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2021-07-04Makefile: Replace top_builddir with builddir.Arun Isaac
Since we only have a top-level Makefile, top_builddir and builddir are the same. Use builddir in the interest of brevity. * Makefile.am (%.go, SCM_LOG_DRIVER, doc/ccwl.info, doc/ccwl.html): Replace top_builddire with builddir.
2021-07-04Makefile: Pass image path to skribilo.Arun Isaac
* Makefile.am (SKRIBILO_FLAGS): Add --image-path=$(builddir).
2021-07-04doc: Use PNG images instead of SVG.Arun Isaac
PNG images are supported by both the info and html engines. * doc/ccwl.skb (Tutorial)[Workflow with multiple steps]: Use PNG images instead of SVG. * Makefile.am (CLEANFILES): Replace doc/*.svg with doc/*.png. (%.svg): Delete rule. (%.png): New rule. * .gitignore: Replace doc/*.svg with doc/*.png.
2021-07-04Makefile: Pass source path to skribilo.Arun Isaac
* Makefile.am (SKRIBILO_FLAGS): New variable. (doc/ccwl.info, doc/ccwl.html): Pass $(SKRIBILO_FLAGS) to skribilo.
2021-07-04doc: Search for source-ref referenced files in source-path.Arun Isaac
* doc/skribilo.scm: Import (skribilo parameters). (source-ref): Search for files in source-path.
2021-07-04doc: Remove redundant file open.Arun Isaac
* doc/skribilo.scm (source-ref): Remove redundant file open.
2021-07-04Makefile: Distribute documentation.Arun Isaac
* Makefile.am (EXTRA_DIST): Add doc/skribilo.scm, doc/ccwl.skb, $(DOC_OTHER).
2021-07-04Makefile: Include .depends with automake.Arun Isaac
* bootstrap.sh: Generate .depends. * Makefile.am: Include .depends with automake, not with make. (.depends): Delete rule. (doc/ccwl.html, doc/ccwl.info): Use DOC_OTHER instead of DOC_OTHER_DEPENDENCIES. (CLEANFILES): Remove .depends. * build-aux/find-dependencies.scm: Output DOC_OTHER instead of DOC_OTHER_DEPENDENCIES. _DEPENDENCIES variables are special in automake.
2021-07-04Makefile: Clean only directories in clean-local.Arun Isaac
* Makefile.am (CLEANFILES): Add .depends, website/index.html. (CLEAN_DIRECTORIES): Add doc/ccwl.html, website/manual. (clean-local): Delete $(CLEAN_DIRECTORIES) only.
2021-07-04Makefile: Build skribilo documentation in-place.Arun Isaac
* Makefile.am (SKRIBILO_BUILD_DIR): Delete variable. (CLEANFILES): Add doc/*.cwl, doc/*.dot, doc/*.svg, doc/ccwl.info, doc/skribilo.go. ($(SKRIBILO_BUILD_DIR)/%.cwl): Rename to %.cwl. (info-local, install-info-local): Depend on doc/ccwl.info instead of $(SKRIBILO_BUILD_DIR)/ccwl.info. (html-local, install-html-local, website/manual/dev/en): Depend on doc/ccwl.html instead of $(SKRIBILO_BUILD_DIR)/ccwl.html. ($(SKRIBILO_BUILD_DIR)/ccwl.info): Rename to doc/ccwl.info. ($(SKRIBILO_BUILD_DIR)/ccwl.html): Rename to doc/ccwl.html. (clean-local): Do not delete doc/skribilo.go and $(SKRIBILO_BUILD_DIR). * .gitignore: Add doc/*.cwl, doc/*.html, doc/*.info, doc/*.svg. Remove doc/skribilo. * doc/ccwl.skb (Tutorial)[Workflow with multiple steps]: Reference images in the doc directory instead of in the doc/skribilo directory.
2021-07-04Makefile: List files in a single line.Arun Isaac
There are so few that it makes no sense to list them one on a line. * Makefile.am (SOURCES, SCM_TESTS): List files in a single line.
2021-07-04scripts: Do not compile ccwl files.Arun Isaac
* scripts/ccwl.in: Do not compile ccwl files.
2021-07-04Makefile: Do not create website directory.Arun Isaac
The website directory is checked into the git repository and need not be created. * Makefile.am (website/index.html): Do not create website directory.
