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2024-03-22ccwl: Implement js-expression.Arun Isaac
js-expression corresponds to ExpressionTool in the CWL specification. * ccwl/ccwl.scm (<js-expression>): New type. (js-expression): New macro. (function-inputs, function-outputs, function-object): Support <js-expression> objects. (function-input-keys): Mention <js-expression> objects in docstring. * ccwl/cwl.scm (function->cwl, workflow->cwl-scm): Support <js-expression> objects. (command->cwl-scm): Move staging requirements handling to ... (staging-requirements): ... this new function. (js-expression->cwl, js-expression->cwl-scm): New functions. * ccwl/graphviz.scm (function->dot): Support <js-expression> objects. (command->graph): Abstract to ... (single-node-workflow->graph): ... this new function. (js-expression->dot, js-expression->graph): New functions. * scripts/ccwl (main): Support <js-expression> objects. * doc/ccwl.skb (Cookbook){Javascript expressions via ExpressionTool}: New section. * doc/js-expression-iota.scm: New file.
2024-03-22scripts: Use unified function terminology.Arun Isaac
Call workflows and commands by our unified notion of "function". This makes it more succinct when adding more kinds of functions. * ccwl/cwl.scm (workflow-or-command->cwl): Rename to function->cwl. * ccwl/graphviz.scm (workflow-or-command->dot): Rename to function->dot. * scripts/ccwl (main): Use function->cwl and function->dot.
2024-03-12ccwl: Find run argument directly without finding the position first.Arun Isaac
* ccwl/ccwl.scm (run-arg-position): Delete function. (find-run-arg): New function. (command): Use find-run-arg instead of run-arg-position.
2024-03-12ccwl: Count argument positions on flattened run arguments.Arun Isaac
* ccwl/ccwl.scm (command): Count argument positions on flattened run arguments. * tests/ccwl.scm ("count argument positions correctly when left-flanked by prefixed string arguments"): New test.
2024-03-12tests: Fix command definition in test.Arun Isaac
* tests/ccwl.scm ("outputs with #:other parameters that fail to evaluate must raise a &ccwl-violation condition"): Define command inputs, not outputs.
2024-01-26NEWS: Mark (term ansi-color) as code.Arun Isaac
* NEWS.org (Changes in 0.3.0)[Other]: Mark (term ansi-color) as code.
2024-01-26Add v0.3.0 release tarballs.Arun Isaac
* website/releases/ccwl-0.3.0.tar.lz, website/releases/ccwl-0.3.0.tar.lz.asc: New files. * build-aux/build-home-page.el (org-dblock-write:download): Add v0.3.0 release.
2024-01-26NEWS: Update for version 0.3.0.v0.3.0Arun Isaac
* NEWS.org (Changes in 0.3.0): New section.
2024-01-26guix: Add recipe to create a distribution tarball.Arun Isaac
* .guix/ccwl-distribution.scm: New file.
2024-01-26Makefile: Split up release tarball signature into separate target.Arun Isaac
* Makefile (dist): Move $(dist_archive).asc to ... (distsign): ... here.
2024-01-26Makefile: Clean up .depends.Arun Isaac
* Makefile (clean): Delete .depends.
2024-01-26build-aux: Do not infer release information from git tags.Arun Isaac
We now build the website as a computed-file G-expression in a Guix channel. Guix channels always discard the git repository information, and don't have access to the git tags. We can fix this problem later if and when we switch to using tissue for the website. * build-aux/build-home-page.el (org-dblock-write:download): Do not infer release information from git tags. Hard-code them.
2024-01-25Revert "guix: Use source with complete git repo to build website."Arun Isaac
This reverts commit af2f18534bd38703b98cb329d3110a8073d39fb6. When building as a Guix channel, the complete git repository is not available anyway.
2024-01-25configure: Sort tags latest first when picking version.Arun Isaac
* configure.scm (version): Sort tags latest first when picking out the version.
