singular: 4.1.1p2 -> 4.2.0p2

Adds proper tests. Also removes the "enableFactory" option because
singular actually enables factory by default and explicitly disabling it
breaks the build. So the option was never really available.

pkgs/applications/science/math/singular/default.nix

@@ -1,57 +1,84 @@
-{ stdenv, fetchurl, gmp, bison, perl, ncurses, readline, coreutils, pkg-config
+{ stdenv, fetchFromGitHub, gmp, bison, perl, ncurses, readline, coreutils, pkg-config
 , lib
 , fetchpatch
-, autoreconfHook
+, autoreconfHook269
+, sharutils
 , file
 , flint
 , ntl
 , cddlib
-, enableFactory ? true
+, gfan
+, lrcalc
+, doxygen
+, graphviz
+# upstream generates docs with texinfo 4. later versions of texinfo
+# use letters instead of numbers for post-appendix chapters, and we
+# want it to match the upstream format because sage depends on it.
+, texinfo4
+, texlive
+, enableDocs ? true
 , enableGfanlib ? true
 }:
 
 stdenv.mkDerivation rec {
   pname = "singular";
-  version = "4.1.1p2";
+  version = "4.2.0p2";
 
-  src = let
+  # since the tarball does not contain tests or documentation (and
-    # singular sorts its tarballs in directories by base release (without patch version)
+  # there is no separate tests tarball for 4.2.0), we fetch from
-    # for example 4.1.1p1 will be in the directory 4-1-1
+  # GitHub.
-    baseVersion = builtins.head (lib.splitString "p" version);
+  src = fetchFromGitHub {
-    urlVersion = builtins.replaceStrings [ "." ] [ "-" ] baseVersion;
+    owner = "Singular";
-  in
+    repo = "Singular";
-  fetchurl {
+
-    url = "http://www.mathematik.uni-kl.de/ftp/pub/Math/Singular/SOURCES/${urlVersion}/singular-${version}.tar.gz";
+    # 4.2.0p2 is not tagged, but the tarball matches commit
-    sha256 = "07x9kri8vl4galik7lr6pscq3c51n8570pyw64i7gbj0m706f7wf";
+    # 6f68939ddf612d96e3caaaaa8275f77613ac1da8. the commit below has
+    # two extra fixes.
+    rev = "3cda50c00a849455efa2502e56596955491a353a";
+    sha256 = "sha256-OizPhGE6L2LTOrKfeDdDB6BSdvYkDVXvbbYjV14hnHM=";
+
+    # if a release is tagged it will be in the format below.
+    # rev = "Release${lib.replaceStrings ["."] ["-"] version}";
+
+    # the repository's .gitattributes file contains the lines "/Tst/
+    # export-ignore" and "/doc/ export-ignore" so some directories are
+    # not included in the tarball downloaded by fetchzip. setting
+    # fetchSubmodules works around this by using fetchgit instead of
+    # fetchzip.
+    fetchSubmodules = true;
   };
 
+  patches = lib.optionals enableDocs [
+    # singular supports building without 4ti2, bertini, normaliz or
+    # topcom just fine, but the docbuilding does not skip manual pages
+    # tagged as depending on those binaries (probably a bug in
+    # doc2tex.pl::HandleLib, since it seems to ignore "-exclude"
+    # argumens). skip them manually.
+    ./disable-docs-for-optional-unpackaged-deps.patch
+  ];
+
   configureFlags = [
     "--with-ntl=${ntl}"
-  ] ++ lib.optionals enableFactory [
+    "--disable-pyobject-module"
-    "--enable-factory"
+  ] ++ lib.optionals enableDocs [
+    "--enable-doc-build"
   ] ++ lib.optionals enableGfanlib [
     "--enable-gfanlib"
   ];
 
-  postUnpack = ''
+  prePatch = ''
+    # don't let the tests depend on `hostname`
+    substituteInPlace Tst/regress.cmd --replace 'mysystem_catch("hostname")' 'nix_test_runner'
+
     patchShebangs .
+  '' + lib.optionalString enableDocs ''
+    # work around encoding problem
+    sed -i -e 's/\xb7/@cdot{}/g' doc/decodegb.doc
   '';
 
