Merge staging-next into staging

9 files changed, 107 insertions, 105 deletions

diff --git a/pkgs/applications/science/astronomy/stellarium/default.nix b/pkgs/applications/science/astronomy/stellarium/default.nix
index fb7963416167..2480b80316eb 100644
--- a/pkgs/applications/science/astronomy/stellarium/default.nix
+++ b/pkgs/applications/science/astronomy/stellarium/default.nix
@@ -6,13 +6,13 @@
 
 mkDerivation rec {
   name = "stellarium-${version}";
-  version = "0.19.0";
+  version = "0.19.1";
 
   src = fetchFromGitHub {
     owner = "Stellarium";
     repo = "stellarium";
     rev = "v${version}";
-    sha256 = "1x9s9v9ann93nyqd8n8adwhx66xgq5vp0liyzl1h1ji6qk8jla3c";
+    sha256 = "0hf1wv2bb5j7ny2xh29mj9m4hjblhn02zylay8gl85w7xlqs7s5r";
   };
 
   nativeBuildInputs = [ cmake perl ];
diff --git a/pkgs/applications/science/biology/mosdepth/default.nix b/pkgs/applications/science/biology/mosdepth/default.nix
index 3cd83a5cdd27..1bdb31616e4d 100644
--- a/pkgs/applications/science/biology/mosdepth/default.nix
+++ b/pkgs/applications/science/biology/mosdepth/default.nix
@@ -4,26 +4,26 @@ let
   hts-nim = fetchFromGitHub {
     owner = "brentp";
     repo = "hts-nim";
-    rev = "v0.2.5";
-    sha256 = "1fma99rjqxgg9dihkd10hm1jjp5amsk5wsxnvq1lk4mcsjix5xqb";
+    rev = "v0.2.14";
+    sha256 = "0d1z4b6mrppmz3hgkxd4wcy79w68icvhi7q7n3m2k17n8f3xbdx3";
   };
 
   docopt = fetchFromGitHub {
     owner = "docopt";
     repo = "docopt.nim";
-    rev = "v0.6.5";
-    sha256 = "0yx79m4jkdcazwlky55nwf39zj5kdhymrrdrjq29mahiwx83x5zr";
+    rev = "v0.6.7";
+    sha256 = "1ga7ckg21fzwwvh26jp2phn2h3pvkn8g8sm13dxif33rp471bv37";
   };
 
 in stdenv.mkDerivation rec {
   name = "mosdepth-${version}";
-  version = "0.2.3";
+  version = "0.2.6";
 
   src = fetchFromGitHub {
     owner = "brentp";
     repo = "mosdepth";
     rev = "v${version}";
-    sha256 = "1b9frrwhcvay3alhn0d02jccc2qlbij1732hzq9nhwnr4kvsvxx7";
+    sha256 = "0i9pl9lsli3y84ygxanrr525gfg8fs9h481944cbzsmqmbldwvgk";
   };
 
   buildInputs = [ nim ];
diff --git a/pkgs/applications/science/biology/octopus/default.nix b/pkgs/applications/science/biology/octopus/default.nix
new file mode 100644
index 000000000000..0a2074a06e97
--- /dev/null
+++ b/pkgs/applications/science/biology/octopus/default.nix
@@ -0,0 +1,30 @@
+{stdenv, fetchFromGitHub, cmake, boost, gmp, htslib, zlib, lzma, pkg-config}:
+
+stdenv.mkDerivation rec {
+  pname = "octopus";
+  version = "0.6.3-beta";
+  name = "${pname}-${version}";
+
+  src = fetchFromGitHub {
+    owner = "luntergroup";
+    repo = "octopus";
+    rev = "v${version}";
+    sha256 = "042fycg8ppld7iajpzq2d8h8wr0nw43zbl57y125sfihryvr373n";
+  };
+
+  nativeBuildInputs = [ cmake pkg-config ];
+  buildInputs = [ boost gmp htslib zlib lzma ];
+
+  postInstall = ''
+    mkdir $out/bin
+    mv $out/octopus $out/bin
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Bayesian haplotype-based mutation calling";
+    license = licenses.mit;
+    homepage = "https://github.com/luntergroup/octopus";
+    maintainers = with maintainers; [ jbedo ];
+    platforms = platforms.x86_64;
+  };
+}
diff --git a/pkgs/applications/science/electronics/verilator/default.nix b/pkgs/applications/science/electronics/verilator/default.nix
index 36a504e86faf..b531563c5c1c 100644
--- a/pkgs/applications/science/electronics/verilator/default.nix
+++ b/pkgs/applications/science/electronics/verilator/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   name    = "verilator-${version}";
-  version = "4.014";
+  version = "4.016";
 
