;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2019 Ricardo Wurmus <rekado@elephly.net>
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix 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.
;;;
;;; GNU Guix 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 GNU Guix.  If not, see <http://www.gnu.org/licenses/>.

(define-module (gnu packages java-maths)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (guix packages)
  #:use-module (guix download)
  #:use-module (guix git-download)
  #:use-module (guix utils)
  #:use-module (guix build-system ant)
  #:use-module (guix build-system gnu)
  #:use-module (gnu packages)
  #:use-module (gnu packages gcc)
  #:use-module (gnu packages java)
  #:use-module (gnu packages maths)
  #:use-module (gnu packages ruby))

(define-public java-jblas
  (package
    (name "java-jblas")
    (version "1.2.4")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/mikiobraun/jblas")
                    (commit (string-append "jblas-" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "0afh48hq8i8li5z11x415c8slwsfrlib0w1xjfbg186mximqvv3g"))))
    (build-system gnu-build-system)
    (arguments
     `(#:tests? #f                      ; there are none
       #:configure-flags
       (list (string-append "--libpath="
                            (assoc-ref %build-inputs "openblas")
                            "/lib")
             "--build-type=openblas")
       #:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'make-writable
           (lambda _
             (map make-file-writable
                  (find-files "." ".*"))
             #t))
         (add-before 'build 'setenv-JAVA_HOME
           (lambda* (#:key inputs #:allow-other-keys)
             (setenv "JAVA_HOME" (assoc-ref inputs "jdk"))
             #t))
         (add-after 'build 'build-jar
           (lambda* (#:key inputs outputs #:allow-other-keys)
             (setenv "M2_HOME" (assoc-ref outputs "out"))
             (invoke "ant" "jar" (string-append "-Dversion=" ,version))))
         (replace 'install
           (lambda* (#:key outputs #:allow-other-keys)
             (let ((target (string-append (assoc-ref outputs "out")
                                          "/share/java")))
               (mkdir-p target)
               (install-file (string-append "jblas-" ,version ".jar") target))
             #t)))))
    (inputs
     (list openblas))
    (native-inputs
     `(("ant" ,ant)
       ("ruby" ,ruby)                   ; for configure script
       ("gfortran" ,gfortran)
       ("jdk" ,icedtea "jdk")))
    (home-page "http://jblas.org")
    (synopsis "Linear algebra for Java")
    (description
     "jblas is a fast linear algebra library for Java.  jblas is based on BLAS
and LAPACK, the de-facto industry standard for matrix computations, and uses
state-of-the-art implementations for all its computational routines, making
jBLAS very fast.")
    (license license:bsd-3)))
ltip'>* gnu/build/accounts.scm (catch-ENOSYS): Remove.
(database-writer): Use 'fsync' instead of 'fdatasync'.
</span></span></td><td>Ludovic Courtès</td></tr>
<tr><td><span title='2019-06-05 23:10:37 +0200'>2019-06-05</span></td><td><a href='/guix/commit/gnu/build/accounts.scm?id=d088d5c4848f08bd62e722789132f9345659c52c'>accounts: Call 'fdatasync' when writing databases.</a><span class='msg-avail'>...<span class='msg-tooltip'>* gnu/build/accounts.scm (catch-ENOSYS): New macro.
(database-writer): Call 'fdatasync'.
</span></span></td><td>Ludovic Courtès</td></tr>
<tr><td><span title='2019-06-05 23:10:37 +0200'>2019-06-05</span></td><td><a href='/guix/commit/gnu/build/accounts.scm?id=ed8570dce3683b73bdf668b3ad0f529a1cea30c5'>accounts: Close database before renaming it.</a><span class='msg-avail'>...<span class='msg-tooltip'>Fixes &lt;https://bugs.gnu.org/35996&gt;.
Reported by Florian Pelz &lt;pelzflorian@pelzflorian.de&gt;.

* gnu/build/accounts.scm (database-writer): Move 'close-port' call
before 'rename-file'.
</span></span></td><td>Ludovic Courtès</td></tr>
<tr><td><span title='2019-06-05 23:10:36 +0200'>2019-06-05</span></td><td><a href='/guix/commit/gnu/build/accounts.scm?id=d497b6ab397273cd250003b6266f22ad74f4c20d'>activation: Lock /etc/.pwd.lock before accessing databases.</a><span class='msg-avail'>...<span class='msg-tooltip'>Suggested by Florian Pelz &lt;pelzflorian@pelzflorian.de&gt;
in &lt;http://bugs.gnu.org/35996&gt;.

* gnu/build/accounts.scm (%password-lock-file): New variable.
* gnu/build/activation.scm (activate-users+groups): Wrap calls to
'user+group-databases', 'write-group', etc. into 'with-file-lock'.
</span></span></td><td>Ludovic Courtès</td></tr>
<tr><td><span title='2019-04-26 14:19:36 +0200'>2019-04-26</span></td><td><a href='/guix/commit/gnu/build/accounts.scm?id=504a0fc636ec591e65b4a229a37e522e425d8a0c'>accounts: Always honor the configured user account shell.</a><span class='msg-avail'>...<span class='msg-tooltip'>Starting from commit 0ae735bcc8ff7fdc89d67b492bdee9091ee19e86, Guix
System would preserve the user shell across reconfigure and reboot.
This was done so as to allow for the use of 'chsh'.

This proved to be a misguided decision.  This commit goes back to
considering user shells as config and not "state."

* gnu/build/accounts.scm (allocate-passwd): Do not use shell from
PREVIOUS.
</span></span></td><td>Ludovic Courtès</td></tr>
<tr><td><span title='2019-03-07 20:05:09 +0100'>2019-03-07</span></td><td><a href='/guix/commit/gnu/build/accounts.scm?id=ec600e4544729f1aaf46fa5162bba334515d0de5'>Add (gnu build accounts).</a><span class='msg-avail'>...<span class='msg-tooltip'>* gnu/build/accounts.scm, tests/accounts.scm: New files.
* Makefile.am (SCM_TESTS): Add tests/accounts.scm.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add build/accounts.scm.
</span></span></td><td>Ludovic Courtès</td></tr>