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authorArun Isaac2022-10-14 00:15:39 +0530
committerArun Isaac2022-10-14 00:15:39 +0530
commit6ea40c00f1ce9224c0324a5beb9196c20361d71c (patch)
treee8b342f5aebc2e3a1490922c7d032096a9a0588e
parentdc3d27b29f7c50a55baf8ee259e5ca4854f62a68 (diff)
downloadgn-machines-6ea40c00f1ce9224c0324a5beb9196c20361d71c.tar.gz
Pull in latest genenetwork3 when running genenetwork2 tests.
So far, whenever genenetwork2 code needed the latest updates from genenetwork3, the guix-bioinformatics channel had to be updated and the development container had to be rebuilt. No more. From now on, the latest genenetwork3 code will be pulled in at all times. The development container need only be rebuilt when the dependencies of genenetwork2 or genenetwork3 change. We may revisit this decision once genenetwork2 and genenetwork3 are better decoupled and we have semantically versioned releases. * genenetwork-development.scm (genenetwork2-tests): Pull in latest genenetwork3 when running genenetwork2 tests.
-rw-r--r--genenetwork-development.scm24
1 files changed, 18 insertions, 6 deletions
diff --git a/genenetwork-development.scm b/genenetwork-development.scm
index 852711f..2b7ea79 100644
--- a/genenetwork-development.scm
+++ b/genenetwork-development.scm
@@ -204,24 +204,36 @@ to be executed."
(display (make-string 50 #\=))
(newline)
(force-output))
-
+
+ (define (show-head-commit)
+ (hline)
+ (invoke "git" "log" "--max-count" "1")
+ (hline))
+
+ (invoke "git" "clone" "--depth" "1"
+ "https://github.com/genenetwork/genenetwork3")
+ (with-directory-excursion "genenetwork3"
+ (show-head-commit))
(invoke "git" "clone" "--depth" "1"
"--branch" #$(forge-project-repository-branch project)
- #$(forge-project-repository project)
- ".")
- (hline)
- (invoke "git" "log" "--max-count" "1")
- (hline)
+ #$(forge-project-repository project))
+ (with-directory-excursion "genenetwork2"
+ (show-head-commit))
(setenv "SERVER_PORT" "8080")
+ ;; Use a profile with all dependencies except genenetwork3.
(setenv "GN2_PROFILE"
#$(profile
(content (package->development-manifest genenetwork2))
(allow-collisions? #t)))
+ ;; Set GN3_PYTHONPATH to the latest genenetwork3.
+ (setenv "GN3_PYTHONPATH"
+ (string-append (getcwd) "/genenetwork3"))
(setenv "GN_PROXY_URL" "http://genenetwork.org/gn3-proxy/")
(setenv "GN3_LOCAL_URL" (string-append "http://localhost:" (number->string #$%genenetwork3-port)))
(setenv "GENENETWORK_FILES" #$%genotype-files)
(setenv "HOME" "/tmp")
(setenv "SQL_URI" "mysql://webqtlout:webqtlout@localhost/db_webqtl")
+ (chdir "genenetwork2")
(apply invoke '#$test-command)))))
(define (genenetwork2-project config)