JakeHillion/nixpkgs
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Merge pull request #39125 from mpickering/darwin-saga

Browse Source 
SAGA, SAGA LTS release, dependencies and QGIS SAGA plugin
This commit is contained in:
Michael Raskin 2018-10-14 19:14:48 +00:00 committed by GitHub
commit 878c6c090d
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
11 changed files with 166 additions and 15 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

7
pkgs/applications/gis/qgis/default.nix
View File

@ -1,14 +1,15 @@
{ stdenv, fetchurl, fetchpatch, gdal, cmake, qt4, flex, bison, proj, geos, xlibsWrapper, sqlite, gsl
, qwt, fcgi, python2Packages, libspatialindex, libspatialite, qscintilla, postgresql, makeWrapper
, qjson, qca2, txt2tags, openssl, darwin, pkgconfig
, withGrass ? true, grass, IOKit, ApplicationServices
, withGrass ? true, grass, saga, IOKit, ApplicationServices
}:
stdenv.mkDerivation rec {
name = "qgis-2.18.22";
buildInputs = [ gdal qt4 flex openssl bison proj geos xlibsWrapper sqlite gsl qwt qscintilla
fcgi libspatialindex libspatialite postgresql qjson qca2 txt2tags pkgconfig ]
fcgi libspatialindex libspatialite postgresql qjson qca2 txt2tags pkgconfig
saga ]
++
(stdenv.lib.optionals stdenv.isDarwin [IOKit ApplicationServices])
++
@ -68,6 +69,8 @@ stdenv.mkDerivation rec {
# Necessary for QGIS to find the correct default GRASS path
# Plugins look for gdal tools like deminfo on the PATH
${stdenv.lib.optionalString withGrass "ln -sf ${grass} $out/QGIS.app/Contents/MacOS/grass"}
# Necessary for QGIS to find the right SAGA installation
ln -sf ${saga}/bin/saga_cmd $out/QGIS.app/Contents/MacOS/bin/saga_cmd
for file in $(find $out -type f -name "QGIS"); do
wrapProgram "$file" \
--prefix DYLD_LIBRARY_PATH : "${qwt}/lib" \

19
pkgs/applications/gis/saga/clang_patch.patch Normal file
View File

@ -0,0 +1,19 @@
commit e92b250968e9656084ab5984689747ca615ff6e7
Author: Volker Wichmann <wichmann@laserdata.at>
Date: Sun Mar 5 13:49:53 2017 +0100
saga_api, CSG_Table::Del_Records(): bug fix, check record count correctly
diff --git a/src/saga_core/saga_api/table.cpp b/src/saga_core/saga_api/table.cpp
index 76a1d8d..fa1a66f 100644
--- a/src/saga_core/saga_api/table.cpp
+++ b/src/saga_core/saga_api/table.cpp
@@ -901,7 +901,7 @@ bool CSG_Table::Del_Record(int iRecord)
//---------------------------------------------------------
bool CSG_Table::Del_Records(void)
{
- if( m_Records > 0 )
+ if( m_nRecords > 0 )
{
_Index_Destroy();

22
pkgs/applications/gis/saga/default.nix
View File

@ -1,23 +1,33 @@
{ stdenv, fetchurl, gdal, wxGTK30, proj, libiodbc, lzma, jasper,
libharu, opencv, vigra, postgresql }:
libharu, opencv, vigra, postgresql, Cocoa,
unixODBC , poppler, hdf4, hdf5, netcdf, sqlite, qhull, giflib }:
stdenv.mkDerivation rec {
name = "saga-6.3.0";
buildInputs = [ gdal wxGTK30 proj libharu opencv vigra postgresql libiodbc lzma jasper ];
# See https://groups.google.com/forum/#!topic/nix-devel/h_vSzEJAPXs
# for why the have additional buildInputs on darwin
buildInputs = [ gdal wxGTK30 proj libharu opencv vigra postgresql libiodbc lzma
jasper qhull giflib ]
++ stdenv.lib.optionals stdenv.isDarwin
[ Cocoa unixODBC poppler hdf4.out hdf5 netcdf sqlite ];
enableParallelBuilding = true;
patches = [ ./finite-6.3.0.patch];
CXXFLAGS = stdenv.lib.optionalString stdenv.cc.isClang "-std=c++11 -Wno-narrowing";
src = fetchurl {
url = "mirror://sourceforge/project/saga-gis/SAGA%20-%206/SAGA%20-%206.3.0/saga-6.3.0.tar.gz";
sha256 = "0hyjim8fcp3mna1hig22nnn4ki3j6b7096am2amcs99sdr09jjxv";
};
meta = {
meta = with stdenv.lib; {
description = "System for Automated Geoscientific Analyses";
homepage = http://www.saga-gis.org;
license = stdenv.lib.licenses.gpl2Plus;
maintainers = [ stdenv.lib.maintainers.michelk ];
platforms = ["x86_64-linux" ];
license = licenses.gpl2Plus;
maintainers = [ maintainers.michelk ];
platforms = with platforms; unix;
};
}

