[PATCH] Add libsvm.

[PATCH] Add libsvm.

[Ricardo Wurmus]

[-- Attachment #1: 0001-gnu-Add-libsvm.patch --]
[-- Type: text/x-patch, Size: 4207 bytes --]

From bbd4a72d89762f93816cfe4ed917c55ffe19bac8 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 28 May 2015 15:53:14 +0200
Subject: [PATCH] gnu: Add libsvm.

* gnu/packages/machine-learning.scm: New file.
* gnu-system.am (GNU_SYSTEM_MODULES): Add it.
---
 gnu-system.am                     |  1 +
 gnu/packages/machine-learning.scm | 72 +++++++++++++++++++++++++++++++++++++++
 2 files changed, 73 insertions(+)
 create mode 100644 gnu/packages/machine-learning.scm

diff --git a/gnu-system.am b/gnu-system.am
index 43ced12..c699da8 100644
--- a/gnu-system.am
+++ b/gnu-system.am
@@ -196,6 +196,7 @@ GNU_SYSTEM_MODULES =				\
   gnu/packages/lxqt.scm				\
   gnu/packages/lynx.scm				\
   gnu/packages/m4.scm				\
+  gnu/packages/machine-learning.scm		\
   gnu/packages/man.scm				\
   gnu/packages/mail.scm				\
   gnu/packages/make-bootstrap.scm		\
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
new file mode 100644
index 0000000..e368fc5
--- /dev/null
+++ b/gnu/packages/machine-learning.scm
@@ -0,0 +1,72 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2015 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 machine-learning)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix packages)
+  #:use-module (guix utils)
+  #:use-module (guix download)
+  #:use-module (guix build-system gnu)
+  #:use-module (gnu packages))
+
+(define-public libsvm
+  (package
+    (name "libsvm")
+    (version "3.20")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://github.com/cjlin1/libsvm/archive/v"
+             (string-join (string-split version #\.) "") ".tar.gz"))
+       (sha256
+        (base32
+         "1jpjlql3frjza7zxzrqqr2firh44fjb8fqsdmvz6bjz7sb47zgp4"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f ;no "check" target
+       #:phases (modify-phases %standard-phases
+                  (delete 'configure)
+                  (add-after
+                   'build 'build-library
+                   (lambda _
+                     (zero? (system* "make" "lib"))))
+                  (replace
+                   'install
+                   (lambda* (#:key outputs #:allow-other-keys)
+                     (let* ((out (assoc-ref outputs "out"))
+                            (bin (string-append out "/bin/"))
+                            (lib (string-append out "/lib/")))
+                       (mkdir-p lib)
+                       (mkdir bin)
+                       (for-each (lambda (file)
+                                   (copy-file file (string-append bin file)))
+                                 '("svm-train"
+                                   "svm-predict"
+                                   "svm-scale"))
+                       (copy-file "libsvm.so.2"
+                                  (string-append lib "libsvm.so.2")))
+                     #t)))))
+    (home-page "http://www.csie.ntu.edu.tw/~cjlin/libsvm/")
+    (synopsis "Library for Support Vector Machines")
+    (description
+     "LIBSVM is an integrated software for support vector
+classification, (C-SVC, nu-SVC), regression (epsilon-SVR, nu-SVR) and
+distribution estimation (one-class SVM).  It supports multi-class
+classification.")
+    (license license:bsd-3)))
-- 
2.1.0

Re: [PATCH] Add libsvm.

[Mark H Weaver]

Hi Ricardo.  Please see below for comments.

Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> writes:

> From bbd4a72d89762f93816cfe4ed917c55ffe19bac8 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Thu, 28 May 2015 15:53:14 +0200
> Subject: [PATCH] gnu: Add libsvm.
>
> * gnu/packages/machine-learning.scm: New file.
> * gnu-system.am (GNU_SYSTEM_MODULES): Add it.
> ---
>  gnu-system.am                     |  1 +
>  gnu/packages/machine-learning.scm | 72 +++++++++++++++++++++++++++++++++++++++
>  2 files changed, 73 insertions(+)
>  create mode 100644 gnu/packages/machine-learning.scm
>
> diff --git a/gnu-system.am b/gnu-system.am
> index 43ced12..c699da8 100644
> --- a/gnu-system.am
> +++ b/gnu-system.am
> @@ -196,6 +196,7 @@ GNU_SYSTEM_MODULES =				\
>    gnu/packages/lxqt.scm				\
>    gnu/packages/lynx.scm				\
>    gnu/packages/m4.scm				\
> +  gnu/packages/machine-learning.scm		\
>    gnu/packages/man.scm				\
>    gnu/packages/mail.scm				\
>    gnu/packages/make-bootstrap.scm		\
> diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
> new file mode 100644
> index 0000000..e368fc5
> --- /dev/null
> +++ b/gnu/packages/machine-learning.scm
> @@ -0,0 +1,72 @@
> +;;; GNU Guix --- Functional package management for GNU
> +;;; Copyright © 2015 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 machine-learning)
> +  #:use-module ((guix licenses) #:prefix license:)
> +  #:use-module (guix packages)
> +  #:use-module (guix utils)
> +  #:use-module (guix download)
> +  #:use-module (guix build-system gnu)
> +  #:use-module (gnu packages))
> +
> +(define-public libsvm
> +  (package
> +    (name "libsvm")
> +    (version "3.20")
> +    (source
> +     (origin
> +       (method url-fetch)
> +       (uri (string-append
> +             "https://github.com/cjlin1/libsvm/archive/v"
> +             (string-join (string-split version #\.) "") ".tar.gz"))

(string-delete #\. version)

Also, please add a 'file-name' field so that the source filename in the
store will be called *-libsvm-3.20.tar.gz instead of *-v320.tar.gz.

> +       (sha256
> +        (base32
> +         "1jpjlql3frjza7zxzrqqr2firh44fjb8fqsdmvz6bjz7sb47zgp4"))))
> +    (build-system gnu-build-system)
> +    (arguments
> +     `(#:tests? #f ;no "check" target
> +       #:phases (modify-phases %standard-phases
> +                  (delete 'configure)
> +                  (add-after
> +                   'build 'build-library
> +                   (lambda _
> +                     (zero? (system* "make" "lib"))))

(zero? (system* "make"
                "-j" (number->string (parallel-job-count))
                "lib"))

> +                  (replace
> +                   'install
> +                   (lambda* (#:key outputs #:allow-other-keys)
> +                     (let* ((out (assoc-ref outputs "out"))
> +                            (bin (string-append out "/bin/"))
> +                            (lib (string-append out "/lib/")))
> +                       (mkdir-p lib)
> +                       (mkdir bin)
> +                       (for-each (lambda (file)
> +                                   (copy-file file (string-append bin file)))
> +                                 '("svm-train"
> +                                   "svm-predict"
> +                                   "svm-scale"))
> +                       (copy-file "libsvm.so.2"
> +                                  (string-append lib "libsvm.so.2")))

I tried building this, I noticed that the installed binaries (svm-train,
svm-predict, and scm-scale) don't reference libsvm.so.2.  In the build
output, I see no header files and no libsvm.so symlink, so I don't see
how this library could be used.

     Thanks,
       Mark

Re: [PATCH] Add libsvm.

[Ricardo Wurmus]

>> +       (uri (string-append
>> +             "https://github.com/cjlin1/libsvm/archive/v"
>> +             (string-join (string-split version #\.) "") ".tar.gz"))
>
> (string-delete #\. version)

Oh, that's better, indeed!

> Also, please add a 'file-name' field so that the source filename in the
> store will be called *-libsvm-3.20.tar.gz instead of *-v320.tar.gz.

Ouch!  That's one of the things I usually do first (since I was made
aware of it), but this time I completely forgot about it.  Thanks for
the reminder!

