| Age | Commit message (Expand) | Author |
|---|
| 2021-11-02 | ccwl: Rename graphviz to dot.•••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.
| Arun Isaac |
| 2021-10-19 | configure: Warn if emacs is not found.•••* configure.ac (OPTIONAL_PROGRAM): New macro.
Use OPTIONAL_PROGRAM to check for emacs.
| Arun Isaac |
| 2021-10-19 | configure: Error out if required programs are not found.•••* configure.ac (CHECK_FOR_PROGRAM, REQUIRED_PROGRAM): New macros.
Use REQUIRED_PROGRAM to check for dot, cwltool and skribilo.
| Arun Isaac |
| 2021-10-19 | guix.scm: Use git-predicate from (guix git-download).•••* 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?.
| Arun Isaac |
| 2021-10-18 | doc: Say that inputs, not workflow inputs, come into pipe and tee.•••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.
| Arun Isaac |
| 2021-10-18 | ccwl: Fix indentation and paragraph filling.•••* ccwl/ccwl.scm (collect-steps): Fix indentation.
(key->output): Fill paragraph.
| Arun Isaac |
| 2021-10-18 | ccwl: Implement rename to rename keys between steps.•••* ccwl/ccwl.scm (collect-steps): Implement rename to rename keys
between steps.
| Arun Isaac |
| 2021-10-18 | ccwl: Improve comment describing handling of single input commands.•••* 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.
| Arun Isaac |
| 2021-10-18 | ccwl: Add setter for name field of <key> type.•••* ccwl/ccwl.scm (<key>): Add setter set-key-name.
| Arun Isaac |
| 2021-10-18 | ccwl: Separate ccwl key from CWL input/output id.•••* 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.
| Arun Isaac |
| 2021-10-12 | tests: Fix quoting of type.•••* tests/ccwl.scm ("stdin input should not have inputBinding"): Fix
quoting of type File.
| Arun Isaac |
| 2021-10-12 | Makefile: Use ccwl to generate graphviz graph.•••* Makefile.am (%.dot): Use ccwl to build %.dot from %.scm instead of
cwltool to build %.dot from %.cwl.
| Arun Isaac |
| 2021-10-12 | scripts: Allow compiling to graphviz.•••* scripts/ccwl.in: Import (ccwl graphviz).
(main): Implement the --to option.
| Arun Isaac |
| 2021-10-12 | scripts: Print usage information on --help and incorrect usage.•••* scripts/ccwl.in: Import (srfi srfi-28).
(invalid-operand): New function.
(%help-option): New variable.
(main): Print usage information on --help and incorrect usage.
| Arun Isaac |
| 2021-10-12 | scripts: Use args-fold.•••* scripts/ccwl.in: Import (srfi srfi-37).
(invalid-option): New function.
(main): Use args-fold to extract source filename.
| Arun Isaac |
| 2021-10-12 | scripts: Wrap main body in function.•••This makes it easier to record changes in the changelog of commit
messages.
* scripts/ccwl.in: Invoke main.
(main): New function.
| Arun Isaac |
| 2021-10-12 | ccwl: Implement compiling to graphviz.•••* 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.
| Arun Isaac |
| 2021-10-11 | ccwl: Remove unused invoke-command function.•••* ccwl/ccwl.scm (invoke-command): Delete function.
| Arun Isaac |
| 2021-10-11 | ccwl: Factorize out CWL generation code to separate file.•••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).
| Arun Isaac |
| 2021-10-11 | ccwl: Remove unused write-cwl function.•••* ccwl/ccwl.scm: Do not export write-cwl.
(write-cwl): Delete function.
| Arun Isaac |
| 2021-10-07 | ccwl: Pass workflow inputs through every command.•••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.
| Arun Isaac |
| 2021-10-06 | ccwl: Fix the docstring of workflow-steps.•••Before this commit, the docstring of workflow-steps did not correctly
describe its function.
