Age | Commit message (Expand) | Author |
2024-03-22 | ccwl: Implement js-expression.•••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.
| Arun Isaac |
2024-03-22 | scripts: Use unified function terminology.•••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.
| Arun Isaac |
2024-03-12 | ccwl: Find run argument directly without finding the position first.•••* ccwl/ccwl.scm (run-arg-position): Delete function.
(find-run-arg): New function.
(command): Use find-run-arg instead of run-arg-position.
| Arun Isaac |
2024-03-12 | ccwl: Count argument positions on flattened run arguments.•••* 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.
| Arun Isaac |
2024-03-12 | tests: Fix command definition in test.•••* tests/ccwl.scm ("outputs with #:other parameters that fail to
evaluate must raise a &ccwl-violation condition"): Define command
inputs, not outputs.
| Arun Isaac |
2024-01-26 | NEWS: Mark (term ansi-color) as code.•••* NEWS.org (Changes in 0.3.0)[Other]: Mark (term ansi-color) as code.
| Arun Isaac |
2024-01-26 | Add v0.3.0 release tarballs.•••* 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.
| Arun Isaac |
2024-01-26 | NEWS: Update for version 0.3.0.•••* NEWS.org (Changes in 0.3.0): New section.
v0.3.0 | Arun Isaac |
2024-01-26 | guix: Add recipe to create a distribution tarball.•••* .guix/ccwl-distribution.scm: New file.
| Arun Isaac |
2024-01-26 | Makefile: Split up release tarball signature into separate target.•••* Makefile (dist): Move $(dist_archive).asc to ...
(distsign): ... here.
| Arun Isaac |
2024-01-26 | Makefile: Clean up .depends.•••* Makefile (clean): Delete .depends.
| Arun Isaac |
2024-01-26 | build-aux: Do not infer release information from git tags.•••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.
| Arun Isaac |
2024-01-25 | Revert "guix: Use source with complete git repo to build website."•••This reverts commit af2f18534bd38703b98cb329d3110a8073d39fb6. When
building as a Guix channel, the complete git repository is not
available anyway.
| Arun Isaac |
2024-01-25 | configure: Sort tags latest first when picking version.•••* configure.scm (version): Sort tags latest first when picking out the
version.
| Arun Isaac |
2024-01-25 | guix: Use source with complete git repository to build website.•••* .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.
| Arun Isaac |
2024-01-13 | guix: Add G-expression computed-file to build website.•••* .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.
| Arun Isaac |
2023-12-01 | ccwl: Deduplicate global workflow input keys across tee branches.•••* 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.
| Arun Isaac |
2023-12-01 | tests: Put expected expression before actual expression.•••* tests/ccwl.scm ("rename should work even on the final output of a
workflow"): Put expected expression before actual expression.
| Arun Isaac |
2023-12-01 | ccwl: Implement identity construct.•••* ccwl/ccwl.scm (collect-steps): Implement identity construct.
* doc/ccwl.skb (Cookbook)[The identity construct]: New section.
* doc/identity-construct.scm: New file.
| Arun Isaac |
2023-11-23 | tests: Bump copyright year.•••This was missed out on an earlier commit this year.
* tests/yaml.scm: Bump copyright year.
| Arun Isaac |
2023-11-23 | yaml: Escape all indicator characters.•••* ccwl/yaml.scm (display-atom): Escape strings if they contain any
indicator character.
| Arun Isaac |
2023-11-23 | ccwl: Implement item separators for array inputs.•••* 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.
| Arun Isaac |
2023-11-23 | ccwl: Scan run-args only once when constructing inputs.•••* 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.
| Arun Isaac |
2023-11-23 | ccwl: Parse run arguments recursively.•••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.
| Arun Isaac |
2023-11-23 | dir-locals: Indent test-condition correctly.•••* .dir-locals.el (scheme-mode): Indent test-condition.
| Arun Isaac |
2023-11-21 | doc: Update source reference to rename.•••* doc/ccwl.skb (Tutorial)[Let's write a spell check workflow]: Update
source reference to rename.
| Arun Isaac |
2023-11-21 | ccwl: Comment on passing global workflow inputs through all commands.•••* ccwl/ccwl.scm (collect-steps): Comment on passing global workflow
inputs through all commands.
| Arun Isaac |
2023-11-21 | ccwl: Reimplement rename recursively.•••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.
| Arun Isaac |
2023-11-21 | ccwl: Report unknown keys passed to rename.•••* 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.
| Arun Isaac |
2023-11-21 | tests: Report non-keyword arguments to rename.•••* tests/ccwl.scm ("rename with non-keyword arguments must raise a
&ccwl-violation condition"): New test.
| Arun Isaac |
2023-11-21 | tests: Abstract out testing for conditions.•••* tests/ccwl.scm (test-condition): New syntax.
(ccwl-violation-with-message?): New function.
Rewrite almost all tests using test-condition.
| Arun Isaac |
2023-11-19 | ccwl: Delete code remnant from previous editing.•••This code remnant actually compiled successfully and was well-hidden
from sight!
* ccwl/ccwl.scm (key->output): Delete code remnant from previous
editing.
| Arun Isaac |
2023-11-18 | ccwl: Error out if arguments have been supplied more than once.•••* ccwl/ccwl.scm (collect-steps): Error out if arguments have been
supplied more than once.
| Arun Isaac |
2023-11-18 | scripts: When ccwl crashes, say so explicitly.•••* scripts/ccwl (main): When ccwl crashes, say so explicitly.
| Arun Isaac |
2023-11-18 | ccwl: Never set other and binding fields of inputs/outputs to #f.•••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.
| Arun Isaac |
2023-11-18 | ccwl: Report non-existent external CWL workflow files.•••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.
| Arun Isaac |
2023-11-18 | ccwl: Allow nested workflows in workflow body.•••* 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.
| Arun Isaac |
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 | ccwl: Report errors in rename mappings.•••* ccwl/ccwl.scm (collect-steps): Report errors in rename mappings.
| Arun Isaac |
2023-11-17 | utils: Define pairify behaviour on odd number of elements.•••* 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.
| Arun Isaac |
2023-11-17 | ccwl: Implement cross product scattering operations.•••* ccwl/ccwl.scm (collect-steps): Implement scatter-cross and
scatter-nested-cross.
(key->output): Nest output array types for nested cross product
scatters.
| Arun Isaac |
2023-11-17 | ccwl: Recreate types using syntax.•••* ccwl/ccwl.scm (type->syntax): New function.
(key->output): Use type->syntax.
| Arun Isaac |
2023-11-17 | ui: Colorize format specifiers not format arguments.•••* 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.
| Arun Isaac |
2023-11-17 | yaml: Serialize atomic dictionary values on the same line.•••* 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.
| 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 | yaml: Comment on various cases handled by scm->yaml.•••* ccwl/yaml.scm (scm->yaml): Comment on cases handled.
| Arun Isaac |
2023-11-16 | yaml: Display arrays with a single atomic element on the same line.•••* 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.
| 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 |