| Age | Commit message (Expand) | Author |
|---|
| 2021-05-15 | Make stdin a unary key of command.•••* ccwl/ccwl.scm (command): Make stdin a unary key.
| Arun Isaac |
| 2021-05-15 | Do not convert YAML symbols from kebab case to camel case.•••Doing this conversion effectively forbids kebab case symbols in YAML.
* ccwl/yaml.scm (kebab->camel): Delete function.
(display-atom): Do not convert symbols from kebab case to camel case.
* ccwl/ccwl.scm (make-workflow, output->cwl, command->cwl): Write
camel case explicitly.
| Arun Isaac |
| 2021-05-15 | Add list functions for multi-valued functions.•••* ccwl/utils.scm (mapn, append-mapn, foldn): New public functions.
| Arun Isaac |
| 2021-05-14 | Rewrite pre-inst-env in scheme.•••Scheme code is more readable than arcane bash.
* pre-inst-env.in: Rewrite in scheme.
| Arun Isaac |
| 2021-04-26 | Remove deprecated pipeline function.•••* ccwl/ccwl.scm (pipeline): Delete function.
| Arun Isaac |
| 2021-04-26 | Escape asterisk characters in scm->yaml.•••* ccwl/yaml.scm (display-atom): Escape asterisk characters.
* tests/yaml.scm ("strings with asterisk characters should be
escaped"): New test.
| Arun Isaac |
| 2021-04-26 | Test if scm->yaml escapes hyphen characters.•••* tests/yaml.scm ("strings with hyphen characters should be escaped"):
New test.
| Arun Isaac |
| 2021-04-26 | Add .gitignore.•••* .gitignore: New file.
| Arun Isaac |
| 2021-04-26 | Run tests in autotools build system.•••* build-aux/test-driver.scm.in: New file.
* configure.ac: Generate build-aux/test-driver.scm.
* Makefile.am (TEST_EXTENSIONS): Add .scm.
(SCM_TESTS): Add tests/ccwl.scm and tests/yaml.scm.
(TESTS): Set to SCM_TESTS.
(EXTRA_DIST): Distribute test files.
| Arun Isaac |
| 2021-04-26 | Remove deprecated break-pair tests.•••* tests/ccwl.scm (break-pair): Delete function.
("break-pair", "break-pair: check last elemet handling"): Delete
tests.
| Arun Isaac |
| 2021-04-26 | Add Guix build script.•••* guix.scm: New file.
| Arun Isaac |
| 2021-04-26 | Set path to guile in shebang from configure.•••* configure.ac: Generate scripts/ccwl.
* scripts/ccwl: Rename to ...
* scripts/ccwl.in: ... this. Set path to guile in shebang as an
autoconf substitution.
| Arun Isaac |
| 2021-04-26 | Add autotools build system.•••* Makefile.am, bootstrap.sh, configure.ac, pre-inst-env.in: New files.
| Arun Isaac |
| 2021-04-26 | Add ccwl script.•••* scripts/ccwl: New file.
| Arun Isaac |
| 2021-04-26 | Redefine command using lambda**.•••* ccwl/ccwl.scm (command): Redefine using lambda**.
| Arun Isaac |
| 2021-04-26 | Implement the CCWL embedded domain specific language.•••* ccwl/ccwl.scm: Import (ccwl utils).
(command): Return <command> object.
(auto-connect): Delete function.
(invoke-command, make-workflow, workflow-steps): New functions.
(workflow): Replace function with macro.
| Arun Isaac |
| 2021-04-26 | Add setter for source field of <output> type.•••* ccwl/ccwl.scm (<output>): Add functional setter set-output-source
for source field.
* .dir-locals.el (scheme-mode): Specify indentation for
set-output-source.
| Arun Isaac |
| 2021-04-26 | Add plist->alist.•••* ccwl/utils.scm (pairify, plist->alist): New public functions.
| Arun Isaac |
| 2021-04-25 | Upgrade to CWL version 1.2.•••Version 1.2 of the CWL specification is required to support
conditional steps.
* ccwl/ccwl.scm (%cwl-version): Set to "v1.2".
| Arun Isaac |
| 2021-04-17 | Add copyright section to test files.•••* tests/ccwl.scm, tests/yaml.scm: Add copyright section.
| Arun Isaac |
| 2021-04-17 | Expand name Arun I to Arun Isaac.•••* ccwl/ccwl.scm, ccwl/utils.scm, ccwl/yaml.scm: Expand name Arun I to
Arun Isaac.
| Arun Isaac |
| 2021-04-16 | Add copyright and commentary sections to files.•••* ccwl/ccwl.scm, ccwl/utils.scm, ccwl/yaml.scm: Add copyright and
commentary sections.
| Arun Isaac |
| 2021-04-16 | Add .dir-locals.el for emacs.•••* .dir-locals.el: New file.
| Arun Isaac |
| 2021-04-16 | Implement lambda** n-ary keyword function.•••* ccwl/utils.scm: Export lambda** instead of group-arguments.
