ccwl/doc, branch v0.3.0

ccwl: Implement identity construct.

2023-12-01T22:35:23+00:00

* ccwl/ccwl.scm (collect-steps): Implement identity construct. * doc/ccwl.skb (Cookbook)[The identity construct]: New section. * doc/identity-construct.scm: New file.

ccwl: Implement item separators for array inputs.

2023-11-23T19:02:58+00:00

* ccwl/ccwl.scm ()[separator]: New field. * ccwl/ccwl.scm (run-arg-position, run-args): Support array input specifiers. (run-arg-separator): New function. (command): Set separator on input objects. * ccwl/cwl.scm (input->cwl-scm): Serialize itemSeparator. * tests/ccwl.scm ("commands with non-string #:separator parameters must raise a &ccwl-violation condition"): New test. * doc/ccwl.skb (Cookbook)[Array input item separators]: New section. * doc/array-input-item-separators.scm: New file.

doc: Update source reference to rename.

2023-11-21T23:32:46+00:00

* doc/ccwl.skb (Tutorial)[Let's write a spell check workflow]: Update source reference to rename.

ccwl: Restrict #:binding parameter to YAML serializable trees.

2023-11-18T00:02:57+00:00

* 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.

doc: Add chapter and section identifiers.

2023-11-17T10:09:20+00:00

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.

ccwl: Support nested arrays.

2023-11-16T13:59:33+00:00

* 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.

doc: Add scatter-gather snippet.

2023-11-14T23:23:57+00:00

I forgot to add this file in my previous commit. * doc/scatter-gather.scm: New file.

ccwl: Implement scatter.

2023-11-14T22:52:03+00:00

* ccwl/ccwl.scm (): 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 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.

doc: Add staging-input-files.scm snippet source file.

2023-10-17T18:35:05+00:00

This file was required by the previous commit, but I forgot to commit it! * doc/staging-input-files.scm: New file.

ccwl: Support staging input files.

2023-10-17T18:16:50+00:00

* ccwl/ccwl.scm ()[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.