NixOS · Nov 24, 2018 · Nov 24, 2018 · Nov 24, 2018 · Nov 24, 2018 · Nov 24, 2018
diff --git a/pkgs/applications/science/math/sage/README.md b/pkgs/applications/science/math/sage/README.md
@@ -2,46 +2,7 @@
 
 Sage is a pretty complex package that depends on many other complex packages and patches some of those. As a result, the sage nix package is also quite complex.
 
-Don't feel discouraged to fix, simplify or improve things though. Here's a quick overview over the functions of the individual files:
-
-- `sage-src.nix`  
-  Downloads the source code and applies patches. This makes sure that all the other files work with the same sage source. If you want to apply a patch to sage or update sage to a new version, this is the place to do it.
-
-- `env-locations.nix`  
-  Creates a bash file that sets a bunch of environment variables telling sage where to find various packages and files. The definitions of those environment variables can be found in the sage source in the `src/env.py` file. This bash file needs to be sourced before sage is started (done in `sage-env.nix` and `sagedoc.nix`).
-
-- `sage-env.nix`  
-  Sets all environment variables sage needs to run. This includes the package locations defined in `env-locations.nix` as well as the location of sage itself and its various subdirectories.
-
-- `sagelib.nix`  
-  Defines the main sage package (without setting the necessary environments or running any tests).
-
-- `sage-with-env.nix`  
-  Wraps sage in the necessary environment.
-
-- `sage.nix`  
-  Runs sages doctests.
-
-- `sage-wrapper.nix`  
-  Optionally tells sage where do find the docs.
-
-- `sagedoc.nix`  
-  Builds and tests the sage html documentation. Can be used for offline documentation viewing as well as the sage `browse_sage_doc` and `search_doc` functions.
-
-- `sagenb.nix`  
-  The (semi deprecated) sage notebook.
-
-- `default.nix`  
-  Introduces necessary overrides, defines new packages and ties everything together (returning the `sage` package).
-
-- `flask-oldsessions.nix`, `flask-openid.nix`, `python-openid.nix`
-  These are python packages that were rejected from the main nixpkgs tree because they appear unmaintained. They are needed for the (semi-deprecated) sage notebook. Since that notebook is still needed to run the sage doctests, these packages are included but not exposed to the rest of nixpkgs.
-
-- `pybrial.nix`  
-  pybrial is a dependency of sage. However, pybrial itself also has sage as a dependency. Because of that circular dependency, pybrial is hidden from the rest of nixpkgs (just as the flask packages and python-openid.
-
-- `openblas-pc.nix`  
-  This creates a `.pc` file to be read by `pkg-config` that allows openblas to take on different roles, like `cblas` or `lapack`.
+Don't feel discouraged to fix, simplify or improve things though. The individual files have comments explaining their purpose. The most importent ones are `default.nix` linking everything together, `sage-src.nix` adding patches and `sagelib.nix` building the actual sage package.
 
 ## The sage build is broken
 

diff --git a/pkgs/applications/science/math/sage/default.nix b/pkgs/applications/science/math/sage/default.nix
@@ -1,68 +1,85 @@
-{ nixpkgs
+{ pkgs
 , withDoc ? false
 }:
 
+# Here sage and its dependencies are put together. Some dependencies may be pinned
+# as a last resort. Patching sage for compatibility with newer dependency versions
+# is always preferred, see `sage-src.nix` for that.
+
 let
-  inherit (nixpkgs) fetchpatch fetchurl symlinkJoin callPackage nodePackages;
+  inherit (pkgs) fetchurl symlinkJoin callPackage nodePackages;
 
