GNU bug report logs - #47966
[PATCH] gnu: Add python-graph-tool.

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Alexandre Hannud Abdo <abdo <at> member.fsf.org>
To: guix-patches <at> gnu.org
Subject: [PATCH] gnu: Add python-graph-tool.
Date: Fri, 23 Apr 2021 08:17:52 +0200

* gnu/packages/graph.scm (python-graph-tool): New variable.
---
 gnu/packages/graph.scm | 62 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 62 insertions(+)

diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index d2e4c875a1..94125ebdba 100644
--- a/gnu/packages/graph.scm
+++ b/gnu/packages/graph.scm
@@ -6,6 +6,7 @@
 ;;; Copyright © 2019 Andreas Enge <andreas <at> enge.fr>
 ;;; Copyright © 2020 Alexander Krotov <krotov <at> iitp.ru>
 ;;; Copyright © 2020 Pierre Langlois <pierre.langlos <at> gmx.com>
+;;; Copyright © 2021 Alexandre Hannud Abdo <abdo <at> member.fsf.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -37,13 +38,18 @@
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages bioconductor)
   #:use-module (gnu packages bioinformatics)
+  #:use-module (gnu packages boost)
   #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages cran)
+  #:use-module (gnu packages datastructures)
   #:use-module (gnu packages gd)
+  #:use-module (gnu packages graphics)
   #:use-module (gnu packages graphviz)
+  #:use-module (gnu packages gtk)
   #:use-module (gnu packages maths)
   #:use-module (gnu packages multiprecision)
+  #:use-module (gnu packages ncurses)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-science)
@@ -510,3 +516,59 @@ MSCs need not be complicated to create or use.  Mscgen aims to provide a simple
 text language that is clear to create, edit and understand, which can also be
 transformed into common image formats for display or printing.")
     (license license:gpl2+)))
+
+(define-public python-graph-tool
+  (package
+    (name "python-graph-tool")
+    (version "2.37")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "https://downloads.skewed.de/graph-tool/graph-tool-"
+                    version
+                    ".tar.bz2"))
+              (sha256
+               (base32
+                "0w2i4d4zyk051zkykcg0ksngspajznwmp523hbsx50xnxc6jliyz"))))
+    (build-system gnu-build-system)
+    ;; (arguments '(#:configure-flags '("--disable-openmp")))
+    (arguments
+     `(#:configure-flags
+       (list (string-append "--with-boost="
+                            (assoc-ref %build-inputs "boost"))
+             (string-append "--with-python-module-path="
+                            (assoc-ref %outputs "out")
+                            "/lib/python"
+                            ((lambda (version)
+                               (substring version 0 (string-rindex version #\.)))
+                             ,(package-version
+                               (car (assoc-ref
+                                     (package-propagated-inputs this-package)
+                                     "python"))))
+                            "/site-packages/"))))
+    (native-inputs `(("pkg-config" ,pkg-config)
+                     ("gcc-10" ,gcc-10)
+                     ("ncurses" ,ncurses)))
+    (inputs `(("boost" ,boost)
+              ("expat" ,expat)
+              ("gmp" ,gmp)
+              ("cgal" ,cgal)
+              ("sparsehash" ,sparsehash)
+              ("gtk+" ,gtk+)
+              ("cairomm" ,cairomm)))
+    (propagated-inputs `(("python" ,python-wrapper)
+                         ("python-scipy" ,python-scipy)
+                         ("python-numpy" ,python-numpy)
+                         ("python-pycairo" ,python-pycairo)
+                         ("python-matplotlib" ,python-matplotlib)))
+    (synopsis "Efficient python module for analysis of graphs")
+    (description "Graph-tool is an efficient Python module for
+manipulation and statistical analysis of graphs (a.k.a. networks).
+Contrary to most other Python modules with similar functionality, the
+core data structures and algorithms are implemented in C++, making
+extensive use of template metaprogramming, based heavily on the Boost
+Graph Library.  This confers it a level of performance that is
+comparable (both in memory usage and computation time) to that of a
+pure C/C++ library.")
+    (home-page "https://graph-tool.skewed.de/")
+    (license license:lgpl3+)))

Message #8 received at 47966 <at> debbugs.gnu.org (full text, mbox):

From: Marius Bakke <marius <at> gnu.org>
To: Alexandre Hannud Abdo <abdo <at> member.fsf.org>, 47966 <at> debbugs.gnu.org
Subject: Re: [bug#47966] [PATCH] gnu: Add python-graph-tool.
Date: Thu, 13 May 2021 19:04:25 +0200

[Message part 1 (text/plain, inline)]

Hi Alexandre,

Alexandre Hannud Abdo <abdo <at> member.fsf.org> skriver:

> * gnu/packages/graph.scm (python-graph-tool): New variable.

