GNU bug report logs - #61204
Scilab scientific software

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

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: guix-patches <at> gnu.org
Subject: Scilab scientific software
Date: Wed, 01 Feb 2023 02:07:00 +0100

Hi guix!

I took a job where I have to use the scientific software suite Scilab in
an old version (5.4.1). I'll probably update it during this job.

I managed to package this version in the non-graphical version of Scilab
5.5.X versions this weekend.

It needs some old software libraries (metis <at> 4, suitesparse <at> 3), which
releases are not even in guix's history, and some compilation errors
fixes.

I go ahead and propose these patches in the next patches. I may continue
to work to propose updates up to the latest versions, but they need some
more work.

-- 
Best regards,
Nicolas Graves

Message #8 received at 61204 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 61204 <at> debbugs.gnu.org
Cc: ngraves <at> ngraves.fr
Subject: [PATCH 1/6] gnu: matio: Add header file.
Date: Wed,  1 Feb 2023 02:12:10 +0100

* gnu/packages/maths.scm (matio):
  [arguments] (phases): Add phase install-matioConfig.h.
---
 gnu/packages/maths.scm | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 4640237968..962b7d117c 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -5922,6 +5922,14 @@ (define-public matio
         (base32
          "0vr8c1mz1k6mz0sgh6n3scl5c3a71iqmy5fnydrgq504icj4vym4"))))
     (build-system gnu-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'install 'install-matioConfig.h
+            (lambda _
+              (install-file "src/matioConfig.h"
+                            (string-append #$output "/include")))))))
     (inputs
      (list zlib hdf5-1.8))
     (home-page "http://matio.sourceforge.net/")
-- 
2.39.1

Message #11 received at 61204 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 61204 <at> debbugs.gnu.org
Cc: ngraves <at> ngraves.fr
Subject: [PATCH 2/6] gnu: Add metis-4.
Date: Wed,  1 Feb 2023 02:12:11 +0100

* gnu/packages/maths.scm (metis-4): New variable.
---
 gnu/packages/maths.scm | 48 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 48 insertions(+)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 962b7d117c..f00f4f58be 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -4354,6 +4354,54 @@ (define-public metis
 schemes.")
     (license license:asl2.0)))          ;As of version 5.0.3
 
+;; This outdated version contains only library and header files. It is used
+;; to build the scilab package.
+(define-public metis-4
+  (package
+    (inherit metis)
+    (name "metis")
+    (version "4.0.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/"
+                           "metis-" version ".tar.gz"))
+       (sha256
+        (base32
+         "0m8shi202vprs8d9l51178v0skngzgx81q0d9ln1ng3hh3g3byjy"))))
+    (build-system gnu-build-system)
+    (arguments
+     (list #:tests? #f                      ;no tests
+           #:make-flags
+           #~(list "CC=gcc"
+                   "AR=gcc -shared -o"
+                   "RANLIB=touch"
+                   "OPTFLAGS= -O3 "
+                   "COPTIONS= -fPIC"
+                   (string-append
+                    "LDOPTIONS=-Wl,rpath," #$output "/lib")
+                   "METISLIB=../libmetis.so")
+           #:phases
+           #~(modify-phases %standard-phases
+               (replace 'configure
+                 ;; Make the library shared.
+                 (lambda _
+                   (substitute* "Lib/Makefile"
+                     (("libmetis\\.a")
+                      "libmetis.so"))
+                   (chdir "Lib")))
+               (replace 'install
+                 (lambda _
+                   ;; Library
+                   (chdir "..")
+                   (install-file "libmetis.so"
+                                 (string-append #$output "/lib"))
+                   ;; Includes
+                   (for-each
+                    (lambda (x)
+                      (install-file x (string-append #$output "/include")))
+                    (find-files "Lib" "\\.h$")))))))))
+
 (define-public p4est
   (package
     (name "p4est")
-- 
2.39.1

Message #14 received at 61204 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 61204 <at> debbugs.gnu.org
Cc: ngraves <at> ngraves.fr
Subject: [PATCH 3/6] gnu: Add suitesparse-3.
Date: Wed,  1 Feb 2023 02:12:12 +0100

* gnu/packages/maths.scm (suitesparse-3): New variable.
---
 gnu/packages/maths.scm | 95 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 95 insertions(+)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index f00f4f58be..cc138de940 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -5116,6 +5116,101 @@ (define-public suitesparse
     ;;  GPUQREngine, RBio, SuiteSparse_GPURuntime, SuiteSparseQR, UMFPACK
     (license (list license:gpl2+ license:lgpl2.1+))))
 