2021-07-04Makefile: Add prefix variables for silencing commands.Arun Isaac
* Makefile.am (CCWL_GEN*, CWLTOOL_GEN*, DOT_GEN*, EMACS_GEN*, GUILD_GEN*, SKRIBILO_GEN*): New variables. (%.go): Prefix with GUILD_GEN instead of AM_V_GEN. ($(SKRIBILO_BUILD_DIR)/%.cwl): Prefix with CCWL_GEN instead of AM_V_GEN. (%.dot): Prefix with CWLTOOL_GEN instead of AM_V_GEN. (%.svg): Prefix with DOT_GEN. ($(SKRIBILO_BUILD_DIR)/ccwl.info, $(SKRIBILO_BUILD_DIR)/ccwl.html): Prefix with SKRIBILO_GEN instead of AM_V_GEN. (website/index.html): Prefix with EMACS_GEN.
2021-07-03doc: Use emph instead of quotes for emphasis.Arun Isaac
* doc/ccwl.skb (Tutorial)[First example, Capturing the standard output stream of a command]: Use emph instead of double quotes for emphasis.
2021-07-03doc: Move skribilo configuration into doc directory.Arun Isaac
* ccwl/skribilo.scm: Move to ... * doc/skribilo.scm: ... here. * doc/ccwl.skb: Import (doc skribilo) instead of (ccwl skribilo). * Makefile.am ($(SKRIBILO_BUILD_DIR)/ccwl.info, $(SKRIBILO_BUILD_DIR)/ccwl.html): Depend on doc/skribilo.go instead of ccwl/skribilo.go. * Makefile.am (clean-local): Delete doc/skribilo.go instead of ccwl/skribilo.go.
2021-07-03Makefile: Build skribilo configuration before documentation.Arun Isaac
* Makefile.am ($(SKRIBILO_BUILD_DIR)/ccwl.info, $(SKRIBILO_BUILD_DIR)/ccwl.html): Depend on ccwl/skribilo.go instead of ccwl/skribilo.scm. * Makefile.am (clean-local): Delete ccwl/skribilo.go.
2021-07-03guix.scm: Depend on cwltool and graphviz.Arun Isaac
* guix.scm: Import (gnu packages bioinformatics) and (gnu packages graphviz). (ccwl)[native-inputs]: Add cwltool and graphviz.
2021-07-03guix.scm: Import (gnu packages skribilo).Arun Isaac
This is a follow-up to commit bf485dd43386305177a2ba3ea1a5ee7e164984c6 where this import was missed out. * guix.scm: Import (gnu packages skribilo).
2021-07-03doc: Squeeze double space.Arun Isaac
* doc/ccwl.skb (Tutorial)[Capturing output files]: Squeeze double space.
2021-07-03Makefile: Comment on -local targets.Arun Isaac
* Makefile.am: Comment on use of install-data-local, install-info-local, install-html-local and uninstall-local targets.
2021-07-02.dir-locals.el: Indent syntax-lambda** correctly.Arun Isaac
* .dir-locals.el (scheme-mode): Indent syntax-lambda**.
2021-07-02.dir.locals.el: Remove unused indentation specifiers.Arun Isaac
* .dir-locals.el (scheme-mode): Remove indentation specification for set-input-source, set-output-source and set-step-in.
2021-07-02doc: Add copyright headers.Arun Isaac
* doc/ccwl.skb: Add copyright headers.
2021-07-02build-aux: Do not make backup files.Arun Isaac
* build-aux/build-home-page.el (make-backup-files): Set to nil.
2021-07-02tests: Ensure stdin input has no inputBinding.Arun Isaac
* tests/ccwl.scm: Import (ccwl ccwl) ("stdin input should not have inputBinding"): New test.
2021-07-02tests: Remove unnecessary import.Arun Isaac
* tests/ccwl.scm: Do not import (srfi srfi-71).
2021-07-02Makefile: Track dependencies automatically.Arun Isaac
* build-aux/find-dependencies.scm: New file. * Makefile.am (DOC_IMAGES): Delete variable. (.depends): New target. Include it in the Makefile. ($(SKRIBILO_BUILD_DIR)/ccwl.info, $(SKRIBILO_BUILD_DIR)/ccwl.html): Depend on DOC_OTHER_DEPENDENCIES. (clean-local): Delete .depends. * .gitignore: Add .depends.