   src = fetchurl {
     url    = "https://www.veripool.org/ftp/${name}.tgz";
-    sha256 = "1srk9a03hbq8rdp4mma817aiq61c2hbrs66qv25zj3dfnfqigxgd";
+    sha256 = "18fqm6pgscy504ql27i150fdsd2j91hw5qsnpymws3pvqj2qz2ij";
   };
 
   enableParallelBuilding = true;
diff --git a/pkgs/applications/science/math/gap/default.nix b/pkgs/applications/science/math/gap/default.nix
index 9b42bcd9f13a..7eb10d1f9525 100644
--- a/pkgs/applications/science/math/gap/default.nix
+++ b/pkgs/applications/science/math/gap/default.nix
@@ -61,11 +61,11 @@ in
 stdenv.mkDerivation rec {
   pname = "gap";
   # https://www.gap-system.org/Releases/
-  version = "4.10.1";
+  version = "4.10.2";
 
   src = fetchurl {
     url = "https://www.gap-system.org/pub/gap/gap-${lib.versions.major version}.${lib.versions.minor version}/tar.bz2/gap-${version}.tar.bz2";
-    sha256 = "136s0zvhcw41fshj5zgsrjcy2kd58cdh2m3ddp5rdizi4rx54f10";
+    sha256 = "0cp6ddk0469zzv1m1vair6gm27ic6c5m77ri8rn0znq3gaps6x94";
   };
 
   # remove all non-essential packages (which take up a lot of space)
diff --git a/pkgs/applications/science/math/sage/default.nix b/pkgs/applications/science/math/sage/default.nix
index 061b3beeb3f2..caf51c3da251 100644
--- a/pkgs/applications/science/math/sage/default.nix
+++ b/pkgs/applications/science/math/sage/default.nix
@@ -130,7 +130,7 @@ let
   singular = pkgs.singular.override { inherit flint; };
 
