Merge commit '84d74ae9c9cbed73274b8e4e00be14688ffc93fe'

8 files changed, 233 insertions, 26 deletions

diff --git a/nixpkgs/pkgs/applications/gis/gmt/dcw.nix b/nixpkgs/pkgs/applications/gis/gmt/dcw.nix
new file mode 100644
index 000000000000..58390e892903
--- /dev/null
+++ b/nixpkgs/pkgs/applications/gis/gmt/dcw.nix
@@ -0,0 +1,32 @@
+{ stdenv, fetchurl }:
+
+stdenv.mkDerivation rec {
+  pname = "dcw-gmt";
+  version = "1.1.4";
+  src = fetchurl {
+    url = "ftp://ftp.soest.hawaii.edu/gmt/dcw-gmt-${version}.tar.gz";
+    sha256 = "8d47402abcd7f54a0f711365cd022e4eaea7da324edac83611ca035ea443aad3";
+  };
+
+  installPhase = ''
+    mkdir -p $out/share/dcw-gmt
+    cp -rv ./* $out/share/dcw-gmt
+  '';
+
+  meta = with stdenv.lib; {
+    homepage = "https://www.soest.hawaii.edu/pwessel/dcw/";
+    description = "Vector basemap of the world, for use with GMT";
+    longDescription = ''
+      DCW-GMT is an enhancement to the original 1:1,000,000 scale vector basemap
+      of the world, available from the Princeton University Digital Map and
+      Geospatial Information Center. It contains more state boundaries (the
+      largest 8 countries are now represented) than the original data
+      source. Information about DCW can be found on Wikipedia
+      (https://en.wikipedia.org/wiki/Digital_Chart_of_the_World). This data is
+      for use by GMT, the Generic Mapping Tools.
+    '';
+    license = licenses.lgpl3Plus;
+    maintainers = with maintainers; [ tviti ];
+  };
+
+}
diff --git a/nixpkgs/pkgs/applications/gis/gmt/default.nix b/nixpkgs/pkgs/applications/gis/gmt/default.nix
new file mode 100644
index 000000000000..f045ec067fee
--- /dev/null
+++ b/nixpkgs/pkgs/applications/gis/gmt/default.nix
@@ -0,0 +1,73 @@
+{ stdenv, fetchurl, cmake, curl, Accelerate, CoreGraphics, CoreVideo
+, fftwSinglePrec, netcdf, pcre, gdal, blas, lapack, glibc, ghostscript, dcw-gmt
+, gshhg-gmt }:
+
+/* The onus is on the user to also install:
+    - ffmpeg for webm or mp4 output
+    - graphicsmagick for gif output
+*/
+
+stdenv.mkDerivation rec {
+  pname = "gmt";
+  version = "6.1.1";
+  src = fetchurl {
+    url = "https://github.com/GenericMappingTools/gmt/releases/download/${version}/gmt-${version}-src.tar.gz";
+    sha256 = "04mdxxcild56jhg9ax522xh78v1wl1x8iqv2f6wv32x9b2lgy1lp";
+  };
+
+  nativeBuildInputs = [ cmake ];
+
+  buildInputs = [ curl gdal netcdf pcre dcw-gmt gshhg-gmt ]
+    ++ (if stdenv.isDarwin then [
+      Accelerate
+      CoreGraphics
+      CoreVideo
+    ] else [
+      glibc
+      fftwSinglePrec
+      blas
+      lapack
+    ]);
+
+  propagatedBuildInputs = [ ghostscript ];
+
+  cmakeFlags = [
+    "-DGMT_DOCDIR=share/doc/gmt"
+    "-DGMT_MANDIR=share/man"
+    "-DGMT_LIBDIR=lib"
+    "-DCOPY_GSHHG:BOOL=FALSE"
+    "-DGSHHG_ROOT=${gshhg-gmt.out}/share/gshhg-gmt"
+    "-DCOPY_DCW:BOOL=FALSE"
+    "-DDCW_ROOT=${dcw-gmt.out}/share/dcw-gmt"
+    "-DGDAL_ROOT=${gdal.out}"
+    "-DNETCDF_ROOT=${netcdf.out}"
+    "-DPCRE_ROOT=${pcre.out}"
+    "-DGMT_INSTALL_TRADITIONAL_FOLDERNAMES:BOOL=FALSE"
+    "-DGMT_ENABLE_OPENMP:BOOL=TRUE"
+    "-DGMT_INSTALL_MODULE_LINKS:BOOL=FALSE"
+    "-DLICENSE_RESTRICTED=LGPL" # "GPL" and "no" also valid
+  ] ++ (with stdenv;
+    lib.optional (!isDarwin) [
+      "-DFFTW3_ROOT=${fftwSinglePrec.dev}"
+      "-DLAPACK_LIBRARY=${lapack}/lib/liblapack.so"
+      "-DBLAS_LIBRARY=${blas}/lib/libblas.so"
+    ]);
+
+  meta = with stdenv.lib; {
