diff options
| -rw-r--r-- | .guix/ccwl-package.scm | 8 | ||||
| -rw-r--r-- | Makefile | 10 | ||||
| -rw-r--r-- | README.org | 11 | ||||
| -rw-r--r-- | build-aux/test-driver.scm | 92 | ||||
| -rw-r--r-- | ccwl/cwl.scm | 9 | ||||
| -rwxr-xr-x | scripts/ccwl | 101 | ||||
| -rw-r--r-- | tests/ccwl.scm | 3 | ||||
| -rw-r--r-- | tests/cwl.scm | 16 | ||||
| -rw-r--r-- | tests/ui.scm | 5 |
9 files changed, 104 insertions, 151 deletions
diff --git a/.guix/ccwl-package.scm b/.guix/ccwl-package.scm index a70e3e0..d585daa 100644 --- a/.guix/ccwl-package.scm +++ b/.guix/ccwl-package.scm @@ -1,5 +1,5 @@ ;;; ccwl --- Concise Common Workflow Language -;;; Copyright © 2021, 2023–2024 Arun Isaac <arunisaac@systemreboot.net> +;;; Copyright © 2021, 2023–2025 Arun Isaac <arunisaac@systemreboot.net> ;;; ;;; This file is part of ccwl. ;;; @@ -20,6 +20,7 @@ #:use-module ((gnu packages bioinformatics) #:prefix guix:) #:use-module ((gnu packages emacs) #:select (emacs-minimal)) #:use-module ((gnu packages fonts) #:select (font-charter font-fira-code)) + #:use-module ((gnu packages guile-xyz) #:select (guile-run64)) #:use-module ((guix build-system guile) #:select (%guile-build-system-modules)) #:use-module (guix gexp) #:use-module (guix git-download) @@ -34,7 +35,10 @@ "ccwl-checkout" #:recursive? #t #:select? (or (git-predicate (dirname (current-source-directory))) - (const #t)))))) + (const #t)))) + (native-inputs + (modify-inputs (package-native-inputs guix:ccwl) + (prepend guile-run64))))) (define ccwl-website-gexp (let ((development-profile diff --git a/Makefile b/Makefile index f4487d9..5a9b07f 100644 --- a/Makefile +++ b/Makefile @@ -1,5 +1,5 @@ # ccwl --- Concise Common Workflow Language -# Copyright © 2022, 2024 Arun Isaac <arunisaac@systemreboot.net> +# Copyright © 2022, 2024–2025 Arun Isaac <arunisaac@systemreboot.net> # # This file is part of ccwl. # @@ -24,12 +24,12 @@ GIT = git GPG = gpg GUILD = guild GUILE = guile +GUILE_RUN64 = guile-run64 LZIP = lzip SKRIBILO = skribilo FIND_DEPENDENCIES = build-aux/find-dependencies.scm GENERATE_CWL_OUTPUT = build-aux/generate-cwl-output.sh -TEST_DRIVER = build-aux/test-driver.scm top_level_module_dir = $(project) sources = $(wildcard $(top_level_module_dir)/*.scm) @@ -46,7 +46,7 @@ fonts = $(addprefix $(GUIX_ENVIRONMENT)/share/fonts/web/, charter_regular.woff2 distribute_files = $(sources) $(scripts) $(tests) $(test_data) \ $(doc_sources) doc/skribilo.scm $(doc_data) $(DOC_SCM) $(DOC_OTHER) \ pre-inst-env guix.scm Makefile configure configure.scm \ - $(FIND_DEPENDENCIES) $(GENERATE_CWL_OUTPUT) $(TEST_DRIVER) \ + $(FIND_DEPENDENCIES) $(GENERATE_CWL_OUTPUT) \ COPYING NEWS.org README.org scmdir = $(datarootdir)/guile/site/$(guile_effective_version)/$(top_level_module_dir) @@ -63,8 +63,8 @@ all: $(objects) # Run tests -check: $(tests) $(TEST_DRIVER) - $(GUILE) --no-auto-compile -L . $(TEST_DRIVER) $(tests) +check: + ./pre-inst-env $(GUILE_RUN64) $(tests) # Build documentation diff --git a/README.org b/README.org index 3d8e31a..3084234 100644 --- a/README.org +++ b/README.org @@ -36,14 +36,14 @@ Download the Docker image from [[https://github.com/arunisaac/ccwl/releases][the it. Then, run ccwl with command-line arguments of your choice. #+BEGIN_SRC shell $ docker load -i ccwl-docker.tar.gz - $ docker run ccwl [ARGS...] + $ docker run ccwl ccwl [ARGS...] #+END_SRC When passing files into the Docker container, remember to share the filesystem. The following command is one way to share the current directory with the container. #+BEGIN_SRC shell - $ docker run -v "$PWD:$PWD" -w "$PWD" ccwl