| Age | Commit message (Expand) | Author |
|---|
| 2023-11-18 | ccwl: Restrict #:binding parameter to YAML serializable trees.•••* ccwl/ccwl.scm (ensure-yaml-serializable): Accept parameter name for
&formatted-message condition.
(input): Explicitly pass parameter name #:other. Restrict #:binding
parameter to YAML serializable trees.
*
doc/capture-output-file-with-parameter-reference.scm (extract-specific-file),
doc/capture-output-file.scm (extract),
doc/decompress-compile-run.scm (compile): Pass an YAML serializable
tree, not an expression, as the #:binding parameter.
| Arun Isaac |
| 2023-11-17 | doc: Add chapter and section identifiers.•••Identifiers are important so the generated HTML documentation can have
permanent URIs to all chapters and sections. We are not too concerned
with adding identifiers to subsections since we don't list them in the
table of contents.
* doc/ccwl.skb: Add chapter and section identifiers to all chapters
and sections.
| Arun Isaac |
| 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 | doc: Add scatter-gather snippet.•••I forgot to add this file in my previous commit.
* doc/scatter-gather.scm: New file.
| 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 | doc: Add staging-input-files.scm snippet source file.•••This file was required by the previous commit, but I forgot to commit
it!
* doc/staging-input-files.scm: New file.
| 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: Search source-path in scheme-source-form.•••* doc/skribilo.scm (scheme-source-form): Search source-path.
| 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: Support extracting specific forms from a scheme file.•••* doc/skribilo.scm (scheme-source-form): New public function.
| 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 |
| 2021-08-17 | ccwl: Define output objects using a macro instead of a function.•••This allows us to do sophisticated syntax checking at an early stage,
very close to the user interface. That way error messages from ccwl
will make a lot more sense.
* ccwl/ccwl.scm (output): Re-implement as macro.
(command): Use the new macro interface.
* 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: Use new quoting syntax for output
types.
| 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 |
| 2021-08-16 | ccwl: Define input objects using a macro instead of a function.•••This allows us to do sophisticated syntax checking at an early stage,
very close to the user interface. That way error messages from ccwl
will make a lot more sense.
* ccwl/ccwl.scm (input): Re-implement as macro.
(<input>): Add new functional setters set-input-position and
set-input-prefix.
(input-spec-id, run-arg-position, run-arg-prefix): New functions.
(command, workflow): Use the new macro interface.
* 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,
doc/pass-stdin.scm: Use new quoting syntax for input types.
| 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 | doc: Search for source-ref referenced files in source-path.•••* doc/skribilo.scm: Import (skribilo parameters).
(source-ref): Search for files in source-path.
| Arun Isaac |
| 2021-07-04 | doc: Remove redundant file open.•••* doc/skribilo.scm (source-ref): Remove redundant file open.
| 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 |
| 2021-05-25 | Add table of contents to manual.•••* doc/ccwl.texi: Add table of contents.
| Arun Isaac |
| 2021-05-25 | Add title and copyright pages to manual.•••* doc/ccwl.texi: Add title and copyright pages.
| Arun Isaac |
| 2021-05-25 | Hide Top node introduction in printed manual.•••* doc/ccwl.texi (Top): Move introduction into ifnottex block.
| Arun Isaac |
| 2021-05-25 | Mention version in manual.•••* doc/ccwl.texi: Include version.texi.
(Top): Mention version.
| Arun Isaac |
| 2021-05-24 | Add "Workflow with multiple steps" to tutorial.•••* doc/ccwl.texi (Workflow with multiple steps): New node.
(Tutorial): Link to "Workflow with multiple steps" node from menu.
| Arun Isaac |
| 2021-05-24 | Add "Capturing output files" to tutorial.•••* doc/ccwl.texi (Capturing output files): New section.
(Tutorial): Link to "Capturing output files" node from menu.
| Arun Isaac |
| 2021-05-24 | Add "Capturing stdout" section to tutorial.•••* doc/ccwl.texi (Capturing the standard output stream of a command):
New section.
* doc/ccwl.texi (Tutorial): Link to "Capturing stdout" node from menu.
| Arun Isaac |
| 2021-05-24 | Add "First example" section to tutorial.•••* doc/ccwl.texi (First example): New section.
(Tutorial): Link to "First example" node from menu.
| Arun Isaac |
| 2021-05-24 | Add tutorial.•••* doc/ccwl.texi (Tutorial): New chapter.
(Top): Link to "Tutorial" node from menu.
| Arun Isaac |
| 2021-05-23 | Add manual.•••* doc/ccwl.texi: New file.
* Makefile.am (bin_SCRIPTS): Add doc/ccwl.texi.
| Arun Isaac |