+
+;; This outdated version is used to build the scilab package.
+(define-public suitesparse-3
+  (package
+    (inherit suitesparse)
+    (name "suitesparse")
+    (version "3.1.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/DrTimothyAldenDavis/SuiteSparse")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0wxk755nzps0c9la24zqknqkzjp6rcj5q9jhd973mff1pqja3clz"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f  ;no "check" target
+       #:make-flags
+       ,#~(list
+           (string-append "CC=gcc")
+           "AR=gcc -shared -o"
+           "RANLIB=touch"
+           "CFLAGS=-O3 -fPIC -I../Include"
+           "TBB=-ltbb"
+           (string-append
+            "METIS=" (search-input-file %build-inputs "lib/libmetis.so"))
+           (string-append
+            "METIS_PATH="
+            (string-drop-right
+             (search-input-file %build-inputs "lib/libmetis.so")
+             (string-length "/lib/libmetis.so")))
+
+           ;; The default is to link against netlib lapack.  Use OpenBLAS
+           ;; instead.
+           "BLAS=-lopenblas" "LAPACK=-lopenblas"
+
+           (string-append "INSTALL_LIB="
+                          (assoc-ref %outputs "out") "/lib")
+           (string-append "INSTALL_INCLUDE="
+                          (assoc-ref %outputs "out") "/include")
+           "library")
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'correct-build-configuration
+           (lambda _
+             ;; Correct metis path.
+             (substitute* "CHOLMOD/Lib/Makefile"
+               (("\\$\\(METIS_PATH\\)\\/Lib")
+                "$(METIS_PATH)/include"))
+             ;; Invert build order: CHOLMOD before KLU.
+             (substitute* "Makefile"
+               (("\t\\( cd CHOLMOD ; \\$\\(MAKE\\) \\)\n$")
+                "")
+               (("\\( cd KLU ; \\$\\(MAKE\\) \\)")
+                (string-append "( cd CHOLMOD ; $(MAKE) )\n\t"
+                               "( cd KLU ; $(MAKE) )")))
+             ;; Build shared libraries.
+             (substitute* (find-files "." "akefile$")
+               (("lib([a-z]+)\\.a" all libname)
+                (string-append "lib" libname ".so")))
+             ;; Delete broken KLU Demo step.
+             (substitute* "KLU/Makefile"
+               (("\\( cd Demo ; \\$\\(MAKE\\) \\)")
+                ""))))
+         (replace 'install
+           (lambda _
+             ;; Install libraries.
+             (for-each
+              (lambda (x)
+                (install-file
+                 x
+                 (string-append (assoc-ref %outputs "out") "/lib")))
+              (find-files "." "\\.so$"))
+             ;; Install header files.
+             (for-each
+              (lambda (x)
+                (install-file
+                 x
+                 (string-append (assoc-ref %outputs "out") "/include")))
+              (find-files "." "\\.h$"))))
+         ,@(if (target-riscv64?)
+               ;; GraphBLAS FTBFS on riscv64-linux
+               `((add-after 'unpack 'skip-graphblas
+                   (lambda _
+                     (substitute* "Makefile"
+                       ((".*cd GraphBLAS.*") "")
+                       (("metisinstall gbinstall moninstall")
+                        "metisinstall moninstall")))))
+               '())
+         (delete 'configure))))         ;no configure script
+    (inputs
+     (list tbb openblas gmp mpfr metis-4))))
+
 (define-public atlas
   (package
     (name "atlas")
-- 
2.39.1

Message #17 received at 61204 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 61204 <at> debbugs.gnu.org
Cc: ngraves <at> ngraves.fr
Subject: [PATCH 5/6] gnu: scilab: Update to 5.5.1.
Date: Wed,  1 Feb 2023 02:12:14 +0100

* gnu/packages/maths.scm (scilab): Update to 5.5.1.
---
 gnu/packages/maths.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 937c829a0b..5f944a1d50 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -8324,7 +8324,7 @@ (define-public optizelle
 (define-public scilab
   (package
     (name "scilab")
-    (version "5.5.0")
+    (version "5.5.1")
     (source
      (origin
        (method url-fetch)
@@ -8332,7 +8332,7 @@ (define-public scilab
         (string-append "https://oos.eu-west-2.outscale.com/scilab-releases/"
                        version "/scilab-" version "-src.tar.gz"))
        (sha256
-        (base32 "1hx57aji5d78brwqcf8a34i1hasm3h4nw46xjg7cgxj09s8yz5kq"))))
+        (base32 "0ab7h0hdra4fjy505pivg6dbgcdxa4vd30g8gjhk8x7i28z24mn0"))))
     (build-system gnu-build-system)
     (native-inputs (list pkg-config gfortran))
     (inputs (list libxml2
-- 
2.39.1