* ccwl/ccwl.scm (workflow-steps): Fix docstring.
| Arun Isaac |
| 2021-10-04 | ccwl: Quote source code in error messages.•••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.
| Arun Isaac |
| 2021-10-04 | ccwl: Support #:allow-other-keys in lambda** and syntax-lambda**.•••* 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.
| Arun Isaac |
| 2021-10-04 | ccwl: Error out on invalid keywords to lambda**.•••* 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.
| Arun Isaac |
| 2021-10-04 | tests: Remove stray syntax-lambda** form.•••* tests/utils.scm: Remove stray syntax-lambda** form.
| Arun Isaac |
| 2021-10-04 | Revert "In pipe, pass through input keys to all expressions."•••This reverts commit 35bcaaa67efbe9b60e69b0f7c17acc186c74e7c3. This was
not such a good idea. It is better to introduce the notion of global
parameters.
| Arun Isaac |
| 2021-10-04 | website: Upcase SVG in comment.•••* website/style.css (object): Upcase SVG in comment.
| Arun Isaac |
| 2021-09-29 | README: Add a Download section using a dynamic block.•••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.
| Arun Isaac |
| 2021-09-29 | README: Add GitHub link using an org dynamic block.•••* 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'.
| Arun Isaac |
| 2021-09-29 | Makefile: Record dependency on build-home-page.el.•••* Makefile.am (website/index.html): Depend on
build-aux/build-home-page.el.
| Arun Isaac |
| 2021-08-17 | build-aux: Remove redundant beginning-of-line.•••* build-aux/build-home-page.el (build-website): Remove redundant
beginning-of-line.
| Arun Isaac |
| 2021-08-17 | build-aux: Link to GitHub repo on website.•••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.
| Arun Isaac |
| 2021-08-17 | ccwl: Define output objects using a macro instead of a function.•••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.
| Arun Isaac |
| 2021-08-17 | build-aux: Preserve only the LIBRARY_PATH environment in cwltool runs.•••* build-aux/generate-cwl-output.sh.in: Preserve only the LIBRARY_PATH
environment variable.
| Arun Isaac |
| 2021-08-16 | Makefile: Generate sample output when building documentation.•••* 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.
| Arun Isaac |
| 2021-08-16 | Makefile: Clean dot files correctly.•••* Makefile.am (CLEANFILES): Clean *.dot, not %.dot.
| Arun Isaac |
| 2021-08-16 | Makefile: Allow tabs when editing in Emacs.•••* Makefile.am: Set indent-tabs-mode to t.
| Arun Isaac |
| 2021-08-16 | ccwl: Define input objects using a macro instead of a function.•••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.
| Arun Isaac |
| 2021-07-27 | ccwl: Make syntax-lambda** more like lambda**.•••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.
| Arun Isaac |
| 2021-07-27 | build-aux: Use #t as the expected value for test-assert tests.•••* build-aux/test-driver.scm.in: Import (ice-9 match).
(my-gnu-runner): Use #t as the expected value for test-assert tests.
| Arun Isaac |
| 2021-07-20 | ccwl: Do not specify '() as the default value for n-ary arguments.•••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.
| Arun Isaac |
| 2021-07-20 | ccwl: Set default value of lambda** n-ary arguments to '().•••* ccwl/utils.scm (lambda**): Set default value of lambda** n-ary
arguments to the empty list. Document this in the 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"): New tests.
| Arun Isaac |
| 2021-07-20 | ccwl: Document syntax-lambda** support for default arguments.•••* ccwl/utils.scm (syntax-lambda**): Add example to docstring
documenting support for default arguments.
* tests/utils.scm ("syntax-lambda** with default values"): New test.
| Arun Isaac |
| 2021-07-20 | ccwl: Clarify difference between and lambda** and syntax-lambda**.•••* ccwl/utils.scm (syntax-lambda**): Clarify difference between and
lambda** and syntax-lambda**.
| Arun Isaac |
| 2021-07-20 | ccwl: Support default values for arguments in lambda**.•••* ccwl/utils.scm (lambda**): Support default values for arguments,
both unary and n-ary.
* tests/utils.scm ("lambda** with default values"): New test.
| Arun Isaac |
| 2021-07-20 | tests: Add tests for ccwl/utils.scm.•••* tests/utils.scm: New file.
* Makefile.am (SCM_TESTS): Register it.
| Arun Isaac |
| 2021-07-20 | ccwl: Add examples to docstrings.•••* ccwl/utils.scm (pairify, plist->alist, group-keyword-arguments,
plist-ref, syntax-lambda**, filter-mapi, mapn, append-mapn, foldn):
Add examples to docstrings.
| Arun Isaac |
| 2021-07-19 | build-aux: Put website building code into a function.•••This will be useful when we want build-home-page.el to build both a
website and a gemini capsule.
* build-aux/build-home-page.el (build-website): New function.
* Makefile.am (website/index.html): Call build-website.
| Arun Isaac |
| 2021-07-19 | ccwl: Add missing syntax in unsyntax-keywords docstring example.•••* ccwl/utils.scm (unsyntax-keywords): Add missing syntax in docstring
example.
| Arun Isaac |
