVXNdhcS3UiiGKGWPRGh57VVDUKu6O5nFJHVfz9YVIO9ktVL3uZePK3e6IBEcqo9fFP6JPDWKdImhyUim9gCbpu0ocVJtx1+tJ5/SOS3k1YyPb9i3nNE8YxeZuh9agGwizqy9TvnDH9zrO5vbvlJ14regUfRTemDi32Sw==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1u0mZI-0007SD-K4 for guix-patches@gnu.org; Fri, 04 Apr 2025 15:19:08 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77541] [PATCH 34/38] gnu: Remove python-cookies. 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(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") From patchwork Fri Apr 4 19:17:07 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 41295 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 53BF127BBE2; Fri, 4 Apr 2025 20:19:50 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-7.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED,RCVD_IN_MSPIKE_H2, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 5662B27BBEE for ; Fri, 4 Apr 2025 20:19:46 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1u0mZR-0007QE-Cy; Fri, 04 Apr 2025 15:19:17 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1u0mZK-0007FW-25 for guix-patches@gnu.org; Fri, 04 Apr 2025 15:19:11 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1u0mZJ-0007z9-Ap for guix-patches@gnu.org; Fri, 04 Apr 2025 15:19:09 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=8Q+Bexx4JALbjsRYXFa1MTUUmaOvVTbnkSw45waWiTE=; b=YIFYDrA3GQ5a3yV/qmOhhO2dKxhufmjmPND3fhyNkdXqx7bvk/44LErYxRj9EdQvrDbMBWuSnKfMDaGbF/uiqPpldVfuQgF1sozCK6TxOdC2ax9CkP2N0InIl6Kzl4iqEnHuxSFVSyOju4LqQInAibZ85MUfbT0JStAeGN5nyN+MHmxb8D7x+Sxj5bjxmvz2+31BEjMYN+15QrdyC08w1adUu6q5OjR1wml/6cgmM4O4B7mWiv+saELFqKEB54MxTYDfXPhUmdZjsCMR7QqgrvHmKQWvZO0Uzcrt+yIxSklXWAInlj8Itnc+2KDou5kZyPAqidzAWFZHlNXwqOd2Bg==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1u0mZJ-0007SM-45 for guix-patches@gnu.org; Fri, 04 Apr 2025 15:19:09 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77541] [PATCH 35/38] gnu: python-django-rq: Update to 3.0.0. 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[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.") 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#false)) ;there are none From patchwork Fri Apr 4 19:17:09 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 41299 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 4EB3F27BBEA; Fri, 4 Apr 2025 20:19:54 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-7.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED,RCVD_IN_MSPIKE_H2, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS,URIBL_BLOCKED autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 1ECCF27BBE2 for ; Fri, 4 Apr 2025 20:19:54 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1u0mZS-0007SJ-Fv; Fri, 04 Apr 2025 15:19:18 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1u0mZL-0007G6-2N for guix-patches@gnu.org; Fri, 04 Apr 2025 15:19:11 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1u0mZK-0007zV-Dy for guix-patches@gnu.org; Fri, 04 Apr 2025 15:19:10 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=PkBd/vL4Kd7PUCO9tku6o7JQikgZf8fuXAKfVmIzT9c=; b=dmcWjnDxScwH+uGXlTKj1Gi8L7l9DIGrqFKooG6Z1u6gs3bNYJ06beeI2f7KJnU/S96jscJstPpGmzSpgH0fI8baEgMJgY3t3dwxD1P3vHNI4mdPoSEOKn9+cFP0WHl0WwZDMcfnp9nTm2tXqJHIps1mNgmFtWkqbGKncKDK5Je6wFL9nZfCM2Po/2APdy42Rb35/Ifg2Osf169jFGTfHRFxN4i9Dq9ZSbJz3AJvJjKQeGKRprqQ/8ObJBn7uMnfGq3VSEQoLdC9ONegaZigknMHRvB5OITgQEVYJrXAFh2vyAz2uOrcAAchknprIUjGFXMCu/tC53jBsXSYB5NHWw==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1u0mZK-0007Sb-37 for guix-patches@gnu.org; Fri, 04 Apr 2025 15:19:10 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77541] [PATCH 37/38] gnu: python-country-converter: Add missing native-input. 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[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