From 712fba51916fe5bcc99aa80bfa82c25490a7926a Mon Sep 17 00:00:00 2001 From: Florian Klink Date: Wed, 19 Feb 2020 15:38:11 +0100 Subject: [PATCH 1/3] python.pkgs.scikits-odes: 2.4.0-9-g93075ae -> 2.6.1 --- .../python-modules/scikits-odes/default.nix | 13 +++++-------- 1 file changed, 5 insertions(+), 8 deletions(-) diff --git a/pkgs/development/python-modules/scikits-odes/default.nix b/pkgs/development/python-modules/scikits-odes/default.nix index 89ffe334e7ff..32809be7bde9 100644 --- a/pkgs/development/python-modules/scikits-odes/default.nix +++ b/pkgs/development/python-modules/scikits-odes/default.nix @@ -1,7 +1,7 @@ { stdenv , lib , buildPythonPackage -, fetchFromGitHub +, fetchPypi , fetchurl , cython , enum34 @@ -16,14 +16,11 @@ buildPythonPackage rec { pname = "scikits.odes"; - version = "2.4.0-9-g93075ae"; + version = "2.6.1"; - # 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"; + src = fetchPypi { + inherit pname version; + sha256 = "0kbf2n16h9s35x6pavlx6sff0pqr68i0x0609z92a4vadni32n6b"; }; nativeBuildInputs = [ From 10f9b277d596e7fb9558d3a603db2ebcad685acc Mon Sep 17 00:00:00 2001 From: Florian Klink Date: Wed, 19 Feb 2020 15:29:38 +0100 Subject: [PATCH 2/3] python.pkgs.scikits-odes: use latest sundials --- pkgs/development/python-modules/scikits-odes/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/development/python-modules/scikits-odes/default.nix b/pkgs/development/python-modules/scikits-odes/default.nix index 32809be7bde9..ba3d5eaaff0e 100644 --- a/pkgs/development/python-modules/scikits-odes/default.nix +++ b/pkgs/development/python-modules/scikits-odes/default.nix @@ -11,7 +11,7 @@ , pytest , python , scipy -, sundials_3 +, sundials }: buildPythonPackage rec { @@ -30,7 +30,7 @@ buildPythonPackage rec { propagatedBuildInputs = [ numpy - sundials_3 + sundials scipy ] ++ lib.optionals (!isPy3k) [ enum34 ]; From fb17ac37863ebd9733a0642d9205952d2fb271e0 Mon Sep 17 00:00:00 2001 From: Florian Klink Date: Wed, 19 Feb 2020 15:32:06 +0100 Subject: [PATCH 3/3] sundials_3: remove This package has only been used for python.pkgs.scikits-odes, which should compile with sundials 5 by now. --- pkgs/development/libraries/sundials/3.x.nix | 52 --------------------- pkgs/top-level/aliases.nix | 1 + pkgs/top-level/all-packages.nix | 4 +- 3 files changed, 2 insertions(+), 55 deletions(-) delete mode 100644 pkgs/development/libraries/sundials/3.x.nix diff --git a/pkgs/development/libraries/sundials/3.x.nix b/pkgs/development/libraries/sundials/3.x.nix deleted file mode 100644 index 879f13e8bf53..000000000000 --- a/pkgs/development/libraries/sundials/3.x.nix +++ /dev/null @@ -1,52 +0,0 @@ -{ 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; - }; -} diff --git a/pkgs/top-level/aliases.nix b/pkgs/top-level/aliases.nix index dabbfcd6d49b..42478f38b84d 100644 --- a/pkgs/top-level/aliases.nix +++ b/pkgs/top-level/aliases.nix @@ -423,6 +423,7 @@ mapAliases ({ smbclient = samba; # added 2018-04-25 slim = throw "slim has been removed. Please use a different display-manager"; # added 2019-11-11 slimThemes = throw "slimThemes has been removed because slim has been also"; # added 2019-11-11 + sundials_3 = throw "removed 2020-02. outdated and no longer needed"; net_snmp = net-snmp; # added 2019-12-21 spaceOrbit = space-orbit; # addewd 2016-05-23 speech_tools = speech-tools; # added 2018-04-25 diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index 8accbf10b664..34604e53a43d 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -14398,8 +14398,6 @@ 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 { }; @@ -15414,7 +15412,7 @@ in miniHttpd = callPackage ../servers/http/mini-httpd {}; mlflow-server = callPackage ../servers/mlflow-server { }; - + mlmmj = callPackage ../servers/mail/mlmmj { }; moodle = callPackage ../servers/web-apps/moodle { };