Message #20 received at 61204 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 61204 <at> debbugs.gnu.org
Cc: ngraves <at> ngraves.fr
Subject: [PATCH 6/6] gnu: scilab: Update to 5.5.2.
Date: Wed,  1 Feb 2023 02:12:15 +0100

* gnu/packages/maths.scm (scilab): Update to 5.5.2.
---
 gnu/packages/maths.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 5f944a1d50..bdc9e75498 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -8324,7 +8324,7 @@ (define-public optizelle
 (define-public scilab
   (package
     (name "scilab")
-    (version "5.5.1")
+    (version "5.5.2")
     (source
      (origin
        (method url-fetch)
@@ -8332,7 +8332,7 @@ (define-public scilab
         (string-append "https://oos.eu-west-2.outscale.com/scilab-releases/"
                        version "/scilab-" version "-src.tar.gz"))
        (sha256
-        (base32 "0ab7h0hdra4fjy505pivg6dbgcdxa4vd30g8gjhk8x7i28z24mn0"))))
+        (base32 "0phg9pn24yw98hbh475ik84dnikf1225b2knh7qbhdbdx6fm2d57"))))
     (build-system gnu-build-system)
     (native-inputs (list pkg-config gfortran))
     (inputs (list libxml2
-- 
2.39.1

Message #23 received at 61204 <at> debbugs.gnu.org (full text, mbox):

From: Ludovic Courtès <ludo <at> gnu.org>
To: Nicolas Graves <ngraves <at> ngraves.fr>
Cc: 61204 <at> debbugs.gnu.org
Subject: Re: bug#61204: Scilab scientific software
Date: Sat, 11 Feb 2023 00:08:09 +0100

Hi Nicolas,

Nicolas Graves <ngraves <at> ngraves.fr> skribis:

> I took a job where I have to use the scientific software suite Scilab in
> an old version (5.4.1). I'll probably update it during this job.

Heh, congrats on the new job, and yay for free software! :-)

> I managed to package this version in the non-graphical version of Scilab
> 5.5.X versions this weekend.
>
> It needs some old software libraries (metis <at> 4, suitesparse <at> 3), which
> releases are not even in guix's history, and some compilation errors
> fixes.
>
> I go ahead and propose these patches in the next patches. I may continue
> to work to propose updates up to the latest versions, but they need some
> more work.

Looks like we’re missing patch 4/6, which actually adds Scilab.

Did it get stuck on its way?

Ludo’.

Message #26 received at 61204 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 61204 <at> debbugs.gnu.org
Cc: ngraves <at> ngraves.fr
Subject: [PATCH] gnu: Add scilab.
Date: Sat, 11 Feb 2023 11:09:37 +0100

