Subject: [bug#66201] [PATCH 1/2] gnu: scilab: Update to 2023.1.0.

From: David Elsing <[email-masked]>
Date: Mon, 25 Sep 2023 21:13:12 +0000

* gnu/packages/maths.scm (scilab): Update to 2023.1.0.
[source] Use git-fetch.
<modules>: Add (guix build utils) and (ice-9 ftw).
<patches>: Add patch for hdf5 >= 1.10.
<snippet>: Move contents of the "scilab" directory to its parents. Remove
the other files and autogenerated files.
[native-inputs]: Add autoconf, autoconf-archive, automake, bison, eigen, flex,
libtool, ocaml and ocaml-findlib.
[inputs]: Add ocaml-num, replace hdf5-1.8 by hdf5-1.14 and suitesparse-3 by
suitesparse.
[arguments]: Remove quasiquote. Add --enable-build-parser,
--with-eigen-include=..., OCAMLC=... and OCAMLOPT=... to #:configure-flags.
<#:phases>: Add fix-ocaml-num, remove-desktop-files,
bootstrap-dynamic_link-scripts and build-parsers phases. Remove fixes for
compilation and linker errors from the pre-build phase.
[home-page]: Update URL.
[description]: Add two spaces between sentences.
[license]: Update to gpl2 and bsd-3.
---
 gnu/packages/maths.scm                        | 256 +++++++++++-------
 .../patches/scilab-hdf5-1.8-api.patch         |  71 +++++
 2 files changed, 236 insertions(+), 91 deletions(-)
 create mode 100644 gnu/packages/patches/scilab-hdf5-1.8-api.patch

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 62d4adfbd1..ff50a99599 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -61,6 +61,7 @@
 ;;; Copyright © 2022 Roman Scherer <[email-masked]>
 ;;; Copyright © 2023 Jake Leporte <[email-masked]>
 ;;; Copyright © 2023 Camilo Q.S. (Distopico) <[email-masked]>
+;;; Copyright © 2023 David Elsing <[email-masked]>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -8422,112 +8423,185 @@ (define-public optizelle
 (define-public scilab
   (package
     (name "scilab")
-    (version "5.5.2")
+    (version "2023.1.0")
     (source
      (origin
-       (method url-fetch)
-       (uri
-        (string-append "https://www.scilab.org/download/"
-                       version "/scilab-" version "-src.tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://gitlab.com/scilab/scilab")
+             (commit version)))
+       (file-name (git-file-name name version))
        (sha256
-        (base32 "0phg9pn24yw98hbh475ik84dnikf1225b2knh7qbhdbdx6fm2d57"))))
+        (base32
+         "0hbqsnc67b4f8zc690kl79bwhjaasykjlmqbln8iymnjcn3l5ypd"))
+       (modules '((guix build utils)
+                  (ice-9 ftw)))
+       (patches (search-patches "scilab-hdf5-1.8-api.patch"))
+       (snippet
+        #~(begin
+            (for-each
+             (lambda (file)
+               (unless (member file '("." ".." "scilab"))
+                 (delete-file-recursively file)))
+             (scandir "."))
+            (for-each
+             (lambda (file)
+               (unless (member file '("." ".."))