2024-01-25guix: Use source with complete git repository to build website.Arun Isaac
* .guix/ccwl-package.scm: Import git-minimal from (gnu packages version-control). (ccwl-source-with-git-repo): New variable. (ccwl-website-gexp): Make git visible via PATH. Use ccwl-source-with-git-repo.
2024-01-13guix: Add G-expression computed-file to build website.Arun Isaac
* .guix/ccwl-package.scm: Import emacs-minimal from (gnu packages emacs), font-charter and font-fira-code from (gnu packages fonts), %guile-build-system-modules from (guix build-system guile), and (guix profiles). (ccwl-website-gexp, ccwl-website): New variables.
2023-12-01ccwl: Deduplicate global workflow input keys across tee branches.Arun Isaac
* ccwl/ccwl.scm (collect-steps): Deduplicate global workflow input keys across branches of tees. * tests/ccwl.scm (key, collect-steps): New variables. ("rename should work even on the final output of a workflow"): Update order of elements in expected list. ("tee must deduplicate global workflow input keys"): New test. * ccwl/utils.scm (append-mapn): Delete function. * tests/utils.scm ("append-mapn"): Delete test.
2023-12-01tests: Put expected expression before actual expression.Arun Isaac
* tests/ccwl.scm ("rename should work even on the final output of a workflow"): Put expected expression before actual expression.
2023-12-01ccwl: Implement identity construct.Arun Isaac
* ccwl/ccwl.scm (collect-steps): Implement identity construct. * doc/ccwl.skb (Cookbook)[The identity construct]: New section. * doc/identity-construct.scm: New file.
2023-11-23tests: Bump copyright year.Arun Isaac
This was missed out on an earlier commit this year. * tests/yaml.scm: Bump copyright year.
2023-11-23yaml: Escape all indicator characters.Arun Isaac
* ccwl/yaml.scm (display-atom): Escape strings if they contain any indicator character.
2023-11-23ccwl: Implement item separators for array inputs.Arun Isaac
* ccwl/ccwl.scm (<input>)[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.
2023-11-23ccwl: Scan run-args only once when constructing inputs.Arun Isaac
* ccwl/ccwl.scm (run-arg-prefix): Operate on a specific run argument, rather than on a list of them. (command): Scan run-args only once when constructing inputs.
2023-11-23ccwl: Parse run arguments recursively.Arun Isaac
Parsing run arguments recursively allows us to share code between different pattern matchers. For example, the input matcher and the (prefix input) matcher can share code. This will come in handy as our pattern matchers grow more complex. * ccwl/ccwl.scm (run-args): Parse run arguments recursively.
2023-11-23dir-locals: Indent test-condition correctly.Arun Isaac
* .dir-locals.el (scheme-mode): Indent test-condition.
2023-11-21doc: Update source reference to rename.Arun Isaac
* doc/ccwl.skb (Tutorial)[Let's write a spell check workflow]: Update source reference to rename.
2023-11-21ccwl: Comment on passing global workflow inputs through all commands.Arun Isaac
* ccwl/ccwl.scm (collect-steps): Comment on passing global workflow inputs through all commands.
2023-11-21ccwl: Reimplement rename recursively.Arun Isaac
With recursion, we no longer need an explicit call to map, and the code is less deeply nested. This is good for clarity. * ccwl/ccwl.scm (collect-steps): Reimplement rename recursively.
2023-11-21ccwl: Report unknown keys passed to rename.Arun Isaac
* ccwl/ccwl.scm (collect-steps): Report unknown keys passed to rename. * tests/ccwl.scm ("rename with unknown key must raise a &ccwl-violation condition"): New test.
2023-11-21tests: Report non-keyword arguments to rename.Arun Isaac
* tests/ccwl.scm ("rename with non-keyword arguments must raise a &ccwl-violation condition"): New test.
2023-11-21tests: Abstract out testing for conditions.Arun Isaac
* tests/ccwl.scm (test-condition): New syntax. (ccwl-violation-with-message?): New function. Rewrite almost all tests using test-condition.
