diff options
Diffstat (limited to '.guix')
| -rw-r--r-- | .guix/cwl-conformance.scm | 114 | ||||
| -rw-r--r-- | .guix/cwltest-package.scm | 117 | ||||
| -rw-r--r-- | .guix/e2e-tests.scm | 78 | ||||
| -rw-r--r-- | .guix/ravanan-package.scm | 13 |
4 files changed, 320 insertions, 2 deletions
diff --git a/.guix/cwl-conformance.scm b/.guix/cwl-conformance.scm new file mode 100644 index 0000000..3e25c71 --- /dev/null +++ b/.guix/cwl-conformance.scm @@ -0,0 +1,114 @@ +;;; 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 (cwl-conformance) + #:use-module ((cwltest-package) #:select (cwltest)) + #:use-module ((ravanan-package) #:select (ravanan)) + #:use-module ((gnu packages python) #:select (python)) + #:use-module ((gnu packages python-web) #:select (python-pybadges)) + #:use-module (guix gexp) + #:use-module (guix git-download) + #:use-module (guix packages) + #:use-module (guix profiles) + #:use-module (guix utils) + #:use-module (ice-9 match) + #:export (cwltest-suite-gexp)) + +(define* (cwltest-suite-gexp cwltest-suite manifest-file #:key (skip-tests '())) + (with-imported-modules '((guix build utils)) + #~(begin + (use-modules (guix build utils) + (ice-9 match)) + + ;; Guix peeks into HOME. + (setenv "HOME" (getcwd)) + ;; cwltest writes out output directories to TMPDIR, but does not clean + ;; up after. So, we set TMPDIR to our own temporary directory that we + ;; can manage easily. See pending issue on cleaning up temporary output + ;; directories: + ;; https://github.com/common-workflow-language/cwltest/issues/249 + (mkdir "tmpdir") + (setenv "TMPDIR" "tmpdir") + (apply invoke + #$(file-append cwltest "/bin/cwltest") + "--test" #$cwltest-suite + "--tool" #$(file-append ravanan "/bin/ravanan") + "--badgedir" "badges" + (append '#$(match skip-tests + (() '()) + (_ (list "-S" (string-join skip-tests ",")))) + (list "--" + "--store=store" + (string-append "--guix-manifest=" #$manifest-file))))))) + +(define cwl-v1.2-conformance-suite + (let ((version "1.2.1")) + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/common-workflow-language/cwl-v1.2") + (commit (string-append "v" version)))) + (file-name (git-file-name "cwl-v1.2" version)) + (sha256 + (base32 + "03q8pd0niaaff52n6sn07l3rjnvwi4da649lnc8mn928sh0vywf3"))))) + +(define-public cwl-v1.2-conformance + (program-file "cwl-v1.2-conformance" + (cwltest-suite-gexp + (file-append cwl-v1.2-conformance-suite + "/conformance_tests.yaml") + (local-file "../cwl-conformance/manifest.scm") + ;; With these tests, evil things happen and too much memory is + ;; consumed. So, disable for now. + #:skip-tests (list "env_home_tmpdir" + "env_home_tmpdir_docker" + "env_home_tmpdir_docker_no_return_code")))) + +(define generate-badges-gexp + (with-imported-modules '((guix build utils)) + #~(begin + (use-modules (guix build utils) + (ice-9 match)) + + (match (command-line) + ((_ cwltest-badgedir output-directory) + (set-path-environment-variable + "GUIX_PYTHONPATH" + '(#$(string-append "lib/python" + (version-major+minor (package-version python)) + "/site-packages")) + (list #$(profile + (content (packages->manifest + (list python python-pybadges)))))) + (invoke #$(file-append python "/bin/python3") + #$(local-file "../cwl-conformance/badgegen.py") + cwltest-badgedir + #$(local-file "../cwl-conformance/commonwl.svg") + output-directory)) + ((program _ ...) + (format (current-error-port) + "Usage: ~a CWLTEST_BADGEDIR OUTPUT-DIRECTORY~%" + program) + (exit #f)))))) + +(define-public generate-badges + (program-file "generate-badges" + generate-badges-gexp)) + +cwl-v1.2-conformance 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 diff --git a/.guix/e2e-tests.scm b/.guix/e2e-tests.scm new file mode 100644 index 0000000..58ba480 --- /dev/null +++ b/.guix/e2e-tests.scm @@ -0,0 +1,78 @@ +;;; 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 (e2e-tests) + #:use-module ((cwl-conformance) #:select (cwltest-suite-gexp)) + #:use-module ((gnu packages bioinformatics) #:select (ccwl)) + #:use-module (guix gexp) + #:use-module (ice-9 match)) + +(define (ccwl-compile source-file) + #~(begin + (use-modules (rnrs io ports) + (srfi srfi-26) + (ice-9 match) + (ice-9 popen)) + + (define (call-with-input-pipe command proc) + (match command + ((prog args ...) + (let ((port #f)) + (dynamic-wind + (lambda () + (set! port (apply open-pipe* OPEN_READ prog args))) + (cut proc port) + (lambda () + (unless (zero? (close-pipe port)) + (error "Command invocation failed" command)))))))) + + (call-with-output-file #$output + (cut display + (call-with-input-pipe '(#$(file-append ccwl "/bin/ccwl") + "compile" + #$source-file) + get-string-all) + <>)))) + +(define e2e-tools-ccwl-sources + `(("hello-world.scm" . ,(local-file "../e2e-tests/tools/hello-world.scm")))) + +(define e2e-tools + (file-union "e2e-tools" + (map (match-lambda + ((ccwl-source-filename . ccwl-source-file) + (let ((cwl-filename (string-append (basename ccwl-source-filename ".scm") + ".cwl"))) + (list cwl-filename + (computed-file cwl-filename + (ccwl-compile ccwl-source-file)))))) + e2e-tools-ccwl-sources))) + +(define e2e-test-suite + (file-union "e2e-test-suite" + `(("tests.yaml" ,(local-file "../e2e-tests/tests.yaml")) + ("tools" ,e2e-tools) + ("jobs" ,(local-file "../e2e-tests/jobs" + #:recursive? #t))))) + +(define-public e2e-tests + (program-file "e2e-tests" + (cwltest-suite-gexp (file-append e2e-test-suite "/tests.yaml") + (local-file "../e2e-tests/manifest.scm")))) + +e2e-tests diff --git a/.guix/ravanan-package.scm b/.guix/ravanan-package.scm index a59ec68..508e8ce 100644 --- a/.guix/ravanan-package.scm +++ b/.guix/ravanan-package.scm @@ -29,7 +29,16 @@ (source (local-file ".." "ravanan-checkout" #:recursive? #t - #:select? (or (git-predicate (dirname (current-source-directory))) - (const #t)))))) + #:select? (lambda (file stat) + ;; If .guix is included, changes to other + ;; files under .guix—such as the CWL + ;; conformance tests—unnecessarily trigger a + ;; rebuild of ravanan. This could be a + ;; nuisance when hacking on the CWL + ;; conformance test scripts. + (and (not (string-contains file "/.guix/")) + ((or (git-predicate (dirname (current-source-directory))) + (const #t)) + file stat))))))) ravanan |