Age | Commit message (Collapse) | Author |
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* ccwl/ccwl.scm (command-variable, command-syntax->object): Delete
functions.
(command-object): New function.
(workflow-steps): Use command-object instead of command-variable and
command-syntax->object.
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* ccwl/ccwl.scm (workflow): When input has no properties, support only
specifying the symbol.
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* ccwl/ccwl.scm (command-syntax->object): When command accepts only a
single input and there is only a single key available, support
implicit key pairing.
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* ccwl/ccwl.scm (workflow-steps): When command does not specify step
identifier, assume the step identifier is the same as the command
symbol.
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* ccwl/ccwl.scm (command-variable, command-syntax->object): New
functions.
(workflow-steps): Use command-variable and command-syntax->object.
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* ccwl/ccwl.scm (%stdin, %stdout): Delete variables.
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* ccwl/ccwl.scm: Import (srfi srfi-71).
(command-input-keys, workflow-steps): New function.
(workflow): Support general Directed Acyclic Graph (DAG) workflows.
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* ccwl/ccwl.scm (<key>): New type.
(key, cwl-key-address): New functions.
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* ccwl/ccwl.scm (make-workflow): Accept inputs explicitly.
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* ccwl/ccwl.scm (input=?): Compare using eq? instead of string=?.
(command->cwl, write-cwl): Convert input-id to string before
appending.
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* ccwl/ccwl.scm (command): Make stdin a unary key.
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Doing this conversion effectively forbids kebab case symbols in YAML.
* ccwl/yaml.scm (kebab->camel): Delete function.
(display-atom): Do not convert symbols from kebab case to camel case.
* ccwl/ccwl.scm (make-workflow, output->cwl, command->cwl): Write
camel case explicitly.
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* ccwl/utils.scm (mapn, append-mapn, foldn): New public functions.
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* ccwl/ccwl.scm (pipeline): Delete function.
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* ccwl/yaml.scm (display-atom): Escape asterisk characters.
* tests/yaml.scm ("strings with asterisk characters should be
escaped"): New test.
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* ccwl/ccwl.scm (command): Redefine using lambda**.
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* ccwl/ccwl.scm: Import (ccwl utils).
(command): Return <command> object.
(auto-connect): Delete function.
(invoke-command, make-workflow, workflow-steps): New functions.
(workflow): Replace function with macro.
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* ccwl/ccwl.scm (<output>): Add functional setter set-output-source
for source field.
* .dir-locals.el (scheme-mode): Specify indentation for
set-output-source.
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* ccwl/utils.scm (pairify, plist->alist): New public functions.
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Version 1.2 of the CWL specification is required to support
conditional steps.
* ccwl/ccwl.scm (%cwl-version): Set to "v1.2".
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* ccwl/ccwl.scm, ccwl/utils.scm, ccwl/yaml.scm: Expand name Arun I to
Arun Isaac.
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* ccwl/ccwl.scm, ccwl/utils.scm, ccwl/yaml.scm: Add copyright and
commentary sections.
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* ccwl/utils.scm: Export lambda** instead of group-arguments.
(group-arguments): Delete function.
(lambda**): New macro.
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* ccwl/utils.scm (group-keyword-arguments): Make unary-keywords
optional.
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* ccwl/utils.scm: Import (srfi srfi-26).
(plist-ref): New function.
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* ccwl/utils.scm: New file.
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* ccwl/ccwl.scm (command->cwl): List additional-inputs in inputs
array.
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* ccwl/ccwl.scm (<command>): Add additional-inputs field.
(command): Initialize additional-inputs field.
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<input> objects need to be expanded into CWL in context sensitive
ways. There is no simple generalization.
* ccwl/ccwl.scm (input->tree): Delete function.
(workflow): Expand input->tree.
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* ccwl/ccwl.scm (<command>): Delete input field.
(command): Do not set inputs field.
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* ccwl/ccwl.scm (write-cwl): Invoke command->cwl if step encloses
<command> object.
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* ccwl/ccwl.scm (<cli-element>): New type.
(command->cwl): Put string and expression arguments into the arguments
array. Put <input> arguments into the inputs array.
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* ccwl/ccwl.scm (filter-alist): New function.
(input->tree): Use filter-alist.
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* ccwl/ccwl.scm (pipeline): Set the stdout of the last command to be
the default output of the pipeline.
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* ccwl/ccwl.scm (%cwl-version): New variable.
(workflow, command->cwl): Use %cwl-version.
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* ccwl/ccwl.scm (<input>): Add prefix field.
(input): Initialize prefix field.
(input-with-prefix): New public function.
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* ccwl/ccwl.scm (append-command-inputs): Delete function.
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* ccwl/ccwl.scm (output): Set default type to File.
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* ccwl/ccwl.scm (input): Set default type to File.
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* ccwl/ccwl.scm: Import (srfi srfi-26) and (ccwl yaml).
(write-cwl): New public function.
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* ccwl/ccwl.scm (<input>): Remove field binding from constructor.
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* ccwl/yaml.scm (display-atom): Escape string if it contains the
hyphen character.
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* ccwl/ccwl.scm (auto-connect): New function.
(workflow): Auto-connect step inputs and outputs before generating
<step> record.
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* ccwl/ccwl.scm (%stdin, %stdout): New variables.
(pipeline): New function.
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All user exposed functions should output a <step> record so that they
are composable.
* ccwl/ccwl.scm (workflow): Rewrite workflow function to output a
<step> record.
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* ccwl/ccwl.scm (input=?): New function.
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* ccwl/ccwl.scm (<input>): Add source field.
(input): Initialize source field to #f in constructor.
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* ccwl/ccwl.scm (clitool, clitool-step): Delete functions.
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* ccwl/ccwl.scm (output->cwl, command->cwl): New functions.
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* ccwl/ccwl.scm (modify-step-run): New function.
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