   # https://trac.sagemath.org/ticket/26625
-  maxima-ecl = pkgs.maxima-ecl-5_41;
+  maxima-ecl = pkgs.maxima-ecl;
 
   # *not* to confuse with the python package "pynac"
   pynac = pkgs.pynac.override { inherit singular flint; };
diff --git a/pkgs/applications/science/math/sage/patches/do-not-test-package-manifests.patch b/pkgs/applications/science/math/sage/patches/do-not-test-package-manifests.patch
deleted file mode 100644
index 9e3f0f5ae880..000000000000
--- a/pkgs/applications/science/math/sage/patches/do-not-test-package-manifests.patch
+++ /dev/null
@@ -1,26 +0,0 @@
-diff --git a/src/sage/misc/package.py b/src/sage/misc/package.py
-index 3bca15d53b..7cf04ff8d1 100644
---- a/src/sage/misc/package.py
-+++ b/src/sage/misc/package.py
-@@ -478,16 +478,16 @@ def package_manifest(package):
- 
-     EXAMPLES::
- 
--        sage: from sage.misc.package import package_manifest
--        sage: sagetex_manifest = package_manifest('sagetex')
--        sage: sagetex_manifest['package_name'] == 'sagetex'
-+        sage: from sage.misc.package import package_manifest # optional - buildsystem
-+        sage: sagetex_manifest = package_manifest('sagetex') # optional - buildsystem
-+        sage: sagetex_manifest['package_name'] == 'sagetex' # optional - buildsystem
-         True
--        sage: 'files' in sagetex_manifest
-+        sage: 'files' in sagetex_manifest # optional - buildsystem
-         True
- 
-     Test a nonexistent package::
- 
--        sage: package_manifest('dummy-package')
-+        sage: package_manifest('dummy-package') # optional - buildsystem
-         Traceback (most recent call last):
-         ...
-         KeyError: 'dummy-package'
diff --git a/pkgs/applications/science/math/sage/patches/sphinx-docbuild-subprocesses.patch b/pkgs/applications/science/math/sage/patches/sphinx-docbuild-subprocesses.patch
new file mode 100644
index 000000000000..933344aa5591
--- /dev/null
+++ b/pkgs/applications/science/math/sage/patches/sphinx-docbuild-subprocesses.patch
@@ -0,0 +1,57 @@
+diff --git a/src/sage_setup/docbuild/__init__.py b/src/sage_setup/docbuild/__init__.py
+index 0f2700168a..60f71357d2 100644
+--- a/src/sage_setup/docbuild/__init__.py
++++ b/src/sage_setup/docbuild/__init__.py
+@@ -86,26 +86,6 @@ def builder_helper(type):
+     """
+     Returns a function which builds the documentation for
+     output type ``type``.
+-
+-    TESTS:
+-
+-    Check that :trac:`25161` has been resolved::
+-
+-        sage: from sage_setup.docbuild import DocBuilder, setup_parser
+-        sage: DocBuilder._options = setup_parser().parse_args([])[0] # builder_helper needs _options to be set
+-
+-        sage: import sage_setup.docbuild.sphinxbuild
+-        sage: def raiseBaseException():
+-        ....:     raise BaseException("abort pool operation")
+-        sage: original_runsphinx, sage_setup.docbuild.sphinxbuild.runsphinx = sage_setup.docbuild.sphinxbuild.runsphinx, raiseBaseException
+-
+-        sage: from sage_setup.docbuild import builder_helper, build_many, build_ref_doc
+-        sage: helper = builder_helper("html")
+-        sage: try:
+-        ....:     build_many(build_ref_doc, [("docname", "en", "html", {})])
+-        ....: except Exception as E:
+-        ....:     "Non-exception during docbuild: abort pool operation" in str(E)
+-        True
+     """
+     def f(self, *args, **kwds):
+         output_dir = self._output_dir(type)
+@@ -127,10 +107,9 @@ def builder_helper(type):
+         logger.debug(build_command)
+ 
+         # Run Sphinx with Sage's special logger
+-        sys.argv = ["sphinx-build"] + build_command.split()
+-        from .sphinxbuild import runsphinx
++        args = "python -um sage_setup.docbuild.sphinxbuild -N".split() + build_command.split()
+         try:
+-            runsphinx()
++            subprocess.check_call(args)
+         except Exception:
+             if ABORT_ON_ERROR:
+                 raise
+diff --git a/src/sage_setup/docbuild/sphinxbuild.py b/src/sage_setup/docbuild/sphinxbuild.py
+index 9a2fba79bc..77c8ed3592 100644
+--- a/src/sage_setup/docbuild/sphinxbuild.py
++++ b/src/sage_setup/docbuild/sphinxbuild.py
+@@ -318,3 +318,8 @@ def runsphinx():
+         sys.stderr = saved_stderr
+         sys.stdout.flush()
+         sys.stderr.flush()
++
++if __name__ == '__main__':
++    import sys
++    sys.argv[0] = "sphinx-build"
++    runsphinx()
diff --git a/pkgs/applications/science/math/sage/sage-src.nix b/pkgs/applications/science/math/sage/sage-src.nix
index 013b1bca9308..51460154c5de 100644
--- a/pkgs/applications/science/math/sage/sage-src.nix
+++ b/pkgs/applications/science/math/sage/sage-src.nix
@@ -10,14 +10,14 @@
 # all get the same sources with the same patches applied.
 
 stdenv.mkDerivation rec {
-  version = "8.7";
+  version = "8.8";
   pname = "sage-src";
 
   src = fetchFromGitHub {
     owner = "sagemath";
     repo = "sage";
     rev = version;
-    sha256 = "05vvrd6syh0hlmrk6kzjrwd0hpmvxp8vr8p3mkjb0jh5p2kjdd27";
+    sha256 = "0jm7zdkz8wfgrmf6620jfr8kgvprrz3qfl8gzx6rl5z5cm734b6x";
   };
 
   # Patches needed because of particularities of nix or the way this is packaged.
@@ -45,46 +45,23 @@ stdenv.mkDerivation rec {
     # Fixes a potential race condition which can lead to transient doctest failures.
     ./patches/fix-ecl-race.patch
 
-    # Parallelize docubuild using subprocesses, fixing an isolation issue. See
-    # https://groups.google.com/forum/#!topic/sage-packaging/YGOm8tkADrE
-    (fetchpatch {
-      name = "sphinx-docbuild-subprocesses.patch";
-      url = "https://salsa.debian.org/science-team/sagemath/raw/8a215b17e6f791ddfae6df8ce6d01dfb89acb434/debian/patches/df-subprocess-sphinx.patch";
-      sha256 = "07p9i0fwjgapmfvmi436yn6v60p8pvmxqjc93wsssqgh5kd8qw3n";
-      stripLen = 1;
-    })
-
-    # Part of the build system. Should become unnecessary with sage 8.8.
-    # Upstream discussion here: https://trac.sagemath.org/ticket/27124#comment:33
-    ./patches/do-not-test-package-manifests.patch
-
     # Not necessary since library location is set explicitly
     # https://trac.sagemath.org/ticket/27660#ticket
     ./patches/do-not-test-find-library.patch
 
