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8 daysscripts: Use raise-exception instead of scm-error. HEAD mainArun Isaac
8 daysscripts: Do not wrap simple condition in condition.Arun Isaac
8 daysscripts: Add --output option.Arun Isaac
8 daysscripts: Only guard load function for ccwl-violation.Arun Isaac
8 daysscripts: Spin out compilation into separate function.Arun Isaac
8 daysscripts: Move options to separate variable.Arun Isaac
12 dayscwl: Serialize #f default values.Arun Isaac
12 daysUse guile-run64 for tests.Arun Isaac
2025-02-28README: Mention that we do not work on GitHub.Arun Isaac
* README.org (Contributing): Mention that we do not work on GitHub.
2025-02-28README: Mention public inbox.Arun Isaac
* README.org (Contributing): Mention public inbox.
2025-01-28REAME: Add image name to docker commands.Arun Isaac
* README.org (Installation)[Using binary software bundles]{Using the Docker image}: Add image name to docker commands.
2025-01-28Add v0.4.0 release tarball.Arun Isaac
* website/releases/ccwl-0.4.0.tar.lz, website/releases/ccwl-0.4.0.tar.lz.asc: New files * build-aux/build-home-page.el (org-dblock-write:download): Update website.
2025-01-28NEWS: Update for version 0.4.0. v0.4.0Arun Isaac
* NEWS.org (Changes in 0.4.0 (since 0.3.0)): New section.
2024-05-30doc: Use section- prefix in section identifier.Arun Isaac
* doc/ccwl.skb (Cookbook)[Prefix arguments]: Use section- prefix in identifier.
2024-05-30doc: Document prefixing arguments.Arun Isaac
* doc/ccwl.skb (Cookbook)[Prefix arguments]: New section. * doc/prefix-arguments.scm: New file.
2024-05-30doc: Document passing in arbitrary CWL Requirements.Arun Isaac
* doc/ccwl.skb (Cookbook)[Pass in arbitrary CWL Requirements]: New section. * doc/inline-javascript-requirement.scm, doc/resource-requirement.scm: New files.
2024-04-13ccwl: Restrict #:requirements parameter to YAML serializable trees.Arun Isaac
This is in keeping with the way the #:other parameter is handled. * ccwl/ccwl.scm (command, js-expression): Restrict #:requirements parameter to YAML serializable trees.
2024-04-12doc: Use curly single quotation marks.Arun Isaac
Curly quotation marks are better typography than straight quotation marks. Straight quotation marks were introduced only due to the physical limitations of the typewriter. * doc/ccwl.skb: Use curly single quotation marks.
2024-04-12doc: Write guide to the source code.Arun Isaac
* doc/ccwl.skb (Guide to the source code): New chapter. (Contributing): Demote to section inside "Guide to the source code".
2024-03-22doc: Markup "0" and "n-1" as code.Arun Isaac
* doc/ccwl.skb (Cookbook)[Javascript expressions via ExpressionTool]: Markup "0" and "n-1" as code.
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.
generated by cgit-pink 1.4.1 (git 2.36.1) at 2025-12-10 01:35:36 +0000