+                 (rename-file (string-append "scilab/" file) file)))
+             (scandir "scilab"))
+            (delete-file-recursively "scilab")
+            (delete-file "aclocal.m4")
+            (for-each
+             delete-file
+             (find-files "." "^Makefile\\.in$"))
+            (delete-file-recursively "config")
+            (delete-file "configure")
+            (delete-file-recursively "libs/GetWindowsVersion")
+            (delete-file "m4/ax_cxx_compile_stdcxx.m4")
+            (delete-file "m4/lib-ld.m4")
+            (delete-file "m4/libtool.m4")
+            (delete-file "m4/ltoptions.m4")
+            (delete-file "m4/ltsugar.m4")
+            (delete-file "m4/ltversion.m4")
+            (delete-file "m4/lt~obsolete.m4")
+            (delete-file "m4/pkg.m4")
+            (for-each
+             (lambda (file)
+               (delete-file
+                (string-append "modules/dynamic_link/src/scripts/" file)))
+             '("aclocal.m4"
+               "configure"
+               "compile"
+               "config.guess"
+               "config.sub"
+               "ltmain.sh"
+               "depcomp"
+               "install-sh"
+               "missing"))
+            (delete-file-recursively "modules/dynamic_link/src/scripts/m4")
+            (delete-file "modules/ast/src/cpp/parse/scanscilab.cpp")
+            (delete-file "modules/ast/src/cpp/parse/bison/parsescilab.output")
+            (delete-file "modules/ast/includes/parse/parsescilab.hxx")
+            (delete-file "modules/ast/src/cpp/parse/parsescilab.cpp")))))
     (build-system gnu-build-system)
-    (native-inputs (list pkg-config gfortran))
-    (inputs (list libxml2
-                  `(,pcre "bin")
+    (native-inputs
+     (list autoconf
+           autoconf-archive
+           automake
+           bison
+           eigen
+           flex
+           gfortran
+           libtool
+           ocaml
+           ocaml-findlib
+           pkg-config))
+    (inputs (list `(,pcre "bin")
                   `(,pcre "out")
-                  readline
-                  hdf5-1.8
-                  curl
-                  openblas
-                  lapack
+                  libxml2
                   arpack-ng
+                  curl
                   fftw
                   gettext-minimal
-                  suitesparse-3
-                  tcl
-                  tk
+                  hdf5-1.14
+                  lapack
                   libx11
-                  matio))
+                  matio
+                  ocaml-num
+                  openblas
+                  readline
+                  suitesparse
+                  tcl
+                  tk))
     (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")))
-                ;; Fix CPP compilation errors.
-                (substitute* "modules/output_stream/src/cpp/diary_manager.cpp"
-                  (("if \\(array_size > 0\\)")
-                   "if (*array_size > 0)"))
-                ;; Set SCIHOME to /tmp before macros compilation.
-                (setenv "SCIHOME" "/tmp"))))))
-    (home-page "https://scilab.org")
+     (list
+      ;; The tests require java code.
+      #:tests? #f
+      #:configure-flags
+      #~(list
+         "--enable-relocatable"
+         "--disable-static-system-lib"
+         "--enable-build-parser"
+         ;; 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")))
+         (string-append "--with-eigen-include="
+                        #$(this-package-native-input "eigen")
+                        "/include/eigen3")
+         ;; Find and link to the OCaml Num package
+         "OCAMLC=ocamlfind ocamlc -package num"
+         "OCAMLOPT=ocamlfind ocamlopt -package num -linkpkg"
+         ;; There are some 2018-fortran errors that are ignored
+         ;; with this fortran compiler flag.
+         "FFLAGS=-fallow-argument-mismatch")
+      #:phases
+      #~(modify-phases %standard-phases
+          ;; The Num library is specified with the OCAMLC and
+          ;; OCAMLOPT variables above.
+          (add-after 'unpack 'fix-ocaml-num
+            (lambda _
+              (substitute*
+                  '("modules/scicos/Makefile.modelica.am"
+                    "modules/scicos/src/translator/makefile.mak"
+                    "modules/scicos/src/modelica_compiler/makefile.mak")
+                (("nums\\.cmx?a") ""))))
+          ;; Install only scilab-cli.desktop
+          (add-after 'unpack 'remove-desktop-files
+            (lambda _
+              (substitute* "desktop/Makefile.am"
+                (("desktop_DATA =")
+                 "desktop_DATA = scilab-cli.desktop\nDUMMY ="))))
+          ;; These generated files are assumed to be present during
+          ;; the build.
+          (add-after 'bootstrap 'bootstrap-dynamic_link-scripts
+            (lambda _
+              (with-directory-excursion "modules/dynamic_link/src/scripts"
+                (invoke "autoreconf" "-i"))))
+          (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"))
+              ;; Set SCIHOME to /tmp before macros compilation.