55
pkgs/applications/gis/saga/finite-6.3.0.patch Normal file
View File

@ -0,0 +1,55 @@
diff --git a/src/tools/imagery/imagery_maxent/me.cpp b/src/tools/imagery/imagery_maxent/me.cpp
index c5da854..d3e9cff 100755
--- a/src/tools/imagery/imagery_maxent/me.cpp
+++ b/src/tools/imagery/imagery_maxent/me.cpp
@@ -21,7 +21,7 @@
#ifdef _SAGA_MSW
#define isinf(x) (!_finite(x))
#else
-#define isinf(x) (!finite(x))
+#define isinf(x) (!isfinite(x))
#endif
/** The input array contains a set of log probabilities lp1, lp2, lp3
@@ -47,7 +47,7 @@ double sumLogProb(vector<double>& logprobs)
/** returns log (e^logprob1 + e^logprob2). */
double sumLogProb(double logprob1, double logprob2)
{
- if (isinf(logprob1) && isinf(logprob2))
+ if (isinf(logprob1) && isinf(logprob2))
return logprob1; // both prob1 and prob2 are 0, return log 0.
if (logprob1>logprob2)
return logprob1+log(1+exp(logprob2-logprob1));
@@ -70,8 +70,8 @@ void MaxEntModel::print(ostream& ostrm, MaxEntTrainer& trainer)
for (FtMap::iterator it = _index.begin(); it!=_index.end(); it++) {
unsigned long i = it->second;
for (unsigned long c = 0; c<_classes; c++) {
- ostrm << "lambda(" << trainer.className(c) << ", "
- << trainer.getStr(it->first) << ")="
+ ostrm << "lambda(" << trainer.className(c) << ", "
+ << trainer.getStr(it->first) << ")="
<< _lambda[i+c] << endl;
}
}
@@ -86,7 +86,7 @@ int MaxEntModel::getProbs(MaxEntEvent& event, vector<double>& probs)
double s = 0;
for (unsigned int f = 0; f<event.size(); f++) {
FtMap::iterator it = _index.find(event[f]);
- if (it!=_index.end())
+ if (it!=_index.end())
s += _lambda[it->second+c];
}
probs[c] = s;
@@ -142,10 +142,10 @@ double MaxEntModel::getObsCounts(EventSet& events, vector<double>& obsCounts)
double ftSum = 0;
for (unsigned long j=0; j<e.size(); j++) {
FtMap::iterator it = _index.find(e[j]);
- if (it!=_index.end())
+ if (it!=_index.end())
obsCounts[it->second+c] += count;
else { // new feature, need to expand obsCounts and _lambda
- for (unsigned int k = 0; k<_classes; k++)
+ for (unsigned int k = 0; k<_classes; k++)
obsCounts.push_back(0);
obsCounts[_lambda.size()+c] += count;
addFeature(e[j]);

13
pkgs/applications/gis/saga/finite.patch Normal file
View File

@ -0,0 +1,13 @@
diff --git a/saga-gis/src/modules/imagery/imagery_maxent/me.cpp b/saga-gis/src/modules/imagery/imagery_maxent/me.cpp
index c5da854..d3e9cff 100755
--- a/src/modules/imagery/imagery_maxent/me.cpp
+++ b/src/modules/imagery/imagery_maxent/me.cpp
@@ -21,7 +21,7 @@
#ifdef _SAGA_MSW
#define isinf(x) (!_finite(x))
#else
-#define isinf(x) (!finite(x))
+#define isinf(x) (!isfinite(x))
#endif
/** The input array contains a set of log probabilities lp1, lp2, lp3

36
pkgs/applications/gis/saga/lts.nix Normal file
View File

@ -0,0 +1,36 @@
{ stdenv, fetchgit, gdal, wxGTK30, proj, libiodbc, lzma, jasper,
libharu, opencv, vigra, postgresql, autoreconfHook, Cocoa
, unixODBC , poppler, hdf4, hdf5, netcdf, sqlite, qhull, giflib }:
stdenv.mkDerivation rec {
name = "saga-2.3.2";
# See https://groups.google.com/forum/#!topic/nix-devel/h_vSzEJAPXs
# for why the have additional buildInputs on darwin
buildInputs = [ autoreconfHook gdal wxGTK30 proj libharu opencv vigra
postgresql libiodbc lzma jasper
unixODBC poppler hdf4.out hdf5 netcdf sqlite qhull giflib ]
++ stdenv.lib.optional stdenv.isDarwin Cocoa ;
enableParallelBuilding = true;
CXXFLAGS = stdenv.lib.optionalString stdenv.cc.isClang "-std=c++11 -Wno-narrowing";
sourceRoot = "code-b6f474f/saga-gis";
patches = [ ./clang_patch.patch ./finite.patch];
src = fetchgit {
url = "https://git.code.sf.net/p/saga-gis/code.git";
rev = "b6f474f8af4af7f0ff82548cc6f88c53547d91f5";
sha256 = "0iakynai8mhcwj6wxvafkqhd7b417ss7hyhbcp9wf6092l6vc2zd";
};
meta = with stdenv.lib; {
description = "System for Automated Geoscientific Analyses";
homepage = http://www.saga-gis.org;
license = licenses.gpl2Plus;
maintainers = [ maintainers.mpickering ];
platforms = with platforms; unix;
};
}

