Merge pull request #64195 from flokli/scikits-odes

scikits-odes: init at 2.4.0

pkgs/development/libraries/sundials/3.x.nix

@@ -0,0 +1,52 @@
+{ stdenv
+, cmake
+, fetchurl
+, python
+, liblapack
+, gfortran
+, lapackSupport ? true }:
+
+let liblapackShared = liblapack.override {
+  shared = true;
+};
+
+in stdenv.mkDerivation rec {
+  pname = "sundials";
+  version = "3.2.1";
+
+  buildInputs = [ python ] ++ stdenv.lib.optionals (lapackSupport) [ gfortran ];
+  nativeBuildInputs = [ cmake ];
+
+  src = fetchurl {
+    url = "https://computation.llnl.gov/projects/${pname}/download/${pname}-${version}.tar.gz";
+    sha256 = "0238r1qnwqz13wcjzfsbcfi8rfnlxcjjmxq2vpf2qf5jgablvna7";
+  };
+
+  patches = [
+    (fetchurl {
+      # https://github.com/LLNL/sundials/pull/19
+      url = "https://github.com/LLNL/sundials/commit/1350421eab6c5ab479de5eccf6af2dcad1eddf30.patch";
+      sha256 = "0g67lixp9m85fqpb9rzz1hl1z8ibdg0ldwq5z6flj5zl8a7cw52l";
+    })
+  ];
+
+  cmakeFlags = [
+    "-DEXAMPLES_INSTALL_PATH=${placeholder "out"}/share/examples"
+  ] ++ stdenv.lib.optionals (lapackSupport) [
+    "-DSUNDIALS_INDEX_TYPE=int32_t"
+    "-DLAPACK_ENABLE=ON"
+    "-DLAPACK_LIBRARIES=${liblapackShared}/lib/liblapack${stdenv.hostPlatform.extensions.sharedLibrary};${liblapackShared}/lib/libblas${stdenv.hostPlatform.extensions.sharedLibrary}"
+  ];
+
+  # flaky tests, and patch in https://github.com/LLNL/sundials/pull/21 doesn't apply cleanly for sundials_3
+  doCheck = false;
+  checkPhase = "make test";
+
+  meta = with stdenv.lib; {
+    description = "Suite of nonlinear differential/algebraic equation solvers";
+    homepage    = https://computation.llnl.gov/projects/sundials;
+    platforms   = platforms.all;
+    maintainers = with maintainers; [ flokli idontgetoutmuch ];
+    license     = licenses.bsd3;
+  };
+}

pkgs/development/libraries/sundials/default.nix

@@ -1,28 +1,58 @@
-{ cmake, fetchurl, python, stdenv }:
+{ stdenv
+, cmake
+, fetchurl
+, python
+, liblapack
+, gfortran
+, lapackSupport ? true }:
 
-stdenv.mkDerivation rec {
+let liblapackShared = liblapack.override {
+  shared = true;
+};
 
+in stdenv.mkDerivation rec {
   pname = "sundials";
   version = "4.1.0";
 
+  buildInputs = [ python ] ++ stdenv.lib.optionals (lapackSupport) [ gfortran ];
+  nativeBuildInputs = [ cmake ];
+
   src = fetchurl {
     url = "https://computation.llnl.gov/projects/${pname}/download/${pname}-${version}.tar.gz";
     sha256 = "19ca4nmlf6i9ijqcibyvpprxzsdfnackgjs6dw51fq13gg1f2398";
   };
 
-  preConfigure = ''
+  patches = [
-    export cmakeFlags="-DCMAKE_INSTALL_PREFIX=$out -DEXAMPLES_INSTALL_PATH=$out/share/examples $cmakeFlags"
+    (fetchurl {
-  '';
+      # https://github.com/LLNL/sundials/pull/19
+      url = "https://github.com/LLNL/sundials/commit/1350421eab6c5ab479de5eccf6af2dcad1eddf30.patch";
+      sha256 = "0g67lixp9m85fqpb9rzz1hl1z8ibdg0ldwq5z6flj5zl8a7cw52l";
+    })
+    (fetchurl {
+      # https://github.com/LLNL/sundials/pull/20
+      url = "https://github.com/LLNL/sundials/pull/20/commits/2d951bbe1ff7842fcd0dafa28c61b0aa94015f66.patch";
+      sha256 = "0lcr6m4lk14yqrxah4rdscpczny5l7m1zpfsjh8bgspadfsgk512";
+    })
+    # https://github.com/LLNL/sundials/pull/21
+    ./tests-parallel.patch
+  ];
 
