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2021-07-03doc: Move skribilo configuration into doc directory.•••* ccwl/skribilo.scm: Move to ... * doc/skribilo.scm: ... here. * doc/ccwl.skb: Import (doc skribilo) instead of (ccwl skribilo). * Makefile.am ($(SKRIBILO_BUILD_DIR)/ccwl.info, $(SKRIBILO_BUILD_DIR)/ccwl.html): Depend on doc/skribilo.go instead of ccwl/skribilo.go. * Makefile.am (clean-local): Delete doc/skribilo.go instead of ccwl/skribilo.go. Arun Isaac
2021-07-03Makefile: Build skribilo configuration before documentation.•••* Makefile.am ($(SKRIBILO_BUILD_DIR)/ccwl.info, $(SKRIBILO_BUILD_DIR)/ccwl.html): Depend on ccwl/skribilo.go instead of ccwl/skribilo.scm. * Makefile.am (clean-local): Delete ccwl/skribilo.go. Arun Isaac
2021-07-03guix.scm: Depend on cwltool and graphviz.•••* guix.scm: Import (gnu packages bioinformatics) and (gnu packages graphviz). (ccwl)[native-inputs]: Add cwltool and graphviz. Arun Isaac
2021-07-03guix.scm: Import (gnu packages skribilo).•••This is a follow-up to commit bf485dd43386305177a2ba3ea1a5ee7e164984c6 where this import was missed out. * guix.scm: Import (gnu packages skribilo). Arun Isaac
2021-07-03doc: Squeeze double space.•••* doc/ccwl.skb (Tutorial)[Capturing output files]: Squeeze double space. Arun Isaac
2021-07-03Makefile: Comment on -local targets.•••* Makefile.am: Comment on use of install-data-local, install-info-local, install-html-local and uninstall-local targets. Arun Isaac
2021-07-02.dir-locals.el: Indent syntax-lambda** correctly.•••* .dir-locals.el (scheme-mode): Indent syntax-lambda**. Arun Isaac
2021-07-02.dir.locals.el: Remove unused indentation specifiers.•••* .dir-locals.el (scheme-mode): Remove indentation specification for set-input-source, set-output-source and set-step-in. Arun Isaac
2021-07-02doc: Add copyright headers.•••* doc/ccwl.skb: Add copyright headers. Arun Isaac
2021-07-02build-aux: Do not make backup files.•••* build-aux/build-home-page.el (make-backup-files): Set to nil. Arun Isaac
2021-07-02tests: Ensure stdin input has no inputBinding.•••* tests/ccwl.scm: Import (ccwl ccwl) ("stdin input should not have inputBinding"): New test. Arun Isaac
2021-07-02tests: Remove unnecessary import.•••* tests/ccwl.scm: Do not import (srfi srfi-71). Arun Isaac
2021-07-02Makefile: Track dependencies automatically.•••* build-aux/find-dependencies.scm: New file. * Makefile.am (DOC_IMAGES): Delete variable. (.depends): New target. Include it in the Makefile. ($(SKRIBILO_BUILD_DIR)/ccwl.info, $(SKRIBILO_BUILD_DIR)/ccwl.html): Depend on DOC_OTHER_DEPENDENCIES. (clean-local): Delete .depends. * .gitignore: Add .depends. Arun Isaac
2021-06-29doc: Document passing input into stdin.•••* doc/ccwl.skb (Tutorial)[Passing input into the standard input stream of a command]: New section. * doc/pass-stdin.scm, doc/pass-stdin.out: New files. Arun Isaac
2021-06-29ccwl: Return #f if alist is empty after filtering.•••This way, filter-alist composes better with other invocations of filter-alist. * ccwl/ccwl.scm (filter-alist): Return #f if alist is empty after filtering. (command->cwl): Remove FIXME note about the inputBinding dictionary being empty. Arun Isaac
2021-06-28Makefile: Clean entire website manual directory.•••* Makefile.am (clean-local): Delete entire website manual directory. (website/manual/dev/en): Create directory before copying files. Arun Isaac
2021-06-28ccwl: Import (srfi srfi-2).•••* ccwl/ccwl.scm: Import (srfi srfi-2). Arun Isaac
2021-06-28ccwl: Fix indentation.•••* ccwl/skribilo.scm (sexp-file-lines): Fix indentation. Arun Isaac
2021-06-28website: Constrain images within their containers.•••* website/style.css (img): Set max-width to 100%. Arun Isaac
