From 2c125cf37ad8ed4d971325bf127745a2768a9872 Mon Sep 17 00:00:00 2001
From: Allen Nelson <anelson@narrativescience.com>
Date: Thu, 28 May 2015 11:56:29 -0500
Subject: [PATCH 1/3] removed default dependency of liblapack on ATLAS. was
 causing an unnecessary double-build of atlas

---
 .../science/math/liblapack/3.5.0.nix          | 49 -------------------
 .../science/math/liblapack/default.nix        | 39 ++++++++++++---
 pkgs/top-level/all-packages.nix               |  5 +-
 3 files changed, 36 insertions(+), 57 deletions(-)
 delete mode 100644 pkgs/development/libraries/science/math/liblapack/3.5.0.nix

diff --git a/pkgs/development/libraries/science/math/liblapack/3.5.0.nix b/pkgs/development/libraries/science/math/liblapack/3.5.0.nix
deleted file mode 100644
index 0b4badf26e7..00000000000
--- a/pkgs/development/libraries/science/math/liblapack/3.5.0.nix
+++ /dev/null
@@ -1,49 +0,0 @@
-{ stdenv, fetchurl, gfortran, atlas, cmake, python, shared ? false }:
-let
-  atlasMaybeShared = atlas.override { inherit shared; };
-  usedLibExtension = if shared then ".so" else ".a";
-in
-stdenv.mkDerivation rec {
-  version = "3.5.0";
-  name = "liblapack-${version}";
-  src = fetchurl {
-    url = "http://www.netlib.org/lapack/lapack-${version}.tgz";
-    sha256 = "0lk3f97i9imqascnlf6wr5mjpyxqcdj73pgj97dj2mgvyg9z1n4s";
-  };
-
-  propagatedBuildInputs = [ atlasMaybeShared ];
-  buildInputs = [ gfortran cmake ];
-  nativeBuildInputs = [ python ];
-
-  cmakeFlags = [
-    "-DUSE_OPTIMIZED_BLAS=ON"
-    "-DBLAS_ATLAS_f77blas_LIBRARY=${atlasMaybeShared}/lib/libf77blas${usedLibExtension}"
-    "-DBLAS_ATLAS_atlas_LIBRARY=${atlasMaybeShared}/lib/libatlas${usedLibExtension}"
-    "-DCMAKE_Fortran_FLAGS=-fPIC"
-  ]
-  ++ (stdenv.lib.optional shared "-DBUILD_SHARED_LIBS=ON")
-  ;
-
-  doCheck = ! shared;
-
-  checkPhase = "
-    sed -i 's,^#!.*,#!${python}/bin/python,' lapack_testing.py
-    ctest
-  ";
-
-  enableParallelBuilding = true;
-
-  passthru = {
-    blas = atlas;
-  };
-
-  meta = {
-    inherit version;
-    description = "Linear Algebra PACKage";
-    homepage = "http://www.netlib.org/lapack/";
-    license = "revised-BSD";
-
-    platforms = stdenv.lib.platforms.all;
-    maintainers = [ stdenv.lib.maintainers.simons ];
-  };
-}
diff --git a/pkgs/development/libraries/science/math/liblapack/default.nix b/pkgs/development/libraries/science/math/liblapack/default.nix
index 25667e11264..18aceeba177 100644
--- a/pkgs/development/libraries/science/math/liblapack/default.nix
+++ b/pkgs/development/libraries/science/math/liblapack/default.nix
@@ -1,15 +1,38 @@
-{ stdenv, fetchurl, gfortran, atlas, cmake, python, shared ? false }:
+{
+  stdenv,
+  fetchurl,
+  gfortran,
+  cmake,
+  python,
+  atlas ? null,
+  shared ? false,
+  version ? "3.4.1"
+}:
 let
-  atlasMaybeShared = atlas.override { inherit shared; };
+  atlasMaybeShared = if atlas != null then atlas.override { inherit shared; }
+                     else null;
   usedLibExtension = if shared then ".so" else ".a";
-  version = "3.4.1";
-  inherit (stdenv.lib) optional;
+  inherit (stdenv.lib) optional optionals concatStringsSep;
+  inherit (builtins) hasAttr attrNames;
+  # Hashes of the versions of liblapack we know about.
+  versions2sha = {
+    "3.4.1" = "93b910f94f6091a2e71b59809c4db4a14655db527cfc5821ade2e8c8ab75380f";
+    "3.5.0" = "0lk3f97i9imqascnlf6wr5mjpyxqcdj73pgj97dj2mgvyg9z1n4s";
+  };
 in
+
+if !(builtins.hasAttr version versions2sha)
+then throw ''
+  Unknown liblapack version ${version}.
+  Available versions: ${concatStringsSep ", " (attrNames versions2sha)}
+''
+else
+
 stdenv.mkDerivation rec {
   name = "liblapack-${version}";
   src = fetchurl {
     url = "http://www.netlib.org/lapack/lapack-${version}.tgz";
-    sha256 = "93b910f94f6091a2e71b59809c4db4a14655db527cfc5821ade2e8c8ab75380f";
+    sha256 = versions2sha."${version}";
   };
 
