From patchwork Wed Apr 12 21:05:26 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Sharlatan Hellseher X-Patchwork-Id: 49122 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 4DB58174EE; Wed, 12 Apr 2023 22:07:05 +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=-3.7 required=5.0 tests=BAYES_00,DKIM_ADSP_CUSTOM_MED, DKIM_INVALID,DKIM_SIGNED,FREEMAIL_FROM,MAILING_LIST_MULTI, RCVD_IN_MSPIKE_H2,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 54FB7174BB for ; Wed, 12 Apr 2023 22:07:04 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pmhfL-0008BN-KB; Wed, 12 Apr 2023 17:06:08 -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 1pmhfH-00089y-6v for guix-patches@gnu.org; Wed, 12 Apr 2023 17:06:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1pmhfG-0007r3-Tu for guix-patches@gnu.org; Wed, 12 Apr 2023 17:06:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pmhfG-0000nk-PE for guix-patches@gnu.org; Wed, 12 Apr 2023 17:06:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#62801] [PATCH 1/4] gnu: Add python-astroscrappy. 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[82.25.93.113]) by smtp.gmail.com with ESMTPSA id y9-20020adffa49000000b002c592535839sm18031381wrr.17.2023.04.12.14.05.30 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Wed, 12 Apr 2023 14:05:30 -0700 (PDT) From: Sharlatan Hellseher Date: Wed, 12 Apr 2023 22:05:26 +0100 Message-Id: <20230412210529.30189-1-sharlatanus@gmail.com> X-Mailer: git-send-email 2.39.2 MIME-Version: 1.0 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/astronomy.scm (python-astroscrappy): New variable. --- gnu/packages/astronomy.scm | 48 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 48 insertions(+) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index db290f5987..f162be6006 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -1302,6 +1302,54 @@ (define-public python-astroquery to access online Astronomical data. Each web service has its own sub-package.") (license license:bsd-3))) +(define-public python-astroscrappy + (package + (name "python-astroscrappy") + (version "1.1.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "astroscrappy" version)) + (sha256 + (base32 "0shmfilvzpmlwz4fh0bx4kqmzr0y39fgga6vipxb5d1rx1y6q6by")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'preparations + (lambda _ (setenv "HOME" "/tmp"))) + (add-before 'install 'writable-compiler + (lambda _ (make-file-writable "astroscrappy/_compiler.c"))) + (add-before 'check 'writable-compiler + (lambda _ (make-file-writable "astroscrappy/_compiler.c"))) + (replace 'check + (lambda* (#:key inputs outputs tests? #:allow-other-keys) + (when tests? + (add-installed-pythonpath inputs outputs) + ;; Extensions have to be rebuilt before running the tests. + (invoke "python" "setup.py" "build_ext" "--inplace") + (invoke "python" "-m" "pytest" "--pyargs" "astroscrappy"))))))) + (native-inputs + (list python-cython + python-extension-helpers + python-h5py + python-pandas + python-pytest-astropy + python-scikit-image + python-setuptools-scm + python-scipy)) + (propagated-inputs (list python-astropy python-numpy)) + (home-page "https://github.com/astropy/astroscrappy") + (synopsis "Speedy Cosmic Ray Annihilation Package in Python") + (description + "Astro-SCRAPPY is designed to detect cosmic rays in images (numpy +arrays), based on Pieter van Dokkum's L.A.Cosmic algorithm. Much of this was +originally adapted from cosmics.py written by Malte Tewes. This is designed to +be as fast as possible so some of the readability has been sacrificed, +specifically in the C code.") + (license license:bsd-3))) + (define-public python-cdflib (package (name "python-cdflib") From patchwork Wed Apr 12 21:05:27 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Sharlatan Hellseher X-Patchwork-Id: 49120 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 0199C174EE; Wed, 12 Apr 2023 22:06:35 +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=-3.7 required=5.0 tests=BAYES_00,DKIM_ADSP_CUSTOM_MED, DKIM_INVALID,DKIM_SIGNED,FREEMAIL_FROM,MAILING_LIST_MULTI, RCVD_IN_MSPIKE_H2,SPF_HELO_PASS 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 41448174BB for ; Wed, 12 Apr 2023 22:06:34 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pmhfJ-0008A5-MQ; Wed, 12 Apr 2023 17:06:06 -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 1pmhfG-00089Y-EB for guix-patches@gnu.org; Wed, 12 Apr 2023 17:06:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1pmhfG-0007qS-5Z for guix-patches@gnu.org; Wed, 12 Apr 2023 17:06:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pmhfF-0000nO-Lc for guix-patches@gnu.org; Wed, 12 Apr 2023 17:06:01 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#62801] [PATCH 2/4] gnu: Add python-memory-profiler. 