* gnu/packages/maths.scm (scilab): New variable.
---
 gnu/packages/maths.scm | 106 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 106 insertions(+)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 741ecc2798..81dba14674 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -8319,3 +8319,109 @@ (define-public optizelle
 provided for applications written in C++ and Python.  Parallel
 computation is supported via MPI.")
     (license license:bsd-2))))
+
+(define-public scilab
+  (package
+    (name "scilab")
+    (version "5.5.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri
+        (string-append "https://oos.eu-west-2.outscale.com/scilab-releases/"
+                       version "/scilab-" version "-src.tar.gz"))
+       (sha256
+        (base32 "1hx57aji5d78brwqcf8a34i1hasm3h4nw46xjg7cgxj09s8yz5kq"))))
+    (build-system gnu-build-system)
+    (native-inputs (list pkg-config gfortran))
+    (inputs (list libxml2
+                  `(,pcre "bin")
+                  `(,pcre "out")
+                  readline
+                  hdf5-1.8
+                  curl
+                  openblas
+                  lapack
+                  arpack-ng
+                  fftw
+                  gettext-minimal
+                  suitesparse-3
+                  tcl
+                  tk
+                  libx11
+                  matio))
+    (arguments
+     `(#:tests? #f
+       #:configure-flags
+       ,#~(list
+           "--enable-relocatable"
+           "--disable-static-system-lib"
+           ;; Disable all java code.
+           "--without-gui"
+           "--without-javasci"
+           "--disable-build-help"
+           "--with-external-scirenderer"
+           ;; Tcl and Tk library locations.
+           (string-append "--with-tcl-include="
+                          (string-drop-right
+                           (search-input-file %build-inputs "include/tcl.h")
+                           (string-length "/tcl.h")))
+           (string-append "--with-tcl-library="
+                          (string-drop-right
+                           (search-input-directory %build-inputs "lib/tcl8")
+                           (string-length "/tcl8")))
+           (string-append "--with-tk-include="
+                          (string-drop-right
+                           (search-input-file %build-inputs "include/tk.h")
+                           (string-length "/tk.h")))
+           (string-append "--with-tk-library="
+                          (string-drop-right
+                           (search-input-directory %build-inputs "lib/tk8.6")
+                           (string-length "/tk8.6")))
+           ;; There are some 2018-fortran errors that are ignored
+           ;; with this fortran compiler flag.
+           "FFLAGS=-fallow-argument-mismatch")
+       #:phases
+       ,#~(modify-phases %standard-phases
+            (add-before 'build 'pre-build
+              (lambda _
+                ;; Fix scilab script.
+                (substitute* "bin/scilab"
+                  (("\\/bin\\/ls")
+                   (which "ls")))
+                ;; Fix core.start.
+                (substitute* "modules/core/etc/core.start"
+                  (("'SCI/modules")
+                   "SCI+'/modules"))
+                ;; Fix fortran compilation error.
+                (substitute*
+                    "modules/differential_equations/src/fortran/twodq.f"
+                  (("node\\(10\\),node1\\(10\\),node2\\(10\\),coef")
+                   "node(9),node1(9),node2(9),coef"))
+                ;; Fix C compilation errors.
+                ;; remove &
+                (substitute* "modules/hdf5/src/c/h5_readDataFromFile_v1.c"
+                  (("(H5Rdereference\\(_iDatasetId, H5R_OBJECT, )&(.*)\\);$"
+                    all common ref)
+                   (string-append common ref)))
+                ;; fix multiple definitions
+                (substitute* "modules/tclsci/src/c/TCL_Command.h"
+                  (("^__thread")
+                   "extern __thread"))
+                (substitute* "modules/tclsci/src/c/InitTclTk.c"
+                  (("BOOL TK_Started = FALSE;" all)
+                   (string-append all "\n"
+                                  "__threadId TclThread;" "\n"
+                                  "__threadSignal InterpReady;" "\n"
+                                  "__threadSignalLock InterpReadyLock;"
+                                  "\n")))
+                ;; Set SCIHOME to /tmp before macros compilation.
+                (setenv "SCIHOME" "/tmp"))))))
+    (home-page "https://scilab.org")
+    (synopsis "Software for engineers and scientists")
+    (description "This package provides the non-graphical version of the Scilab
+software for engineers and scientists. Scilab is used for signal processing,
+statistical analysis, image enhancement, fluid dynamics simulations, numerical
+optimization, and modeling, simulation of explicit and implicit dynamical
+systems and symbolic manipulations.")
+    (license license:gpl2)))
-- 
2.39.1

Message #29 received at 61204 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: Ludovic Courtès <ludo <at> gnu.org>
Cc: 61204 <at> debbugs.gnu.org
Subject: Re: [bug#61204] Scilab scientific software
Date: Sat, 11 Feb 2023 11:11:42 +0100

On 2023-02-11 00:08, Ludovic Courtès wrote:

> Heh, congrats on the new job, and yay for free software! :-)

Thanks!

> Looks like we’re missing patch 4/6, which actually adds Scilab.
> Did it get stuck on its way?

Most likely yes, I've just resent this patch here.

-- 
Best regards,
Nicolas Graves

Message #32 received at 61204 <at> debbugs.gnu.org (full text, mbox):

From: Simon Tournier <zimon.toutoune <at> gmail.com>
To: Nicolas Graves <ngraves <at> ngraves.fr>, 61204 <at> debbugs.gnu.org
Subject: Re: [bug#61204] Scilab scientific software
Date: Wed, 15 Feb 2023 16:57:19 +0100

Hi,

On Wed, 01 Feb 2023 at 02:07, Nicolas Graves via Guix-patches via <guix-patches <at> gnu.org> wrote:

> I took a job where I have to use the scientific software suite Scilab in
> an old version (5.4.1). I'll probably update it during this job.

Congrats!


> I managed to package this version in the non-graphical version of Scilab
> 5.5.X versions this weekend.

Cool!  Well, I was tweaking and reviewing the series when…

> It needs some old software libraries (metis <at> 4, suitesparse <at> 3), which
> releases are not even in guix's history, and some compilation errors
> fixes.

…I see two issues about licenses:

 1. Metis 4 is not free software
 2. Scilab is Cecill v2.1 and not gpl2 as the patch suggests.

About #2, the fix is easy. :-)

About #1, it will be difficult.

Well, maybe these 3 old versions of Scilab could go to the channel
guix-science [1] or guix-science-non-free [2].

If Scilab 6 works with Metis 5, then there is no issue with the licenses
and could be included.

WDYT?