   # https://trac.sagemath.org/ticket/15980 for tracking of python3 support
-  python = nixpkgs.python2.override {
+  python = pkgs.python2.override {
     packageOverrides = self: super: {
       # python packages that appear unmaintained and were not accepted into the nixpkgs
       # tree because of that. These packages are only dependencies of the more-or-less
       # deprecated sagenb. However sagenb is still a default dependency and the doctests
       # depend on it.
       # See https://github.com/NixOS/nixpkgs/pull/38787 for a discussion.
+      # The dependency on the sage notebook (and therefore these packages) will be
+      # removed in the future:
+      # https://trac.sagemath.org/ticket/25837
       flask-oldsessions = self.callPackage ./flask-oldsessions.nix {};
       flask-openid = self.callPackage ./flask-openid.nix {};
       python-openid = self.callPackage ./python-openid.nix {};
-
-      pybrial = self.callPackage ./pybrial.nix {};
-
-      sagelib = self.callPackage ./sagelib.nix {
-        inherit flint ecl arb;
-        inherit sage-src openblas-blas-pc openblas-cblas-pc openblas-lapack-pc pynac singular;
-        linbox = nixpkgs.linbox.override { withSage = true; };
-      };
-
       sagenb = self.callPackage ./sagenb.nix {
         mathjax = nodePackages.mathjax;
       };
 
-      sagedoc = self.callPackage ./sagedoc.nix {
-        inherit sage-src;
-      };
+      # Package with a cyclic dependency with sage
+      pybrial = self.callPackage ./pybrial.nix {};
 
-      env-locations = self.callPackage ./env-locations.nix {
-        inherit pari_data ecl;
-        inherit singular;
-        three = nodePackages.three;
-        mathjax = nodePackages.mathjax;
+      # `sagelib`, i.e. all of sage except some wrappers and runtime dependencies
+      sagelib = self.callPackage ./sagelib.nix {
+        inherit flint ecl arb;
+        inherit sage-src pynac singular;
+        linbox = pkgs.linbox.override { withSage = true; };
       };
+    };
+  };
 
-      sage-env = self.callPackage ./sage-env.nix {
-        inherit sage-src python rWrapper openblas-cblas-pc ecl singular palp flint pynac pythonEnv;
-        pkg-config = nixpkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig
-      };
+  # A bash script setting various environment variables to tell sage where
+  # the files its looking fore are located. Also see `sage-env`.
+  env-locations = callPackage ./env-locations.nix {
+    inherit pari_data ecl;
+    inherit singular;
+    cysignals = python.pkgs.cysignals;
+    three = nodePackages.three;
+    mathjax = nodePackages.mathjax;
+  };
 
-      sage-with-env = self.callPackage ./sage-with-env.nix {
-        inherit pythonEnv;
-        inherit sage-src openblas-blas-pc openblas-cblas-pc openblas-lapack-pc pynac singular;
-        pkg-config = nixpkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig
-        three = nodePackages.three;
-      };
+  # The shell file that gets sourced on every sage start. Will also source
+  # the env-locations file.
+  sage-env = callPackage ./sage-env.nix {
+    sagelib = python.pkgs.sagelib;
+    inherit env-locations;
+    inherit python rWrapper ecl singular palp flint pynac pythonEnv;
+    pkg-config = pkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig
+  };
 
-      sage = self.callPackage ./sage.nix { };
+  # The documentation for sage, building it takes a lot of ram.
+  sagedoc = callPackage ./sagedoc.nix {
+    inherit sage-with-env;
+    inherit python;
+  };
 
-      sage-wrapper = self.callPackage ./sage-wrapper.nix {
-        inherit sage-src withDoc;
-      };
-    };
+  # sagelib with added wrappers and a dependency on sage-tests to make sure thet tests were run.
+  sage-with-env = callPackage ./sage-with-env.nix {
+    inherit pythonEnv;
+    inherit sage-env;
+    inherit pynac singular;
+    pkg-config = pkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig
+    three = nodePackages.three;
   };
 
-  openblas-blas-pc = callPackage ./openblas-pc.nix { name = "blas"; };
-  openblas-cblas-pc = callPackage ./openblas-pc.nix { name = "cblas"; };
-  openblas-lapack-pc = callPackage ./openblas-pc.nix { name = "lapack"; };
+  # Doesn't actually build anything, just runs sages testsuite. This is a
+  # separate derivation to make it possible to re-run the tests without
+  # rebuilding sagelib (which takes ~30 minutes).
+  # Running the tests should take something in the order of 1h.
+  sage-tests = callPackage ./sage-tests.nix {
+    inherit sage-with-env;
+  };
 
   sage-src = callPackage ./sage-src.nix {};
 
