Age | Commit message (Collapse) | Author |
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This is required to support VPATH builds.
* Makefile.am (doc/capture-output-file.out,
doc/capture-output-file-with-parameter-reference.out,
doc/checksum.out, doc/decompress-compile-run.out, doc/pass-stdin.out):
Pass auxiliary dependencies from automatic variables.
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This removes the assumption that the source tree and the build tree
are the same, and is required to support VPATH builds.
* build-aux/generate-cwl-output.sh.in: Accept and write to paths
relative to the top-level directory. Do not change directory.
* Makefile.am (doc/capture-output-file.out,
doc/capture-output-file-with-parameter-reference.out,
doc/checksum.out, doc/decompress-compile-run.out, doc/pass-stdin.out):
Pass relative paths in input arguments.
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* configure.ac: Check for (yaml) guile module.
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doc/hello.tar is used to build doc/hello.tar.out.
* Makefile.am (EXTRA_DIST): Add doc/hello.tar.
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The *.out files are generated by running ccwl workflows. They need not
be distributed.
* build-aux/find-dependencies.scm (find-dependencies): Return *.out
files and *.scm files as different kinds of dependencies.
Output *.out and *.scm files separately as DOC_OUT and DOC_SCM instead
of together as DOC_OTHER.
* Makefile.am (doc/ccwl.info, doc/ccwl.html): Depend on DOC_SCM and
DOC_OUT instead of DOC_OTHER.
(EXTRA_DIST): Remove DOT_OTHER. Add DOC_SCM.
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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.
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* 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.
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This make it easier to refer to it in the changelog.
* guix.scm (ccwl): New variable.
Return ccwl.
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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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* configure.ac (OPTIONAL_PROGRAM): New macro.
Use OPTIONAL_PROGRAM to check for emacs.
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* configure.ac (CHECK_FOR_PROGRAM, REQUIRED_PROGRAM): New macros.
Use REQUIRED_PROGRAM to check for dot, cwltool and skribilo.
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* guix.scm: Do not import (srfi srfi-1), (srfi srfi-26), (ice-9
match), (ice-9 popen), (ice-9 rdelim) and (guix build
utils). Import (guix git-download).
(git-file?): Delete function.
Use git-predicate from (guix git-download) instead of git-file?.
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Workflow inputs are now global. It is misleading to say that they come
into the first expression, namely pipe and tee, in these examples.
* doc/ccwl.skb (Tutorial)[Workflow with multiple steps]: Say that
inputs, not workflow inputs, come into pipe and tee.
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* ccwl/ccwl.scm (collect-steps): Fix indentation.
(key->output): Fill paragraph.
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* ccwl/ccwl.scm (collect-steps): Implement rename to rename keys
between steps.
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* ccwl/ccwl.scm (collect-steps): Improve comment describing handling
of single input commands. Mention that it applies only when no inputs
are passed to it.
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* ccwl/ccwl.scm (<key>): Add setter set-key-name.
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* ccwl/ccwl.scm (<key>): Add cwl-id field.
(key): Initialize cwl-id field.
(key->output): Match the cwl-id of keys to the id of outputs, instead
of matching the name of keys to the id of outputs.
(cwl-key-address): Use the cwl-id of keys when outputting to CWL.
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* tests/ccwl.scm ("stdin input should not have inputBinding"): Fix
quoting of type File.
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* Makefile.am (%.dot): Use ccwl to build %.dot from %.scm instead of
cwltool to build %.dot from %.cwl.
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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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* ccwl/yaml.scm (indent-level): Import (ccwl utils). Move to ...
* ccwl/utils.scm (indent-level): ... here.
Export indent-level.
* ccwl/graphviz.scm: New file.
* Makefile.am (SOURCES): Register it.
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* ccwl/ccwl.scm (invoke-command): Delete 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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* ccwl/ccwl.scm: Do not export write-cwl.
(write-cwl): Delete function.
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We pass workflow inputs through all commands and constructs (pipe,
tee, etc.). Thus, these parameters are globally visible to all steps,
and are a kind of "global variable".
* ccwl/ccwl.scm (workflow-steps): Pass to the output, input keys that
correspond to workflow inputs.
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Before this commit, the docstring of workflow-steps did not correctly
describe its function.
* ccwl/ccwl.scm (workflow-steps): Fix docstring.
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This makes it easier to distinct source code from the regular text of
the error messages.
* ccwl/ccwl.scm (workflow-steps): Quote source code in error messages.
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* 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.
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* 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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* tests/utils.scm: Remove stray syntax-lambda** form.
