Merge pull request #529 from imincik/weekly-update-2024.39

pkgs: weekly update (weekly-update-2024.39)
imincik · Sep 29, 2024 · eb59a3a · eb59a3a
2 parents a468642 + f7fc337
commit eb59a3a
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Showing 20 changed files with 127 additions and 92 deletions.
diff --git a/flake.lock b/flake.lock
diff --git a/pkgs/gdal/default.nix b/pkgs/gdal/default.nix
@@ -4,7 +4,7 @@
 , fetchFromGitHub
 
 , useMinimalFeatures ? false
-, useTiledb ? (!useMinimalFeatures) && !(stdenv.isDarwin && stdenv.isx86_64)
+, useTiledb ? (!useMinimalFeatures) && !(stdenv.hostPlatform.isDarwin && stdenv.hostPlatform.isx86_64)
 , useLibHEIF ? (!useMinimalFeatures)
 , useLibJXL ? (!useMinimalFeatures)
 , useMysql ? (!useMinimalFeatures)
@@ -107,9 +107,9 @@ stdenv.mkDerivation (finalAttrs: {
     "-DMYSQL_LIBRARY=${lib.getLib libmysqlclient}/lib/${lib.optionalString (libmysqlclient.pname != "mysql") "mysql/"}libmysqlclient${stdenv.hostPlatform.extensions.sharedLibrary}"
   ] ++ lib.optionals finalAttrs.doInstallCheck [
     "-DBUILD_TESTING=ON"
-  ] ++ lib.optionals (!stdenv.isDarwin) [
+  ] ++ lib.optionals (!stdenv.hostPlatform.isDarwin) [
     "-DCMAKE_SKIP_BUILD_RPATH=ON" # without, libgdal.so can't find libmariadb.so
-  ] ++ lib.optionals stdenv.isDarwin [
+  ] ++ lib.optionals stdenv.hostPlatform.isDarwin [
     "-DCMAKE_BUILD_WITH_INSTALL_NAME_DIR=ON"
   ] ++ lib.optionals (!useTiledb) [
     "-DGDAL_USE_TILEDB=OFF"
@@ -145,8 +145,8 @@ stdenv.mkDerivation (finalAttrs: {
       netCdfDeps = lib.optionals useNetCDF [ netcdf ];
       armadilloDeps = lib.optionals useArmadillo [ armadillo ];
 
-      darwinDeps = lib.optionals stdenv.isDarwin [ libiconv ];
-      nonDarwinDeps = lib.optionals (!stdenv.isDarwin) ([
+      darwinDeps = lib.optionals stdenv.hostPlatform.isDarwin [ libiconv ];
+      nonDarwinDeps = lib.optionals (!stdenv.hostPlatform.isDarwin) ([
         # tests for formats enabled by these packages fail on macos
         openexr
         xercesc
@@ -256,10 +256,10 @@ stdenv.mkDerivation (finalAttrs: {
     # failing with PROJ 9.3.1
     # https://github.com/OSGeo/gdal/issues/8908
     "test_osr_esri_28"
-  ] ++ lib.optionals (!stdenv.isx86_64) [
+  ] ++ lib.optionals (!stdenv.hostPlatform.isx86_64) [
     # likely precision-related expecting x87 behaviour
     "test_jp2openjpeg_22"
-  ] ++ lib.optionals stdenv.isDarwin [
+  ] ++ lib.optionals stdenv.hostPlatform.isDarwin [
     # flaky on macos
     "test_rda_download_queue"
   ] ++ lib.optionals (lib.versionOlder proj.version "8") [

diff --git a/pkgs/gdal/master-rev.nix b/pkgs/gdal/master-rev.nix
@@ -1,4 +1,4 @@
 {
-  rev = "33dd00c";
-  hash = "sha256-HqSy7UzeYxYHjouIQ+NdwOoZk6AcAjztZ2ejuteSUaA=";
+  rev = "8055974";
+  hash = "sha256-uEU7QpCsArZVYNByIs/Stp34p9j36DJA4I2mSF+/jME=";
 }
diff --git a/pkgs/gdal/master.nix b/pkgs/gdal/master.nix
@@ -16,5 +16,11 @@ in
     };
 