-  nativeBuildInputs = [ cmake ];
+  cmakeFlags = [
-  buildInputs = [ python ];
+    "-DEXAMPLES_INSTALL_PATH=${placeholder "out"}/share/examples"
+  ] ++ stdenv.lib.optionals (lapackSupport) [
+    "-DSUNDIALS_INDEX_TYPE=int32_t"
+    "-DLAPACK_ENABLE=ON"
+    "-DLAPACK_LIBRARIES=${liblapackShared}/lib/liblapack${stdenv.hostPlatform.extensions.sharedLibrary};${liblapackShared}/lib/libblas${stdenv.hostPlatform.extensions.sharedLibrary}"
+  ];
+
+  doCheck = true;
+  checkPhase = "make test";
 
   meta = with stdenv.lib; {
     description = "Suite of nonlinear differential/algebraic equation solvers";
     homepage    = https://computation.llnl.gov/projects/sundials;
     platforms   = platforms.all;
-    maintainers = [ maintainers.idontgetoutmuch ];
+    maintainers = with maintainers; [ flokli idontgetoutmuch ];
     license     = licenses.bsd3;
   };
-
 }

pkgs/development/libraries/sundials/tests-parallel.patch

@@ -0,0 +1,45 @@
+diff --git a/config/SundialsAddTest.cmake b/config/SundialsAddTest.cmake
+index e965fed..a7fb1d2 100644
+--- a/config/SundialsAddTest.cmake
++++ b/config/SundialsAddTest.cmake
+@@ -70,7 +70,7 @@ MACRO(SUNDIALS_ADD_TEST NAME EXECUTABLE)
+         "--verbose"
+         "--testname=${NAME}"
+         "--executablename=$<TARGET_FILE:${EXECUTABLE}>"
+-        "--outputdir=${CMAKE_BINARY_DIR}/Testing/output"
++        "--outputdir=${TEST_OUTPUT_DIR}"
+         )
+ 
+       # do not diff the output and answer files
+diff --git a/config/SundialsTesting.cmake b/config/SundialsTesting.cmake
+index 815576a..d91801a 100644
+--- a/config/SundialsTesting.cmake
++++ b/config/SundialsTesting.cmake
+@@ -29,6 +29,13 @@ IF(SUNDIALS_DEVTESTS)
+     ENDIF()
+   ENDIF()
+ 
++  # Directory for test output
++  SET(TEST_OUTPUT_DIR ${PROJECT_BINARY_DIR}/Testing/output)
++
++  IF(NOT EXISTS ${TEST_OUTPUT_DIR})
++    FILE(MAKE_DIRECTORY ${TEST_OUTPUT_DIR})
++  ENDIF()
++
+   # look for the testRunner script in the test directory
+   FIND_PROGRAM(TESTRUNNER testRunner PATHS test)
+   HIDE_VARIABLE(TESTRUNNER)
+diff --git a/test/testRunner b/test/testRunner
+index f450ec2..f1c8deb 100755
+--- a/test/testRunner
++++ b/test/testRunner
+@@ -106,7 +106,8 @@ def main():
+ 
+     # create output directory if necessary
+     if not os.path.exists(outDir):
+-        os.makedirs(outDir)
++        error("Output directory does not exist, it must be created.", outDir)
++        sys.exit(1)
+     elif not os.path.isdir(outDir):
+         error("Output directory exists but is not a directory, it must be deleted.", outDir)
+         sys.exit(1)

pkgs/development/python-modules/scikits-odes/default.nix

@@ -0,0 +1,55 @@
+{ stdenv
+, lib
+, buildPythonPackage
+, fetchFromGitHub
+, fetchurl
+, cython
+, enum34
+, gfortran
+, isPy3k
+, numpy
+, pytest
+, python
+, scipy
+, sundials_3
+}:
+
+buildPythonPackage rec {
+  pname = "scikits.odes";
+  version = "2.4.0-9-g93075ae";
+
+  # we fetch github instead of Pypi, as we want #104 and #105, which don't apply cleanly on 2.4.0
+  src = fetchFromGitHub {
+    owner = "bmcage";
+    repo = "odes";
+    rev = "93075ae25c409f572f13ca7207fada5706f73c73";
+    sha256 = "161rab7hy6r1a9xw1zby9xhnnmxi0zwdpzxfpjkw9651xn2k5xyw";
+  };
+
+  nativeBuildInputs = [
+    gfortran
+    cython
+  ];
+
+  propagatedBuildInputs = [
+    numpy
+    sundials_3
+    scipy
+  ] ++ lib.optionals (!isPy3k) [ enum34 ];
+
+  doCheck = true;
+  checkInputs = [ pytest ];
+
+  checkPhase = ''
+    cd $out/${python.sitePackages}/scikits/odes/tests
+    pytest
+  '';
+
+  meta = with stdenv.lib; {
+    description = "A scikit offering extra ode/dae solvers, as an extension to what is available in scipy";
+    homepage = https://github.com/bmcage/odes;
+    license = licenses.bsd3;
+    maintainers = with maintainers; [ flokli idontgetoutmuch ];
+    platforms = [ "aarch64-linux" "x86_64-linux" "x86_64-darwin" ];
+  };
+}

pkgs/top-level/all-packages.nix

@@ -13746,6 +13746,8 @@ in
 
   sundials = callPackage ../development/libraries/sundials { };
 
+  sundials_3 = callPackage ../development/libraries/sundials/3.x.nix { };
+
   sutils = callPackage ../tools/misc/sutils { };
 
   svrcore = callPackage ../development/libraries/svrcore { };

pkgs/top-level/python-packages.nix

@@ -4846,6 +4846,8 @@ in {
 
   scikit-build = callPackage ../development/python-modules/scikit-build { };
 
+  scikits-odes = callPackage ../development/python-modules/scikits-odes { };
+
   scikit-optimize = callPackage ../development/python-modules/scikit-optimize { };
 
   scikit-tda = callPackage ../development/python-modules/scikit-tda { };