+    homepage = "https://www.generic-mapping-tools.org";
+    description = "Tools for manipulating geographic and cartesian data sets";
+    longDescription = ''
+      GMT is an open-source collection of command-line tools for manipulating
+      geographic and Cartesian data sets (including filtering, trend fitting,
+      gridding, projecting, etc.) and producing high-quality illustrations
+      ranging from simple x–y plots via contour maps to artificially illuminated
+      surfaces and 3D perspective views. It supports many map projections and
+      transformations and includes supporting data such as coastlines, rivers,
+      and political boundaries and optionally country polygons.
+    '';
+    platforms = [ "x86_64-linux" "x86_64-darwin" ];
+    license = licenses.lgpl3Plus;
+    maintainers = with maintainers; [ tviti ];
+  };
+
+}
diff --git a/nixpkgs/pkgs/applications/gis/gmt/gshhg.nix b/nixpkgs/pkgs/applications/gis/gmt/gshhg.nix
new file mode 100644
index 000000000000..0f22f87c89b5
--- /dev/null
+++ b/nixpkgs/pkgs/applications/gis/gmt/gshhg.nix
@@ -0,0 +1,31 @@
+{ stdenv, fetchurl }:
+
+stdenv.mkDerivation rec {
+  pname = "gshhg-gmt";
+  version = "2.3.7";
+  src = fetchurl {
+    url = "ftp://ftp.soest.hawaii.edu/gmt/gshhg-gmt-${version}.tar.gz";
+    sha256 = "9bb1a956fca0718c083bef842e625797535a00ce81f175df08b042c2a92cfe7f";
+  };
+
+  installPhase = ''
+    mkdir -p $out/share/gshhg-gmt
+    cp -rv ./* $out/share/gshhg-gmt
+  '';
+
+  meta = with stdenv.lib; {
+    homepage = "https://www.soest.hawaii.edu/pwessel/gshhg/";
+    description = "High-resolution shoreline data set, for use with GMT";
+    longDescription = ''
+      GSHHG is a high-resolution shoreline data set amalgamated from two
+      databases: Global Self-consistent Hierarchical High-resolution Shorelines
+      (GSHHS) and CIA World Data Bank II (WDBII). GSHHG contains vector
+      descriptions at five different resolutions of land outlines, lakes,
+      rivers, and political boundaries. This data is for use by GMT, the Generic
+      Mapping Tools.
+    '';
+    license = licenses.lgpl3Plus;
+    maintainers = with maintainers; [ tviti ];
+  };
+
+}
diff --git a/nixpkgs/pkgs/applications/gis/openorienteering-mapper/default.nix b/nixpkgs/pkgs/applications/gis/openorienteering-mapper/default.nix
index 39f8694dd177..540fa2718975 100644
--- a/nixpkgs/pkgs/applications/gis/openorienteering-mapper/default.nix
+++ b/nixpkgs/pkgs/applications/gis/openorienteering-mapper/default.nix
@@ -56,8 +56,6 @@ mkDerivation rec {
     "-DLICENSING_PROVIDER:BOOL=OFF"
     "-DMapper_MANUAL_QTHELP:BOOL=OFF"
   ] ++ stdenv.lib.optionals stdenv.isDarwin [
-    # Usually enabled on Darwin
-    "-DCMAKE_FIND_FRAMEWORK=never"
     # FindGDAL is broken and always finds /Library/Framework unless this is
     # specified
     "-DGDAL_INCLUDE_DIR=${gdal}/include"
diff --git a/nixpkgs/pkgs/applications/gis/qgis/unwrapped.nix b/nixpkgs/pkgs/applications/gis/qgis/unwrapped.nix
index 2e11f22f517b..130c0af6ee20 100644
--- a/nixpkgs/pkgs/applications/gis/qgis/unwrapped.nix
+++ b/nixpkgs/pkgs/applications/gis/qgis/unwrapped.nix
@@ -10,7 +10,7 @@ let
     [ qscintilla-qt5 gdal jinja2 numpy psycopg2
       chardet dateutil pyyaml pytz requests urllib3 pygments pyqt5 sip owslib six ];
 in mkDerivation rec {
-  version = "3.10.4";
+  version = "3.10.9";
   pname = "qgis";
   name = "${pname}-unwrapped-${version}";
 