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This reverts commit 35bcaaa67efbe9b60e69b0f7c17acc186c74e7c3. This was
not such a good idea. It is better to introduce the notion of global
parameters.
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* website/style.css (object): Upcase SVG in comment.
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In addition, we link to the GitHub repo in this new Download section
rather than in the Contributing section.
* README.org (download): Add dynamic block.
(Contributing): Delete github-link dynamic block.
* build-aux/build-home-page.el (org-dblock-write:github-link): Delete
function.
(org-dblock-write:download): New function.
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* README.org (Contributing): Add github-link dynamic block.
* build-aux/build-home-page.el (org-dblock-write:github-link): New
function.
(build-website): Update all org dynamic blocks. Do not insert GitHub
link using `search-forward' and `insert'.
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* Makefile.am (website/index.html): Depend on
build-aux/build-home-page.el.
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* build-aux/build-home-page.el (build-website): Remove redundant
beginning-of-line.
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We programmatically add a link to the GitHub repo before building the
website. This way, the GitHub link will appear only on the website,
and not on the README.org rendered on GitHub.
* build-aux/build-home-page.el (build-website): Add a link to the
GitHub repo before building the website.
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This allows us to do sophisticated syntax checking at an early stage,
very close to the user interface. That way error messages from ccwl
will make a lot more sense.
* ccwl/ccwl.scm (output): Re-implement as macro.
(command): Use the new macro interface.
* doc/capture-output-file-with-parameter-reference.scm,
doc/capture-output-file.scm, doc/capture-stdout.scm, doc/checksum.scm,
doc/decompress-compile-run.scm: Use new quoting syntax for output
types.
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* build-aux/generate-cwl-output.sh.in: Preserve only the LIBRARY_PATH
environment variable.
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* Makefile.am (CLEANFILES): Add doc/*.out.
(CLEAN_DIRECTORIES): Add doc/cwl-output.
(GENERATE_CWL_OUTPUT): New variable.
(doc/capture-output-file.out,
doc/capture-output-file-with-parameter-reference.out,
doc/capture-stdout.out, doc/checksum.out,
doc/decompress-compile-run.out, doc/hello-world.out,
doc/pass-stdin.out, doc/hello.tar.out): New targets.
* doc/capture-output-file-with-parameter-reference.out,
doc/capture-output-file.out, doc/capture-stdout.out, doc/checksum.out,
doc/decompress-compile-run.out, doc/hello-world.out,
doc/hello.tar.out, doc/pass-stdin.out: Delete files.
* build-aux/generate-cwl-output.sh.in, doc/hello.c.gz, doc/hello.tar,
doc/hello.txt: New files.
* configure.ac: Configure build-aux/generate-cwl-output.sh.
* doc/ccwl.skb (Tutorial)[Passing input into the standard input stream
of a command]: Replace file "foo" with "hello.txt".
* .gitignore: Add build-aux/generate-cwl-output.sh, doc/*.out and
doc/cwl-output.
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* Makefile.am (CLEANFILES): Clean *.dot, not %.dot.
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* Makefile.am: Set indent-tabs-mode to t.
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This allows us to do sophisticated syntax checking at an early stage,
very close to the user interface. That way error messages from ccwl
will make a lot more sense.
* ccwl/ccwl.scm (input): Re-implement as macro.
(<input>): Add new functional setters set-input-position and
set-input-prefix.
(input-spec-id, run-arg-position, run-arg-prefix): New functions.
(command, workflow): Use the new macro interface.
* doc/capture-output-file-with-parameter-reference.scm,
doc/capture-output-file.scm, doc/capture-stdout.scm, doc/checksum.scm,
doc/decompress-compile-run.scm, doc/hello-world.scm,
doc/pass-stdin.scm: Use new quoting syntax for input types.
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I have tripped up several times on the differences between lambda**
and syntax-lambda**. No longer! Making syntax-lambda** as close as
possible to lambda** makes the code much more readable and align
better with common sense.
* ccwl/utils.scm (syntax-lambda**): Do not ignore the first
identifier. Accept multiple values as arguments, not a single syntax
object.
* ccwl/ccwl.scm (command): Update use of syntax-lambda**.
* tests/utils.scm ("syntax-lambda**", "syntax-lambda** with default
values"): Update tests.
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* build-aux/test-driver.scm.in: Import (ice-9 match).
(my-gnu-runner): Use #t as the expected value for test-assert tests.
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Specifying '() as the default value for n-ary arguments is now
equivalent to specifying '(()) as the default value. This is wrong.
* ccwl/ccwl.scm (command): Do not explicitly specify the emtpy list as
the default value for n-ary arguments.
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