-  patches = [
-    # NTL error handler was introduced in the library part, preventing users of
-    # the library from implementing their own error handling
-    # https://www.singular.uni-kl.de/forum/viewtopic.php?t=2769
-    (fetchpatch {
-      name = "move_error_handler_out_of_libsingular.patch";
-      # rebased version of https://github.com/Singular/Sources/commit/502cf86d0bb2a96715be6764774b64a69c1ca34c.patch
-      url = "https://git.sagemath.org/sage.git/plain/build/pkgs/singular/patches/singular-ntl-error-handler.patch?h=50b9ae2fd233c30860e1cbb3e63a26f2cc10560a";
-      sha256 = "0vgh4m9zn1kjl0br68n04j4nmn5i1igfn28cph0chnwf7dvr9194";
-    })
-  ];
-
   # For reference (last checked on commit 75f460d):
-  # https://github.com/Singular/Sources/blob/spielwiese/doc/Building-Singular-from-source.md
+  # https://github.com/Singular/Singular/blob/spielwiese/doc/Building-Singular-from-source.md
-  # https://github.com/Singular/Sources/blob/spielwiese/doc/external-packages-dynamic-modules.md
+  # https://github.com/Singular/Singular/blob/spielwiese/doc/external-packages-dynamic-modules.md
   buildInputs = [
     # necessary
     gmp
@@ -60,6 +87,8 @@ stdenv.mkDerivation rec {
     readline
     ntl
     flint
+    lrcalc
+    gfan
   ] ++ lib.optionals enableGfanlib [
     cddlib
   ];
@@ -67,7 +96,13 @@ stdenv.mkDerivation rec {
     bison
     perl
     pkg-config
-    autoreconfHook
+    autoreconfHook269
+    sharutils # needed for regress.cmd install checks
+  ] ++ lib.optionals enableDocs [
+    doxygen
+    graphviz
+    texinfo4
+    texlive.combined.scheme-small
   ];
 
   preAutoreconf = ''
@@ -85,23 +120,62 @@ stdenv.mkDerivation rec {
     # do nothing
   '';
 
+  doCheck = true; # very basic checks, does not test any libraries
+
   installPhase = ''
     mkdir -p "$out"
     cp -r Singular/LIB "$out/lib"
     make install
-
+  '' + lib.optionalString enableDocs ''
+    # Sage uses singular.hlp (which is not in the tarball)
+    mkdir -p $out/share/info
+    cp doc/singular.hlp $out/share/info
+  '' + ''
     # Make sure patchelf picks up the right libraries
     rm -rf libpolys factory resources omalloc Singular
   '';
 
+  # singular tests are a bit complicated, see
+  # https://github.com/Singular/Singular/tree/spielwiese/Tst
+  # https://www.singular.uni-kl.de/forum/viewtopic.php&t=2773
+  testsToRun = [
+    "Old/universal.lst"
+    "Buch/buch.lst"
+    "Plural/short.lst"
+    "Old/factor.tst"
+  ] ++ lib.optionals enableGfanlib [
+    # tests that require gfanlib
+    "Short/ok_s.lst"
+  ];
+
   # simple test to make sure singular starts and finds its libraries
   doInstallCheck = true;
   installCheckPhase = ''
+    # Very basic sanity check to make sure singular starts and finds its libraries.
+    # This is redundant with the below tests. It is only kept because the singular test
+    # runner is a bit complicated. In case we decide to give up those tests in the future,
+    # this will still be useful. It takes barely any time.
     "$out/bin/Singular" -c 'LIB "freegb.lib"; exit;'
     if [ $? -ne 0 ]; then
         echo >&2 "Error loading the freegb library in Singular."
         exit 1
     fi
+
+    # Run the test suite
+    cd Tst
+    perl ./regress.cmd \
+      -s "$out/bin/Singular" \
+      ${lib.concatStringsSep " " (map lib.escapeShellArg testsToRun)} \
+      2>"$TMPDIR/out-err.log"
+
+    # unfortunately regress.cmd always returns exit code 0, so check stderr
+    # https://www.singular.uni-kl.de/forum/viewtopic.php&t=2773
+    if [[ -s "$TMPDIR/out-err.log" ]]; then
+      cat "$TMPDIR/out-err.log"
+      exit 1
+    fi
+
+    echo "Exit status $?"
   '';
 
   enableParallelBuilding = true;
@@ -110,6 +184,7 @@ stdenv.mkDerivation rec {
     description = "A CAS for polynomial computations";
     maintainers = teams.sage.members;
     # 32 bit x86 fails with some link error: `undefined reference to `__divmoddi4@GCC_7.0.0'`
+    # https://www.singular.uni-kl.de:8002/trac/ticket/837
     platforms = subtractLists platforms.i686 platforms.unix;
     license = licenses.gpl3; # Or GPLv2 at your option - but not GPLv4
     homepage = "http://www.singular.uni-kl.de";

pkgs/applications/science/math/singular/disable-docs-for-optional-unpackaged-deps.patch