@@ -18,7 +18,7 @@ in mkDerivation rec {
     owner = "qgis";
     repo = "QGIS";
     rev = "final-${lib.replaceStrings ["."] ["_"] version}";
-    sha256 = "0d1rsgjgnnq6jgms5bgppz8lkh4518nf90fk0qvxajdfi9j4jn12";
+    sha256 = "0d646hvrhhgsw789qc2g3iblmsvr64qh15jck1jkaljzrj3qbml6";
   };
 
   passthru = {
diff --git a/nixpkgs/pkgs/applications/gis/saga/default.nix b/nixpkgs/pkgs/applications/gis/saga/default.nix
index 053272b1efa7..aa418148209e 100644
--- a/nixpkgs/pkgs/applications/gis/saga/default.nix
+++ b/nixpkgs/pkgs/applications/gis/saga/default.nix
@@ -1,27 +1,90 @@
-{ stdenv, fetchurl, gdal, wxGTK30, proj, libiodbc, lzma,
-  libharu, opencv2, vigra, postgresql, Cocoa,
-  unixODBC , poppler, hdf4, hdf5, netcdf, sqlite, qhull, giflib }:
+{ stdenv
+, fetchurl
+# native
+, autoreconfHook
+, pkg-config
+# not native
+, gdal
+, wxGTK31-gtk3
+, proj
+, dxflib
+, curl
+, libiodbc
+, lzma
+, libharu
+, opencv
+, vigra
+, postgresql
+, Cocoa
+, unixODBC
+, poppler
+, hdf4
+, hdf5
+, netcdf
+, sqlite
+, qhull
+, giflib
+, libsvm
+, fftw
+}:
 
-stdenv.mkDerivation {
+stdenv.mkDerivation rec {
   pname = "saga";
-  version = "7.6.3";
+  version = "7.7.0";
 
+  src = fetchurl {
+    url = "https://sourceforge.net/projects/saga-gis/files/SAGA%20-%20${stdenv.lib.versions.major version}/SAGA%20-%20${version}/saga-${version}.tar.gz";
+    sha256 = "1nmvrlcpcm2pas9pnav13iydnym9d8yqqnwq47lm0j6b0a2wy9zk";
+  };
+
+  nativeBuildInputs = [
+    # Upstream's gnerated ./configure is not reliable
+    autoreconfHook
+    pkg-config
+  ];
+  configureFlags = [
+    "--with-system-svm"
+    # hdf is no detected otherwise
+    "HDF5_LIBS=-l${hdf5}/lib"
+    "HDF5_CFLAGS=-I${hdf5.dev}/include"
+  ];
+  buildInputs = [
+    curl
+    dxflib
+    fftw
+    libsvm
+    hdf5
+    gdal
+    wxGTK31-gtk3
+    proj
+    libharu
+    opencv
+    vigra
+    postgresql
+    libiodbc
+    lzma
+    qhull
+    giflib
+  ]
   # See https://groups.google.com/forum/#!topic/nix-devel/h_vSzEJAPXs
   # for why the have additional buildInputs on darwin
-  buildInputs = [ gdal wxGTK30 proj libharu opencv2 vigra postgresql libiodbc lzma
-                  qhull giflib ]
-                ++ stdenv.lib.optionals stdenv.isDarwin
-                  [ Cocoa unixODBC poppler hdf4.out hdf5 netcdf sqlite ];
+  ++ stdenv.lib.optionals stdenv.isDarwin [
+    Cocoa
+    unixODBC
+    poppler
+    netcdf
+    sqlite
+  ];
+
+  patches = [
+    # See https://sourceforge.net/p/saga-gis/bugs/280/
+    ./opencv4.patch
+  ];
 
   enableParallelBuilding = true;
 