2021-06-29doc: Document passing input into stdin.Arun Isaac
* doc/ccwl.skb (Tutorial)[Passing input into the standard input stream of a command]: New section. * doc/pass-stdin.scm, doc/pass-stdin.out: New files.
2021-06-29ccwl: Return #f if alist is empty after filtering.Arun Isaac
This way, filter-alist composes better with other invocations of filter-alist. * ccwl/ccwl.scm (filter-alist): Return #f if alist is empty after filtering. (command->cwl): Remove FIXME note about the inputBinding dictionary being empty.
2021-06-28Makefile: Clean entire website manual directory.Arun Isaac
* Makefile.am (clean-local): Delete entire website manual directory. (website/manual/dev/en): Create directory before copying files.
2021-06-28ccwl: Import (srfi srfi-2).Arun Isaac
* ccwl/ccwl.scm: Import (srfi srfi-2).
2021-06-28ccwl: Fix indentation.Arun Isaac
* ccwl/skribilo.scm (sexp-file-lines): Fix indentation.
2021-06-28website: Constrain images within their containers.Arun Isaac
* website/style.css (img): Set max-width to 100%.
2021-06-28doc: Add workflow graphs.Arun Isaac
* Makefile.am (DOC_IMAGES): Add checksum.svg and decompres-compile-run.svg. * doc/ccwl.skb (Tutorial)[Workflow with multiple steps]: Add workflow graphs checksum.svg and decompres-compile-run.svg.
2021-06-28Makefile: Build workflow images.Arun Isaac
* configure.ac: Search for cwltool, dot and sed. * Makefile.am (DOC_IMAGES): New variable. ($(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 $(DOC_IMAGES) into that directory.
2021-06-28ccwl: Support SVG images in HTML documentation.Arun Isaac
* ccwl/skribilo.scm: Add "svg" to the image-format custom of the HTML engine.
2021-06-22doc: Specify command inputs in a separate argument.Arun Isaac
* doc/capture-output-file-with-parameter-reference.scm, doc/capture-output-file.scm, doc/capture-stdout.scm, doc/checksum.scm, doc/decompress-compile-run.scm, doc/hello-world.scm: Specify command inputs in a separate argument. * doc/ccwl.skb (Tutorial)[First example]: Update description of command definition accordingly.
2021-06-22doc: Fix comma position.Arun Isaac
Lispy mode normalizes comma positions incorrectly for Skribilo mode. This needs to be fixed upstream or elsewhere. * doc/ccwl.skb (Tutorial)[Important concepts, Capturing the standard output stream of a command, Capturing output files, Workflow with multiple steps]: Fix comma position.
2021-06-21doc: Fill paragraph.Arun Isaac
* doc/ccwl.skb (Tutorial)[Workflow with multiple steps]: Fill paragraph.
2021-06-21ccwl: Link source links to entire s-exp.Arun Isaac
* ccwl/skribilo.scm (sexp-position, position->line-number, sexp-file-lines): New functions. (source-ref): Refer to entire s-exp, not just a single line.
2021-06-19website: Set foreground color to black.Arun Isaac
We want a high contrast black text on white background. * website/style.css (body): Unset color property.
2021-06-19website: Italicize code symbols.Arun Isaac
* website/style.css (code): Italicize.
2021-06-19website: Add background color and padding to code snippets.Arun Isaac
* website/style.css (pre): Add background color and padding.
2021-06-19README: Remove broken link to tutorial.Arun Isaac
* README.org (Documentation): Remove broken link to tutorial.
2021-06-19.gitignore: Add files.Arun Isaac
* .gitignore: Add build-aux/test-driver.scm and website.
2021-06-19Makefile: Let info and html targets depend on skribilo config.Arun Isaac
* Makefile.am ($(SKRIBILO_BUILD_DIR)/ccwl.info, $(SKRIBILO_BUILD_DIR)/ccwl.html): Depend on skribilo config ccwl/skribilo.scm.
2021-06-19doc: Link to source for pipe and tee.Arun Isaac
* doc/ccwl.skb (Tutorial)[Workflow with multiple steps]: Link to source for pipe and tee.
2021-06-19ccwl: Add source links.Arun Isaac
* 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.
2021-06-19configure: Search for emacs.Arun Isaac
* configure.ac: Search for emacs. * Makefile.am: Use EMACS set by configure.
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