-    # https://trac.sagemath.org/ticket/27697#ticket
-    (fetchpatch {
-      name = "pplpy-doc-location-configurable.patch";
-      url = "https://git.sagemath.org/sage.git/patch/?h=c4d966e7cb0c7b87c55d52dc6f46518433a2a0a2";
-      sha256 = "0pqbbsx8mriwny422s9mp3z5d095cnam32sm62q4mxk8g8jb9vm9";
-    })
 
     # https://trac.sagemath.org/ticket/28007
     ./patches/threejs-offline.patch
+
+    # Parallelize docubuild using subprocesses, fixing an isolation issue. See
+    # https://groups.google.com/forum/#!topic/sage-packaging/YGOm8tkADrE
+    ./patches/sphinx-docbuild-subprocesses.patch
   ];
 
   # Since sage unfortunately does not release bugfix releases, packagers must
   # fix those bugs themselves. This is for critical bugfixes, where "critical"
   # == "causes (transient) doctest failures / somebody complained".
-  bugfixPatches = [
-    # Transient doctest failure in src/sage/modular/abvar/torsion_subgroup.py
-    # https://trac.sagemath.org/ticket/27477
-    (fetchpatch {
-      name = "sig_on_in_matrix_sparce.patch";
-      url = "https://git.sagemath.org/sage.git/patch?id2=10407524b18659e14e184114b61c043fb816f3c2&id=c9b0cc9d0b8748ab85e568f8f57f316c5e8cbe54";
-      sha256 = "0wgp7yvn9sm1ynlhcr4l0hzmvr2n28llg4xc01p6k1zz4im64c17";
-    })
-  ];
+  bugfixPatches = [ ];
 
   # Patches needed because of package updates. We could just pin the versions of
   # dependencies, but that would lead to rebuilds, confusion and the burdons of
@@ -116,35 +93,6 @@ stdenv.mkDerivation rec {
       stripLen = 1;
     })
 
-    # https://trac.sagemath.org/ticket/26451
-    (fetchSageDiff {
-      name = "sphinx-1.8.patch";
-      base = "8.7";
-      rev = "737afd8f314bd1e16feaec562bb4b5efa2effa8b";
-      sha256 = "0n56ss88ds662bp49j23z5c2i6hsn3jynxw13wv76hyl0h7l1hjh";
-    })
-
-    # https://trac.sagemath.org/ticket/27653
-    (fetchpatch {
-      name = "sympy-1.4.patch";
-      url = "https://git.sagemath.org/sage.git/patch/?h=3277ba76d0ba7174608a31a0c6623e9210c63e3d";
-      sha256 = "09avaanwmdgqv14mmllbgw9z2scf4lc0y0kzdhlriiq8ss9j8iir";
-    })
-
-    # https://trac.sagemath.org/ticket/27094
-    (fetchpatch {
-      name = "gap-4.10.1.patch";
-      url = "https://git.sagemath.org/sage.git/patch?id=d3483110474591ea6cc8e3210cd884f3e0018b3e";
-      sha256 = "028i6h8l8npwzx5z0ax0rcywl85gc83qw1jf93zf523msdfcsk0n";
-    })
-
-    # https://trac.sagemath.org/ticket/27738
-    (fetchpatch {
-      name = "R-3.6.0.patch";
-      url = "https://git.sagemath.org/sage.git/patch/?h=8b7dbd0805d02d0e8674a272e161ceb24a637966";
-      sha256 = "1c81f13z1w62s06yvp43gz6vkp8mxcs289n6l4gj9xj10slimzff";
-    })
-
     # https://trac.sagemath.org/ticket/26932
     (fetchSageDiff {
       name = "givaro-4.1.0_fflas-ffpack-2.4.0_linbox-1.6.0.patch";
@@ -152,13 +100,6 @@ stdenv.mkDerivation rec {
       rev = "c11d9cfa23ff9f77681a8f12742f68143eed4504";
       sha256 = "0xzra7mbgqvahk9v45bjwir2mqz73hrhhy314jq5nxrb35ysdxyi";
     })
-
-    # https://trac.sagemath.org/ticket/26718
-    (fetchpatch {
-      name = "threejs-r100.patch";
-      url = "https://git.sagemath.org/sage.git/patch/?h=86c5bb000259e6de5d7c60afc608a4b0d010b690";
-      sha256 = "0sgqqd4df2bxsq19b6kfy7dvgyxprlpg7f3xx7g3fs8ij937m352";
-    })
   ];
 
   patches = nixPatches ++ bugfixPatches ++ packageUpgradePatches;