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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.
2023-11-23ccwl: 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.
2023-11-21ccwl: 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.
2023-11-21tests: Abstract out testing for conditions.Arun Isaac
* tests/ccwl.scm (test-condition): New syntax. (ccwl-violation-with-message?): New function. Rewrite almost all tests using test-condition.
2023-11-16ccwl: Support nested arrays.Arun Isaac
* 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.
2023-11-06ccwl: Error out if #:other parameters are not serializable to YAML.Arun Isaac
* 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.
2023-10-17ccwl: Add "Invalid parameter" to #:stderr and #:stdout error messages.Arun Isaac
* 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.
2023-10-17ccwl: Support staging input files.Arun Isaac
* 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.
2023-10-16ccwl: Error out on prefixes that are not strings.Arun Isaac
* 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.
2023-10-16ccwl: Flatten prefixed string arguments in command definitions.Arun Isaac
* ccwl/ccwl.scm (run-args): Flatten prefixed string arguments in command definitions. * tests/ccwl.scm ("tolerate prefixed string arguments in command definitions"): New test.
2023-10-16ccwl: Raise &ccwl-violation on invalid command #:run arguments.Arun Isaac
* 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.
2023-10-16ccwl: Check if inputs in command definitions are defined.Arun Isaac
* 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.
2023-10-16tests: Allow literal ints as arguments.Arun Isaac
* 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.
2023-10-15ccwl: Make #:stderr and #:stdout first class parameters.Arun Isaac
#: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.
2023-10-14ccwl: Detect multiple expressions in workflow body.Arun Isaac
* ccwl/ccwl.scm (workflow): Detect multiple expressions in workflow body and raise an exception. * tests/ccwl.scm ("unrecognized workflow syntaxes must raise a &ccwl-violation condition"): Test for the formatted message too. ("multiple expressions in workflow body must raise a &ccwl-violation condition"): New test.
2023-10-14ccwl: Raise &ccwl-violation when workflow syntax is not recognized.Arun Isaac
* ccwl/ccwl.scm (workflow): Raise &ccwl-violation when workflow syntax is not recognized. * tests/ccwl.scm ("unrecognized workflow syntaxes must raise a &ccwl-violation condition"): New test.
2023-10-13tests: Raise a &ccwl-violation on unknown keys.Arun Isaac
* tests/ccwl.scm ("step supplied with an unknown key must raise a &ccwl-violation condition"): New test.
2023-10-09ccwl: Allow literals as arguments.Arun Isaac
* ccwl/ccwl.scm (<input>)[set-input-default]: New setter. * ccwl/ccwl.scm (<command>)[set-command-inputs]: Add setter. * ccwl/ccwl.scm (apply-partially): New function. (collect-steps): Support literal strings as arguments. * tests/ccwl.scm ("allow literal strings as arguments"): New test. * .dir-locals.el (scheme-mode): Indent set-command-inputs and set-input-default.
2023-10-09tests: Catch expressions that don't raise exceptions.Arun Isaac
Many tests that use guard to catch and ensure that certain conditions are raised actually leak and let through cases where the expressions result in a truthy value. * tests/ccwl.scm ("input, when passed more than one positional argument, must raise a &ccwl-violation condition", "input, when passed an unrecognized keyword, must raise a &ccwl-violation condition", "input, when passed multiple arguments to a unary keyword, must raise a &ccwl-violation condition", "output, when passed more than one positional argument, must raise a &ccwl-violation condition", "output, when passed an unrecognized keyword, must raise a &ccwl-violation condition", "output, when passed multiple arguments to a unary keyword, must raise a &ccwl-violation condition", "command, when passed positional arguments, must raise a &ccwl-violation condition", "command, when passed an unrecognized keyword, must raise a &ccwl-violation condition", "command, when passed multiple arguments to a unary keyword, must raise a &ccwl-violation condition"): Catch expressions that don't raise exceptions.
2023-10-09ccwl: Error out if steps with expression commands have no identifier.Arun Isaac
* ccwl/ccwl.scm (collect-steps): Error out if steps with expressions that evaluate to commands have no identifier. * tests/ccwl.scm ("step with expression that evaluates to a command but without a step identifier must raise a &ccwl-violation condition"): New test.
2023-10-09ccwl: In macro expansion, use eval instead of module introspection.Arun Isaac
eval is not just more portable but also more flexible. It lets us allow steps with expressions that evaluate to commands. Sadly, we do not yet properly support commands defined in lexical scope. * ccwl/ccwl.scm (function-object): Use eval instead of module introspection. * tests/ccwl.scm ("allow steps with expressions that evaluate to commands"): New test.
2023-09-29ccwl: Allow steps with unspecified default arguments.Arun Isaac
* ccwl/ccwl.scm (function-inputs): New function. (function-input-keys): Use function-inputs. (collect-steps): Do not error out on steps with unspecified default arguments. * tests/ccwl.scm (print-with-default): New variable. ("allow steps with unspecified default arguments"): New test.
2023-09-20tests: Test that rename works even on a final workflow output.Arun Isaac
* tests/ccwl.scm (print): New variable. ("rename should work even on the final output of a workflow"): New test.