1: https://github.com/guix-science/guix-science
2: https://github.com/guix-science/guix-science-nonfree

Cheers,
simon

Message #35 received at 61204 <at> debbugs.gnu.org (full text, mbox):

From: Ludovic Courtès <ludo <at> gnu.org>
To: Nicolas Graves <ngraves <at> ngraves.fr>
Cc: 61204 <at> debbugs.gnu.org, Simon Tournier <zimon.toutoune <at> gmail.com>
Subject: Re: bug#61204: Scilab scientific software
Date: Thu, 16 Mar 2023 12:26:47 +0100

Hi Nicolas,

Simon Tournier <zimon.toutoune <at> gmail.com> skribis:

> …I see two issues about licenses:
>
>  1. Metis 4 is not free software
>  2. Scilab is Cecill v2.1 and not gpl2 as the patch suggests.
>
> About #2, the fix is easy. :-)
>
> About #1, it will be difficult.

[...]

> If Scilab 6 works with Metis 5, then there is no issue with the licenses
> and could be included.

Could you check whether using Metis 5 is possible, or whether Metis is
an optional dependency, or whether scotch:metis can be used (Scotch is
another graph partitioner with a Metis compatibility layer)?

TIA,
Ludo’.

Message #38 received at 61204 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 61204 <at> debbugs.gnu.org
Cc: ludo <at> gnu.org, ngraves <at> ngraves.fr
Subject: [PATCH v2 1/3] gnu: matio: Add header file.
Date: Sat, 25 Mar 2023 15:15:20 +0100

* gnu/packages/maths.scm (matio):
  [arguments] (phases): Add phase install-matioConfig.h.
---
 gnu/packages/maths.scm | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 93afc6ed40..5d8e2f0159 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -6056,6 +6056,14 @@ (define-public matio
         (base32
          "0vr8c1mz1k6mz0sgh6n3scl5c3a71iqmy5fnydrgq504icj4vym4"))))
     (build-system gnu-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'install 'install-matioConfig.h
+            (lambda _
+              (install-file "src/matioConfig.h"
+                            (string-append #$output "/include")))))))
     (inputs
      (list zlib hdf5-1.8))
     (home-page "http://matio.sourceforge.net/")
-- 
2.39.2

Message #41 received at 61204 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 61204 <at> debbugs.gnu.org
Cc: ludo <at> gnu.org, ngraves <at> ngraves.fr
Subject: [PATCH v2 2/3] gnu: Add suitesparse-3.
Date: Sat, 25 Mar 2023 15:15:21 +0100

* gnu/packages/maths.scm (suitesparse-3): New variable.
---
 gnu/packages/maths.scm | 89 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 89 insertions(+)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 5d8e2f0159..be20e5b581 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -5202,6 +5202,95 @@ (define-public suitesparse
     ;;  GPUQREngine, RBio, SuiteSparse_GPURuntime, SuiteSparseQR, UMFPACK
     (license (list license:gpl2+ license:lgpl2.1+))))
 
+
+;; This outdated version is used to build the scilab package.
+(define-public suitesparse-3
+  (package
+    (inherit suitesparse)
+    (name "suitesparse")
+    (version "3.1.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/DrTimothyAldenDavis/SuiteSparse")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0wxk755nzps0c9la24zqknqkzjp6rcj5q9jhd973mff1pqja3clz"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f  ;no "check" target
+       #:make-flags
+       ,#~(list
+           (string-append "CC=gcc")
+           "AR=gcc -shared -o"
+           "RANLIB=touch"
+           "CFLAGS=-O3 -fPIC -I../Include"
+           "TBB=-ltbb"
+
+           ;; Disable metis <at> 4 (nonfree) support.
+           "CHOLMOD_CONFIG=-DNPARTITION"
+           "METIS="
+           "METIS_PATH="
+
+           ;; The default is to link against netlib lapack.  Use OpenBLAS
+           ;; instead.
+           "BLAS=-lopenblas" "LAPACK=-lopenblas"
+
+           (string-append "INSTALL_LIB="
+                          (assoc-ref %outputs "out") "/lib")
+           (string-append "INSTALL_INCLUDE="
+                          (assoc-ref %outputs "out") "/include")
+           "library")
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'correct-build-configuration
+           (lambda _
+             ;; Invert build order: CHOLMOD before KLU.
+             (substitute* "Makefile"
+               (("\t\\( cd CHOLMOD ; \\$\\(MAKE\\) \\)\n$")
+                "")
+               (("\\( cd KLU ; \\$\\(MAKE\\) \\)")
+                (string-append "( cd CHOLMOD ; $(MAKE) )\n\t"
+                               "( cd KLU ; $(MAKE) )")))
+             ;; Build shared libraries.
+             (substitute* (find-files "." "akefile$")
+               (("lib([a-z]+)\\.a" all libname)
+                (string-append "lib" libname ".so")))
+             ;; Delete broken KLU Demo step.
+             (substitute* "KLU/Makefile"
+               (("\\( cd Demo ; \\$\\(MAKE\\) \\)")
+                ""))))
+         (replace 'install
+           (lambda _
+             ;; Install libraries.
+             (for-each
+              (lambda (x)
+                (install-file
+                 x
+                 (string-append (assoc-ref %outputs "out") "/lib")))
+              (find-files "." "\\.so$"))
+             ;; Install header files.
+             (for-each
+              (lambda (x)
+                (install-file
+                 x
+                 (string-append (assoc-ref %outputs "out") "/include")))
+              (find-files "." "\\.h$"))))
+         ,@(if (target-riscv64?)
+               ;; GraphBLAS FTBFS on riscv64-linux
+               `((add-after 'unpack 'skip-graphblas
+                   (lambda _
+                     (substitute* "Makefile"
+                       ((".*cd GraphBLAS.*") "")
+                       (("metisinstall gbinstall moninstall")
+                        "moninstall")))))
+               '())
+         (delete 'configure))))         ;no configure script
+    (inputs
+     (list tbb openblas gmp mpfr))))
+
 (define-public atlas
   (package
     (name "atlas")
-- 
2.39.2