     patches = [ ];
+
+    disabledTests = prev.disabledTests ++ [
+      # failing with master
+      # https://github.com/OSGeo/gdal/pull/10806#issuecomment-2362054085
+      "test_ogr_gmlas_billion_laugh"
+    ];
   });
 }
diff --git a/pkgs/geopandas/default.nix b/pkgs/geopandas/default.nix
@@ -13,6 +13,17 @@
   pyproj,
   rtree,
   shapely,
+
+  # optional-dependencies
+  folium,
+  geoalchemy2,
+  geopy,
+  mapclassify,
+  matplotlib,
+  psycopg,
+  pyarrow,
+  sqlalchemy,
+  xyzservices,
 }:
 
 buildPythonPackage rec {
@@ -39,12 +50,32 @@ buildPythonPackage rec {
     shapely
   ];
 
+  optional-dependencies = {
+    all = [
+      # prevent infinite recursion
+      (folium.overridePythonAttrs (prevAttrs: {
+        doCheck = false;
+      }))
+      geoalchemy2
+      geopy
+      # prevent infinite recursion
+      (mapclassify.overridePythonAttrs (prevAttrs: {
+        doCheck = false;
+      }))
+      matplotlib
+      psycopg
+      pyarrow
+      sqlalchemy
+      xyzservices
+    ];
+  };
+
   nativeCheckInputs = [
     pytestCheckHook
     rtree
-  ];
+  ] ++ optional-dependencies.all;
 
-  doCheck = !stdenv.isDarwin;
+  doCheck = !stdenv.hostPlatform.isDarwin;
 
   preCheck = ''
     export HOME=$(mktemp -d);

diff --git a/pkgs/geos/default.nix b/pkgs/geos/default.nix
@@ -19,7 +19,7 @@ stdenv.mkDerivation (finalAttrs: {
   nativeBuildInputs = [ cmake ];
 
   # https://github.com/libgeos/geos/issues/930
-  cmakeFlags = lib.optionals (stdenv.isDarwin && stdenv.isx86_64) [
+  cmakeFlags = lib.optionals (stdenv.hostPlatform.isDarwin && stdenv.hostPlatform.isx86_64) [
     "-DCMAKE_CTEST_ARGUMENTS=--exclude-regex;unit-geom-Envelope"
   ];
 

diff --git a/pkgs/grass/clang-integer-conversion.patch b/pkgs/grass/clang-integer-conversion.patch
diff --git a/pkgs/grass/default.nix b/pkgs/grass/default.nix
@@ -5,7 +5,7 @@
 , makeWrapper
 , wrapGAppsHook3
 
-, withOpenGL ? true
+, withOpenGL ? !stdenv.hostPlatform.isDarwin
 
 , bison
 , blas
@@ -23,6 +23,7 @@
 , libsvm
 , libtiff
 , libxml2
+, llvmPackages
 , netcdf
 , pdal
 , pkg-config
@@ -51,6 +52,12 @@ stdenv.mkDerivation (finalAttrs: {
     hash = "sha256-NKMshd6pr2O62ZjmQ/oPttmeVBYVD0Nqhh3SwQrhZf8=";
   };
 
+  patches = [
+    # Backport of https://github.com/OSGeo/grass/pull/3899
+    # by @landam . Remove for GRASS 8.5.
+    ./grass_config_dir.patch
+  ];
+
   nativeBuildInputs = [
     makeWrapper
     wrapGAppsHook3
@@ -86,19 +93,11 @@ stdenv.mkDerivation (finalAttrs: {
     zlib
     zstd
   ] ++ lib.optionals withOpenGL [ libGLU ]
-  ++ lib.optionals stdenv.isDarwin [ libiconv ];
+  ++ lib.optionals stdenv.hostPlatform.isDarwin [ libiconv ]
+  ++ lib.optionals stdenv.cc.isClang [ llvmPackages.openmp ];
 
   strictDeps = true;
 
