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2021-04-26Add ccwl script.Arun Isaac
* scripts/ccwl: New file.
2021-04-26Redefine command using lambda**.Arun Isaac
* ccwl/ccwl.scm (command): Redefine using lambda**.
2021-04-26Implement the CCWL embedded domain specific language.Arun Isaac
* 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.
2021-04-26Add setter for source field of <output> type.Arun Isaac
* ccwl/ccwl.scm (<output>): Add functional setter set-output-source for source field. * .dir-locals.el (scheme-mode): Specify indentation for set-output-source.
2021-04-26Add plist->alist.Arun Isaac
* ccwl/utils.scm (pairify, plist->alist): New public functions.
2021-04-25Upgrade to CWL version 1.2.Arun Isaac
Version 1.2 of the CWL specification is required to support conditional steps. * ccwl/ccwl.scm (%cwl-version): Set to "v1.2".
2021-04-17Add copyright section to test files.Arun Isaac
* tests/ccwl.scm, tests/yaml.scm: Add copyright section.
2021-04-17Expand name Arun I to Arun Isaac.Arun Isaac
* ccwl/ccwl.scm, ccwl/utils.scm, ccwl/yaml.scm: Expand name Arun I to Arun Isaac.
2021-04-16Add copyright and commentary sections to files.Arun Isaac
* ccwl/ccwl.scm, ccwl/utils.scm, ccwl/yaml.scm: Add copyright and commentary sections.
2021-04-16Add .dir-locals.el for emacs.Arun Isaac
* .dir-locals.el: New file.
2021-04-16Implement lambda** n-ary keyword function.Arun Isaac
* ccwl/utils.scm: Export lambda** instead of group-arguments. (group-arguments): Delete function. (lambda**): New macro.
2021-04-16Make unary-keywords argument of group-keyword-arguments optional.Arun Isaac
* ccwl/utils.scm (group-keyword-arguments): Make unary-keywords optional.
2021-04-16Add plist-ref utility.Arun Isaac
* ccwl/utils.scm: Import (srfi srfi-26). (plist-ref): New function.
2021-04-12Support n-ary keyword arguments.Arun Isaac
* ccwl/utils.scm: New file.
2021-03-26Add README.Arun Isaac
* README.org: New file.
2021-03-26Add copy of GPLv3.Arun Isaac
* COPYING: New file.
2021-03-22List additional-inputs while generating CWL.Arun Isaac
* ccwl/ccwl.scm (command->cwl): List additional-inputs in inputs array.
2021-03-22Add additional-inputs field to <command> type.Arun Isaac
* ccwl/ccwl.scm (<command>): Add additional-inputs field. (command): Initialize additional-inputs field.
2021-03-22Remove input->tree abstraction.Arun Isaac
<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.
2021-03-22Delete input field of <command> object.Arun Isaac
* ccwl/ccwl.scm (<command>): Delete input field. (command): Do not set inputs field.
2021-03-21Print steps enclosing <command> objects correctly.Arun Isaac
* ccwl/ccwl.scm (write-cwl): Invoke command->cwl if step encloses <command> object.
2021-03-21Use both CWL arguments and inputs arrays.Arun Isaac
* 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.
2021-03-21Add alist filtering utility function.Arun Isaac
* ccwl/ccwl.scm (filter-alist): New function. (input->tree): Use filter-alist.
2021-03-21Set the default output of a pipeline.Arun Isaac
* ccwl/ccwl.scm (pipeline): Set the stdout of the last command to be the default output of the pipeline.
2021-03-21Pull out cwl-version as a separate variable.Arun Isaac
* ccwl/ccwl.scm (%cwl-version): New variable. (workflow, command->cwl): Use %cwl-version.
2021-03-21Add prefix field to <input> object.Arun Isaac
* ccwl/ccwl.scm (<input>): Add prefix field. (input): Initialize prefix field. (input-with-prefix): New public function.
2021-03-21Remove appender for inputs field of <command>.Arun Isaac
* ccwl/ccwl.scm (append-command-inputs): Delete function.
2021-03-17Set default type of outputs to File.Arun Isaac
* ccwl/ccwl.scm (output): Set default type to File.