Message #44 received at 61204 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 61204 <at> debbugs.gnu.org
Cc: ludo <at> gnu.org, ngraves <at> ngraves.fr
Subject: [PATCH v2 3/3] gnu: Add scilab.
Date: Sat, 25 Mar 2023 15:15:22 +0100

* gnu/packages/maths.scm (scilab): New variable.
---
 gnu/packages/maths.scm | 106 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 106 insertions(+)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index be20e5b581..2bebc51bf9 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -8650,3 +8650,109 @@ (define-public optizelle
 provided for applications written in C++ and Python.  Parallel
 computation is supported via MPI.")
     (license license:bsd-2))))
+
+(define-public scilab
+  (package
+    (name "scilab")
+    (version "5.5.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri
+        (string-append "https://oos.eu-west-2.outscale.com/scilab-releases/"
+                       version "/scilab-" version "-src.tar.gz"))
+       (sha256
+        (base32 "1hx57aji5d78brwqcf8a34i1hasm3h4nw46xjg7cgxj09s8yz5kq"))))
+    (build-system gnu-build-system)
+    (native-inputs (list pkg-config gfortran))
+    (inputs (list libxml2
+                  `(,pcre "bin")
+                  `(,pcre "out")
+                  readline
+                  hdf5-1.8
+                  curl
+                  openblas
+                  lapack
+                  arpack-ng
+                  fftw
+                  gettext-minimal
+                  suitesparse-3
+                  tcl
+                  tk
+                  libx11
+                  matio))
+    (arguments
+     `(#:tests? #f
+       #:configure-flags
+       ,#~(list
+           "--enable-relocatable"
+           "--disable-static-system-lib"
+           ;; Disable all java code.
+           "--without-gui"
+           "--without-javasci"
+           "--disable-build-help"
+           "--with-external-scirenderer"
+           ;; Tcl and Tk library locations.
+           (string-append "--with-tcl-include="
+                          (string-drop-right
+                           (search-input-file %build-inputs "include/tcl.h")
+                           (string-length "/tcl.h")))
+           (string-append "--with-tcl-library="
+                          (string-drop-right
+                           (search-input-directory %build-inputs "lib/tcl8")
+                           (string-length "/tcl8")))
+           (string-append "--with-tk-include="
+                          (string-drop-right
+                           (search-input-file %build-inputs "include/tk.h")
+                           (string-length "/tk.h")))
+           (string-append "--with-tk-library="
+                          (string-drop-right
+                           (search-input-directory %build-inputs "lib/tk8.6")
+                           (string-length "/tk8.6")))
+           ;; There are some 2018-fortran errors that are ignored
+           ;; with this fortran compiler flag.
+           "FFLAGS=-fallow-argument-mismatch")
+       #:phases
+       ,#~(modify-phases %standard-phases
+            (add-before 'build 'pre-build
+              (lambda _
+                ;; Fix scilab script.
+                (substitute* "bin/scilab"
+                  (("\\/bin\\/ls")
+                   (which "ls")))
+                ;; Fix core.start.
+                (substitute* "modules/core/etc/core.start"
+                  (("'SCI/modules")
+                   "SCI+'/modules"))
+                ;; Fix fortran compilation error.
+                (substitute*
+                    "modules/differential_equations/src/fortran/twodq.f"
+                  (("node\\(10\\),node1\\(10\\),node2\\(10\\),coef")
+                   "node(9),node1(9),node2(9),coef"))
+                ;; Fix C compilation errors.
+                ;; remove &
+                (substitute* "modules/hdf5/src/c/h5_readDataFromFile_v1.c"
+                  (("(H5Rdereference\\(_iDatasetId, H5R_OBJECT, )&(.*)\\);$"
+                    all common ref)
+                   (string-append common ref)))
+                ;; fix multiple definitions
+                (substitute* "modules/tclsci/src/c/TCL_Command.h"
+                  (("^__thread")
+                   "extern __thread"))
+                (substitute* "modules/tclsci/src/c/InitTclTk.c"
+                  (("BOOL TK_Started = FALSE;" all)
+                   (string-append all "\n"
+                                  "__threadId TclThread;" "\n"
+                                  "__threadSignal InterpReady;" "\n"
+                                  "__threadSignalLock InterpReadyLock;"
+                                  "\n")))
+                ;; Set SCIHOME to /tmp before macros compilation.
+                (setenv "SCIHOME" "/tmp"))))))
+    (home-page "https://scilab.org")
+    (synopsis "Software for engineers and scientists")
+    (description "This package provides the non-graphical version of the Scilab
+software for engineers and scientists. Scilab is used for signal processing,
+statistical analysis, image enhancement, fluid dynamics simulations, numerical
+optimization, and modeling, simulation of explicit and implicit dynamical
+systems and symbolic manipulations.")
+    (license license:gpl2)))
-- 
2.39.2

