| Age | Commit message (Expand) | Author |
|---|
| 2023-11-16 | ccwl: Support nested arrays.•••* ccwl/ccwl.scm (construct-type-syntax): Construct types recursively
to support nested arrays.
(key->output): Recursively convert stdout types to File types.
* ccwl/cwl.scm (type->cwl): New function.
(input->cwl-scm, output->cwl-scm): Use type->cwl.
* tests/ccwl.scm (make-array-type): New function.
(construct-type-syntax-wrapper): New syntax.
("construct-type-syntax on primitive types", "construct-type-syntax on
array types", "construct-type-syntax on nested array types"): New
tests.
* tests/cwl.scm, doc/array-types.scm, doc/nested-array-types.scm: New
files.
* doc/ccwl.skb (Cookbook)[Array types]: New section.
| Arun Isaac |
| 2023-11-14 | ccwl: Implement scatter.•••* ccwl/ccwl.scm (<step>): Wrap constructor make-step.
[scattered-inputs, scatter-method]: New fields.
(collect-scatter-step): New function.
(collect-steps): Implement scatter.
(key->output): If step scatters, convert output to an array type.
(workflow): Add syntax to initialize scattered-inputs and
scatter-method fields of <step> object.
* ccwl/cwl.scm (workflow->cwl-scm): Add ScatterFeatureRequirement if
workflow contains scattering steps. Serialize scattered-inputs and
scatter-method.
* doc/ccwl.skb (Cookbook)[Scatter/gather]: New section.
| Arun Isaac |
| 2023-10-17 | ccwl: Support staging input files.•••* ccwl/ccwl.scm (<input>)[stage?]: New field.
* ccwl/ccwl.scm (input): Add #:stage argument.
* ccwl/cwl.scm (command->cwl-scm): Serialize requirements for staged
inputs.
* doc/ccwl.skb (Cookbook)[Stage input files]: New section.
* tests/ccwl.scm ("inputs with an invalid #:stage? parameter must
raise a &ccwl-violation condition"): New test.
| Arun Isaac |
| 2023-10-15 | ccwl: Make #:stderr and #:stdout first class parameters.•••#:stderr and #:stdout, especially #:stdout, are commonly
required. They ought to be first class parameters and not tucked away
into #:other.
* ccwl/ccwl.scm (<command>)[stderr, stdout]: New fields.
* ccwl/ccwl.scm (command): Accept #:stderr and #:stdout as first class
parameters.
* ccwl/cwl.scm (command->cwl-scm): Serialize stderr and stdout fields.
* doc/capture-stdout.scm (print),
doc/decompress-compile-run.scm (run), doc/checksum.scm (md5sum,
sha1sum, sha256sum), doc/spell-check.scm (find-misspellings): Capture
stdout in file.
* doc/checksum.scm, doc/decompress-compile-run.scm:
* doc/ccwl.skb (Tutorial)[Capturing the standard output stream of a
command]: Document #:stdout first class parameter.
* doc/ccwl.skb (Tutorial)[Workflow with multiple steps]: Capture
stdout in explicitly named files.
* tests/ccwl.scm ("commands with non-string #:stderr parameters must
raise a &ccwl-violation condition", "commands with non-string #:stdout
parameters must raise a &ccwl-violation condition"): New tests.
| Arun Isaac |
| 2022-04-09 | doc: Add table of contents.•••* doc/ccwl.skb: Add table of contents.
| Arun Isaac |
| 2021-11-05 | doc: Add spell check workflow to tutorial.•••* doc/ccwl.skb (Tutorial)[Let's write a spell check workflow]: New
section.
* Makefile.am (doc/spell-check.out): New target.
(EXTRA_DIST): Add doc/spell-check-text.txt and doc/dictionary.
* doc/dictionary, doc/spell-check-text.txt,
doc/spell-check-workflow-1.scm, doc/spell-check-workflow-2.scm,
doc/spell-check.scm: New files.
| Arun Isaac |
| 2021-11-05 | doc: Document reuse of external CWL workflows.•••* doc/ccwl.skb (Cookbook): New chapter.
