| Age | Commit message (Expand) | Author |
|---|
| 2021-11-05 | doc: Add spell check workflow to tutorial.•••* doc/ccwl.skb (Tutorial)[Let's write a spell check workflow]: New
section.
* Makefile.am (doc/spell-check.out): New target.
(EXTRA_DIST): Add doc/spell-check-text.txt and doc/dictionary.
* doc/dictionary, doc/spell-check-text.txt,
doc/spell-check-workflow-1.scm, doc/spell-check-workflow-2.scm,
doc/spell-check.scm: New files.
| Arun Isaac |
| 2021-11-05 | doc: Support extracting specific forms from a scheme file.•••* doc/skribilo.scm (scheme-source-form): New public function.
| Arun Isaac |
| 2021-11-05 | build-aux: Hide doc/cwl-output in the manual output snippets.•••* build-aux/generate-cwl-output.sh.in: In the sed invocation, replace
doc/cwl-output too.
| Arun Isaac |
| 2021-11-05 | website: Do not specify line-height on h1, h2 and h3.•••* website/style.css (h1, h2, h3): Delete line-height CSS property.
| Arun Isaac |
| 2021-11-05 | Makefile: Copy images without recursion.•••* Makefile.am (doc/ccwl.html): Copy images without recursion.
| Arun Isaac |
| 2021-11-05 | Makefile: Delete target if recipe fails.•••Without this, when recipes involving output redirection fail, their
targets are not deleted.
* Makefile.am (.DELETE_ON_ERROR): New target.
| Arun Isaac |
| 2021-11-05 | Makefile: Create doc directory before populating it.•••* Makefile.am (doc/.dirstamp): New target.
($(DOC_IMAGES:.png=.dot), $(DOC_OUT)): Depend on doc/.dirstamp.
(CLEAN_DIRECTORIES): Add doc/.dirstamp.
| Arun Isaac |
| 2021-11-05 | Makefile: Do not clean files based on extension.•••* Makefile.am (CLEANFILES): Replace doc/*.cwl, doc/*.dot, doc/*.out
and doc/*.png with DOC_SCM, DOC_IMAGES and DOC_OUT variables.
| Arun Isaac |
| 2021-11-05 | Makefile: Distinguish DOC_OTHER from DOC_OUT.•••DOC_OTHER includes dependencies that are neither scm files nor out
files, but are primary sources required for the build.
* Makefile.am (EXTRA_DIST): Add DOC_OTHER.
(doc/ccwl.info, doc/ccwl.html): Depend on DOC_OTHER.
* build-aux/find-dependencies.scm: Output DOC_OTHER.
(find-dependencies): Classify source forms as type 'out or type 'other
based on extension.
| Arun Isaac |
| 2021-11-05 | doc: Document reuse of external CWL workflows.•••* doc/ccwl.skb (Cookbook): New chapter.
* doc/external-cwl-workflow.scm, doc/echo.cwl: New files.
* .gitignore: Add !doc/echo.cwl.
| Arun Isaac |
| 2021-11-04 | Makefile: Distribute doc/hello.c.gz. and doc/hello.txt.•••These files are source files required for the build. They were missed
out in an earlier commit.
* Makefile.am (EXTRA_DIST): Add doc/hello.c.gz and doc/hello.txt.
| Arun Isaac |
| 2021-11-04 | Makefile: Pass auxiliary dependencies from automatic variables.•••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.
| Arun Isaac |
| 2021-11-04 | build-aux: Use paths relative to top-level in generate-cwl-output.sh.•••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.
| Arun Isaac |
| 2021-11-02 | configure: Check for (yaml) guile module.•••* configure.ac: Check for (yaml) guile module.
| Arun Isaac |
| 2021-11-02 | Makefile: Distribute doc/hello.tar.•••doc/hello.tar is used to build doc/hello.tar.out.
* Makefile.am (EXTRA_DIST): Add doc/hello.tar.
| Arun Isaac |
| 2021-11-02 | Makefile: Do not distribute *.out files.•••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.
| Arun Isaac |
| 2021-11-02 | tests: Add input-output-parameters.cwl.•••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.
| Arun Isaac |
| 2021-11-02 | ccwl: Support external CWL workflows.•••* 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.
| Arun Isaac |
| 2021-11-02 | guix.scm: Define ccwl as a separate variable.•••This make it easier to refer to it in the changelog.
* guix.scm (ccwl): New variable.
Return ccwl.
| Arun Isaac |
| 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 |