   propagatedBuildInputs = [ atlasMaybeShared ];
@@ -18,10 +41,12 @@ stdenv.mkDerivation rec {
 
   cmakeFlags = [
     "-DUSE_OPTIMIZED_BLAS=ON"
-    "-DBLAS_ATLAS_f77blas_LIBRARY=${atlasMaybeShared}/lib/libf77blas${usedLibExtension}"
-    "-DBLAS_ATLAS_atlas_LIBRARY=${atlasMaybeShared}/lib/libatlas${usedLibExtension}"
     "-DCMAKE_Fortran_FLAGS=-fPIC"
   ]
+  ++ (optionals (atlas != null) [
+    "-DBLAS_ATLAS_f77blas_LIBRARY=${atlasMaybeShared}/lib/libf77blas${usedLibExtension}"
+    "-DBLAS_ATLAS_atlas_LIBRARY=${atlasMaybeShared}/lib/libatlas${usedLibExtension}"
+  ])
   ++ (optional shared "-DBUILD_SHARED_LIBS=ON")
   # If we're on darwin, CMake will automatically detect impure paths. This switch
   # prevents that.
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 368ec616654..bb3b696e23a 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -13836,7 +13836,10 @@ let
   jags = callPackage ../applications/science/math/jags { };
 
   liblapack = callPackage ../development/libraries/science/math/liblapack { };
-  liblapack_3_5_0 = callPackage ../development/libraries/science/math/liblapack/3.5.0.nix { };
+
+  liblapackWithAtlas = liblapack.override { inherit atlas; };
+
+  liblapack_3_5_0 = liblapack.override { version = "3.5.0"; };
 
   liblbfgs = callPackage ../development/libraries/science/math/liblbfgs { };
 

From e001340cf659eb7f3c97d172710c21b3df35003c Mon Sep 17 00:00:00 2001
From: Allen Nelson <anelson@narrativescience.com>
Date: Thu, 28 May 2015 21:46:09 -0500
Subject: [PATCH 2/3] returned to two-file structure for liblapack

---
 .../science/math/liblapack/3.5.0.nix          | 66 +++++++++++++++++++
 .../science/math/liblapack/default.nix        | 18 +----
 pkgs/top-level/all-packages.nix               |  6 +-
 3 files changed, 73 insertions(+), 17 deletions(-)
 create mode 100644 pkgs/development/libraries/science/math/liblapack/3.5.0.nix

diff --git a/pkgs/development/libraries/science/math/liblapack/3.5.0.nix b/pkgs/development/libraries/science/math/liblapack/3.5.0.nix
new file mode 100644
index 00000000000..510b18a5548
--- /dev/null
+++ b/pkgs/development/libraries/science/math/liblapack/3.5.0.nix
@@ -0,0 +1,66 @@
+{
+  stdenv,
+  fetchurl,
+  gfortran,
+  cmake,
+  python,
+  atlas ? null,
+  shared ? false
+}:
+let
+  atlasMaybeShared = if atlas != null then atlas.override { inherit shared; }
+                     else null;
+  usedLibExtension = if shared then ".so" else ".a";
+  inherit (stdenv.lib) optional optionals concatStringsSep;
+  inherit (builtins) hasAttr attrNames;
+  version = "3.5.0";
+in
+
+stdenv.mkDerivation rec {
+  name = "liblapack-${version}";
+  src = fetchurl {
+    url = "http://www.netlib.org/lapack/lapack-${version}.tgz";
+    sha256 = "0lk3f97i9imqascnlf6wr5mjpyxqcdj73pgj97dj2mgvyg9z1n4s";
+  };
+
+  propagatedBuildInputs = [ atlasMaybeShared ];
+  buildInputs = [ gfortran cmake ];
+  nativeBuildInputs = [ python ];
+
+  cmakeFlags = [
+    "-DUSE_OPTIMIZED_BLAS=ON"
+    "-DCMAKE_Fortran_FLAGS=-fPIC"
+  ]
+  ++ (optionals (atlas != null) [
+    "-DBLAS_ATLAS_f77blas_LIBRARY=${atlasMaybeShared}/lib/libf77blas${usedLibExtension}"
+    "-DBLAS_ATLAS_atlas_LIBRARY=${atlasMaybeShared}/lib/libatlas${usedLibExtension}"
+  ])
+  ++ (optional shared "-DBUILD_SHARED_LIBS=ON")
+  # If we're on darwin, CMake will automatically detect impure paths. This switch
+  # prevents that.
+  ++ (optional stdenv.isDarwin "-DCMAKE_OSX_SYSROOT:PATH=''")
+  ;
+
+  doCheck = ! shared;
+
+  checkPhase = "
+    sed -i 's,^#!.*,#!${python}/bin/python,' lapack_testing.py
+    ctest
+  ";
+
+  enableParallelBuilding = true;
+
+  passthru = {
+    blas = atlas;
+  };
+
+  meta = {
+    inherit version;
+    description = "Linear Algebra PACKage";
+    homepage = "http://www.netlib.org/lapack/";
+    license = "revised-BSD";
+
+    platforms = stdenv.lib.platforms.all;
+    maintainers = [ stdenv.lib.maintainers.simons ];
+  };
+}
diff --git a/pkgs/development/libraries/science/math/liblapack/default.nix b/pkgs/development/libraries/science/math/liblapack/default.nix
index 18aceeba177..0487af4e9f4 100644
--- a/pkgs/development/libraries/science/math/liblapack/default.nix
+++ b/pkgs/development/libraries/science/math/liblapack/default.nix
@@ -5,8 +5,7 @@
   cmake,
   python,
   atlas ? null,
-  shared ? false,
-  version ? "3.4.1"
+  shared ? false
 }:
 let
   atlasMaybeShared = if atlas != null then atlas.override { inherit shared; }
@@ -14,25 +13,14 @@ let
   usedLibExtension = if shared then ".so" else ".a";
   inherit (stdenv.lib) optional optionals concatStringsSep;
   inherit (builtins) hasAttr attrNames;
-  # Hashes of the versions of liblapack we know about.
-  versions2sha = {
-    "3.4.1" = "93b910f94f6091a2e71b59809c4db4a14655db527cfc5821ade2e8c8ab75380f";
-    "3.5.0" = "0lk3f97i9imqascnlf6wr5mjpyxqcdj73pgj97dj2mgvyg9z1n4s";
-  };
+  version = "3.4.1";
 in
 