compile foo.scm + $ docker run -v "$PWD:$PWD" -w "$PWD" ccwl ccwl compile foo.scm #+END_SRC ** Using Guix @@ -80,8 +80,11 @@ introduction to ccwl. * Contributing Feedback, suggestions, feature requests, bug reports and pull requests -are all welcome. Unclear and unspecific error messages are considered -a bug. Do report them! +are all welcome. Please write to [[mailto:ccwl@systemreboot.net][ccwl@systemreboot.net]]. You may also +browse the [[https://lists.systemreboot.net/ccwl][archives]] of previous discussions. Unclear and unspecific +error messages are considered a bug. Do report them! + +We do not accept issues or pull requests on GitHub. Thank you! To hack on ccwl, you can use GNU Guix to quickly drop into a development environment by running diff --git a/build-aux/test-driver.scm b/build-aux/test-driver.scm deleted file mode 100644 index adac481..0000000 --- a/build-aux/test-driver.scm +++ /dev/null @@ -1,92 +0,0 @@ -;;; ccwl --- Concise Common Workflow Language -;;; Copyright © 2021, 2022 Arun Isaac <arunisaac@systemreboot.net> -;;; -;;; This file is part of ccwl. -;;; -;;; ccwl 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. -;;; -;;; ccwl 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 ccwl. If not, see <https://www.gnu.org/licenses/>. - -;;; Commentary: - -;; This is a better test driver for Guile's (srfi srfi-64). -;; -;; TODO: Improve Guile's test driver so this module won't be -;; necessary. - -;;; Code: - -(use-modules (ice-9 format) - (ice-9 match) - (srfi srfi-26) - (srfi srfi-64) - (term ansi-color)) - -(define (color color-symbol str color?) - (if color? - (colorize-string str color-symbol) - str)) - -(define red (cut color 'RED <> <>)) -(define green (cut color 'GREEN <> <>)) -(define magenta (cut color 'MAGENTA <> <>)) - -(define (my-gnu-runner color?) - (let ((runner (test-runner-null))) - (test-runner-on-group-begin! runner - (lambda (runner suite-name count) - (format #t (magenta "%%%% ~a~%" color?) suite-name))) - (test-runner-on-group-end! runner - (lambda _ - (newline))) - (test-runner-on-test-end! runner - (lambda (runner) - (let ((name (test-runner-test-name runner)) - (result (string-upcase - (symbol->string (test-result-kind runner)))) - (result-alist (test-result-alist runner))) - (format #t "~a ~a~%" - (case (test-result-kind runner) - ((pass) (green result color?)) - (else (red result color?))) - name) - ;; If test did not pass, print details. - (unless (eq? (test-result-kind runner) 'pass) - (format (current-error-port) - "~a:~a~%expected: ~s~%actual: ~s~%" - (assq-ref result-alist 'source-file) - (assq-ref result-alist 'source-line) - (match (assq-ref result-alist 'source-form) - (('test-assert _ ...) #t) - (_ (assq-ref result-alist 'expected-value))) - (assq-ref result-alist 'actual-value)))))) - runner)) - -(match (command-line) - ((_ test-files ...) - (let ((runner (my-gnu-runner #t))) - (test-with-runner runner - (for-each load-from-path test-files) - (display (magenta "SUMMARY" #t)) - (newline) - (format #t "PASS: ~a -FAIL: ~a -XPASS: ~a -XFAIL: ~a -SKIP: ~a -" - (test-runner-pass-count runner) - (test-runner-fail-count runner) - (test-runner-xpass-count runner) - (test-runner-xfail-count runner) - (test-runner-skip-count runner)) - (exit (zero? (test-runner-fail-count runner))))))) diff --git a/ccwl/cwl.scm b/ccwl/cwl.scm index baef519..0f600ca 100644 --- a/ccwl/cwl.scm +++ b/ccwl/cwl.scm @@ -1,5 +1,5 @@ ;;; ccwl --- Concise Common Workflow Language -;;; Copyright © 2021, 2023–2024 Arun Isaac <arunisaac@systemreboot.net> +;;; Copyright © 2021, 2023–2025 Arun