   CXXFLAGS = stdenv.lib.optionalString stdenv.cc.isClang "-std=c++11 -Wno-narrowing";
 
-  src = fetchurl {
-    url = "https://sourceforge.net/projects/saga-gis/files/SAGA%20-%207/SAGA%20-%207.6.3/saga-7.6.3.tar.gz";
-    sha256 = "0f1qy2y929gd9y7h45bkv9x71xapbzyn06v6wqivjaiydsi1qycb";
-  };
-
   meta = with stdenv.lib; {
     description = "System for Automated Geoscientific Analyses";
     homepage = "http://www.saga-gis.org";
diff --git a/nixpkgs/pkgs/applications/gis/saga/opencv4.patch b/nixpkgs/pkgs/applications/gis/saga/opencv4.patch
new file mode 100644
index 000000000000..0b26192bf09b
--- /dev/null
+++ b/nixpkgs/pkgs/applications/gis/saga/opencv4.patch
@@ -0,0 +1,14 @@
+--- a/src/tools/imagery/imagery_opencv/Makefile.am
++++ b/src/tools/imagery/imagery_opencv/Makefile.am
+@@ -7,9 +7,9 @@
+ 
+ if HAVE_CV
+ DEF_SAGA           = -D_SAGA_LINUX -D_TYPEDEF_BYTE -D_TYPEDEF_WORD
+-CXX_INCS           = -I$(top_srcdir)/src/saga_core -I/usr/include/opencv
++CXX_INCS           = -I$(top_srcdir)/src/saga_core `pkg-config opencv4 --cflags`
+ AM_CXXFLAGS        = -fPIC $(CXX_INCS) $(DEF_SAGA) $(DBGFLAGS) $(GOMPFLAGS)
+-AM_LDFLAGS         = -fPIC -shared -avoid-version `pkg-config opencv --libs`
++AM_LDFLAGS         = -fPIC -shared -avoid-version `pkg-config opencv4 --libs`
+ pkglib_LTLIBRARIES = libimagery_opencv.la
+ libimagery_opencv_la_SOURCES =\
+ MLB_Interface.cpp\
diff --git a/nixpkgs/pkgs/applications/gis/whitebox-tools/default.nix b/nixpkgs/pkgs/applications/gis/whitebox-tools/default.nix
index d81a08e29008..0ac19c0d1336 100644
--- a/nixpkgs/pkgs/applications/gis/whitebox-tools/default.nix
+++ b/nixpkgs/pkgs/applications/gis/whitebox-tools/default.nix
@@ -1,27 +1,23 @@
 { stdenv, rustPlatform , fetchFromGitHub, Security }:
 rustPlatform.buildRustPackage rec {
   pname = "whitebox_tools";
-  version = "1.2.0";
+  version = "1.3.0";
 
   src = fetchFromGitHub {
     owner = "jblindsay";
     repo = "whitebox-tools";
     rev = "v${version}";
-    sha256 = "0zi32d0wrbl2763dcllv2g0liwacsfiza5lkx52620prjjbhby8i";
+    sha256 = "0c9jmfjz6ys65y65zlllv9xvaaavr9jpqc1dc217iywhj07j8k2v";
   };
 
   buildInputs = stdenv.lib.optional stdenv.isDarwin Security;
 
-  cargoSha256 = "13k21akyfqgamywj39bw73sldby1s02vyvxfglxbaqq1x96xcy4i";
-
-  # failures: structures::polyline::test::test_polyline_split
-  doCheck = false;
+  cargoSha256 = "05w2jimmygg7dc93i8bpjpjc5yj5xfpfkjnbbgw2sq4kh06r5ii4";
 
   meta = with stdenv.lib; {
     description = "An advanced geospatial data analysis platform";
-    homepage = "http://www.uoguelph.ca/~hydrogeo/WhiteboxTools/index.html";
+    homepage = "https://jblindsay.github.io/ghrg/WhiteboxTools/index.html";
     license = licenses.mit;
     maintainers = [ maintainers.mpickering ];
-    platforms = platforms.all;
   };
 }