guix: Work with a test suite interned to the store. HEAD main

Instead of cwl-v1.2-conformance being a script that accepts a path to
the CWL v1.2 conformance test suite, we now work with a CWL v1.2 repo
origin object. This is more declarative, and there is no need for
manual cloning of the cwl-v1.2 git repo on the CI. The CI merely has
to run a script with no arguments. This provides more control here in
the ravanan repo and less configuration on the CI server.

We do likewise for the end-to-end tests. In this case, we work with
files from the ravanan repo, but have to first compile ccwl sources to
CWL workflows.

4 files changed, 92 insertions, 71 deletions

diff --git a/.guix/cwl-conformance.scm b/.guix/cwl-conformance.scm
index 8da1645..42d25d1 100644
--- a/.guix/cwl-conformance.scm
+++ b/.guix/cwl-conformance.scm
@@ -19,50 +19,60 @@
 (define-module (cwl-conformance)
   #:use-module ((cwltest-package) #:select (cwltest))
   #:use-module ((ravanan-package) #:select (ravanan))
+  #:use-module ((gnu packages bioinformatics) #:select (ccwl))
   #:use-module ((gnu packages nss) #:select (nss-certs))
   #:use-module ((gnu packages python) #:select (python))
   #:use-module ((gnu packages python-web) #:select (python-pybadges))
+  #:use-module (guix build utils)
   #:use-module (guix gexp)
+  #:use-module (guix git-download)
   #:use-module (guix packages)
   #:use-module (guix profiles)
   #:use-module (guix utils)
   #:use-module (ice-9 match))
 
-(define* (cwltest-suite-gexp manifest-file #:key (skip-tests '()))
+(define* (cwltest-suite-gexp cwltest-suite manifest-file #:key (skip-tests '()))
   (with-imported-modules '((guix build utils))
     #~(begin
         (use-modules (guix build utils)
                      (ice-9 match))
 
-        (match (command-line)
-          ((_ cwltest-suite)
-           ;; cwltest writes out output directories to TMPDIR, but does not
-           ;; clean up after. So, we set TMPDIR to our own temporary directory
-           ;; that we can manage easily. See pending issue on cleaning up
-           ;; temporary output directories:
-           ;; https://github.com/common-workflow-language/cwltest/issues/249
-           (mkdir "tmpdir")
-           (setenv "TMPDIR" "tmpdir")
-           (apply invoke
-                  #$(file-append cwltest "/bin/cwltest")
-                  "--test" cwltest-suite
-                  "--tool" #$(file-append ravanan "/bin/ravanan")
-                  "--badgedir" "badges"
-                  (append '#$(match skip-tests
-                               (() '())
-                               (_ (list "-S" (string-join skip-tests ","))))
-                          (list "--"
-                                "--store=store"
-                                (string-append "--guix-manifest=" #$manifest-file)))))
-          ((program _ ...)
-           (format (current-error-port)
-                   "Usage: ~a CWLTEST-SUITE~%"
-                   program)
-           (exit #f))))))
+        ;; cwltest writes out output directories to TMPDIR, but does not clean
+        ;; up after. So, we set TMPDIR to our own temporary directory that we
+        ;; can manage easily. See pending issue on cleaning up temporary output
+        ;; directories:
+        ;; https://github.com/common-workflow-language/cwltest/issues/249
+        (mkdir "tmpdir")
+        (setenv "TMPDIR" "tmpdir")
+        (apply invoke
+               #$(file-append cwltest "/bin/cwltest")
+               "--test" #$cwltest-suite
+               "--tool" #$(file-append ravanan "/bin/ravanan")
+               "--badgedir" "badges"
+               (append '#$(match skip-tests
+                            (() '())
+                            (_ (list "-S" (string-join skip-tests ","))))
+                       (list "--"
+                             "--store=store"
+                             (string-append "--guix-manifest=" #$manifest-file)))))))
+
+(define cwl-v1.2-conformance-suite
+  (let ((version "1.2.1"))
+    (origin
+      (method git-fetch)
+      (uri (git-reference
+             (url "https://github.com/common-workflow-language/cwl-v1.2")
+             (commit (string-append "v" version))))
+      (file-name (git-file-name "cwl-v1.2" version))
+      (sha256
+       (base32
+        "03q8pd0niaaff52n6sn07l3rjnvwi4da649lnc8mn928sh0vywf3")))))
 
 (define-public cwl-v1.2-conformance
   (program-file "cwl-v1.2-conformance"
                 (cwltest-suite-gexp
+                 (file-append cwl-v1.2-conformance-suite
+                              "/conformance_tests.yaml")
                  (local-file "../cwl-conformance/manifest.scm")
                  ;; With these tests, evil things happen and too much memory is
                  ;; consumed. So, disable for now.
@@ -70,9 +80,58 @@
                                     "env_home_tmpdir_docker"
                                     "env_home_tmpdir_docker_no_return_code"))))
 
