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2022-01-16tests: Use @@ instead of module-ref and resolve-module.Arun Isaac
@@ is shorter and looks neater with fewer quotes. * tests/ccwl.scm ("stdin input should not have inputBinding"), tests/utils.scm ("unsyntax-keywords"): Use @@ instead of module-ref and resolve-module.
2022-01-16ccwl: Indent lambda** docstring examples correctly.Arun Isaac
* ccwl/utils.scm (lambda**): Indent docstring examples correctly.
2022-01-10dir-locals: Allows tabs in Makefiles.Arun Isaac
* .dir-locals.el (makefile-gmake-mode): Set indent-tabs-mode to t.
2022-01-10Migrate to hand-written Makefiles.Arun Isaac
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.
2021-12-17Create specialized type for graphviz edge.Arun Isaac
* ccwl/graphviz.scm (<graph-edge>): New type. (graph-edge): New function. (graph->dot): Support specification of edges using the <graph-edge> type.
2021-12-17Abstract out serialization of graphviz properties.Arun Isaac
* ccwl/graphviz.scm (serialize-properties): New function. (graph->dot): Use serialize-properties.
2021-12-13ccwl: Support graphviz node ports.Arun Isaac
* ccwl/graphviz.scm (<graph-port>): New type. (serialize): Support <graph-port> objects. * tests/graphviz.scm (graph-port): New function. ("serialize ports correctly"): New test case.
2021-12-13ccwl: Organize serialize into a generic function.Arun Isaac
* ccwl/graphviz.scm (serialize): Organize into a generic function that dispatches on input type.
2021-12-13ccwl: Escape only the double quote character in graphviz output.Arun Isaac
* ccwl/graphviz.scm: Import (ice-9 string-fun). (serialize): When quoting strings, escape only the double quote character. * tests/graphviz.scm ("do not escape backslashes"): New test case.
2021-12-13ccwl: Support graphviz HTML strings.Arun Isaac
* ccwl/graphviz.scm (<html-string>): New type. (escape-id): Delete function. (serialize): New function. (graph->dot): Use serialize instead of escape-id. * tests/graphviz.scm: New file. ("serialize HTML strings correctly"): New test case. * Makefile.am (SCM_TESTS): Register it.
2021-12-10guix.scm: Base ccwl package off upstream Guix package.Arun Isaac
* guix.scm: Do not import (gnu packages graphviz), (gnu packages guile), (gnu packages guile-xyz), (gnu packages pkg-config), (gnu packages skribilo), (gnu packages texinfo), (guix build-system gnu), (guix licenses) and (guix utils). Import (gnu packages bioinformatics) with the guix: prefix. (ccwl): Base off upstream Guix package.
2021-12-10README: Recommend Guix to set up a development environment.Arun Isaac
* README.org (Contributing): Recommend Guix to set up a development environment.
2021-12-10README: Recommend upstream Guix package for installation.Arun Isaac
* README.org (Installation)[Using Guix]: Recommend upstream Guix package.
2021-12-09contrib: Add pggb workflow.Arun Isaac
* contrib/pggb.scm: New file.
2021-11-29README: Emphasize that manual installation is from source.Arun Isaac
* README.org (Installation)[Manually]: Rename to "Manually from source".
2021-11-29README: Add instructions for installation using software bundles.Arun Isaac
* README.org (Installation)[Using binary software bundles]: New subsection.
2021-11-29Makefile: Build software bundles.Arun Isaac
* Makefile.am (docker, pack): New targets.
2021-11-29guix.scm: Add a wrap phase.Arun Isaac
* guix.scm (ccwl)[arguments]: Import target-guile-effective-version from (guix build guile-build-system). Add a wrap phase.
2021-11-25guix.scm: Bump version.Arun Isaac
* guix.scm (ccwl)[version]: Set to 0.2.0.
2021-11-25guix.scm: Use the upstream Guix guile-libyaml package.Arun Isaac
* guix.scm: Do not prefix import of (gnu packages guile-xyz) with guix: (guile-libyaml): Delete variable.
2021-11-19README: Add installation instructions.Arun Isaac
* README.org (Installation): New section.
2021-11-19guix.scm: Replace guix environment with guix shell.Arun Isaac
guix environment has been superseded by guix shell. * guix.scm: Replace guix environment with guix shell.