>> +                     (zero? (system* "make" "lib"))))
>
> (zero? (system* "make"
>                 "-j" (number->string (parallel-job-count))
>                 "lib"))

[...]

> I tried building this, I noticed that the installed binaries (svm-train,
> svm-predict, and scm-scale) don't reference libsvm.so.2.  In the build
> output, I see no header files and no libsvm.so symlink, so I don't see
> how this library could be used.

It seems that this library is in fact only used by the Python module
which is built from the "python" subdir and for which I have prepared
another package.  I'll remove the library building phase from this
package and move it to the recipe for "python-libsvm".

My apologies for the confusion!  I'll send an updated patch soon.

~~ Ricardo

Re: [PATCH] Add libsvm.

[Ricardo Wurmus]

[-- Attachment #1: Type: text/plain, Size: 727 bytes --]

>> I tried building this, I noticed that the installed binaries (svm-train,
>> svm-predict, and scm-scale) don't reference libsvm.so.2.  In the build
>> output, I see no header files and no libsvm.so symlink, so I don't see
>> how this library could be used.
>
> It seems that this library is in fact only used by the Python module
> which is built from the "python" subdir and for which I have prepared
> another package.  I'll remove the library building phase from this
> package and move it to the recipe for "python-libsvm".
>
> My apologies for the confusion!  I'll send an updated patch soon.

Attached are two patches for libsvm and python-libsvm (only available
for Python 3), taking the comments into consideration.


[-- Attachment #2: 0001-gnu-Add-libsvm.patch --]
[-- Type: text/x-patch, Size: 3878 bytes --]

From 6a17d83d4bc2512f8089477e70c485e9ca93377a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 28 May 2015 15:53:14 +0200
Subject: [PATCH 1/2] gnu: Add libsvm.

* gnu/packages/machine-learning.scm: New file.
* gnu-system.am (GNU_SYSTEM_MODULES): Add it.
---
 gnu-system.am                     |  1 +
 gnu/packages/machine-learning.scm | 65 +++++++++++++++++++++++++++++++++++++++
 2 files changed, 66 insertions(+)
 create mode 100644 gnu/packages/machine-learning.scm

diff --git a/gnu-system.am b/gnu-system.am
index 2cd4c62..c714062 100644
--- a/gnu-system.am
+++ b/gnu-system.am
@@ -196,6 +196,7 @@ GNU_SYSTEM_MODULES =				\
   gnu/packages/lxqt.scm				\
   gnu/packages/lynx.scm				\
   gnu/packages/m4.scm				\
+  gnu/packages/machine-learning.scm		\
   gnu/packages/man.scm				\
   gnu/packages/mail.scm				\
   gnu/packages/make-bootstrap.scm		\
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
new file mode 100644
index 0000000..c1a33de
--- /dev/null
+++ b/gnu/packages/machine-learning.scm
@@ -0,0 +1,65 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2015 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 machine-learning)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix packages)
+  #:use-module (guix utils)
+  #:use-module (guix download)
+  #:use-module (guix build-system gnu)
+  #:use-module (gnu packages))
+
+(define-public libsvm
+  (package
+    (name "libsvm")
+    (version "3.20")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://github.com/cjlin1/libsvm/archive/v"
+             (string-delete #\. version) ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1jpjlql3frjza7zxzrqqr2firh44fjb8fqsdmvz6bjz7sb47zgp4"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f ;no "check" target
+       #:phases (modify-phases %standard-phases
+                  (delete 'configure)
+                  (replace
+                   'install
+                   (lambda* (#:key outputs #:allow-other-keys)
+                     (let* ((out (assoc-ref outputs "out"))
+                            (bin (string-append out "/bin/")))
+                       (mkdir-p bin)
+                       (for-each (lambda (file)
+                                   (copy-file file (string-append bin file)))
+                                 '("svm-train"
+                                   "svm-predict"
+                                   "svm-scale")))
+                     #t)))))
+    (home-page "http://www.csie.ntu.edu.tw/~cjlin/libsvm/")
+    (synopsis "Library for Support Vector Machines")
+    (description
+     "LIBSVM is an integrated software for support vector
+classification, (C-SVC, nu-SVC), regression (epsilon-SVR, nu-SVR) and
+distribution estimation (one-class SVM).  It supports multi-class
+classification.")
+    (license license:bsd-3)))
-- 
2.1.0