(group-arguments): Delete function.
(lambda**): New macro.
| Arun Isaac |
| 2021-04-16 | Make unary-keywords argument of group-keyword-arguments optional.•••* ccwl/utils.scm (group-keyword-arguments): Make unary-keywords
optional.
| Arun Isaac |
| 2021-04-16 | Add plist-ref utility.•••* ccwl/utils.scm: Import (srfi srfi-26).
(plist-ref): New function.
| Arun Isaac |
| 2021-04-12 | Support n-ary keyword arguments.•••* ccwl/utils.scm: New file.
| Arun Isaac |
| 2021-03-26 | Add README.•••* README.org: New file.
| Arun Isaac |
| 2021-03-26 | Add copy of GPLv3.•••* COPYING: New file.
| Arun Isaac |
| 2021-03-22 | List additional-inputs while generating CWL.•••* ccwl/ccwl.scm (command->cwl): List additional-inputs in inputs
array.
| Arun Isaac |
| 2021-03-22 | Add additional-inputs field to <command> type.•••* ccwl/ccwl.scm (<command>): Add additional-inputs field.
(command): Initialize additional-inputs field.
| Arun Isaac |
| 2021-03-22 | Remove input->tree abstraction.•••<input> objects need to be expanded into CWL in context sensitive
ways. There is no simple generalization.
* ccwl/ccwl.scm (input->tree): Delete function.
(workflow): Expand input->tree.
| Arun Isaac |
| 2021-03-22 | Delete input field of <command> object.•••* ccwl/ccwl.scm (<command>): Delete input field.
(command): Do not set inputs field.
| Arun Isaac |
| 2021-03-21 | Print steps enclosing <command> objects correctly.•••* ccwl/ccwl.scm (write-cwl): Invoke command->cwl if step encloses
<command> object.
| Arun Isaac |
| 2021-03-21 | Use both CWL arguments and inputs arrays.•••* ccwl/ccwl.scm (<cli-element>): New type.
(command->cwl): Put string and expression arguments into the arguments
array. Put <input> arguments into the inputs array.
| Arun Isaac |
| 2021-03-21 | Add alist filtering utility function.•••* ccwl/ccwl.scm (filter-alist): New function.
(input->tree): Use filter-alist.
| Arun Isaac |
| 2021-03-21 | Set the default output of a pipeline.•••* ccwl/ccwl.scm (pipeline): Set the stdout of the last command to be
the default output of the pipeline.
| Arun Isaac |
| 2021-03-21 | Pull out cwl-version as a separate variable.•••* ccwl/ccwl.scm (%cwl-version): New variable.
(workflow, command->cwl): Use %cwl-version.
| Arun Isaac |
| 2021-03-21 | Add prefix field to <input> object.•••* ccwl/ccwl.scm (<input>): Add prefix field.
(input): Initialize prefix field.
(input-with-prefix): New public function.
| Arun Isaac |
| 2021-03-21 | Remove appender for inputs field of <command>.•••* ccwl/ccwl.scm (append-command-inputs): Delete function.
| Arun Isaac |
| 2021-03-17 | Set default type of outputs to File.•••* ccwl/ccwl.scm (output): Set default type to File.
| Arun Isaac |
| 2021-03-17 | Set default type of inputs to File.•••* ccwl/ccwl.scm (input): Set default type to File.
| Arun Isaac |
| 2021-03-07 | Add write-cwl function to write generated CWL to a file.•••* ccwl/ccwl.scm: Import (srfi srfi-26) and (ccwl yaml).
(write-cwl): New public function.
| Arun Isaac |
| 2021-03-07 | Remove field binding from constructor of the <input> type.•••* ccwl/ccwl.scm (<input>): Remove field binding from constructor.
| Arun Isaac |
| 2021-03-07 | Escape YAML strings that contain the hyphen character.•••* ccwl/yaml.scm (display-atom): Escape string if it contains the
hyphen character.
| Arun Isaac |
| 2021-03-06 | Auto-connect steps by matching identifiers.•••* ccwl/ccwl.scm (auto-connect): New function.
(workflow): Auto-connect step inputs and outputs before generating
<step> record.
| Arun Isaac |
| 2021-03-06 | Implement pipeline support.•••* ccwl/ccwl.scm (%stdin, %stdout): New variables.
(pipeline): New function.
| Arun Isaac |
| 2021-03-06 | Rewrite workflow function to output a <step> record.•••All user exposed functions should output a <step> record so that they
are composable.
* ccwl/ccwl.scm (workflow): Rewrite workflow function to output a
<step> record.
| Arun Isaac |
| 2021-03-06 | Define input=? predicate.•••* ccwl/ccwl.scm (input=?): New function.
| Arun Isaac |
| 2021-03-06 | Add source field to <input> type.•••* ccwl/ccwl.scm (<input>): Add source field.
(input): Initialize source field to #f in constructor.
| Arun Isaac |