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[82.25.93.113]) by smtp.gmail.com with ESMTPSA id y9-20020adffa49000000b002c592535839sm18031381wrr.17.2023.04.12.14.05.31 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Wed, 12 Apr 2023 14:05:31 -0700 (PDT) From: Sharlatan Hellseher Date: Wed, 12 Apr 2023 22:05:27 +0100 Message-Id: <20230412210529.30189-2-sharlatanus@gmail.com> X-Mailer: git-send-email 2.39.2 In-Reply-To: <20230412210529.30189-1-sharlatanus@gmail.com> References: <20230412210529.30189-1-sharlatanus@gmail.com> MIME-Version: 1.0 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/python-check.scm (python-memory-profiler): New variable. --- gnu/packages/python-check.scm | 49 +++++++++++++++++++++++++++++++++++ 1 file changed, 49 insertions(+) diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm index 41a6997190..0affd2896b 100644 --- a/gnu/packages/python-check.scm +++ b/gnu/packages/python-check.scm @@ -1771,6 +1771,55 @@ (define-public python-atpublic (license (list license:asl2.0 license:lgpl3)))) ; only for setup_helpers.py +(define-public python-memory-profiler + (package + (name "python-memory-profiler") + (version "0.61") + (source + (origin + ;; PyPi tarball lacks tests. + (method git-fetch) + (uri (git-reference + (url "https://github.com/pythonprofilers/memory_profiler") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0n6g47qqmnn7abh3v25535hd8bmfvhf9bnp72m7bkd89f715m7xh")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + ;; XXX: @profile is not loaded in some test files and there are 3 tests + ;; which were failed, disable them for now. + (add-after 'unpack 'disable-fialing-tests + (lambda _ + (with-directory-excursion "test" + (for-each delete-file + '("test_as.py" + "test_func.py" + "test_gen.py" + "test_loop.py" + "test_loop_decorated.py" + "test_mprofile.py" + "test_nested.py" + "test_precision_command_line.py" + "test_unicode.py"))) + (substitute* "test/test_attributes.py" + (("def test_with_profile") "def __off_test_with_profile")) + (substitute* "test/test_stream_unicode.py" + (("def test_unicode") "def __off_test_unicode")) + (substitute* "test/test_tracemalloc.py" + (("def test_memory_profiler") "def __off_test_memory_profiler"))))))) + (native-inputs (list python-pytest-7.1 python-pytest-fixture-config python-safety)) + (propagated-inputs (list python-psutil)) + (home-page "https://github.com/pythonprofilers/memory_profiler") + (synopsis "Monitor Memory usage of Python code") + (description + "This package provides a module for monitoring memory usage of a python +program.") + (license license:bsd-3))) + (define-public python-mockito (package (name "python-mockito") From patchwork Wed Apr 12 21:05:28 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Sharlatan Hellseher X-Patchwork-Id: 49119 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 CA174174EE; Wed, 12 Apr 2023 22:06:26 +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=-3.7 required=5.0 tests=BAYES_00,DKIM_ADSP_CUSTOM_MED, DKIM_INVALID,DKIM_SIGNED,FREEMAIL_FROM,MAILING_LIST_MULTI, RCVD_IN_MSPIKE_H2,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 E00EF174BB for ; Wed, 12 Apr 2023 22:06:25 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pmhfL-0008BL-Bz; Wed, 12 Apr 2023 17:06:07 -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 1pmhfG-00089q-RU for guix-patches@gnu.org; Wed, 12 Apr 2023 17:06:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1pmhfG-0007qq-Io for guix-patches@gnu.org; Wed, 12 Apr 2023 17:06:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pmhfG-0000nd-Dg for guix-patches@gnu.org; Wed, 12 Apr 2023 17:06:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#62801] [PATCH 3/4] gnu: Add python-ccdproc. 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[82.25.93.113]) by smtp.gmail.com with ESMTPSA id y9-20020adffa49000000b002c592535839sm18031381wrr.17.2023.04.12.14.05.32 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Wed, 12 Apr 2023 14:05:32 -0700 (PDT) From: Sharlatan Hellseher Date: Wed, 12 Apr 2023 22:05:28 +0100 Message-Id: <20230412210529.30189-3-sharlatanus@gmail.com> X-Mailer: git-send-email 2.39.2 In-Reply-To: <20230412210529.30189-1-sharlatanus@gmail.com> References: <20230412210529.30189-1-sharlatanus@gmail.com> MIME-Version: 1.0 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/astronomy.scm (python-ccdproc): New variable. --- gnu/packages/astronomy.scm | 33 ++++++++++++++++++++++++++++++++- 1 file changed, 32 insertions(+), 1 deletion(-) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index f162be6006..9961e19695 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -5,7 +5,7 @@ ;;; Copyright © 2019 by Amar Singh ;;; Copyright © 2020 R Veera Kumar ;;; Copyright © 2020, 2021 Guillaume Le Vaillant -;;; Copyright © 2021, 2022, 2023 Sharlatan Hellseher +;;; Copyright © 2021-2023 Sharlatan Hellseher ;;; Copyright © 2021, 2022 Vinicius Monego ;;; Copyright © 2021 Greg Hogan ;;; Copyright © 2021 Foo Chuan Wei @@ -1350,6 +1350,37 @@ (define-public python-astroscrappy specifically in the C code.") (license license:bsd-3))) +(define-public python-ccdproc + (package + (name "python-ccdproc") + (version "2.4.