+              (setenv "SCIHOME" "/tmp")))
+          ;; Prevent race condition
+          (add-after 'pre-build 'build-parsers
+            (lambda _
+              (with-directory-excursion "modules/ast"
+                (invoke "make" "src/cpp/parse/parsescilab.cpp"
+                        "src/cpp/parse/scanscilab.cpp")))))))
+    (home-page "https://www.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,
+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:cecill)))                    ;CeCILL v2.1
+    (license (list license:gpl2 license:bsd-3))))
 
 (define-public ruy
   (let ((commit "caa244343de289f913c505100e6a463d46c174de")
diff --git a/gnu/packages/patches/scilab-hdf5-1.8-api.patch b/gnu/packages/patches/scilab-hdf5-1.8-api.patch
new file mode 100644
index 0000000000..8b453e4720
--- /dev/null
+++ b/gnu/packages/patches/scilab-hdf5-1.8-api.patch
@@ -0,0 +1,71 @@
+This patch fixes the compilation with hdf5 version >= 1.10. Adapted from
+https://aur.archlinux.org/cgit/aur.git/plain/hdf5_18_api.patch?h=scilab-git.
+
+diff -ur a/scilab/modules/hdf5/includes/HDF5Objects.h b/scilab/modules/hdf5/includes/HDF5Objects.h
+--- a/scilab/modules/hdf5/includes/HDF5Objects.h
++++ b/scilab/modules/hdf5/includes/HDF5Objects.h
+@@ -16,14 +16,12 @@
+ #ifndef __HDF5OBJECTS_H__
+ #define __HDF5OBJECTS_H__
+ 
+-#define H5_NO_DEPRECATED_SYMBOLS
+ #undef H5_USE_16_API
++#define H5_USE_18_API
+ 
+-#define H5Eset_auto_vers 2
+ #include <hdf5.h>
+ #include <hdf5_hl.h>
+ 
+-#undef H5_NO_DEPRECATED_SYMBOLS
+ 
+ //#define __HDF5OBJECTS_DEBUG__
+ //#define __HDF5ERROR_PRINT__
+diff -ur a/scilab/modules/hdf5/Makefile.am b/scilab/modules/hdf5/Makefile.am
+--- a/scilab/modules/hdf5/Makefile.am
++++ b/scilab/modules/hdf5/Makefile.am
+@@ -104,8 +104,7 @@
+     -DH5Gopen_vers=2 \
+     -DH5Tget_array_dims_vers=2 \
+     -DH5Acreate_vers=2 \
+-    -DH5Rdereference_vers=2 \
+-    -DNO_DEPRECATED_SYMBOLS
++    -DH5Rdereference_vers=2
+ 
+ 
+ libscihdf5_la_CPPFLAGS = \
+diff -ur a/scilab/modules/hdf5/sci_gateway/cpp/sci_hdf5_listvar_v3.cpp b/scilab/modules/hdf5/sci_gateway/cpp/sci_hdf5_listvar_v3.cpp
+--- a/scilab/modules/hdf5/sci_gateway/cpp/sci_hdf5_listvar_v3.cpp
++++ b/scilab/modules/hdf5/sci_gateway/cpp/sci_hdf5_listvar_v3.cpp
+@@ -13,6 +13,8 @@
+ *
+ */
+ 
++#define H5_USE_18_API
++
+ #include <vector>
+ #include "function.hxx"
+ #include "string.hxx"
+diff -ur a/scilab/modules/hdf5/src/c/h5_readDataFromFile.c b/scilab/modules/hdf5/src/c/h5_readDataFromFile.c
+--- a/scilab/modules/hdf5/src/c/h5_readDataFromFile.c
++++ b/scilab/modules/hdf5/src/c/h5_readDataFromFile.c
+@@ -13,7 +13,7 @@
+ *
+ */
+ 
+-#define H5_NO_DEPRECATED_SYMBOLS
++#define H5_USE_18_API
+ 
+ #ifndef _MSC_VER
+ #include <sys/time.h>
+diff -ur a/scilab/modules/hdf5/src/c/h5_readDataFromFile_v1.c b/scilab/modules/hdf5/src/c/h5_readDataFromFile_v1.c
+--- a/scilab/modules/hdf5/src/c/h5_readDataFromFile_v1.c
++++ b/scilab/modules/hdf5/src/c/h5_readDataFromFile_v1.c
+@@ -13,7 +13,7 @@
+ *
+ */
+ 
+-#define H5_NO_DEPRECATED_SYMBOLS
++#define H5_USE_18_API
+ 
+ #ifndef _MSC_VER
+ #include <sys/time.h>
-- 
2.41.0