2022-01-16ccwl: Raise exceptions on command syntax errors.Arun Isaac
* ccwl/ccwl.scm (command): Raise &ccwl-violation conditions on syntax errors. * tests/ccwl.scm ("command, when passed positional arguments, must raise a &ccwl-violation condition", "command, when passed an unrecognized keyword, must raise a &ccwl-violation condition", "command, when passed multiple arguments to a unary keyword, must raise a &ccwl-violation condition"): New tests.
2022-01-16ccwl: Raise exceptions on output syntax errors.Arun Isaac
* ccwl/ccwl.scm (output): Raise &ccwl-violation conditions on syntax errors. * tests/ccwl.scm (output): New function. ("output, when passed more than one positional argument, must raise a &ccwl-violation condition", "output, when passed an unrecognized keyword, must raise a &ccwl-violation condition", "output, when passed multiple arguments to a unary keyword, must raise a &ccwl-violation condition"): New tests.
2022-01-16ccwl: Raise exceptions on input syntax errors.Arun Isaac
* ccwl/ccwl.scm: Import (rnrs conditions), (rnrs exceptions) and (ccwl conditions). (input, input-spec-id): Raise &ccwl-violation conditions on syntax errors. * tests/ccwl.scm: Import (rnrs exceptions) and (ccwl conditions). (input): New function. ("input, when passed more than one positional argument, must raise a &ccwl-violation condition", "input, when passed an unrecognized keyword, must raise a &ccwl-violation condition", "input, when passed multiple arguments to a unary keyword, must raise a &ccwl-violation condition"): New tests.
2022-01-16tests: Use @@ instead of module-ref and resolve-module.Arun Isaac
@@ is shorter and looks neater with fewer quotes. * tests/ccwl.scm ("stdin input should not have inputBinding"), tests/utils.scm ("unsyntax-keywords"): Use @@ instead of module-ref and resolve-module.
2021-11-02ccwl: Support external CWL workflows.Arun Isaac
* ccwl/ccwl.scm: Import (yaml). Export cwl-workflow?, cwl-workflow, cwl-workflow-file, cwl-workflow-inputs and cwl-workflow-outputs. (<cwl-workflow>): New type. (cwl-workflow, function-input-keys, function-outputs, function-object): New functions. (command-input-keys, command-object): Delete functions. (collect-steps): Replace command-object with function-object, command-input-keys with function-input-keys and command-outputs with function-outputs. * ccwl/cwl.scm (workflow->cwl-scm): Handle <cwl-workflow> objects. * tests/ccwl.scm ("read all forms of inputs and outputs from a CWL workflow"): New test. * guix.scm: Import (gnu packages guile-xyz) and (guix utils). (guile-libyaml): New variable. (ccwl)[inputs]: Add guile-libyaml.
2021-10-12tests: Fix quoting of type.Arun Isaac
* tests/ccwl.scm ("stdin input should not have inputBinding"): Fix quoting of type File.
2021-10-11ccwl: Factorize out CWL generation code to separate file.Arun Isaac
This factorization is required to support other compilation targets such as graphviz, bash, scheme, etc. * ccwl/cwl.scm: New file. * Makefile.am (SOURCES): Register it. * ccwl/ccwl.scm (ccwl): Export command?, command-inputs, command-outputs, command-args, command-stdin, command-other, workflow?, workflow-steps, workflow-inputs, workflow-outputs, workflow-other, input?, input-id, input-type, input-label, input-default, input-position, input-prefix, input-other, output?, output-id, output-type, output-binding, output-source, output-other, step?, step-id, step-run, step-in, step-out, unspecified-default?. (<workflow>): New type. (filter-alist): Move to cwl.scm. (make-workflow): Refactor into workflow->cwl-scm in cwl.scm. (output->cwl): Move to cwl.scm as output->cwl-scm. (command->cwl): Move to cwl.scm as command->cwl-scm. (workflow-steps): Rename to collect-steps. Clarify docstring. (workflow): Use collect-steps instead of workflow-steps. Explicitly pass empty list as other argument of make-workflow. Add TODO note to implement it properly. * scripts/ccwl.in: Import (ccwl cwl) instead of (ccwl yaml). Use workflow->cwl instead of scm->yaml. * tests/ccwl.scm ("stdin input should not have inputBinding"): Use command->cwl-scm from (ccwl cwl) instead of command->cwl from (ccwl ccwl).
2021-07-19tests: Fix indentation.Arun Isaac
* tests/ccwl.scm ("stdin input should not have inputBinding"): Fix indentation.
2021-07-02tests: Ensure stdin input has no inputBinding.Arun Isaac
* tests/ccwl.scm: Import (ccwl ccwl) ("stdin input should not have inputBinding"): New test.
2021-07-02tests: Remove unnecessary import.Arun Isaac
* tests/ccwl.scm: Do not import (srfi srfi-71).
2021-04-26Remove deprecated break-pair tests.Arun Isaac
* tests/ccwl.scm (break-pair): Delete function. ("break-pair", "break-pair: check last elemet handling"): Delete tests.
2021-04-17Add copyright section to test files.Arun Isaac
* tests/ccwl.scm, tests/yaml.scm: Add copyright section.
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.
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