Message #47 received at 61204 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: Ludovic Courtès <ludo <at> gnu.org>
Cc: 61204 <at> debbugs.gnu.org, Simon Tournier <zimon.toutoune <at> gmail.com>
Subject: Re: [bug#61204] Scilab scientific software
Date: Sat, 25 Mar 2023 15:17:59 +0100

On 2023-03-16 12:26, Ludovic Courtès wrote:

> Hi Nicolas,
>
> Simon Tournier <zimon.toutoune <at> gmail.com> skribis:
>
>> …I see two issues about licenses:
>>
>>  1. Metis 4 is not free software
>>  2. Scilab is Cecill v2.1 and not gpl2 as the patch suggests.
>>
>> About #2, the fix is easy. :-)
>>
>> About #1, it will be difficult.
>
> [...]
>
>> If Scilab 6 works with Metis 5, then there is no issue with the licenses
>> and could be included.
>
> Could you check whether using Metis 5 is possible, or whether Metis is
> an optional dependency, or whether scotch:metis can be used (Scotch is
> another graph partitioner with a Metis compatibility layer)?

Actually, I've seen that it's possible to compile Suitesparse <at> 3 without
support for Metis <at> 4. Scilab seems to work correctly, so I'll stop here
for this version ;)

I've just send a v2 patch thread. 

>
> TIA,
> Ludo’.
>
>
>

-- 
Best regards,
Nicolas Graves

Message #52 received at 61204-done <at> debbugs.gnu.org (full text, mbox):

From: Ludovic Courtès <ludo <at> gnu.org>
To: Nicolas Graves <ngraves <at> ngraves.fr>
Cc: 61204-done <at> debbugs.gnu.org
Subject: Re: [PATCH v2 3/3] gnu: Add scilab.
Date: Thu, 30 Mar 2023 22:43:16 +0200

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

Hi Nicolas,

Nicolas Graves <ngraves <at> ngraves.fr> skribis:

> * gnu/packages/maths.scm (scilab): New variable.

Applied all three patches with the license change below: I checked
‘COPYING’ and scanned a bunch of files, and it’s consistently
CeCILL v2.1.

Thanks!

Ludo’.

[Message part 2 (text/x-patch, inline)]

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 0d7035df4e..72dccd04bf 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -8755,4 +8755,4 @@ (define-public scilab
 statistical analysis, image enhancement, fluid dynamics simulations, numerical
 optimization, and modeling, simulation of explicit and implicit dynamical
 systems and symbolic manipulations.")
-    (license license:gpl2)))
+    (license license:cecill)))                    ;CeCILL v2.1

Message #55 received at 61204 <at> debbugs.gnu.org (full text, mbox):

From: Simon Tournier <zimon.toutoune <at> gmail.com>
To: Nicolas Graves <ngraves <at> ngraves.fr>, Ludovic Courtès
 <ludo <at> gnu.org>
Cc: 61204 <at> debbugs.gnu.org
Subject: Re: [bug#61204] Scilab scientific software
Date: Mon, 03 Apr 2023 17:43:45 +0200

Hi,

On sam., 25 mars 2023 at 15:17, Nicolas Graves via Guix-patches via <guix-patches <at> gnu.org> wrote:

> Actually, I've seen that it's possible to compile Suitesparse <at> 3 without
> support for Metis <at> 4. Scilab seems to work correctly, so I'll stop here
> for this version ;)

Cool!