2021-06-28doc: Add workflow graphs.•••* Makefile.am (DOC_IMAGES): Add checksum.svg and decompres-compile-run.svg. * doc/ccwl.skb (Tutorial)[Workflow with multiple steps]: Add workflow graphs checksum.svg and decompres-compile-run.svg. Arun Isaac
2021-06-28Makefile: Build workflow images.•••* configure.ac: Search for cwltool, dot and sed. * Makefile.am (DOC_IMAGES): New variable. ($(SKRIBILO_BUILD_DIR)/%.cwl, %.dot, %.svg): New rules. ($(SKRIBILO_BUILD_DIR)/ccwl.info): Depend on $(DOC_IMAGES). ($(SKRIBILO_BUILD_DIR)/ccwl.html): Depend on $(DOC_IMAGES). Build HTML into a directory. Copy $(DOC_IMAGES) into that directory. Arun Isaac
2021-06-28ccwl: Support SVG images in HTML documentation.•••* ccwl/skribilo.scm: Add "svg" to the image-format custom of the HTML engine. Arun Isaac
2021-06-22doc: Specify command inputs in a separate argument.•••* doc/capture-output-file-with-parameter-reference.scm, doc/capture-output-file.scm, doc/capture-stdout.scm, doc/checksum.scm, doc/decompress-compile-run.scm, doc/hello-world.scm: Specify command inputs in a separate argument. * doc/ccwl.skb (Tutorial)[First example]: Update description of command definition accordingly. Arun Isaac
2021-06-22doc: Fix comma position.•••Lispy mode normalizes comma positions incorrectly for Skribilo mode. This needs to be fixed upstream or elsewhere. * doc/ccwl.skb (Tutorial)[Important concepts, Capturing the standard output stream of a command, Capturing output files, Workflow with multiple steps]: Fix comma position. Arun Isaac
2021-06-21doc: Fill paragraph.•••* doc/ccwl.skb (Tutorial)[Workflow with multiple steps]: Fill paragraph. Arun Isaac
2021-06-21ccwl: Link source links to entire s-exp.•••* ccwl/skribilo.scm (sexp-position, position->line-number, sexp-file-lines): New functions. (source-ref): Refer to entire s-exp, not just a single line. Arun Isaac
2021-06-19website: Set foreground color to black.•••We want a high contrast black text on white background. * website/style.css (body): Unset color property. Arun Isaac
2021-06-19website: Italicize code symbols.•••* website/style.css (code): Italicize. Arun Isaac
2021-06-19website: Add background color and padding to code snippets.•••* website/style.css (pre): Add background color and padding. Arun Isaac
2021-06-19README: Remove broken link to tutorial.•••* README.org (Documentation): Remove broken link to tutorial. Arun Isaac
2021-06-19.gitignore: Add files.•••* .gitignore: Add build-aux/test-driver.scm and website. Arun Isaac
2021-06-19Makefile: Let info and html targets depend on skribilo config.•••* Makefile.am ($(SKRIBILO_BUILD_DIR)/ccwl.info, $(SKRIBILO_BUILD_DIR)/ccwl.html): Depend on skribilo config ccwl/skribilo.scm. Arun Isaac
2021-06-19doc: Link to source for pipe and tee.•••* doc/ccwl.skb (Tutorial)[Workflow with multiple steps]: Link to source for pipe and tee. Arun Isaac
2021-06-19ccwl: Add source links.•••* ccwl/skribilo.scm: Import (rnrs io ports), (ice-9 match), (ice-9 regex) and (srfi srfi-171). (%source-uri-base): New variable. (source-ref): New public function. Arun Isaac
2021-06-19configure: Search for emacs.•••* configure.ac: Search for emacs. * Makefile.am: Use EMACS set by configure. Arun Isaac
2021-06-19Makefile: Use MKDIR_P instead of `mkdir -p'.•••* Makefile.am (website/index.html): Use MKDIR_P instead of `mkdir -p'. Arun Isaac
2021-06-19Makefile: Delete manual directory before rebuilding.•••* Makefile.am (website/manual/dev/en): Delete directory before rebuilding. Arun Isaac
2021-06-19website: Move CSS into the website directory.•••That way, there is no need to copy it when building the website. * Makefile.am (website/style.css): Delete target. (website): Do not depend on the website/style.css target. (clean-local): Clean up only website/index.html and website/manual/dev/en, not the entire website directory. * style.css: Move to website/style.css. Arun Isaac