-  patches = [
-    # Backport of https://github.com/OSGeo/grass/pull/3899
-    # by @landam . Remove for GRASS 8.5.
-    ./grass_config_dir.patch
-  ] ++ lib.optionals stdenv.isDarwin [
-    # Fix conversion of const char* to unsigned int.
-    ./clang-integer-conversion.patch
-  ];
-
   configureFlags = [
     "--with-blas"
     "--with-cairo-ldflags=-lfontconfig"
@@ -124,14 +123,14 @@ stdenv.mkDerivation (finalAttrs: {
     "--without-odbc"
   ] ++ lib.optionals (! withOpenGL) [
     "--without-opengl"
-  ] ++ lib.optionals stdenv.isDarwin [
+  ] ++ lib.optionals stdenv.hostPlatform.isDarwin [
     "--without-cairo"
     "--without-freetype"
     "--without-x"
   ];
 
   # Otherwise a very confusing "Can't load GDAL library" error
-  makeFlags = lib.optional stdenv.isDarwin "GDAL_DYNAMIC=";
+  makeFlags = lib.optional stdenv.hostPlatform.isDarwin "GDAL_DYNAMIC=";
 
   /* Ensures that the python script run at build time are actually executable;
    * otherwise, patchShebangs ignores them.  */

diff --git a/pkgs/grass/nixpkgs/grass-config-dir.patch b/pkgs/grass/nixpkgs/grass-config-dir.patch
@@ -1,17 +1,17 @@
-diff --git b/pkgs/grass/default.nix a/pkgs/grass/default.nix
-index d27e21a..35b322b 100644
---- b/pkgs/grass/default.nix
-+++ a/pkgs/grass/default.nix
-@@ -90,7 +90,11 @@ stdenv.mkDerivation (finalAttrs: {
+diff --git a/pkgs/grass/default.nix b/pkgs/grass/default.nix
+index 69d6e98..31624cc 100644
+--- a/pkgs/grass/default.nix
++++ b/pkgs/grass/default.nix
+@@ -52,6 +52,12 @@ stdenv.mkDerivation (finalAttrs: {
+     hash = "sha256-NKMshd6pr2O62ZjmQ/oPttmeVBYVD0Nqhh3SwQrhZf8=";
+   };
 
-   strictDeps = true;
-
--  patches = lib.optionals stdenv.isDarwin [
 +  patches = [
 +    # Backport of https://github.com/OSGeo/grass/pull/3899
 +    # by @landam . Remove for GRASS 8.5.
 +    ./grass_config_dir.patch
-+  ] ++ lib.optionals stdenv.isDarwin [
-     # Fix conversion of const char* to unsigned int.
-     ./clang-integer-conversion.patch
-   ];
++  ];
++
+   nativeBuildInputs = [
+     makeWrapper
+     wrapGAppsHook3
diff --git a/pkgs/grass/plugins-list.nix b/pkgs/grass/plugins-list.nix
@@ -56,7 +56,7 @@
 
             g-download-location = {
                 name = "g.download.location";
-                description = ''Download GRASS Location from the web Get GRASS Location from an URL or file path'';
+                description = ''Download GRASS project (location) from the web Get GRASS project from an URL or file path'';
             };
 
 
@@ -468,6 +468,12 @@
             };
 
 
+            r-buildvrt-gdal = {
+                name = "r.buildvrt.gdal";
+                description = ''Build GDAL Virtual Rasters (VRT) over GRASS GIS raster maps'';
+            };
+
+
             r-catchment = {
                 name = "r.catchment";
                 description = ''Creates a raster buffer of specified area around vector points using cost distances using r.walk.'';
@@ -1814,7 +1820,7 @@
 
             v-kriging = {
                 name = "v.kriging";
-                description = ''Interpolates 2D or 3D raster based on input values located on 2D or 3D point vector layer (method ordinary kriging extended to 3D).'';
+                description = ''None'';
             };
 