-if !(builtins.hasAttr version versions2sha)
-then throw ''
-  Unknown liblapack version ${version}.
-  Available versions: ${concatStringsSep ", " (attrNames versions2sha)}
-''
-else
-
 stdenv.mkDerivation rec {
   name = "liblapack-${version}";
   src = fetchurl {
     url = "http://www.netlib.org/lapack/lapack-${version}.tgz";
-    sha256 = versions2sha."${version}";
+    sha256 = "93b910f94f6091a2e71b59809c4db4a14655db527cfc5821ade2e8c8ab75380f";
   };
 
   propagatedBuildInputs = [ atlasMaybeShared ];
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index bb3b696e23a..1da4a9803e5 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -13835,11 +13835,13 @@ let
 
   jags = callPackage ../applications/science/math/jags { };
 
-  liblapack = callPackage ../development/libraries/science/math/liblapack { };
+  liblapack = callPackage ../development/libraries/science/math/liblapack { 
+    atlas = null;
+  };
 
   liblapackWithAtlas = liblapack.override { inherit atlas; };
 
-  liblapack_3_5_0 = liblapack.override { version = "3.5.0"; };
+  liblapack_3_5_0 = callPackage ../development/libraries/science/math/liblapack/3.5.0.nix { };
 
   liblbfgs = callPackage ../development/libraries/science/math/liblbfgs { };
 

From 8a965946cb9f9c8288da985050853aa715a9ca97 Mon Sep 17 00:00:00 2001
From: Allen Nelson <anelson@narrativescience.com>
Date: Fri, 29 May 2015 15:16:12 -0500
Subject: [PATCH 3/3] switched to atlas as a dependency for liblapack by
 default

---
 pkgs/top-level/all-packages.nix | 18 +++++++++++-------
 1 file changed, 11 insertions(+), 7 deletions(-)

diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 1da4a9803e5..cc689f6177d 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -13819,7 +13819,7 @@ let
     # great feature, but it's of limited use with pre-built binaries
     # coming from a central build farm.
     tolerateCpuTimingInaccuracy = true;
-    liblapack = liblapack_3_5_0;
+    liblapack = liblapack_3_5_0WithoutAtlas;
     withLapack = false;
   };
 
@@ -13835,13 +13835,17 @@ let
 
   jags = callPackage ../applications/science/math/jags { };
 
-  liblapack = callPackage ../development/libraries/science/math/liblapack { 
-    atlas = null;
-  };
 
-  liblapackWithAtlas = liblapack.override { inherit atlas; };
-
-  liblapack_3_5_0 = callPackage ../development/libraries/science/math/liblapack/3.5.0.nix { };
+  # We have essentially 4 permutations of liblapack: version 3.4.1 or 3.5.0,
+  # and with or without atlas as a dependency. The default `liblapack` is 3.4.1
+  # with atlas. Atlas, when built with liblapack as a dependency, uses 3.5.0
+  # without atlas. Etc.
+  liblapackWithAtlas = callPackage ../development/libraries/science/math/liblapack {};
+  liblapackWithoutAtlas = liblapackWithAtlas.override { atlas = null; };
+  liblapack_3_5_0WithAtlas = callPackage ../development/libraries/science/math/liblapack/3.5.0.nix {};
+  liblapack_3_5_0WithoutAtlas = liblapack_3_5_0WithAtlas.override { atlas = null; };
+  liblapack = liblapackWithAtlas;
+  liblapack_3_5_0 = liblapack_3_5_0WithAtlas;
 
   liblbfgs = callPackage ../development/libraries/science/math/liblbfgs { };