@@ -0,0 +1,112 @@
+commit 9e8b044d982e132cf35a106a1cc0cf7e77b27f7c
+Author: Mauricio Collares <mauricio@collares.org>
+Date:   Thu Apr 15 20:33:21 2021 -0300
+
+    Disable manual sections using optional packages not yet in Nixpkgs
+
+        * normaliz.lib depends on normaliz.
+        * polymake.lib depends on topcom.
+        * recover.lib depends on bertini.
+        * sing4ti2.lib depends on 4ti2.
+        * tateProdCplxNegGrad.lib uses multigrading.lib, which depends on 4ti2.
+
+diff --git a/doc/singular.doc b/doc/singular.doc
+index 64b969d39..e704f95f0 100644
+--- a/doc/singular.doc
++++ b/doc/singular.doc
+@@ -407,7 +407,6 @@ LIB "all.lib";
+ * nfmodsyz_lib:: Syzygy modules of submodules of free modules over algebraic number fields
+ * noether_lib:: Noether normalization of an ideal
+ * normal_lib:: procedure for normalization
+-* normaliz_lib:: integral closure, normalization for monomial ideals, toric ideals
+ * pointid_lib:: factorized lex GB of the vanishing ideal of a set of points
+ * primdec_lib:: procedures for primary decomposition
+ * primdecint_lib:: primary decomposition over the integers
+@@ -416,7 +415,6 @@ LIB "all.lib";
+ * reesclos_lib:: Rees Algebra and integral closure of an ideal
+ * rstandard_lib:: Janet bases and border bases for ideals
+ * sagbi_lib:: Subalgebras bases Analogous to Groebner bases for ideals
+-* sing4ti2_lib:: interface to program 4ti2
+ * symodstd_lib:: Groebner bases for symmetric ideals
+ * toric_lib:: toric ideals
+ @end menu
+@@ -521,10 +519,6 @@ LIB "all.lib";
+ @node normal_lib
+ @subsection normal_lib
+ @c lib normal.lib
+-@c ---------------------------------------------------------
+-@node normaliz_lib
+-@subsection normaliz_lib
+-@c lib normaliz.lib tag:normaliz
+ @c ----------------------------------------------------------
+ @node pointid_lib
+ @subsection pointid_lib
+@@ -558,10 +552,6 @@ LIB "all.lib";
+ @subsection sagbi_lib
+ @c lib sagbi.lib
+ @c ---------------------------------------------------------
+-@node sing4ti2_lib
+-@subsection sing4ti2_lib
+-@c lib sing4ti2.lib tag:sing4ti2
+-@c ----------------------------------------------------------
+ @node symodstd_lib
+ @subsection symodstd_lib
+ @c lib symodstd.lib
+@@ -873,7 +863,6 @@ iniD, reslist, sumlist, dividelist, createlist
+ * solve_lib:: procedures to solve polynomial systems
+ * triang_lib:: procedures for decomposing zero-dimensional ideals
+ * ntsolve_lib:: one real solution of polynomial systems (Newton iteration)
+-* recover_lib:: Hybrid numerical/symbolical algorithms
+ * rootisolation_lib:: real root isolation with intervals
+ * signcond_lib:: computing realizable sign conditions
+ * zeroset_lib:: procedures for roots and factorization
+@@ -904,10 +893,6 @@ iniD, reslist, sumlist, dividelist, createlist
+ @subsection ntsolve_lib
+ @c lib ntsolve.lib
+ @c ---------------------------------------------------------
+-@node recover_lib
+-@subsection recover_lib
+-@c lib recover.lib tag:bertini
+-@c ----------------------------------------------------------
+ @node rootisolation_lib
+ @subsection rootisolation_lib
+ @c lib rootisolation.lib
+@@ -1108,7 +1093,6 @@ but not for serious computations.
+ * cimonom_lib:: complete intersection for toric ideals
+ * gfan_lib:: A gfanlib interface for Singular
+ * gitfan_lib:: Compute GIT-fans
+-* polymake_lib:: interface to TOPCOM
+ * realizationMatroids_lib:: Realizability for Tropical Fan Curves
+ * tropical_lib:: interface to gfan
+ * tropicalNewton_lib:: Newton polygons in tropical geometry
+@@ -1125,10 +1109,7 @@ but not for serious computations.
+ @node gitfan_lib
+ @subsection gitfan_lib
+ @c lib gitfan.lib
+-@c ----------------------------------------------------------
+-@node polymake_lib
+-@subsection polymake_lib
+-@c lib polymake.lib tag:topcom
++
+ @c ----------------------------------------------------------
+ @node realizationMatroids_lib
+ @subsection realizationMatroids_lib
+@@ -1219,7 +1200,6 @@ Comments should be send to the author of the library directly.
+ * stanleyreisner_lib:: T1 and T2 for a general Stanley-Reiser ring
+ * swalk_lib:: Sagbi Walk Conversion Algorithm
+ * systhreads_lib:: multi-threaded objects
+-* tateProdCplxNegGrad_lib:: sheaf cohomology on product of projective spaces
+ * VecField_lib:: vector fields
+ @end menu
+ @c ----------------------------------------------------------
+@@ -1310,10 +1290,6 @@ Todos/Issues:
+ @subsection systhreads_lib
+ @c lib systhreads.lib
+ @c ---------------------------------------------------------
+-@node tateProdCplxNegGrad_lib
+-@subsection tateProdCplxNegGrad_lib
+-@c lib tateProdCplxNegGrad.lib
+-@c ---------------------------------------------------------
+ @node VecField_lib
+ @subsection VecField_lib
+ @c lib VecField.lib