Add gn-guile.

* gn/packages/guile.scm (gn-guile): New package.

1 files changed, 165 insertions, 0 deletions

diff --git a/gn/packages/guile.scm b/gn/packages/guile.scm
new file mode 100644
index 0000000..6f0b41d
--- /dev/null
+++ b/gn/packages/guile.scm
@@ -0,0 +1,165 @@
+(define-module (gn packages guile)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix gexp)
+  #:use-module (guix packages)
+  #:use-module (guix git-download)
+  #:use-module (guix build-system guile)
+  #:use-module (guix build-system gnu)
+  #:use-module ((gnu packages autotools) #:select (libltdl autoconf automake libtool))
+  #:use-module ((gnu packages databases) #:select (mariadb))
+  #:use-module ((gnu packages compression) #:select (zlib))
+  #:use-module ((gnu packages perl) #:select (perl))
+  #:use-module ((gnu packages texinfo) #:select (texinfo))
+  #:use-module (guix utils)
+  #:use-module (gnu packages build-tools)
+  #:use-module (gnu packages package-management)
+  #:use-module ((gnu packages bash) #:select (bash-minimal))
+  #:use-module ((gnu packages bioinformatics) #:select (gemma))
+  #:use-module ((gnu packages certs) #:select (nss-certs))
+  #:use-module ((gnu packages guile) #:select (guile-json-4 guile-3.0 guile-2.2 guile-readline))
+  #:use-module ((gnu packages guile-xyz) #:select (guile-dbi guile-dbd-mysql guile-fibers guile-redis guile-hashing guile-commonmark))
+  #:use-module ((gnu packages parallel) #:select (parallel))
+  #:use-module ((gnu packages perl) #:select (perl))
+  #:use-module ((gnu packages tls) #:select (guile-gnutls openssl)))
+
+;; Lifted from:
+;; https://lists.gnu.org/archive/html/artanis/2023-03/txtNk7zz7rJAN.txt
+(define-public guile3-dbi
+  (package
+    (name "guile3-dbi")
+    (version "2.1.8")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/opencog/guile-dbi")
+                    (commit (string-append "guile-dbi-" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "123m4j82bi60s1v95pjh4djb7bh6zdwmljbpyg7zq8ni2gyal7lw"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:modules (((guix build guile-build-system)
+                   #:select (target-guile-effective-version))
+                  ,@%default-gnu-imported-modules)
+       #:imported-modules ((guix build guile-build-system)
+                           ,@%default-gnu-imported-modules)
+       #:configure-flags
+       (list (string-append
+              "--with-guile-site-dir=" %output "/share/guile/site/"
+              (target-guile-effective-version (assoc-ref %build-inputs "guile"))))
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'chdir
+           (lambda _
+             ;; The upstream Git repository contains all the code, so change
+             ;; to the directory specific to guile-dbi.
+             (chdir "guile-dbi")))
+         (add-after 'install 'patch-extension-path
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (dbi.scm (string-append out "/share/guile/site/"
+                                            (target-guile-effective-version
+                                             (assoc-ref inputs "guile"))
+                                            "/dbi/dbi.scm"))
+                    (ext (string-append out "/lib/libguile-dbi")))
+               (substitute* dbi.scm (("libguile-dbi") ext))))))))
+    (inputs
+     (list libltdl))
+    (native-inputs
+     (list autoconf automake libtool perl texinfo guile-3.0))
+    (synopsis "Guile database abstraction layer")
+    (home-page "https://github.com/opencog/guile-dbi")
+    (description
+     "guile-dbi is a library for Guile that provides a convenient interface to
+SQL databases.  Database programming with guile-dbi is generic in that the same
+programming interface is presented regardless of which database system is used.
+It currently supports MySQL, Postgres and SQLite3.")
+    (license license:gpl2+)
+    (native-search-paths
+     (list (search-path-specification
+            (variable "GUILE_DBD_PATH")
+            (files '("lib")))))))
+
+(define-public guile3-dbd-mysql
+  (package
+    (inherit guile3-dbi)
+    (name "guile3-dbd-mysql")
+    (arguments
+     (substitute-keyword-arguments (package-arguments guile3-dbi)
+       ((#:phases phases)
+        `(modify-phases ,phases
+           (replace 'chdir
+             (lambda _
+               ;; The upstream Git repository contains all the code, so change
+               ;; to the directory specific to guile-dbd-mysql.
+               (chdir "guile-dbd-mysql")))
+           (add-after 'chdir 'patch-src
+             (lambda _
+               (substitute* "configure.ac"
+                 (("mariadbclient") "mariadb"))
+               (substitute* "src/guile-dbd-mysql.c"
+                 (("<mariadb/") "<mysql/"))))
+           (delete 'patch-extension-path)))))
+    (inputs
+     (modify-inputs (package-inputs guile3-dbi)
+       (prepend `(,mariadb "dev")
+                `(,mariadb "lib")
+                zlib)))
+    (native-inputs
+     (modify-inputs (package-native-inputs guile3-dbi)
+       (prepend guile3-dbi		; only required for headers
+                )))
+    (synopsis "Guile DBI driver for MySQL")
+    (description "@code{guile-dbi} is a library for Guile that provides a
+convenient interface to SQL databases.  This package implements the interface
+for MySQL.")
+    (license license:gpl2+)))
+
+(define-public gn-guile
+  (let ((commit "4623225b0adb0846a4c2e879a33b31884d2e5f05")
+	(revision "0"))
+    (package
+      (name "gn-guile")
+      (version (git-version "4.0.0" revision commit))
+      (source (origin
+		(method git-fetch)
+		(uri (git-reference
+		      (url "https://git.genenetwork.org/gn-guile/")
+		      (commit commit)))
+		(file-name (string-append name "-" version))
+		(sha256
+		 (base32 "1l8q2yi8dqjglv54v2d6yqd498yabhhz193i25kwxwsk6cv9xkyz"))))
+      (build-system guile-build-system)
+      (propagated-inputs
+       (list guile-3.0 guile3-dbi guile3-dbd-mysql guile-fibers guile-gnutls guile-readline
+	     guile-commonmark guile-redis openssl nss-certs gemma parallel guile-hashing
+	     guile-json-4))
+      (arguments
+       (list
+	#:phases
+	#~(modify-phases %standard-phases
+	    ;; When using the guile-build-system, guild doesn't
+	    ;; correctly set the GUILE_LOAD_PATH for the various guile
+	    ;; packages in the build phase leading to build failures.
+	    (add-before 'build 'augment-GUILE_LOAD_PATH
+	      (lambda* (#:key outputs #:allow-other-keys)
+		(let* ((guile-version (target-guile-effective-version)))
+		  ;; guild uses this: "\\.(scm|sls)$" regexp to try and
+		  ;; compile all scm files in this repository.  We don't
+		  ;; need to compile guix.scm and manifest.scm.
+		  (delete-file "guix.scm")
+		  (delete-file "manifest.scm")
+		  (setenv "GUILE_LOAD_PATH"
+			  (string-append
+			   (format
+			    #f "~{~a:~}"
+			    (map (lambda (package)
+				   (format #f "~a/share/guile/site/~a"
+					   package guile-version))
+				 (list #$guile3-dbi #$guile-fibers #$guile-commonmark #$guile-json-4 #$guile-hashing)))
+			   #$(getenv "GUILE_LOAD_PATH")))))))))
+      (home-page "https://git.genenetwork.com/gn-guile")
+      (synopsis "Next generation GN code in guile")
+      (description "Use of guile.")
+      (license license:gpl3))))