ccwl - Concise Common Workflow Language (mirror of https://github.com/arunisaac/ccwl)

Age	Commit message (Collapse)	Author
2023-10-09	tests: 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.
2023-10-09	ccwl: 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.
2023-10-09	ccwl: 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.
2023-09-29	ccwl: 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.
2023-09-20	tests: 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.
2022-01-16	ccwl: 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.
2022-01-16	ccwl: 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.
2022-01-16	ccwl: 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.
2022-01-16	tests: 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.
2021-11-02	ccwl: 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.
2021-10-12	tests: Fix quoting of type.	Arun Isaac
	* tests/ccwl.scm ("stdin input should not have inputBinding"): Fix quoting of type File.
2021-10-11	ccwl: 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).
2021-07-19	tests: Fix indentation.	Arun Isaac
	* tests/ccwl.scm ("stdin input should not have inputBinding"): Fix indentation.
2021-07-02	tests: Ensure stdin input has no inputBinding.	Arun Isaac
	* tests/ccwl.scm: Import (ccwl ccwl) ("stdin input should not have inputBinding"): New test.
2021-07-02	tests: Remove unnecessary import.	Arun Isaac
	* tests/ccwl.scm: Do not import (srfi srfi-71).
2021-04-26	Remove deprecated break-pair tests.	Arun Isaac
	* tests/ccwl.scm (break-pair): Delete function. ("break-pair", "break-pair: check last elemet handling"): Delete tests.
2021-04-17	Add copyright section to test files.	Arun Isaac
	* tests/ccwl.scm, tests/yaml.scm: Add copyright section.
2021-02-27	Add 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.