2021-11-06Release version 0.2.0.v0.2.0Arun Isaac
* configure.ac: Bump version. * NEWS: Update news. * website/releases/ccwl-0.2.0.tar.lz, website/releases/ccwl-0.2.0.tar.lz.asc: New files.
2021-11-05doc: Search source-path in scheme-source-form.Arun Isaac
* doc/skribilo.scm (scheme-source-form): Search source-path.
2021-11-05build-aux: Extract dependencies from scheme-source-form.Arun Isaac
* build-aux/find-dependencies.scm (find-dependencies): Extract dependencies from scheme-source-form.
2021-11-05build-aux: Delete duplicates in dependencies.Arun Isaac
* build-aux/find-dependencies.scm: Delete duplicates before printing out dependencies.
2021-11-05gitignore: Ignore dot files.Arun Isaac
* .gitignore: Add doc/*.dot.
2021-11-05doc: Add spell check workflow to tutorial.Arun Isaac
* 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.
2021-11-05doc: Support extracting specific forms from a scheme file.Arun Isaac
* doc/skribilo.scm (scheme-source-form): New public function.
2021-11-05build-aux: Hide doc/cwl-output in the manual output snippets.Arun Isaac
* build-aux/generate-cwl-output.sh.in: In the sed invocation, replace doc/cwl-output too.
2021-11-05website: Do not specify line-height on h1, h2 and h3.Arun Isaac
* website/style.css (h1, h2, h3): Delete line-height CSS property.
2021-11-05Makefile: Copy images without recursion.Arun Isaac
* Makefile.am (doc/ccwl.html): Copy images without recursion.
2021-11-05Makefile: Delete target if recipe fails.Arun Isaac
Without this, when recipes involving output redirection fail, their targets are not deleted. * Makefile.am (.DELETE_ON_ERROR): New target.
2021-11-05Makefile: Create doc directory before populating it.Arun Isaac
* Makefile.am (doc/.dirstamp): New target. ($(DOC_IMAGES:.png=.dot), $(DOC_OUT)): Depend on doc/.dirstamp. (CLEAN_DIRECTORIES): Add doc/.dirstamp.
2021-11-05Makefile: Do not clean files based on extension.Arun Isaac
* Makefile.am (CLEANFILES): Replace doc/*.cwl, doc/*.dot, doc/*.out and doc/*.png with DOC_SCM, DOC_IMAGES and DOC_OUT variables.
2021-11-05Makefile: Distinguish DOC_OTHER from DOC_OUT.Arun Isaac
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.
2021-11-05doc: Document reuse of external CWL workflows.Arun Isaac
* doc/ccwl.skb (Cookbook): New chapter. * doc/external-cwl-workflow.scm, doc/echo.cwl: New files. * .gitignore: Add !doc/echo.cwl.
2021-11-04Makefile: Distribute doc/hello.c.gz. and doc/hello.txt.Arun Isaac
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.
2021-11-04Makefile: Pass auxiliary dependencies from automatic variables.Arun Isaac
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.
2021-11-04build-aux: Use paths relative to top-level in generate-cwl-output.sh.Arun Isaac
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.
2021-11-02configure: Check for (yaml) guile module.Arun Isaac
* configure.ac: Check for (yaml) guile module.
2021-11-02Makefile: Distribute doc/hello.tar.Arun Isaac
doc/hello.tar is used to build doc/hello.tar.out. * Makefile.am (EXTRA_DIST): Add doc/hello.tar.
2021-11-02Makefile: Do not distribute *.out files.Arun Isaac
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.
2021-11-02tests: Add input-output-parameters.cwl.Arun Isaac
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.
2021-11-02ccwl: Support external CWL workflows.Arun Isaac
* 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.
2021-11-02guix.scm: Define ccwl as a separate variable.Arun Isaac
This make it easier to refer to it in the changelog. * guix.scm (ccwl): New variable. Return ccwl.
2021-11-02ccwl: Rename graphviz to dot.Arun Isaac
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.
2021-10-19configure: Warn if emacs is not found.Arun Isaac
* configure.ac (OPTIONAL_PROGRAM): New macro. Use OPTIONAL_PROGRAM to check for emacs.
2021-10-19configure: Error out if required programs are not found.Arun Isaac
* configure.ac (CHECK_FOR_PROGRAM, REQUIRED_PROGRAM): New macros. Use REQUIRED_PROGRAM to check for dot, cwltool and skribilo.
2021-10-19guix.scm: Use git-predicate from (guix git-download).Arun Isaac
* 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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