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "ccdproc" version)) + (sha256 + (base32 "0fy1sni87cr05dkljd8wb7vgh7z9agh8wv5kiagxcpbcf8l06jv1")))) + (build-system pyproject-build-system) + (arguments + ;; FIXME: Test failed a lot with: DeprecationWarning: distutils Version + ;; classes are deprecated. Use packaging.version instead. + (list #:tests? #f)) + (native-inputs + (list python-memory-profiler python-pytest-astropy)) + (propagated-inputs + (list python-astropy + python-astroscrappy + python-numpy + python-reproject + python-scikit-image + python-scipy)) + (home-page "http://ccdproc.readthedocs.io/") + (synopsis "Basic data reductions of CCD images") + (description "The ccdproc package provides many of the necessary tools for +processing of CCD images built on a framework to provide error propagation and +bad pixel tracking throughout the reduction process.") + (license license:bsd-3))) + (define-public python-cdflib (package (name "python-cdflib") From patchwork Wed Apr 12 21:05:29 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Sharlatan Hellseher X-Patchwork-Id: 49121 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 12B5D174E8; Wed, 12 Apr 2023 22:07:02 +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=-3.7 required=5.0 tests=BAYES_00,DKIM_ADSP_CUSTOM_MED, DKIM_INVALID,DKIM_SIGNED,FREEMAIL_FROM,MAILING_LIST_MULTI, RCVD_IN_MSPIKE_H2,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 CD8ED174BB for ; Wed, 12 Apr 2023 22:06:59 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pmhfL-0008B5-3W; Wed, 12 Apr 2023 17:06:07 -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 1pmhfG-00089Z-H0 for guix-patches@gnu.org; Wed, 12 Apr 2023 17:06:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1pmhfG-0007qY-75 for guix-patches@gnu.org; Wed, 12 Apr 2023 17:06:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pmhfG-0000nW-2D for guix-patches@gnu.org; Wed, 12 Apr 2023 17:06:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#62801] [PATCH 4/4] gnu: python-astroalign: Update to 2.4.2. 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[82.25.93.113]) by smtp.gmail.com with ESMTPSA id y9-20020adffa49000000b002c592535839sm18031381wrr.17.2023.04.12.14.05.32 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Wed, 12 Apr 2023 14:05:33 -0700 (PDT) From: Sharlatan Hellseher Date: Wed, 12 Apr 2023 22:05:29 +0100 Message-Id: <20230412210529.30189-4-sharlatanus@gmail.com> X-Mailer: git-send-email 2.39.2 In-Reply-To: <20230412210529.30189-1-sharlatanus@gmail.com> References: <20230412210529.30189-1-sharlatanus@gmail.com> MIME-Version: 1.0 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/astronomy.scm (python-astroalign): Update to 2.4.2. [source]: Use git checkout instead PyPI to enable tests. [build-system]: Use pyproject-build-system. [propagated-inputs]: Migrate from inputs. Remove labels. Add optional python-bottleneck. [native-inputs]: Add python-astropy, python-ccdproc, python-pillow. --- gnu/packages/astronomy.scm | 30 +++++++++++++++++------------- 1 file changed, 17 insertions(+), 13 deletions(-) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index 9961e19695..0d7212791a 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -3070,22 +3070,26 @@ (define-public python-gwcs (define-public python-astroalign (package (name "python-astroalign") - (version "2.3.1") + (version "2.4.2") (source (origin - (method url-fetch) - (uri (pypi-uri "astroalign" version)) + ;; There are no tests in the PyPI tarball. + (method git-fetch) + (uri (git-reference + (url "https://github.com/quatrope/astroalign") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 - (base32 "19qzv3552lgrd9qmj0rxs51wmx485hw04cbf76ds5pin85kfaiy1")))) - (build-system python-build-system) - (arguments - ;; TODO: (Sharlatan-20210213T162940+0000): I could not make tests run - `(#:tests? #f)) - (inputs - `(("numpy" ,python-numpy) - ("scikit-image" ,python-scikit-image) - ("scipy" ,python-scipy) - ("sep" ,python-sep))) + (base32 "0hly20a65540hr3l1lsd1i4d90a0vdrbwnn6zx3z8s89ha9lq3pb")))) + (build-system pyproject-build-system) + (native-inputs + (list python-astropy python-ccdproc python-pillow)) + (propagated-inputs + (list python-bottleneck + python-numpy + python-scikit-image + python-scipy + python-sep)) (home-page "https://astroalign.readthedocs.io/") (synopsis "Astrometric Alignment of Images") (description