@@ -91,9 +108,9 @@ let
   } // { extraLibs = pythonRuntimeDeps; }; # make the libs accessible
 
   # needs to be rWrapper, standard "R" doesn't include default packages
-  rWrapper = nixpkgs.rWrapper.override {
+  rWrapper = pkgs.rWrapper.override {
     # https://trac.sagemath.org/ticket/25674
-    R = nixpkgs.R.overrideAttrs (attrs: rec {
+    R = pkgs.R.overrideAttrs (attrs: rec {
       name = "R-3.4.4";
       src = fetchurl {
         url = "http://cran.r-project.org/src/base/R-3/${name}.tar.gz";
@@ -102,44 +119,45 @@ let
     });
   };
 
-  arb = nixpkgs.arb.override { inherit flint; };
+  arb = pkgs.arb.override { inherit flint; };
 
-  singular = nixpkgs.singular.override { inherit flint; };
+  singular = pkgs.singular.override { inherit flint; };
 
   # *not* to confuse with the python package "pynac"
-  pynac = nixpkgs.pynac.override { inherit singular flint; };
+  pynac = pkgs.pynac.override { inherit singular flint; };
 
   # With openblas (64 bit), the tests fail the same way as when sage is build with
   # openblas instead of openblasCompat. Apparently other packages somehow use flints
   # blas when it is available. Alternative would be to override flint to use
   # openblasCompat.
-  flint = nixpkgs.flint.override { withBlas = false; };
+  flint = pkgs.flint.override { withBlas = false; };
 
   # Multiple palp dimensions need to be available and sage expects them all to be
   # in the same folder.
   palp = symlinkJoin {
-    name = "palp-${nixpkgs.palp.version}";
+    name = "palp-${pkgs.palp.version}";
     paths = [
-      (nixpkgs.palp.override { dimensions = 4; doSymlink = false; })
-      (nixpkgs.palp.override { dimensions = 5; doSymlink = false; })
-      (nixpkgs.palp.override { dimensions = 6; doSymlink = true; })
-      (nixpkgs.palp.override { dimensions = 11; doSymlink = false; })
+      (pkgs.palp.override { dimensions = 4; doSymlink = false; })
+      (pkgs.palp.override { dimensions = 5; doSymlink = false; })
+      (pkgs.palp.override { dimensions = 6; doSymlink = true; })
+      (pkgs.palp.override { dimensions = 11; doSymlink = false; })
     ];
   };
 
   # Sage expects those in the same directory.
   pari_data = symlinkJoin {
     name = "pari_data";
-    paths = with nixpkgs; [
+    paths = with pkgs; [
       pari-galdata
       pari-seadata-small
     ];
   };
 
   # https://trac.sagemath.org/ticket/22191
-  ecl = nixpkgs.ecl_16_1_2;
+  ecl = pkgs.ecl_16_1_2;
 in
-  python.pkgs.sage-wrapper // {
-    doc = python.pkgs.sagedoc;
-    lib = python.pkgs.sagelib;
-  }
+# A wrapper around sage that makes sure sage finds its docs (if they were build).
+callPackage ./sage.nix {
+  inherit sage-tests sage-with-env sagedoc;
+  inherit withDoc;
+}
diff --git a/pkgs/applications/science/math/sage/env-locations.nix b/pkgs/applications/science/math/sage/env-locations.nix
@@ -16,6 +16,8 @@
 , cysignals
 }:
 
+# A bash script setting various environment variables to tell sage where
+# the files its looking fore are located. Also see `sage-env`.
 writeTextFile rec {
   name = "sage-env-locations";
   destination = "/${name}";

diff --git a/pkgs/applications/science/math/sage/openblas-pc.nix b/pkgs/applications/science/math/sage/openblas-pc.nix
diff --git a/pkgs/applications/science/math/sage/patches/eclib-20180710.patch b/pkgs/applications/science/math/sage/patches/eclib-20180710.patch
diff --git a/pkgs/applications/science/math/sage/patches/eclib-regulator-precision.patch b/pkgs/applications/science/math/sage/patches/eclib-regulator-precision.patch