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js-expression corresponds to ExpressionTool in the CWL specification.
* ccwl/ccwl.scm (<js-expression>): New type.
(js-expression): New macro.
(function-inputs, function-outputs, function-object): Support
<js-expression> objects.
(function-input-keys): Mention <js-expression> objects in docstring.
* ccwl/cwl.scm (function->cwl, workflow->cwl-scm): Support
<js-expression> objects.
(command->cwl-scm): Move staging requirements handling to ...
(staging-requirements): ... this new function.
(js-expression->cwl, js-expression->cwl-scm): New functions.
* ccwl/graphviz.scm (function->dot): Support <js-expression> objects.
(command->graph): Abstract to ...
(single-node-workflow->graph): ... this new function.
(js-expression->dot, js-expression->graph): New functions.
* scripts/ccwl (main): Support <js-expression> objects.
* doc/ccwl.skb (Cookbook){Javascript expressions via ExpressionTool}:
New section.
* doc/js-expression-iota.scm: New file.
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Call workflows and commands by our unified notion of "function". This
makes it more succinct when adding more kinds of functions.
* ccwl/cwl.scm (workflow-or-command->cwl): Rename to function->cwl.
* ccwl/graphviz.scm (workflow-or-command->dot): Rename to
function->dot.
* scripts/ccwl (main): Use function->cwl and function->dot.
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* scripts/ccwl (main): When ccwl crashes, say so explicitly.
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* scripts/ccwl (main): Raise exception when file returns neither
workflow nor command.
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* scripts/ccwl (main): Replace workflow->cwl and workflow->dot with
workflow-or-command->cwl and workflow-or-command->dot.
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* scripts/ccwl (main): Catch and report &formatted-message conditions.
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* scripts/ccwl: Import (ice-9 exceptions).
(main): Do not print backtrace or request the user to report a bug for
quit exceptions.
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* scripts/ccwl: Set scheme mode in Emacs.
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* scripts/ccwl (main): Catch uncaught exceptions and request the user
report them to the issue tracker.
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Call main from the shebang command instead of calling it
directly. This allows us to run "guile -l scripts/ccwl" without
actually running main. This seems to be important for Emacs Geiser as
it freezes up without this fix.
* scripts/ccwl: Call main from shebang. Do not call main directly.
(main): Accept args as regular argument instead of as a rest argument.
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* scripts/ccwl: Do not pass multiple arguments to env. Pass them
through sh.
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* scripts/ccwl: Add --no-auto-compile to shebang.
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* scripts/ccwl (main): Remove FIXME note about compiling ccwl files.
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* ccwl/ui.scm: New file.
* scripts/ccwl: Import (rnrs exceptions), (srfi srfi-28), (ccwl
conditions) and (ccwl ui).
(main): Handle ccwl syntax violations by reporting them and exiting.
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read-syntax gives us get better source properties.
* scripts/ccwl (main): Read using read-syntax.
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The autotools are really overkill for a simple Guile project like
ccwl.
* .gitignore: Delete autotool generated files. Add Makefile.include.
* Makefile.am, Makefile, build-aux/distcheck.scm, configure,
configure.ac, configure.scm: New files.
* NEWS: Rename to NEWS.org. Remove Emacs file-local variable to use
org mode.
* bootstrap.sh: Delete file.
* build-aux/generate-cwl-output.sh.in: Rename to ...
* build-aux/generate-cwl-output.sh: ... this. Replace autoconf
variables for cwltool and sed.
* build-aux/test-driver.scm.in: Rename to ...
* build-aux/test-driver.scm: ... this. Do not import (ice-9
getopt-long).
(%options): Delete variable.
(my-gnu-runner): Do not write to log or trs ports.
Accept test files as command-line arguments. Update invocation of
my-gnu-runner. Print summary of results.
* guix.scm (ccwl)[native-inputs]: Remove autoconf and automake.
* pre-inst-env.in: Rename to ...
* pre-inst-env: ... this. Replace autoconf variables for guile,
abs_top_builddir and abs_top_srcdir.
* scripts/ccwl.in: Rename to ...
* scripts/ccwl: ... this. Replace autoconf variable for guile.
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What we call "graphviz syntax" is actually the "graphviz dot
language". Rename accordingly.
* ccwl/graphviz.scm (workflow->graphviz): Rename to
workflow->dot. Call graph->dot instead of graph->graphviz.
(escape-id): Update docstring to mention dot.
(graph->graphviz): Rename to graph->dot. Update docstring to mention
dot.
* scripts/ccwl.in (main): Accept --to=dot instead of
--to=graphviz. Update --help usage information.
* Makefile.am (%.dot): Pass --to=dot instead of --to=graphviz.
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* scripts/ccwl.in: Import (ccwl graphviz).
(main): Implement the --to option.
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* scripts/ccwl.in: Import (srfi srfi-28).
(invalid-operand): New function.
(%help-option): New variable.
(main): Print usage information on --help and incorrect usage.
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* scripts/ccwl.in: Import (srfi srfi-37).
(invalid-option): New function.
(main): Use args-fold to extract source filename.
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This makes it easier to record changes in the changelog of commit
messages.
* scripts/ccwl.in: Invoke main.
(main): New function.
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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).
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* scripts/ccwl.in: Do not compile ccwl files.
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* pre-inst-env.in, scripts/ccwl.in: Remove unnecessary -s flag from
shebang.
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* configure.ac: Generate scripts/ccwl.
* scripts/ccwl: Rename to ...
* scripts/ccwl.in: ... this. Set path to guile in shebang as an
autoconf substitution.
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* scripts/ccwl: New file.
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