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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.
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* 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.
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* guix.scm (ccwl)[arguments]: Import target-guile-effective-version
from (guix build guile-build-system). Add a wrap phase.
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* guix.scm (ccwl)[version]: Set to 0.2.0.
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* guix.scm: Do not prefix import of (gnu packages guile-xyz) with
guix:
(guile-libyaml): Delete variable.
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guix environment has been superseded by guix shell.
* guix.scm: Replace guix environment with guix shell.
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* 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.
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This make it easier to refer to it in the changelog.
* guix.scm (ccwl): New variable.
Return ccwl.
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* 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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* guix.scm: Import (gnu packages bioinformatics) and (gnu packages
graphviz).
(ccwl)[native-inputs]: Add cwltool and graphviz.
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This is a follow-up to commit bf485dd43386305177a2ba3ea1a5ee7e164984c6
where this import was missed out.
* guix.scm: Import (gnu packages skribilo).
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* 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.
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* guix.scm: Import (gnu packages texinfo).
Add texinfo to native-inputs.
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* guix.scm: New file.
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