Thanks for the patch.

[...]

> +(define-public python-graph-tool
> +  (package
> +    (name "python-graph-tool")
> +    (version "2.37")
> +    (source (origin
> +              (method url-fetch)
> +              (uri (string-append
> +                    "https://downloads.skewed.de/graph-tool/graph-tool-"
> +                    version
> +                    ".tar.bz2"))
> +              (sha256
> +               (base32
> +                "0w2i4d4zyk051zkykcg0ksngspajznwmp523hbsx50xnxc6jliyz"))))
> +    (build-system gnu-build-system)
> +    ;; (arguments '(#:configure-flags '("--disable-openmp")))

This comment can probably be removed?

> +    (arguments
> +     `(#:configure-flags
> +       (list (string-append "--with-boost="
> +                            (assoc-ref %build-inputs "boost"))
> +             (string-append "--with-python-module-path="
> +                            (assoc-ref %outputs "out")
> +                            "/lib/python"
> +                            ((lambda (version)
> +                               (substring version 0 (string-rindex version #\.)))
> +                             ,(package-version
> +                               (car (assoc-ref
> +                                     (package-propagated-inputs this-package)
> +                                     "python"))))
> +                            "/site-packages/"))))

That's clever.  :-)

(guix utils) has a handy (version-major+minor ...) procedure that can be
accessed in the unquoted context.  Thus the expression above can be
simplified to:

  (string-append "--with-python-module-path="
                 (assoc-ref %outputs "out")
                 "/lib/python"
                 ,(version-major+minor
                   (package-version
                    (car (assoc-ref
                          (package-propagated-inputs this-package)
                          "python"))))
                 "/site-packages/")


> +    (native-inputs `(("pkg-config" ,pkg-config)
> +                     ("gcc-10" ,gcc-10)
> +                     ("ncurses" ,ncurses)))

The indentation here and below is unusual.  :-)

> +    (inputs `(("boost" ,boost)
> +              ("expat" ,expat)
> +              ("gmp" ,gmp)
> +              ("cgal" ,cgal)
> +              ("sparsehash" ,sparsehash)
> +              ("gtk+" ,gtk+)
> +              ("cairomm" ,cairomm)))
> +    (propagated-inputs `(("python" ,python-wrapper)

Python should be a regular input.  It will be available in just about
any context where this package is used, and propagating it can cause
conflicts if users have custom variants in their
profile/manifests/packages.

> +                         ("python-scipy" ,python-scipy)
> +                         ("python-numpy" ,python-numpy)
> +                         ("python-pycairo" ,python-pycairo)
> +                         ("python-matplotlib" ,python-matplotlib)))
> +    (synopsis "Efficient python module for analysis of graphs")

Perhaps just 'Analyze graphs with Python' to avoid overlapping with the
description which has more detail?

> +    (description "Graph-tool is an efficient Python module for
> +manipulation and statistical analysis of graphs (a.k.a. networks).
> +Contrary to most other Python modules with similar functionality, the
> +core data structures and algorithms are implemented in C++, making
> +extensive use of template metaprogramming, based heavily on the Boost
> +Graph Library.  This confers it a level of performance that is
> +comparable (both in memory usage and computation time) to that of a
> +pure C/C++ library.")
> +    (home-page "https://graph-tool.skewed.de/")
> +    (license license:lgpl3+)))

Otherwise LGTM.  Can you send an updated patch?

TIA,
Marius

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Message #11 received at 47966 <at> debbugs.gnu.org (full text, mbox):

From: Alexandre Hannud Abdo <abdo <at> member.fsf.org>
To: 47966 <at> debbugs.gnu.org
Subject: [PATCH] gnu: Add python-graph-tool.
Date: Fri, 14 May 2021 22:47:30 +0200