* doc/external-cwl-workflow.scm, doc/echo.cwl: New files.
* .gitignore: Add !doc/echo.cwl.
| Arun Isaac |
| 2021-10-18 | doc: Say that inputs, not workflow inputs, come into pipe and tee.•••Workflow inputs are now global. It is misleading to say that they come
into the first expression, namely pipe and tee, in these examples.
* doc/ccwl.skb (Tutorial)[Workflow with multiple steps]: Say that
inputs, not workflow inputs, come into pipe and tee.
| Arun Isaac |
| 2021-08-16 | Makefile: Generate sample output when building documentation.•••* Makefile.am (CLEANFILES): Add doc/*.out.
(CLEAN_DIRECTORIES): Add doc/cwl-output.
(GENERATE_CWL_OUTPUT): New variable.
(doc/capture-output-file.out,
doc/capture-output-file-with-parameter-reference.out,
doc/capture-stdout.out, doc/checksum.out,
doc/decompress-compile-run.out, doc/hello-world.out,
doc/pass-stdin.out, doc/hello.tar.out): New targets.
* doc/capture-output-file-with-parameter-reference.out,
doc/capture-output-file.out, doc/capture-stdout.out, doc/checksum.out,
doc/decompress-compile-run.out, doc/hello-world.out,
doc/hello.tar.out, doc/pass-stdin.out: Delete files.
* build-aux/generate-cwl-output.sh.in, doc/hello.c.gz, doc/hello.tar,
doc/hello.txt: New files.
* configure.ac: Configure build-aux/generate-cwl-output.sh.
* doc/ccwl.skb (Tutorial)[Passing input into the standard input stream
of a command]: Replace file "foo" with "hello.txt".
* .gitignore: Add build-aux/generate-cwl-output.sh, doc/*.out and
doc/cwl-output.
| Arun Isaac |
| 2021-07-05 | doc: Inline code snippets.•••* doc/ccwl.skb (Tutorial)[Important concepts]: Inline code snippets.
| Arun Isaac |
| 2021-07-05 | doc: Add python named arguments example.•••* doc/ccwl.skb (Tutorial)[Important concepts]: Add python named
arguments example.
| Arun Isaac |
| 2021-07-04 | doc: Use PNG images instead of SVG.•••PNG images are supported by both the info and html engines.
* doc/ccwl.skb (Tutorial)[Workflow with multiple steps]: Use PNG
images instead of SVG.
* Makefile.am (CLEANFILES): Replace doc/*.svg with doc/*.png.
(%.svg): Delete rule.
(%.png): New rule.
* .gitignore: Replace doc/*.svg with doc/*.png.
| Arun Isaac |
| 2021-07-04 | Makefile: Build skribilo documentation in-place.•••* Makefile.am (SKRIBILO_BUILD_DIR): Delete variable.
(CLEANFILES): Add doc/*.cwl, doc/*.dot, doc/*.svg, doc/ccwl.info,
doc/skribilo.go.
($(SKRIBILO_BUILD_DIR)/%.cwl): Rename to %.cwl.
(info-local, install-info-local): Depend on doc/ccwl.info instead of
$(SKRIBILO_BUILD_DIR)/ccwl.info.
(html-local, install-html-local, website/manual/dev/en): Depend on
doc/ccwl.html instead of $(SKRIBILO_BUILD_DIR)/ccwl.html.
($(SKRIBILO_BUILD_DIR)/ccwl.info): Rename to doc/ccwl.info.
($(SKRIBILO_BUILD_DIR)/ccwl.html): Rename to doc/ccwl.html.
(clean-local): Do not delete doc/skribilo.go and
$(SKRIBILO_BUILD_DIR).
* .gitignore: Add doc/*.cwl, doc/*.html, doc/*.info, doc/*.svg. Remove
doc/skribilo.