+(define (ccwl-compile source-file)
+  #~(begin
+      (use-modules (rnrs io ports)
+                   (srfi srfi-26)
+                   (ice-9 match)
+                   (ice-9 popen))
+
+      (define (call-with-input-pipe command proc)
+        (match command
+          ((prog args ...)
+           (let ((port #f))
+             (dynamic-wind
+               (lambda ()
+                 (set! port (apply open-pipe* OPEN_READ prog args)))
+               (cut proc port)
+               (lambda ()
+                 (unless (zero? (close-pipe port))
+                   (error "Command invocation failed" command))))))))
+
+      (call-with-output-file #$output
+        (cut display
+             (call-with-input-pipe '(#$(file-append ccwl "/bin/ccwl")
+                                     "compile"
+                                     #$source-file)
+               get-string-all)
+             <>))))
+
+(define e2e-tools-ccwl-sources
+  `(("hello-world.scm" . ,(local-file "../e2e-tests/tools/hello-world.scm"))))
+
+(define e2e-tools
+  (file-union "e2e-tools"
+              (map (match-lambda
+                     ((ccwl-source-filename . ccwl-source-file)
+                      (let ((cwl-filename (string-append (basename ccwl-source-filename ".scm")
+                                                         ".cwl")))
+                        (list cwl-filename
+                              (computed-file cwl-filename
+                                             (ccwl-compile ccwl-source-file))))))
+                   e2e-tools-ccwl-sources)))
+
+(define e2e-test-suite
+  (file-union "e2e-test-suite"
+              `(("tests.yaml" ,(local-file "../e2e-tests/tests.yaml"))
+                ("tools" ,e2e-tools)
+                ("jobs" ,(local-file "../e2e-tests/jobs"
+                                     #:recursive? #t)))))
+
 (define-public e2e-tests
-  (program-file "ravanan-e2e-tests"
-                (cwltest-suite-gexp (local-file "../e2e-tests/manifest.scm"))))
+  (program-file "e2e-tests"
+                (cwltest-suite-gexp (file-append e2e-test-suite "/tests.yaml")
+                                    (local-file "../e2e-tests/manifest.scm"))))
 
 (define generate-badges-gexp
   (with-imported-modules '((guix build utils))
diff --git a/HACKING.md b/HACKING.md
index 7bb6691..e456242 100644
--- a/HACKING.md
+++ b/HACKING.md
@@ -7,12 +7,12 @@ guix shell -L .guix -Df manifest.scm
 
 # Run end-to-end tests
 
-ravanan comes with a suite of end-to-end tests under `e2e-tests`. To run them, first compile the required CWL workflows from the ccwl sources.
+ravanan comes with a suite of end-to-end tests under `e2e-tests`. End-to-end tests require a running Guix daemon. To run them, create and change into a new empty directory.
 ```
-make -C e2e-tests
+mkdir rundir
+cd rundir
 ```
-Then, run cwltest like so:
+Then, build and run the tests.
 ```
-make -C e2e-tests check
+$(guix build -L ../.guix -e '(@ (cwl-conformance) e2e-tests)')
 ```
-End-to-end tests require a running Guix daemon.
diff --git a/e2e-tests/.gitignore b/e2e-tests/.gitignore
deleted file mode 100644
index 321232f..0000000
--- a/e2e-tests/.gitignore
+++ /dev/null
@@ -1 +0,0 @@
-tools/*.cwl
\ No newline at end of file
diff --git a/e2e-tests/Makefile b/e2e-tests/Makefile
deleted file mode 100644
index 1410a6d..0000000
--- a/e2e-tests/Makefile
+++ /dev/null
@@ -1,37 +0,0 @@
-# ravanan --- High-reproducibility CWL runner powered by Guix
-# Copyright © 2025 Arun Isaac <arunisaac@systemreboot.net>
-#
-# This file is part of ravanan.
-#
-# ravanan is free software: you can redistribute it and/or modify it
-# under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# ravanan is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-# General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with ravanan.  If not, see <https://www.gnu.org/licenses/>.
-
-CCWL ?= ccwl
-CWLTEST ?= cwltest
-
-tools_directory = tools
-tool_ccwl = $(wildcard $(tools_directory)/*.scm)
-tool_cwl = $(tool_ccwl:.scm=.cwl)
-
-all: $(tool_cwl)
-
-%.cwl: %.scm
-	$(CCWL) compile $^ > $@
-
-.PHONY: check clean
-check:
-	mkdir -p /tmp/cwltest-tmpdir
-	TMPDIR=/tmp/cwltest-tmpdir ../pre-inst-env $(CWLTEST) --test tests.yaml --tool ravanan -- --store=store --guix-manifest=manifest.scm
-
-clean:
-	rm -f $(tool_cwl)