Age | Commit message (Collapse) | Author |
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* doc/ccwl.skb (Tutorial)[Let's write a spell check workflow]: Update
source reference to rename.
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* ccwl/ccwl.scm (collect-steps): Comment on passing global workflow
inputs through all commands.
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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.
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* 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.
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* tests/ccwl.scm ("rename with non-keyword arguments must raise a
&ccwl-violation condition"): New test.
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* tests/ccwl.scm (test-condition): New syntax.
(ccwl-violation-with-message?): New function.
Rewrite almost all tests using test-condition.
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This code remnant actually compiled successfully and was well-hidden
from sight!
* ccwl/ccwl.scm (key->output): Delete code remnant from previous
editing.
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* ccwl/ccwl.scm (collect-steps): Error out if arguments have been
supplied more than once.
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* scripts/ccwl (main): When ccwl crashes, say so explicitly.
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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.
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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.
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* 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.
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* 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.
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* ccwl/ccwl.scm (collect-steps): Report errors in rename mappings.
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* 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.
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* ccwl/ccwl.scm (collect-steps): Implement scatter-cross and
scatter-nested-cross.
(key->output): Nest output array types for nested cross product
scatters.
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* ccwl/ccwl.scm (type->syntax): New function.
(key->output): Use type->syntax.
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* 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.
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* 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.
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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.
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* ccwl/yaml.scm (scm->yaml): Comment on cases handled.
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* 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.
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* 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.
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I forgot to add this file in my previous commit.
* doc/scatter-gather.scm: New file.
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* 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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* ccwl/ccwl.scm (key->output): Clarify in the docstring that this is
meant for workflow outputs only.
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This conversation should be in ccwl.scm, not in cwl.scm. cwl.scm
should only deal with CWL serialization concerns.
* ccwl/cwl.scm (output->cwl-scm): Move conversion to ...
* ccwl/ccwl.scm (key->output): ... here.
(<output>)[type]: Add setter.
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It is easier (no need to juggle complex with-syntax constructs) to do
more complicated operations outside of the scope of syntax.
* ccwl/ccwl.scm (key->output): Build output from key outside of
syntax.
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* ccwl/ccwl.scm (<array-type>): New type.
(memoize, make-array-type, construct-type-syntax): New functions.
(input, output): Use construct-type-syntax.
* ccwl/cwl.scm (output->cwl-scm, input->cwl-scm): Render array types.
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* ccwl/cwl.scm (output->cwl-scm): Handle both command and workflow
outputs. Accept #:workflow? argument to indicate workflow outputs.
(workflow->cwl-scm): Use output->cwl-scm.
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* ccwl/cwl.scm (input->cwl-scm): New function.
(workflow->cwl-scm, command->cwl-scm): Use input->cwl-scm.
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* ccwl/ccwl.scm (input=?): Delete function.
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* ccwl/ui.scm (source-in-context): Do not attempt to display the line
preceding the 0th.
* tests/ui.scm ("display source in context on 0th line"): New line.
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* tests/ui.scm: New file.
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* build-aux/test-driver.scm (color): Use colorize-string from (term
ansi-color).
* ccwl/ui.scm (report-formatted-message, source-in-context,
report-ccwl-violation): Use colorize-string from (term ansi-color).
(color, bold, red, magenta): Delete functions.
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* ccwl/ui.scm (source-in-context): Accept port, not filename.
(report-ccwl-violation): Pass port, not filename.
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* ccwl/ccwl.scm (ensure-yaml-serializable): New function.
(input, output, command): Use ensure-yaml-serializable.
* tests/ccwl.scm ("inputs with #:other parameters that fail to
evaluate must raise a &ccwl-violation condition", "outputs with
#:other parameters that fail to evaluate must raise a &ccwl-violation
condition", "commands with #:other parameters that fail to evaluate
must raise a &ccwl-violation condition"): New tests.
