ccwl/tests, branch v0.2.0

tests: Add input-output-parameters.cwl.

2021-11-01T20:07:47+00:00

This is a follow-up to 0b359cf2c32cde81b4311d55273c8f6c14ca6b93 where this file should have been included. * tests/input-output-parameters.cwl: New file. * Makefile.am (EXTRA_DIST): Register it.

ccwl: Support external CWL workflows.

2021-11-01T20:01:56+00:00

* ccwl/ccwl.scm: Import (yaml). Export cwl-workflow?, cwl-workflow, cwl-workflow-file, cwl-workflow-inputs and cwl-workflow-outputs. (): New type. (cwl-workflow, function-input-keys, function-outputs, function-object): New functions. (command-input-keys, command-object): Delete functions. (collect-steps): Replace command-object with function-object, command-input-keys with function-input-keys and command-outputs with function-outputs. * ccwl/cwl.scm (workflow->cwl-scm): Handle objects. * tests/ccwl.scm ("read all forms of inputs and outputs from a CWL workflow"): New test. * guix.scm: Import (gnu packages guile-xyz) and (guix utils). (guile-libyaml): New variable. (ccwl)[inputs]: Add guile-libyaml.

tests: Fix quoting of type.

2021-10-12T11:15:39+00:00

* tests/ccwl.scm ("stdin input should not have inputBinding"): Fix quoting of type File.

ccwl: Factorize out CWL generation code to separate file.

2021-10-11T09:21:22+00:00

This factorization is required to support other compilation targets such as graphviz, bash, scheme, etc. * ccwl/cwl.scm: New file. * Makefile.am (SOURCES): Register it. * ccwl/ccwl.scm (ccwl): Export command?, command-inputs, command-outputs, command-args, command-stdin, command-other, workflow?, workflow-steps, workflow-inputs, workflow-outputs, workflow-other, input?, input-id, input-type, input-label, input-default, input-position, input-prefix, input-other, output?, output-id, output-type, output-binding, output-source, output-other, step?, step-id, step-run, step-in, step-out, unspecified-default?. (): New type. (filter-alist): Move to cwl.scm. (make-workflow): Refactor into workflow->cwl-scm in cwl.scm. (output->cwl): Move to cwl.scm as output->cwl-scm. (command->cwl): Move to cwl.scm as command->cwl-scm. (workflow-steps): Rename to collect-steps. Clarify docstring. (workflow): Use collect-steps instead of workflow-steps. Explicitly pass empty list as other argument of make-workflow. Add TODO note to implement it properly. * scripts/ccwl.in: Import (ccwl cwl) instead of (ccwl yaml). Use workflow->cwl instead of scm->yaml. * tests/ccwl.scm ("stdin input should not have inputBinding"): Use command->cwl-scm from (ccwl cwl) instead of command->cwl from (ccwl ccwl).

ccwl: Support #:allow-other-keys in lambda and syntax-lambda.

2021-10-04T11:25:21+00:00

* ccwl/utils.scm (lambda**): Support #:allow-other-keys. Update docstring. (syntax-lambda**): Update docstring. * tests/utils.scm ("Allow other keys in lambda**", "Allow other keys in syntax-lambda**"): New tests.

ccwl: Error out on invalid keywords to lambda**.

2021-10-04T11:04:55+00:00

* ccwl/utils.scm (lambda**): Error out on invalid keywords (that is, keywords other than #:key, #:key* and #:allow-other-keys). * tests/utils.scm ("lambda** should error out on unrecognized keywords in arguments"): New test.

tests: Remove stray syntax-lambda** form.

2021-10-04T10:24:22+00:00

* tests/utils.scm: Remove stray syntax-lambda** form.

ccwl: Make syntax-lambda more like lambda.

2021-07-27T10:28:02+00:00

I have tripped up several times on the differences between lambda** and syntax-lambda**. No longer! Making syntax-lambda** as close as possible to lambda** makes the code much more readable and align better with common sense. * ccwl/utils.scm (syntax-lambda**): Do not ignore the first identifier. Accept multiple values as arguments, not a single syntax object. * ccwl/ccwl.scm (command): Update use of syntax-lambda**. * tests/utils.scm ("syntax-lambda**", "syntax-lambda** with default values"): Update tests.

ccwl: Set default value of lambda** n-ary arguments to '().

2021-07-20T11:28:48+00:00

* ccwl/utils.scm (lambda**): Set default value of lambda** n-ary arguments to the empty list. Document this in the docstring. * tests/utils.scm ("default value of lambda** unary argument should be #f", "default value of lambda** n-ary argument should be the empty list"): New tests.

ccwl: Document syntax-lambda** support for default arguments.

2021-07-20T11:02:50+00:00

* ccwl/utils.scm (syntax-lambda**): Add example to docstring documenting support for default arguments. * tests/utils.scm ("syntax-lambda** with default values"): New test.