* gnu/packages/graph.scm (python-graph-tool): New variable.
---
 gnu/packages/graph.scm | 62 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 62 insertions(+)

diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index 95506c69a9..10b1b91e41 100644
--- a/gnu/packages/graph.scm
+++ b/gnu/packages/graph.scm
@@ -7,6 +7,7 @@
 ;;; Copyright © 2020 Alexander Krotov <krotov <at> iitp.ru>
 ;;; Copyright © 2020 Pierre Langlois <pierre.langlos <at> gmx.com>
 ;;; Copyright © 2021 Vinicius Monego <monego <at> posteo.net>
+;;; Copyright © 2021 Alexandre Hannud Abdo <abdo <at> member.fsf.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -38,13 +39,18 @@
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages bioconductor)
   #:use-module (gnu packages bioinformatics)
+  #:use-module (gnu packages boost)
   #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages cran)
+  #:use-module (gnu packages datastructures)
   #:use-module (gnu packages gd)
+  #:use-module (gnu packages graphics)
   #:use-module (gnu packages graphviz)
+  #:use-module (gnu packages gtk)
   #:use-module (gnu packages maths)
   #:use-module (gnu packages multiprecision)
+  #:use-module (gnu packages ncurses)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-science)
@@ -532,3 +538,59 @@ MSCs need not be complicated to create or use.  Mscgen aims to provide a simple
 text language that is clear to create, edit and understand, which can also be
 transformed into common image formats for display or printing.")
     (license license:gpl2+)))
+
+(define-public python-graph-tool
+  (package
+    (name "python-graph-tool")
+    (version "2.37")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "https://downloads.skewed.de/graph-tool/graph-tool-"
+                    version
+                    ".tar.bz2"))
+              (sha256
+               (base32
+                "0w2i4d4zyk051zkykcg0ksngspajznwmp523hbsx50xnxc6jliyz"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:configure-flags
+       (list (string-append "--with-boost="
+                            (assoc-ref %build-inputs "boost"))
+             (string-append "--with-python-module-path="
+                            (assoc-ref %outputs "out")
+                            "/lib/python"
+                            ,(version-major+minor
+                              (package-version
+                               (car (assoc-ref
+                                     (package-inputs this-package)
+                                     "python"))))
+                            "/site-packages/"))))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)
+       ("gcc-10" ,gcc-10)
+       ("ncurses" ,ncurses)))
+    (inputs
+     `(("python" ,python-wrapper)
+       ("boost" ,boost)
+       ("expat" ,expat)
+       ("gmp" ,gmp)
+       ("cgal" ,cgal)
+       ("sparsehash" ,sparsehash)
+       ("gtk+" ,gtk+)
+       ("cairomm" ,cairomm)))
+    (propagated-inputs
+     `(("python-scipy" ,python-scipy)
+       ("python-numpy" ,python-numpy)
+       ("python-pycairo" ,python-pycairo)
+       ("python-matplotlib" ,python-matplotlib)))
+    (synopsis "Manipulate and analyze graphs with Python efficiently")
+    (description "Graph-tool is an efficient Python module for manipulation
+and statistical analysis of graphs (a.k.a. networks).  Contrary to most other
+Python modules with similar functionality, the core data structures and
+algorithms are implemented in C++, making extensive use of template
+metaprogramming, based heavily on the Boost Graph Library.  This confers it a
+level of performance that is comparable (both in memory usage and computation
+time) to that of a pure C/C++ library.")
+    (home-page "https://graph-tool.skewed.de/")
+    (license license:lgpl3+)))

Message #14 received at 47966 <at> debbugs.gnu.org (full text, mbox):

From: Alexandre Hannud Abdo <abdo <at> member.fsf.org>
To: 47966 <at> debbugs.gnu.org
Subject: [PATCH] gnu: Add python-graph-tool.
Date: Fri, 14 May 2021 22:53:54 +0200

Ni! Thanks for the tips, Marius.
The new patch should have those issues fixed.
Let me know if there's anything else!
Cheers,
ale .~´

Message #19 received at 47966-done <at> debbugs.gnu.org (full text, mbox):

From: Marius Bakke <marius <at> gnu.org>
To: Alexandre Hannud Abdo <abdo <at> member.fsf.org>, 47966-done <at> debbugs.gnu.org
Subject: Re: [bug#47966] [PATCH] gnu: Add python-graph-tool.
Date: Sat, 15 May 2021 19:26:07 +0200

[Message part 1 (text/plain, inline)]

Alexandre Hannud Abdo <abdo <at> member.fsf.org> skriver:

> * gnu/packages/graph.scm (python-graph-tool): New variable.

Pushed as 5b359e4ba58daee0e08857cfe3a2296a2ac6fca6, thank you!

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