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Perhaps it fits in better with the spirit of ccwl to not evaluate
#:other parameters and instead allow only YAML serializable
trees. This saves users from quoting #:other parameters, of
course. But it also permits more thorough analysis and clearer error
messages. Besides, there is not much reason to allow general
expressions in #:other parameters. Such dynamism is not commonly
required in ccwl or CWL.
* ccwl/ccwl.scm (input, output, command): Restrict #:other parameter
to YAML serializable trees that are not evaluated.
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This file was required by the previous commit, but I forgot to commit
it!
* doc/staging-input-files.scm: New file.
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* ccwl/ccwl.scm (command): Add "Invalid parameter" to #:stderr and
#:stdout error messages.
* tests/ccwl.scm ("commands with non-string #:stderr parameters must
raise a &ccwl-violation condition", "commands with non-string #:stdout
parameters must raise a &ccwl-violation condition"): Adjust tests.
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* ccwl/ccwl.scm (<input>)[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.
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* ccwl/ccwl.scm (<command>)[requirements]: New field.
(command): Add #:requirements argument.
* ccwl/cwl.scm (command->cwl-scm): Serialize requirements.
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Support arbitrary expressions, that are actually evaluated, in #:other
arguments. This means, among other things, that users will have to
quote them correctly. While this complicates matters for novice users
who may not be familiar with scheme, it is the most general and most
flexible solution. In this particular case, we value flexibility over
ease of use since #:other is an escape hatch and if users have to use
it, ease of use has already been lost.
* ccwl/ccwl.scm (input, output, command): Make #:other an actually
evaluated unary argument.
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* ccwl/ccwl.scm (run-args): Error out on prefixes that are not
strings.
* tests/ccwl.scm ("command definitions with non-string prefixes in
prefixed inputs must raise a &ccwl-violation condition"): New test.
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* ccwl/ccwl.scm (run-args): Flatten prefixed string arguments in
command definitions.
* tests/ccwl.scm ("tolerate prefixed string arguments in command
definitions"): New test.
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* ccwl/ccwl.scm (command): Move run arguments construction to ...
(run-args): ... new function.
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* ccwl/ccwl.scm (command): Raise &ccwl-violation on invalid command
#:run arguments.
* tests/ccwl.scm ("command definitions with invalid #:run arguments
must raise a &ccwl-violation condition"): New test.
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* ccwl/ccwl.scm (command): Check if inputs used in #:run arguments of
command definitions are actually defined.
* tests/ccwl.scm ("command definitions with undefined inputs in their
#:run arguments must raise a &ccwl-violation condition", "command
definitions with undefined prefix inputs in their #:run arguments must
raise a &ccwl-violation condition"): New tests.
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* tests/ccwl.scm ("allow literal as arguments"): Rename to "allow
literal strings as arguments".
(print-int): New variable.
("allow literal ints as arguments"): New test.
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#:stderr and #:stdout, especially #:stdout, are commonly
required. They ought to be first class parameters and not tucked away
into #:other.
* ccwl/ccwl.scm (<command>)[stderr, stdout]: New fields.
* ccwl/ccwl.scm (command): Accept #:stderr and #:stdout as first class
parameters.
* ccwl/cwl.scm (command->cwl-scm): Serialize stderr and stdout fields.
* doc/capture-stdout.scm (print),
doc/decompress-compile-run.scm (run), doc/checksum.scm (md5sum,
sha1sum, sha256sum), doc/spell-check.scm (find-misspellings): Capture
stdout in file.
* doc/checksum.scm, doc/decompress-compile-run.scm:
* doc/ccwl.skb (Tutorial)[Capturing the standard output stream of a
command]: Document #:stdout first class parameter.
* doc/ccwl.skb (Tutorial)[Workflow with multiple steps]: Capture
stdout in explicitly named files.
* tests/ccwl.scm ("commands with non-string #:stderr parameters must
raise a &ccwl-violation condition", "commands with non-string #:stdout
parameters must raise a &ccwl-violation condition"): New tests.
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