Just a remark about [PATCH v2 3/3] gnu: Add scilab.

+    (source
+     (origin
+       (method url-fetch)
+       (uri
+        (string-append "https://oos.eu-west-2.outscale.com/scilab-releases/"
+                       version "/scilab-" version "-src.tar.gz"))
+       (sha256
+        (base32 "1hx57aji5d78brwqcf8a34i1hasm3h4nw46xjg7cgxj09s8yz5kq"))))

Is the URL stable?  It looks like the Cloud solution of Dassault
Systèmes, right?  Dassault Systèmes being the maintainer, right?

Well, the main development repository seems gitlab.com, right?

    https://gitlab.com/scilab/scilab

Why not rely on this gitlab.com URL?  Tarball if the Git history of the
repository is too heavy.  For example,

    https://gitlab.com/scilab/scilab/-/archive/5.5.0/scilab-5.5.0.tar.gz

Although some files are only in the outscale link,

--8<---------------cut here---------------start------------->8---
$ diff -r --no-dereference scilab-5.5.0-{1,2}
Only in scilab-5.5.0-1: ACKNOWLEDGEMENTS
Only in scilab-5.5.0-1: aclocal.m4
Only in scilab-5.5.0-1: bin
Only in scilab-5.5.0-1: build.incl.xml
Only in scilab-5.5.0-1: build.qa.incl.xml
Only in scilab-5.5.0-1: CHANGES_2.X
Only in scilab-5.5.0-1: CHANGES_3.X
Only in scilab-5.5.0-1: CHANGES_4.X
Only in scilab-5.5.0-1: CHANGES_5.0.X
Only in scilab-5.5.0-1: CHANGES_5.1.X
Only in scilab-5.5.0-1: CHANGES_5.2.X
Only in scilab-5.5.0-1: CHANGES_5.3.X
Only in scilab-5.5.0-1: CHANGES_5.4.X
Only in scilab-5.5.0-1: CHANGES_5.5.X
Only in scilab-5.5.0-1: checkstyle
Only in scilab-5.5.0-1: config
Only in scilab-5.5.0-1: configure
Only in scilab-5.5.0-1: configure.ac
Only in scilab-5.5.0-1: contrib
Only in scilab-5.5.0-1: COPYING
Only in scilab-5.5.0-1: COPYING-BSD
Only in scilab-5.5.0-1: COPYING-FR
Only in scilab-5.5.0-1: desktop
Only in scilab-5.5.0-1: etc
Only in scilab-5.5.0-2: git_hooks
Only in scilab-5.5.0-2: .gitignore
Only in scilab-5.5.0-1: GIT_info.incl
Only in scilab-5.5.0-1: libs
Only in scilab-5.5.0-1: license.txt
Only in scilab-5.5.0-1: locale
Only in scilab-5.5.0-1: m4
Only in scilab-5.5.0-1: Makefile.am
Only in scilab-5.5.0-1: Makefile.call_scilab.am
Only in scilab-5.5.0-1: Makefile.in
Only in scilab-5.5.0-1: Makefile.incl.am
Only in scilab-5.5.0-1: Makefile.incl.in
Only in scilab-5.5.0-1: modules
Only in scilab-5.5.0-1: README_Unix
Only in scilab-5.5.0-1: Readme_Visual.txt
Only in scilab-5.5.0-1: README_Windows.txt
Only in scilab-5.5.0-1: RELEASE_NOTES_5.0.X
Only in scilab-5.5.0-1: RELEASE_NOTES_5.1.X
Only in scilab-5.5.0-1: RELEASE_NOTES_5.2.X
Only in scilab-5.5.0-1: RELEASE_NOTES_5.3.X
Only in scilab-5.5.0-2: scilab
Only in scilab-5.5.0-1: Scilab_f2c.sln
Only in scilab-5.5.0-1: scilab-lib-doc.properties.in
Only in scilab-5.5.0-1: scilab-lib-doc.properties.vc
Only in scilab-5.5.0-1: scilab-lib.properties.in
Only in scilab-5.5.0-1: scilab-lib.properties.vc
Only in scilab-5.5.0-1: scilab.pc.in
Only in scilab-5.5.0-1: scilab.properties.in
Only in scilab-5.5.0-1: scilab.properties.vc
Only in scilab-5.5.0-1: Scilab.sln
Only in scilab-5.5.0-2: SEP
Only in scilab-5.5.0-1: SVN_revision.incl
Only in scilab-5.5.0-1: tools
Only in scilab-5.5.0-1: Version.incl
Only in scilab-5.5.0-1: Visual-Studio-settings
--8<---------------cut here---------------end--------------->8---

Ah, weird! :-)

Cheers,
simon

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