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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.
2023-11-23tests: Bump copyright year.Arun Isaac
This was missed out on an earlier commit this year. * tests/yaml.scm: Bump copyright year.
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.
2023-11-17utils: Define pairify behaviour on odd number of elements.Arun Isaac
* 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.
2023-11-17ui: Colorize format specifiers not format arguments.Arun Isaac
* 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.
2023-11-17yaml: Serialize atomic dictionary values on the same line.Arun Isaac
* 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.
2023-11-16yaml: Display arrays with a single atomic element on the same line.Arun Isaac
* 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.
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.
2023-11-06ui: Do not attempt to display the line preceding the 0th.Arun Isaac
* 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.
2023-11-06tests: Add tests for ui.scm.Arun Isaac
* tests/ui.scm: New file.
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.
2022-01-16ccwl: Delete plist->alist.Arun Isaac
plist->alist is not used anywhere. pairify is quite sufficient to take on its functionality. * ccwl/utils.scm (plist->alist): Delete function. * tests/utils.scm ("plist->alist"): Delete test.
2022-01-16ccwl: Document default default value of syntax-lambda**.Arun Isaac
* ccwl/utils.scm (syntax-lambda**): Document default default value. * tests/utils.scm ("default default value of syntax-lambda** unary argument should be #f", "default default value of syntax-lambda** n-ary argument should be the empty list"): New tests.
2022-01-16ccwl: Clarify default default value of lambda**.Arun Isaac
* ccwl/utils.scm (lambda**): Change "default value" to "default default value" in docstring. * tests/utils.scm ("default value of lambda** unary argument should be #f", "default value of lambda** n-ary argument should be the empty list"): Change "default value" to "default default value".
2022-01-16tests: Move plist-ref ahead of test-begin.Arun Isaac
This is a purely cosmetic change just to keep definitions outside the test cases. * tests/utils.scm (plist-ref): Move ahead of test-begin.
2022-01-16ccwl: Raise lambda** and syntax-lambda** errors as exceptions.Arun Isaac
* ccwl/conditions.scm (&unrecognized-keyword-assertion, &invalid-keyword-arity-assertion, &invalid-positional-arguments-arity-assertion): New conditions. * ccwl/utils.scm: Import (rnrs conditions), (rnrs exceptions) and (ccwl conditions). (group-keyword-arguments): Raise &invalid-keyword-arity-assertion on error. (lambda**, syntax-lambda**): Raise &unrecognized-keyword-assertion, &invalid-keyword-arity-assertion and &invalid-positional-arguments-arity-assertion on error. * tests/utils.scm: Import (rnrs conditions), (rnrs exceptions), (srfi srfi-1) and (ccwl conditions). ("lambda** should raise an &unrecognized-keyword-assertion on unrecognized keywords in arguments with syntax objects as irritants"): Check for &unrecognized-keyword-assertion. ("Unrecognized keyword argument passed to lambda** should raise an &unrecognized-keyword-assertion condition", "Unary lambda** keyword argument passed multiple arguments should raise an &invalid-keyword-arity-assertion condition", "Wrong number of positional arguments to lambda** should raise an &invalid-positional-arguments-arity-assertion condition", "syntax-lambda** should raise an &unrecognized-keyword-assertion on unrecognized keywords in arguments", "Unrecognized keyword argument passed to syntax-lambda** should raise an &unrecognized-keyword-assertion condition with syntax objects as irritants", "Unary syntax-lambda** keyword argument passed multiple arguments should raise an &invalid-keyword-arity-assertion condition", "Wrong number of positional arguments to syntax-lambda** should raise an &invalid-positional-arguments-arity-assertion 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.
2021-12-13ccwl: Support graphviz node ports.Arun Isaac
* ccwl/graphviz.scm (<graph-port>): New type. (serialize): Support <graph-port> objects. * tests/graphviz.scm (graph-port): New function. ("serialize ports correctly"): New test case.
2021-12-13ccwl: Escape only the double quote character in graphviz output.Arun Isaac
* ccwl/graphviz.scm: Import (ice-9 string-fun). (serialize): When quoting strings, escape only the double quote character. * tests/graphviz.scm ("do not escape backslashes"): New test case.
2021-12-13ccwl: Support graphviz HTML strings.Arun Isaac
* ccwl/graphviz.scm (<html-string>): New type. (escape-id): Delete function. (serialize): New function. (graph->dot): Use serialize instead of escape-id. * tests/graphviz.scm: New file. ("serialize HTML strings correctly"): New test case. * Makefile.am (SCM_TESTS): Register it.
2021-11-02tests: Add input-output-parameters.cwl.Arun Isaac
This is a follow-up to 0b359cf2c32cde81b4311d55273c8f6c14ca6b93 where this file should have been included. * tests/input-output-parameters.cwl: New file. * Makefile.am (EXTRA_DIST): Register it.
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).
2021-10-04ccwl: Support #:allow-other-keys in lambda** and syntax-lambda**.Arun Isaac
* ccwl/utils.scm (lambda**): Support #:allow-other-keys. Update docstring. (syntax-lambda**): Update docstring. * tests/utils.scm ("Allow other keys in lambda**", "Allow other keys in syntax-lambda**"): New tests.
2021-10-04ccwl: Error out on invalid keywords to lambda**.Arun Isaac
* ccwl/utils.scm (lambda**): Error out on invalid keywords (that is, keywords other than #:key, #:key* and #:allow-other-keys). * tests/utils.scm ("lambda** should error out on unrecognized keywords in arguments"): New test.
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