* doc/ccwl.skb (Tutorial)[Workflow with multiple steps]: Reference
images in the doc directory instead of in the doc/skribilo directory.
| Arun Isaac |
| 2021-07-03 | doc: Use emph instead of quotes for emphasis.•••* doc/ccwl.skb (Tutorial)[First example, Capturing the standard output
stream of a command]: Use emph instead of double quotes for emphasis.
| Arun Isaac |
| 2021-07-03 | doc: Move skribilo configuration into doc directory.•••* ccwl/skribilo.scm: Move to ...
* doc/skribilo.scm: ... here.
* doc/ccwl.skb: Import (doc skribilo) instead of (ccwl skribilo).
* Makefile.am ($(SKRIBILO_BUILD_DIR)/ccwl.info,
$(SKRIBILO_BUILD_DIR)/ccwl.html): Depend on doc/skribilo.go instead of
ccwl/skribilo.go.
* Makefile.am (clean-local): Delete doc/skribilo.go instead of
ccwl/skribilo.go.
| Arun Isaac |
| 2021-07-03 | doc: Squeeze double space.•••* doc/ccwl.skb (Tutorial)[Capturing output files]: Squeeze double
space.
| Arun Isaac |
| 2021-07-02 | doc: Add copyright headers.•••* doc/ccwl.skb: Add copyright headers.
| Arun Isaac |
| 2021-06-29 | doc: Document passing input into stdin.•••* doc/ccwl.skb (Tutorial)[Passing input into the standard input stream
of a command]: New section.
* doc/pass-stdin.scm, doc/pass-stdin.out: New files.
| Arun Isaac |
| 2021-06-28 | doc: Add workflow graphs.•••* Makefile.am (DOC_IMAGES): Add checksum.svg and
decompres-compile-run.svg.
* doc/ccwl.skb (Tutorial)[Workflow with multiple steps]: Add workflow
graphs checksum.svg and decompres-compile-run.svg.
| Arun Isaac |
| 2021-06-22 | doc: Specify command inputs in a separate argument.•••* doc/capture-output-file-with-parameter-reference.scm,
doc/capture-output-file.scm, doc/capture-stdout.scm, doc/checksum.scm,
doc/decompress-compile-run.scm, doc/hello-world.scm: Specify command
inputs in a separate argument.
* doc/ccwl.skb (Tutorial)[First example]: Update description of
command definition accordingly.
| Arun Isaac |
| 2021-06-22 | doc: Fix comma position.•••Lispy mode normalizes comma positions incorrectly for Skribilo
mode. This needs to be fixed upstream or elsewhere.
* doc/ccwl.skb (Tutorial)[Important concepts, Capturing the standard
output stream of a command, Capturing output files, Workflow with
multiple steps]: Fix comma position.
| Arun Isaac |
| 2021-06-21 | doc: Fill paragraph.•••* doc/ccwl.skb (Tutorial)[Workflow with multiple steps]: Fill
paragraph.
| Arun Isaac |
| 2021-06-19 | doc: Link to source for pipe and tee.•••* doc/ccwl.skb (Tutorial)[Workflow with multiple steps]: Link to
source for pipe and tee.
| Arun Isaac |
| 2021-06-15 | doc: Move documentation from texinfo to skribilo.•••* doc/ccwl.texi: Delete file.
* ccwl/skribilo.scm, doc/ccwl.skb,
doc/capture-output-file-with-parameter-reference.out,
doc/capture-output-file-with-parameter-reference.scm,
doc/capture-output-file.out, doc/capture-output-file.scm,
doc/capture-stdout.out, doc/capture-stdout.scm, doc/checksum.out,
doc/checksum.scm, doc/decompress-compile-run.out,
doc/decompress-compile-run.scm, doc/hello-world.out,
doc/hello-world.scm, doc/hello.tar.out: New files.
* configure.ac: Check for skribilo.
* Makefile.am: Unregister doc/ccwl.texi. Add documentation build
rules.
* guix.scm (ccwl)[native-inputs]: Replace texinfo with skribilo.
* .gitignore: Add doc/skribilo. Remove doc/version.texi, doc/*.html,
doc/*.info.
| Arun Isaac |
