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Diffstat (limited to '.guix/cwltest-package.scm')
| -rw-r--r-- | .guix/cwltest-package.scm | 117 |
1 files changed, 117 insertions, 0 deletions
diff --git a/.guix/cwltest-package.scm b/.guix/cwltest-package.scm new file mode 100644 index 0000000..f3eeb9d --- /dev/null +++ b/.guix/cwltest-package.scm @@ -0,0 +1,117 @@ +;;; ravanan --- High-reproducibility CWL runner powered by Guix +;;; Copyright © 2025 Arun Isaac <arunisaac@systemreboot.net> +;;; +;;; This file is part of ravanan. +;;; +;;; ravanan is free software: you can redistribute it and/or modify it +;;; under the terms of the GNU General Public License as published by +;;; the Free Software Foundation, either version 3 of the License, or +;;; (at your option) any later version. +;;; +;;; ravanan is distributed in the hope that it will be useful, but +;;; WITHOUT ANY WARRANTY; without even the implied warranty of +;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +;;; General Public License for more details. +;;; +;;; You should have received a copy of the GNU General Public License +;;; along with ravanan. If not, see <https://www.gnu.org/licenses/>. + +(define-module (cwltest-package) + #:use-module ((gnu packages bioinformatics) + #:select (cwltool python-schema-salad)) + #:use-module ((gnu packages check) + #:select (python-pytest python-pytest-xdist)) + #:use-module ((gnu packages node) #:select (node)) + #:use-module ((gnu packages python-build) + #:select (python-setuptools python-setuptools-scm python-wheel)) + #:use-module ((gnu packages python-check) #:select (python-junit-xml)) + #:use-module ((gnu packages xml) #:select (python-defusedxml)) + #:use-module (guix build-system pyproject) + #:use-module (guix build-system python) + #:use-module (guix download) + #:use-module (guix gexp) + #:use-module ((guix licenses) #:prefix license:) + #:use-module (guix packages)) + +;; cwltest uses cwltool as a library. so, create a library version of cwltool +;; where inputs become propagated inputs. +(define python-cwltool + (package + (inherit cwltool) + (name "python-cwltool") + (inputs + (list node)) + (propagated-inputs + (modify-inputs (package-inputs cwltool) + (delete "node"))))) + +;; cwltest requires cwl-runner, the implementation-agnostic entry point to +;; cwltool, for its tests. +(define cwl-runner + (file-union "cwl-runner" + `(("bin/cwl-runner" ,(file-append cwltool "/bin/cwltool"))))) + +(define-public cwltest + (package + (name "cwltest") + (version "2.6.20250314152537") + (source + (origin + (method url-fetch) + (uri (pypi-uri "cwltest" version)) + (sha256 + (base32 "0h2w9bllb6cz8d5pja5lbbd1kj08yga40jdi3300anwllczcnfq6")))) + (build-system pyproject-build-system) + (arguments + (list #:modules `((rnrs io ports) + (srfi srfi-1) + (srfi srfi-26) + (srfi srfi-171) + (guix build pyproject-build-system) + (guix build utils)) + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'disable-docker-in-tests + (lambda _ + ;; Remove DockerRequirement (lines 7–10). + (let* ((file "tests/test-data/v1.0/cat1-testcli.cwl") + (lines (call-with-input-file file + (cut port-transduce + identity + rcons + get-line + <>)))) + (call-with-output-file file + (lambda (port) + (for-each (lambda (line) + (display line port) + (newline port)) + (append (take lines 6) + (drop lines 10)))))))) + (add-after 'install 'fix-permissions + (lambda* (#:key inputs outputs #:allow-other-keys) + ;; Make test scripts executable. + (for-each (lambda (file) + (chmod (string-append (site-packages inputs outputs) + "/cwltest/tests/test-data/" + file) + #o755)) + (list "dummy-executor.sh" + "mock_cwl_runner.py"))))))) + (inputs (list python-defusedxml + python-junit-xml + python-pytest + python-schema-salad)) + (native-inputs (list cwl-runner + python-cwltool + python-pytest + python-pytest-xdist + python-setuptools + python-setuptools-scm + python-wheel)) + (home-page "https://github.com/common-workflow-language/cwltest") + (synopsis "Common Workflow Language testing framework") + (description "Common Workflow Language testing framework.") + (license license:asl2.0))) + +cwltest |