2
pkgs/desktops/gnome-2/platform/GConf/default.nix
View File

@ -27,6 +27,6 @@ stdenv.mkDerivation rec {
meta = with stdenv.lib; {
homepage = https://projects.gnome.org/gconf/;
description = "Deprecated system for storing application preferences";
platforms = platforms.linux;
platforms = platforms.unix;
};
}

2
pkgs/development/libraries/libharu/default.nix
View File

@ -15,6 +15,6 @@ stdenv.mkDerivation {
homepage = http://libharu.org/;
license = stdenv.lib.licenses.zlib;
maintainers = [ stdenv.lib.maintainers.marcweber ];
platforms = stdenv.lib.platforms.linux;
platforms = stdenv.lib.platforms.unix;
};
}

7
pkgs/development/libraries/libiodbc/default.nix
View File

@ -1,4 +1,4 @@
{ stdenv, fetchurl, pkgconfig, gtk2, useGTK ? false }:
{ stdenv, fetchurl, pkgconfig, gtk2, Carbon, useGTK ? false }:
stdenv.mkDerivation rec {
name = "libiodbc-3.52.12";
@ -9,7 +9,8 @@ stdenv.mkDerivation rec {
};
nativeBuildInputs = [ pkgconfig ];
buildInputs = stdenv.lib.optionals useGTK [ gtk2 ];
buildInputs = stdenv.lib.optionals useGTK [ gtk2 ]
++ stdenv.lib.optional stdenv.isDarwin Carbon;
preBuild =
''
@ -19,6 +20,6 @@ stdenv.mkDerivation rec {
meta = {
description = "iODBC driver manager";
homepage = http://www.iodbc.org;
platforms = stdenv.lib.platforms.linux;
platforms = stdenv.lib.platforms.unix;
};
}

8
pkgs/development/libraries/vigra/default.nix
View File

@ -15,6 +15,12 @@ in stdenv.mkDerivation rec {
NIX_CFLAGS_COMPILE = "-I${ilmbase.dev}/include/OpenEXR";
# Fixes compilation with clang (on darwin) see https://github.com/ukoethe/vigra/issues/414
patches =
let clangPatch = fetchurl { url = "https://github.com/ukoethe/vigra/commit/81958d302494e137f98a8b1d7869841532f90388.patch";
sha256 = "1i1w6smijgb5z8bg9jaq84ccy00k2sxm87s37lgjpyix901gjlgi"; };
in [ clangPatch ];
buildInputs = [ boost cmake fftw fftwSinglePrec hdf5 ilmbase libjpeg libpng
libtiff numpy openexr python ];
@ -34,6 +40,6 @@ in stdenv.mkDerivation rec {
homepage = https://hci.iwr.uni-heidelberg.de/vigra;
license = licenses.mit;
maintainers = [ maintainers.viric ];
platforms = platforms.linux;
platforms = platforms.unix;
};
}

10
pkgs/top-level/all-packages.nix
View File

@ -10649,6 +10649,7 @@ with pkgs;
libiodbc = callPackage ../development/libraries/libiodbc {
useGTK = config.libiodbc.gtk or false;
inherit (darwin.apple_sdk.frameworks) Carbon;
};
libivykis = callPackage ../development/libraries/libivykis { };
@ -18410,6 +18411,7 @@ with pkgs;
qgis = callPackage ../applications/gis/qgis {
inherit (darwin.apple_sdk.frameworks) IOKit ApplicationServices;
saga = saga_2_3_2;
};
qgroundcontrol = libsForQt5.callPackage ../applications/science/robotics/qgroundcontrol { };
@ -20377,7 +20379,13 @@ with pkgs;
rrootage = callPackage ../games/rrootage { };
saga = callPackage ../applications/gis/saga { };
saga = callPackage ../applications/gis/saga {
inherit (darwin.apple_sdk.frameworks) Cocoa;
};
saga_2_3_2 = callPackage ../applications/gis/saga/lts.nix {
inherit (darwin.apple_sdk.frameworks) Cocoa;
};
samplv1 = callPackage ../applications/audio/samplv1 { };