[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #3: 0002-gnu-Add-python-libsvm.patch --]
[-- Type: text/x-patch, Size: 2320 bytes --]

From 1103750f0c38c48f69f040b6a2e701f511907e26 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 2 Jun 2015 15:10:37 +0200
Subject: [PATCH 2/2] gnu: Add python-libsvm.

* gnu/packages/machine-learning.scm (python-libsvm): New variable.
---
 gnu/packages/machine-learning.scm | 34 +++++++++++++++++++++++++++++++++-
 1 file changed, 33 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index c1a33de..3b4af19 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -22,7 +22,8 @@
   #:use-module (guix utils)
   #:use-module (guix download)
   #:use-module (guix build-system gnu)
-  #:use-module (gnu packages))
+  #:use-module (gnu packages)
+  #:use-module (gnu packages python))
 
 (define-public libsvm
   (package
@@ -63,3 +64,34 @@ classification, (C-SVC, nu-SVC), regression (epsilon-SVR, nu-SVR) and
 distribution estimation (one-class SVM).  It supports multi-class
 classification.")
     (license license:bsd-3)))
+
+(define-public python-libsvm
+  (package (inherit libsvm)
+    (name "python-libsvm")
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f ;no "check" target
+       #:make-flags '("-C" "python")
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (replace
+          'install
+          (lambda* (#:key inputs outputs #:allow-other-keys)
+            (let ((site (string-append (assoc-ref outputs "out")
+                                       "/lib/python"
+                                       (string-take
+                                        (string-take-right
+                                         (assoc-ref inputs "python") 5) 3)
+                                       "/site-packages/")))
+              (substitute* "python/svm.py"
+                (("../libsvm.so.2") "libsvm.so.2"))
+              (mkdir-p site)
+              (for-each (lambda (file)
+                          (copy-file file (string-append site (basename file))))
+                        (find-files "python" "\\.py"))
+              (copy-file "libsvm.so.2"
+                         (string-append site "libsvm.so.2")))
+            #t)))))
+    (inputs
+     `(("python" ,python)))))
-- 
2.1.0

Re: [PATCH] Add libsvm.

[Ludovic Courtès]

Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:

> From 6a17d83d4bc2512f8089477e70c485e9ca93377a Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Thu, 28 May 2015 15:53:14 +0200
> Subject: [PATCH 1/2] gnu: Add libsvm.
>
> * gnu/packages/machine-learning.scm: New file.
> * gnu-system.am (GNU_SYSTEM_MODULES): Add it.

[...]

> +    (synopsis "Library for Support Vector Machines")
> +    (description
> +     "LIBSVM is an integrated software for support vector

s/software/piece of software/ or “library”.

> +classification, (C-SVC, nu-SVC), regression (epsilon-SVR, nu-SVR) and
> +distribution estimation (one-class SVM).  It supports multi-class
> +classification.")

I think it should mention machine learning because, as ignorant of ν-SVC
and ε-SVR as I am, I find it hard from the description to understand
what it’s about.  :-)

> From 1103750f0c38c48f69f040b6a2e701f511907e26 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Tue, 2 Jun 2015 15:10:37 +0200
> Subject: [PATCH 2/2] gnu: Add python-libsvm.
>
> * gnu/packages/machine-learning.scm (python-libsvm): New variable.

[...]

> +(define-public python-libsvm
> +  (package (inherit libsvm)
> +    (name "python-libsvm")

Also add a specific synopsis like “Python bindings of libSVM”.

OK with these changes.

Thank you!

Ludo’.