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[77.98.0.246]) by smtp.gmail.com with ESMTPSA id ffacd0b85a97d-3675a0e1688sm11076402f8f.60.2024.07.01.13.46.23 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 01 Jul 2024 13:46:23 -0700 (PDT) From: Sharlatan Hellseher Date: Mon, 1 Jul 2024 21:46:19 +0100 Message-ID: <85179153ce289e6ad62faddb3022bc01b3c28afb.1719866387.git.sharlatanus@gmail.com> X-Mailer: git-send-email 2.41.0 In-Reply-To: References: 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/simulation.scm (python-dolfin-adjoint): Fix indentation. Change-Id: I457639a98f1ae49d43042e557352d390afc9419d --- gnu/packages/simulation.scm | 48 ++++++++++++++++++------------------- 1 file changed, 24 insertions(+), 24 deletions(-) diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm index 4fa2e93d81..ab86e1d792 100644 --- a/gnu/packages/simulation.scm +++ b/gnu/packages/simulation.scm @@ -1180,29 +1180,29 @@ (define-public python-dolfin-adjoint (name "python-dolfin-adjoint") (version "2019.1.0") (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/dolfin-adjoint/pyadjoint") - (commit version))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0xhy76a5f33hz94wc9g2mc5qmwkxfccbbc6yxl7psm130afp8lhn")) - (modules '((guix build utils))) - (snippet - '(begin - ;; One of the migration tests attempts to call openmpi - ;; recursively and fails. See - ;; https://bitbucket.org/mpi4py/mpi4py/issues/95. Run the - ;; test sequentially instead. - (with-directory-excursion "tests/migration/optimal_control_mms" - (substitute* "test_optimal_control_mms.py" - (("\\\"mpirun\\\", \\\"-n\\\", \\\"2\\\", ") ""))) - ;; Result files are regenerated in the check phase. - (delete-file-recursively - "tests/migration/viscoelasticity/test-results") - #t)))) + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/dolfin-adjoint/pyadjoint") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0xhy76a5f33hz94wc9g2mc5qmwkxfccbbc6yxl7psm130afp8lhn")) + (modules '((guix build utils))) + (snippet + '(begin + ;; One of the migration tests attempts to call openmpi + ;; recursively and fails. See + ;; https://bitbucket.org/mpi4py/mpi4py/issues/95. Run the + ;; test sequentially instead. + (with-directory-excursion "tests/migration/optimal_control_mms" + (substitute* "test_optimal_control_mms.py" + (("\\\"mpirun\\\", \\\"-n\\\", \\\"2\\\", ") ""))) + ;; Result files are regenerated in the check phase. + (delete-file-recursively + "tests/migration/viscoelasticity/test-results") + #t)))) (build-system python-build-system) (inputs (list fenics openmpi pybind11)) @@ -1219,7 +1219,7 @@ (define-public python-dolfin-adjoint `(#:phases (modify-phases %standard-phases (add-after 'build 'mpi-setup - ,%openmpi-setup) + ,%openmpi-setup) (add-after 'install 'install-doc (lambda* (#:key outputs #:allow-other-keys) (let* ((doc (string-append (assoc-ref outputs "out") From patchwork Mon Jul 1 20:46:20 2024 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Sharlatan Hellseher X-Patchwork-Id: 65822 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 670AA27BBEA; Mon, 1 Jul 2024 21:48:34 +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=-2.7 required=5.0 tests=BAYES_00,DKIM_ADSP_CUSTOM_MED, DKIM_INVALID,DKIM_SIGNED,FREEMAIL_FROM,MAILING_LIST_MULTI, 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 9951B27BBE2 for ; Mon, 1 Jul 2024 21:48:33 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1sONwV-0006hu-ST; Mon, 01 Jul 2024 16:48:07 -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 1sONwR-0006gh-Tx for guix-patches@gnu.org; Mon, 01 Jul 2024 16:48:05 -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 1sONwQ-0007p5-M8 for guix-patches@gnu.org; Mon, 01 Jul 2024 16:48:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1sONwR-0002O2-Az for guix-patches@gnu.org; Mon, 01 Jul 2024 16:48:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#71884] [PATCH 2/3] gnu: python-dolfin-adjoint: Adjust package style. 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[77.98.0.246]) by smtp.gmail.com with ESMTPSA id ffacd0b85a97d-3675a0e1688sm11076402f8f.60.2024.07.01.13.46.24 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 01 Jul 2024 13:46:24 -0700 (PDT) From: Sharlatan Hellseher Date: Mon, 1 Jul 2024 21:46:20 +0100 Message-ID: X-Mailer: git-send-email 2.41.0 In-Reply-To: References: 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/simulation.scm (python-dolfin-adjoint): Move inputs after arguments. [description]: Place it on a new line, fix indentation. Change-Id: I3d971e48b4072258ed0b41af5c202e64af9de8f3 --- gnu/packages/simulation.scm | 40 ++++++++++++++++++------------------- 1 file changed, 20 insertions(+), 20 deletions(-) diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm index ab86e1d792..5341c0ae55 100644 --- a/gnu/packages/simulation.scm +++ b/gnu/packages/simulation.scm @@ -1204,17 +1204,6 @@ (define-public python-dolfin-adjoint "tests/migration/viscoelasticity/test-results") #t)))) (build-system python-build-system) - (inputs - (list fenics openmpi pybind11)) - (native-inputs - (list pkg-config - python-coverage - python-decorator - python-flake8 - python-pkgconfig - python-pytest)) - (propagated-inputs - `(("scipy" ,python-scipy))) (arguments `(#:phases (modify-phases %standard-phases @@ -1245,17 +1234,28 @@ (define-public python-dolfin-adjoint ;; fails with an ImportError if it sees that the backend module ;; has already been loaded. (delete 'sanity-check)))) + (inputs + (list fenics openmpi pybind11)) + (native-inputs + (list pkg-config + python-coverage + python-decorator + python-flake8 + python-pkgconfig + python-pytest)) + (propagated-inputs + (list python-scipy)) (home-page "https://www.dolfin-adjoint.org") (synopsis "Automatic differentiation library") - (description "@code{python-dolfin-adjoint} is a solver of -differential equations associated with a governing system and a -functional of interest. Working from the forward model the solver -automatically derives the discrete adjoint and tangent linear models. -These additional models are key ingredients in many algorithms such as -data assimilation, optimal control, sensitivity analysis, design -optimisation and error estimation. The dolfin-adjoint project -provides the necessary tools and data structures for cases where the -forward model is implemented in @code{fenics} or + (description + "@code{python-dolfin-adjoint} is a solver of differential equations +associated with a governing system and a functional of interest. Working from +the forward model the solver automatically derives the discrete adjoint and +tangent linear models. These additional models are key ingredients in many +algorithms such as data assimilation, optimal control, sensitivity analysis, +design optimisation and error estimation. The dolfin-adjoint project provides +the necessary tools and data structures for cases where the forward model is +implemented in @code{fenics} or @url{https://firedrakeproject.org,firedrake}.") 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[77.98.0.246]) by smtp.gmail.com with ESMTPSA id ffacd0b85a97d-3675a0e1688sm11076402f8f.60.2024.07.01.13.46.25 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 01 Jul 2024 13:46:25 -0700 (PDT) From: Sharlatan Hellseher Date: Mon, 1 Jul 2024 21:46:21 +0100 Message-ID: X-Mailer: git-send-email 2.41.0 In-Reply-To: References: 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/simulation.scm (python-dolfin-adjoint) [source]: Remove trailing #t from snippet. [build-system]: Swap to pyproject-build-system. [arguments]: Apply G-expressions. <#:phases>: Swap back to defaul 'check phase. python-dolfin-adjoint Change-Id: Idf100b718b44d9d6695e598c434fbbac55a38845 --- gnu/packages/simulation.scm | 58 +++++++++++++++++-------------------- 1 file changed, 26 insertions(+), 32 deletions(-) diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm index 5341c0ae55..182e00cec4 100644 --- a/gnu/packages/simulation.scm +++ b/gnu/packages/simulation.scm @@ -1201,39 +1201,33 @@ (define-public python-dolfin-adjoint (("\\\"mpirun\\\", \\\"-n\\\", \\\"2\\\", ") ""))) ;; Result files are regenerated in the check phase. (delete-file-recursively - "tests/migration/viscoelasticity/test-results") - #t)))) - (build-system python-build-system) + "tests/migration/viscoelasticity/test-results"))))) + (build-system pyproject-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'build 'mpi-setup - ,%openmpi-setup) - (add-after 'install 'install-doc - (lambda* (#:key outputs #:allow-other-keys) - (let* ((doc (string-append (assoc-ref outputs "out") - "/share/doc/" ,name "-" - ,version)) - (examples (string-append doc "/examples"))) - (mkdir-p examples) - (copy-recursively "examples" examples)) - #t)) - (replace 'check - (lambda* (#:key inputs outputs tests? #:allow-other-keys) - (when tests? - (add-installed-pythonpath inputs outputs) - (setenv "HOME" (getcwd)) - (and (invoke "py.test" "-v" "tests/fenics_adjoint" - "-k" "not test_read_checkpoint") - (invoke "py.test" "-v" "tests/migration") - (invoke "py.test" "-v" "tests/pyadjoint"))) - #t)) - ;; Remove 'sanity-check, because it tries to import - ;; firedrake_adjoint after importing fenics_adjoint. - ;; Both load a module named 'backend' and firedrake_adjoint - ;; fails with an ImportError if it sees that the backend module - ;; has already been loaded. - (delete 'sanity-check)))) + (list + #:test-flags + #~(list "tests/firedrake_adjoint/" + "tests/migration" + "tests/pyadjoint/" + "-k" "not test_read_checkpoint") + #:phases + #~(modify-phases %standard-phases + (add-after 'build 'mpi-setup ,%openmpi-setup) + (add-before 'check 'set-environment-variables + (lambda _ + (setenv "HOME" "/tmp"))) + (add-after 'install 'install-doc + (lambda _ + (let* ((doc (string-append #$output "/share/doc/" name "-" version)) + (examples (string-append doc "/examples"))) + (mkdir-p examples) + (copy-recursively "examples" examples)))) + ;; Remove 'sanity-check, because it tries to import + ;; firedrake_adjoint after importing fenics_adjoint. + ;; Both load a module named 'backend' and firedrake_adjoint + ;; fails with an ImportError if it sees that the backend module + ;; has already been loaded. + (delete 'sanity-check)))) (inputs (list fenics openmpi pybind11)) (native-inputs