Isaac <arunisaac@systemreboot.net> ;;; ;;; This file is part of ccwl. ;;; @@ -136,10 +136,13 @@ CWL YAML specification." "Render @var{input}, a @code{<input>} object, into a CWL tree." `(,(input-id input) (type . ,(type->cwl (input-type input))) + ;; The default property is special because a value of #f is + ;; meaningful and must be serialized. + ,@(if (unspecified-default? (input-default input)) + '() + `((default . ,(input-default input)))) ,@(or (filter-alist `((label . ,(input-label input)) - (default . ,(and (not (unspecified-default? (input-default input))) - (input-default input))) ;; inputBinding is only relevant to commands, not ;; workflows. But, the input position and prefix are not set ;; for worklow inputs and therefore this sub-expression has diff --git a/scripts/ccwl b/scripts/ccwl index 984d22a..fbd549d 100755 --- a/scripts/ccwl +++ b/scripts/ccwl @@ -3,7 +3,7 @@ exec guile --no-auto-compile -e main -s "$0" "$@" !# ;;; ccwl --- Concise Common Workflow Language -;;; Copyright © 2021–2024 Arun Isaac <arunisaac@systemreboot.net> +;;; Copyright © 2021–2025 Arun Isaac <arunisaac@systemreboot.net> ;;; ;;; This file is part of ccwl. ;;; @@ -28,6 +28,7 @@ exec guile --no-auto-compile -e main -s "$0" "$@" (use-modules (rnrs conditions) (rnrs exceptions) + (srfi srfi-26) (srfi srfi-28) (srfi srfi-37) (ice-9 match) @@ -49,6 +50,52 @@ exec guile --no-auto-compile -e main -s "$0" "$@" (lambda (opt name arg result) (acons 'help #t result)))) +(define %options + (list (option (list #\t "to") #t #f + (lambda (opt name arg result) + (let ((supported (list "cwl" "dot"))) + (unless (member arg supported) + (raise-exception + (formatted-message "Invalid target ~a argument ~s. Supported targets are ~a." + (if (char? name) + (string #\- name) + (string-append "--" name)) + arg + (string-join supported ", "))))) + (acons 'to (string->symbol arg) + result))) + (option (list #\o "output") #t #f + (lambda (opt name arg result) + (acons 'output-file arg result))) + %help-option)) + +(define (ccwl-compile source to port) + "Compile @var{source} file to @var{to} format writing output to +@var{port}. @var{to} is either @code{'cwl} or @code{'dot}." + ;; We don't need to compile ccwl files. Loading is sufficient for + ;; our purposes. Besides, compiling would fail since the workflow + ;; macro cannot access command definitions. + (set! %load-should-auto-compile #f) + ((case to + ((cwl) function->cwl) + ((dot) function->dot)) + (let ((result (guard (exception + ;; Handle syntax violation exceptions by + ;; reporting them and exiting. + ((ccwl-violation? exception) + (report-ccwl-violation exception) + (exit #f))) + (load (canonicalize-path source) + read-syntax)))) + (if (or (command? result) + (js-expression? result) + (workflow? result)) + result + (raise-exception + (formatted-message "Last expression in file ~a returns none of workflow, command or js-expression" + source)))) + port)) + (define (main args) (with-exception-handler (lambda (condition) @@ -75,30 +122,17 @@ Thank you! (match args ((program "compile" args ...) (let* ((args (args-fold args - (list (option (list #\t "to") #t #f - (lambda (opt name arg result) - (let ((supported (list "cwl" "dot"))) - (unless (member arg supported) - (scm-error 'misc-error - #f - "Invalid target ~A argument ~S. Supported targets are ~A." - (list (if (char? name) - (string #\- name) - (string-append "--" name)) - arg - (string-join supported ", ")) - #f))) - (acons 'to arg result))) - %help-option) + %options invalid-option (lambda (arg result) (acons 'source-file arg result)) - '((to . "cwl"))))) + '((to . cwl))))) (when (or (assq 'help args) (not (assq-ref args 'source-file))) (display (format "Usage: ~a compile [OPTIONS] SOURCE-FILE Compile SOURCE-FILE. + -o, --output=FILE write compiled output to file -t, --to=TARGET compile SOURCE-FILE to TARGET language; Supported targets are cwl (default) and dot. @@ -106,30 +140,15 @@ Compile SOURCE-FILE. program) (current-error-port)) (exit (assq 'help args))) - ;; We don't need to compile ccwl files. Loading is sufficient - ;; for our purposes. Besides, compiling would fail since the - ;; workflow macro cannot access command definitions. - (set! %load-should-auto-compile #f) - (let ((to (assq-ref args 'to))) - ((cond - ((string=? to "cwl") function->cwl) - ((string=? to "dot") function->dot)) - (guard (exception - ;; Handle syntax violation exceptions by reporting - ;; them and exiting. - ((ccwl-violation? exception) - (report-ccwl-violation exception) - (exit #f))) - (let ((result (load (canonicalize-path (assq-ref args 'source-file)) - read-syntax))) - (if (or (command? result) - (js-expression? result) - (workflow? result)) - result - (raise-exception - (condition (formatted-message "Last expression in file ~a returns none of workflow, command or js-expression" - (assq-ref args 'source-file))))))) - (current-output-port))))) + (if (assq-ref args 'output-file) + (call-with-output-file (assq-ref args 'output-file) + (cut ccwl-compile + (assq-ref args 'source-file) + (assq-ref args 'to) + <>)) + (ccwl-compile (assq-ref args 'source-file) + (assq-ref args 'to) + (current-output-port))))) ((program args ...) (let ((args (args-fold args (list %help-option) diff --git a/tests/ccwl.scm b/tests/ccwl.scm index 2d755ad..e10d9f2 100644 --- a/tests/ccwl.scm +++ b/tests/ccwl.scm @@ -1,5 +1,5 @@ ;;; ccwl --- Concise Common Workflow Language -;;; Copyright © 2021–2024 Arun Isaac <arunisaac@systemreboot.net> +;;; Copyright © 2021–2025 Arun Isaac <arunisaac@systemreboot.net> ;;; ;;; This file is part of ccwl. ;;; @@ -20,6 +20,7 @@ (srfi srfi-1) (srfi srfi-64) (srfi srfi-71) + (ice-9 match) (ccwl ccwl) (ccwl conditions)) diff --git a/tests/cwl.scm b/tests/cwl.scm index ba619ab..8009a2e 100644 --- a/tests/cwl.scm +++ b/tests/cwl.scm @@ -1,5 +1,5 @@ ;;; ccwl --- Concise Common Workflow Language -;;; Copyright © 2023 Arun Isaac <arunisaac@systemreboot.net> +;;; Copyright © 2023, 2025 Arun Isaac <arunisaac@systemreboot.net> ;;; ;;; This file is part of ccwl. ;;; @@ -18,6 +18,12 @@ (use-modules (srfi srfi-64)) +(define make-input + (@@ (ccwl ccwl) make-input)) + +(define input->cwl-scm + (@@ (ccwl cwl) input->cwl-scm)) + (define type->cwl (@@ (ccwl cwl) type->cwl)) @@ -41,4 +47,12 @@ (items . File)))) (type->cwl (make-array-type (make-array-type 'File)))) +(test-equal "Serialize #f defaults in input values" + '("foo" + (type . boolean) + (default . #f) + (label . "foo")) + (input->cwl-scm + (make-input "foo" 'boolean "foo" #f #f #f #f '()))) + (test-end "cwl") diff --git a/tests/ui.scm b/tests/ui.scm index a5741c0..115a20e 100644 --- a/tests/ui.scm +++ b/tests/ui.scm @@ -1,5 +1,5 @@ ;;; ccwl --- Concise Common Workflow Language -;;; Copyright © 2023 Arun Isaac <arunisaac@systemreboot.net> +;;; Copyright © 2023, 2025 Arun Isaac <arunisaac@systemreboot.net> ;;; ;;; This file is part of ccwl. ;;; @@ -16,7 +16,8 @@ ;;; You should have received a copy of the GNU General Public License ;;; along with ccwl. If not, see <https://www.gnu.org/licenses/>. -(use-modules (srfi srfi-64) +(use-modules (srfi srfi-26) + (srfi srfi-64) (term ansi-color) (ccwl ui) (ccwl conditions)) |