2021-03-17Set default type of inputs to File.Arun Isaac
* ccwl/ccwl.scm (input): Set default type to File.
2021-03-07Add write-cwl function to write generated CWL to a file.Arun Isaac
* ccwl/ccwl.scm: Import (srfi srfi-26) and (ccwl yaml). (write-cwl): New public function.
2021-03-07Remove field binding from constructor of the <input> type.Arun Isaac
* ccwl/ccwl.scm (<input>): Remove field binding from constructor.
2021-03-07Escape YAML strings that contain the hyphen character.Arun Isaac
* ccwl/yaml.scm (display-atom): Escape string if it contains the hyphen character.
2021-03-06Auto-connect steps by matching identifiers.Arun Isaac
* ccwl/ccwl.scm (auto-connect): New function. (workflow): Auto-connect step inputs and outputs before generating <step> record.
2021-03-06Implement pipeline support.Arun Isaac
* ccwl/ccwl.scm (%stdin, %stdout): New variables. (pipeline): New function.
2021-03-06Rewrite workflow function to output a <step> record.Arun Isaac
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.
2021-03-06Define input=? predicate.Arun Isaac
* ccwl/ccwl.scm (input=?): New function.
2021-03-06Add source field to <input> type.Arun Isaac
* ccwl/ccwl.scm (<input>): Add source field. (input): Initialize source field to #f in constructor.
2021-03-06Remove clitool functions.Arun Isaac
* ccwl/ccwl.scm (clitool, clitool-step): Delete functions.
2021-03-06Add command->cwl rendering function.Arun Isaac
* ccwl/ccwl.scm (output->cwl, command->cwl): New functions.
2021-03-06Add modifier for run field of <step> object.Arun Isaac
* ccwl/ccwl.scm (modify-step-run): New function.
2021-03-06Add field appenders.Arun Isaac
* ccwl/ccwl.scm (field-appender, append-step-in, append-step-out, append-command-inputs, append-command-outputs): New functions.
2021-03-06Introduce <command> type.Arun Isaac
* ccwl/ccwl.scm (<command>): New type. (command): New function.
2021-03-06Delete command parsing functions.Arun Isaac
We will not auto-parse commands and try to associate a binding to inputs. If we specify the command using the arguments field of the CWL specification, we don't need to know the base command or the bindings. * ccwl/ccwl.scm: Do not import (srfi srfi-71). (parse-arguments, break-pair, parse-command): Delete functions.
2021-03-06Remove <intermediate> type.Arun Isaac
We will auto-connect inputs and outputs by matching their unique identifiers. * ccwl/ccwl.scm (<intermediate>): Delete type.
2021-03-06Re-order fields of <input> type.Arun Isaac
* ccwl/ccwl.scm (<input>): Re-order <input> fields to be consistent with its constructor.
2021-03-06Combine <workflow-output> type into <output> type.Arun Isaac
The user should not have to distinguish between regular outputs and workflow outputs. * ccwl/ccwl.scm (<output>): Add source field. (output): Add source field to constructor. (<workflow-output>): Delete type. (workflow-output): Delete function.
2021-03-06Migrate to SRFI-9 records.Arun Isaac
Functional setters from (srfi srfi-9 gnu) are very useful. * ccwl/ccwl.scm (<input>, unspecified-default, <output>, <intermediate>, <workflow-output>, <step>): Redefine using SRFI-9 records.
2021-02-27Rewrite parse-command using break-pair.Arun Isaac
* ccwl/ccwl.scm (parse-command): Rewrite using break-pair.
2021-02-27Add break-pair utility.Arun Isaac
* ccwl/ccwl.scm (break-pair): New function. * tests/ccwl.scm: New file. * tests/ccwl.scm ("break-pair", "break-pair: check last elemet handling"): New test cases.
2021-02-27Display dictionary entries with empty values on the same line.Arun Isaac
* ccwl/yaml.scm (display-dictionary-entry): If value is an empty array or dictionary, display it on the same line. (scm->yaml): Go to next line after printing empty array. * tests/yaml.scm: New file. * tests/yaml.scm ("dictionary entries with empty arrays and dictionaries for values must render on the same line"): New test case.
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