2023-11-19ccwl: Delete code remnant from previous editing.Arun Isaac
This code remnant actually compiled successfully and was well-hidden from sight! * ccwl/ccwl.scm (key->output): Delete code remnant from previous editing.
2023-11-18ccwl: Error out if arguments have been supplied more than once.Arun Isaac
* ccwl/ccwl.scm (collect-steps): Error out if arguments have been supplied more than once.
2023-11-18scripts: When ccwl crashes, say so explicitly.Arun Isaac
* scripts/ccwl (main): When ccwl crashes, say so explicitly.
2023-11-18ccwl: Never set other and binding fields of inputs/outputs to #f.Arun Isaac
Setting the other and binding fields to #f is a type violation. It messes with code that expects these fields to always contain lists. * ccwl/ccwl.scm (cwl-workflow): Set other and binding fields of inputs and outputs to the empty list.
2023-11-18ccwl: Report non-existent external CWL workflow files.Arun Isaac
cwl-workflow needs to be a macro so we have access to syntax objects necessary to raise a &cwl-violation condition. * ccwl/ccwl.scm (cwl-workflow): Rewrite as macro. Report error if CWL file does not exist.
2023-11-18ccwl: Allow nested workflows in workflow body.Arun Isaac
* ccwl/ccwl.scm (function-inputs, function-outputs, function-object): Support <workflow> objects as functions. (<workflow>): Move above function-outputs. * ccwl/cwl.scm (workflow->cwl-scm): Allow nested workflows.
2023-11-18ccwl: Restrict #:binding parameter to YAML serializable trees.Arun Isaac
* 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.
2023-11-17ccwl: Report errors in rename mappings.Arun Isaac
* ccwl/ccwl.scm (collect-steps): Report errors in rename mappings.
2023-11-17utils: Define pairify behaviour on odd number of elements.Arun Isaac
* ccwl/utils.scm (pairify): Ignore extra elements when list has an odd number of elements. * tests/utils.scm ("pairify must ignore extra elements when list has an odd number of elements"): New test.
2023-11-17ccwl: Implement cross product scattering operations.Arun Isaac
* ccwl/ccwl.scm (collect-steps): Implement scatter-cross and scatter-nested-cross. (key->output): Nest output array types for nested cross product scatters.
2023-11-17ccwl: Recreate types using syntax.Arun Isaac
* ccwl/ccwl.scm (type->syntax): New function. (key->output): Use type->syntax.
2023-11-17ui: Colorize format specifiers not format arguments.Arun Isaac
* ccwl/ui.scm (report-formatted-message): Colorize format specifiers not format arguments. * tests/ui.scm ("report-formatted-message must not fail on arguments that are not strings"): New test.
2023-11-17yaml: Serialize atomic dictionary values on the same line.Arun Isaac
* ccwl/yaml.scm (display-dictionary-entry): Serialize atomic values on the same line. * tests/yaml.scm ("dictionary keys that map to an atomic value must be serialized on the same line"): New test.
2023-11-17doc: Add chapter and section identifiers.Arun Isaac
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.
2023-11-16yaml: Comment on various cases handled by scm->yaml.Arun Isaac
* ccwl/yaml.scm (scm->yaml): Comment on cases handled.
2023-11-16yaml: Display arrays with a single atomic element on the same line.Arun Isaac
* ccwl/yaml.scm (atom?): New function. (display-dictionary-entry, scm->yaml): Display arrays with a single atomic element on the same line. * tests/yaml.scm ("strings with hyphen characters should be escaped", "strings with asterisk characters should be escaped"): Update tests with new behaviour. ("single element vectors must be serialized on the same line"): New test.
2023-11-16ccwl: Support nested arrays.Arun Isaac
* 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.
2023-11-14doc: Add scatter-gather snippet.Arun Isaac
I forgot to add this file in my previous commit. * doc/scatter-gather.scm: New file.
2023-11-14ccwl: Implement scatter.Arun Isaac
* 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.
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