2021-06-15website: Make SVG badges clickable.•••* style.css (object): Set pointer-events to none. Arun Isaac
2021-06-15doc: Move documentation from texinfo to skribilo.•••* doc/ccwl.texi: Delete file. * ccwl/skribilo.scm, doc/ccwl.skb, doc/capture-output-file-with-parameter-reference.out, doc/capture-output-file-with-parameter-reference.scm, doc/capture-output-file.out, doc/capture-output-file.scm, doc/capture-stdout.out, doc/capture-stdout.scm, doc/checksum.out, doc/checksum.scm, doc/decompress-compile-run.out, doc/decompress-compile-run.scm, doc/hello-world.out, doc/hello-world.scm, doc/hello.tar.out: New files. * configure.ac: Check for skribilo. * Makefile.am: Unregister doc/ccwl.texi. Add documentation build rules. * guix.scm (ccwl)[native-inputs]: Replace texinfo with skribilo. * .gitignore: Add doc/skribilo. Remove doc/version.texi, doc/*.html, doc/*.info. Arun Isaac
2021-06-10build-aux: Do not override org-html--svg-image.•••SVG image export works correctly out of the box in org. * build-aux/build-home-page.el (org-html--svg-image): Delete function. Arun Isaac
2021-06-10pre-inst-env: Handle absent environment variables.•••* pre-inst-env.in (prepend-path-env!): Handle case when environment variable is absent and getenv returns #f. Arun Isaac
2021-06-10README: Do not use org macros.•••Unfortunately, GitHub's org exporter does not support macros. * README.org (ci-badge): Delete macro. Replace ci-badge macro invocations with expansions. Arun Isaac
2021-06-10README: Add continuous integration badges.•••* README.org (ci-badge): New macro. Add continuous integration badges. * build-aux/build-home-page.el (org-html--svg-image): Override org-html--svg-image to export svg using an img tag instead of an object tag. Arun Isaac
2021-06-01Do not export obsolete functions.•••* ccwl/ccwl.scm: Do not export step and pipeline. Arun Isaac
2021-06-01Introduce new command definition syntax.•••* ccwl/ccwl.scm: Do not export input and output. (<input>): Delete source field. Add position field. (input): Accept position and prefix fields in constructor. Do not initialize non-existent source field. (<command>): Delete additional-inputs field. Add inputs field. Delete set-command-outputs and set-command-stdin setters. (command): Rewrite as macro that accepts new command definition syntax. (<cli-element>): Delete type. (command->cwl): Generate CWL from new <command> type. (command-input-keys): Simplify to support new <command> type. Arun Isaac
2021-06-01Remove unused setters, appenders, etc.•••* ccwl/ccwl.scm: Do not export input-with-prefix. (<input>): Delete set-input-prefix. (<step>): Delete set-step-run, set-step-id, set-step-out. (input-with-prefix, field-appender, modify-step-run, append-step-in, append-step-out, append-command-outputs): Delete functions. Arun Isaac
2021-06-01In pipe, pass through input keys to all expressions.•••Earlier, the input keys would only be passed to the first expression. The second expression would only receive the output keys from the first expression. Passing input keys through to all expressions is a common use case, since expressions often need to access global inputs. If the original behavior is desired, we can always introduce a new construct, say `pipe-strict'. * ccwl/ccwl.scm (workflow-steps): In pipe, pass through input keys to all expressions. Arun Isaac
2021-06-01Filter out global workflow inputs from workflow outputs.•••* ccwl/ccwl.scm (key->output): New function. (workflow-steps): Filter out global workflow inputs from workflow-outputs. Arun Isaac
2021-06-01Add filter-mapi.•••* ccwl/utils.scm (filter-mapi): New public function. Arun Isaac
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