 

diff --git a/pkgs/grass/plugins-rev.nix b/pkgs/grass/plugins-rev.nix
@@ -1,4 +1,4 @@
 {
-  rev = "dbc2be3";
-  hash = "sha256-0xM/MzuM+vj8I5hTiFgP0V5ppxYkLpPbZ2qZpcyDxQ8=";
+  rev = "02330fe";
+  hash = "sha256-8xMQ+CHSHuKNVArvNapNxSUH1CWApkKWi07WdiYxFJY=";
 }
diff --git a/pkgs/libspatialindex/package.nix b/pkgs/libspatialindex/package.nix
@@ -21,7 +21,7 @@ stdenv.mkDerivation (finalAttrs: {
     patchShebangs test/
   '';
 
-  nativeBuildInputs = [ cmake ] ++ lib.optional stdenv.isDarwin fixDarwinDylibNames;
+  nativeBuildInputs = [ cmake ] ++ lib.optional stdenv.hostPlatform.isDarwin fixDarwinDylibNames;
 
   cmakeFlags = [
     (lib.cmakeBool "BUILD_TESTING" finalAttrs.finalPackage.doCheck)
@@ -37,7 +37,7 @@ stdenv.mkDerivation (finalAttrs: {
 
   doCheck = true;
 
-  postFixup = lib.optionalString stdenv.isDarwin ''
+  postFixup = lib.optionalString stdenv.hostPlatform.isDarwin ''
     install_name_tool -change "@rpath/libspatialindex.7.dylib" "$out/lib/libspatialindex.7.dylib" $out/lib/libspatialindex_c.dylib
   '';
 

diff --git a/pkgs/libspatialite/default.nix b/pkgs/libspatialite/default.nix
@@ -40,13 +40,13 @@ stdenv.mkDerivation rec {
     proj
     sqlite
     zlib
-  ] ++ lib.optionals stdenv.isDarwin [
+  ] ++ lib.optionals stdenv.hostPlatform.isDarwin [
     libiconv
   ];
 
   enableParallelBuilding = true;
 
-  postInstall = lib.optionalString stdenv.isDarwin ''
+  postInstall = lib.optionalString stdenv.hostPlatform.isDarwin ''
     ln -s $out/lib/mod_spatialite.{so,dylib}
   '';
 

diff --git a/pkgs/postgis/postgis.nix b/pkgs/postgis/postgis.nix
@@ -28,7 +28,7 @@ let
 in
 stdenv.mkDerivation rec {
   pname = "postgis";
-  version = "3.4.2";
+  version = "3.4.3";
 
   outputs = [
     "out"
@@ -37,7 +37,7 @@ stdenv.mkDerivation rec {
 
   src = fetchurl {
     url = "https://download.osgeo.org/postgis/source/postgis-${version}.tar.gz";
-    hash = "sha256-yMh0wAukqYSocDCva/lUSCFQIGCtRz1clvHU0INcWJI=";
+    hash = "sha256-+N7VBdrrj1dlnaK55Xf/ceGDqqCUcI0u7OLFbZM2H2I=";
   };
 
   buildInputs = [
@@ -49,7 +49,7 @@ stdenv.mkDerivation rec {
     json_c
     protobufc
     pcre2.dev
-  ] ++ lib.optional stdenv.isDarwin libiconv;
+  ] ++ lib.optional stdenv.hostPlatform.isDarwin libiconv;
   nativeBuildInputs = [
     perl
     pkg-config
@@ -89,7 +89,7 @@ stdenv.mkDerivation rec {
     ln -s ${postgresql}/bin/postgres $out/bin/postgres
   '';
 
-  doCheck = stdenv.isLinux;
+  doCheck = stdenv.hostPlatform.isLinux;
 
   preCheck = ''
     substituteInPlace regress/run_test.pl --replace-fail "/share/contrib/postgis" "$out/share/postgresql/contrib/postgis"

diff --git a/pkgs/proj/default.nix b/pkgs/proj/default.nix
@@ -51,7 +51,7 @@ stdenv.mkDerivation (finalAttrs: {
 
   preCheck =
     let
-      libPathEnvVar = if stdenv.isDarwin then "DYLD_LIBRARY_PATH" else "LD_LIBRARY_PATH";
+      libPathEnvVar = if stdenv.hostPlatform.isDarwin then "DYLD_LIBRARY_PATH" else "LD_LIBRARY_PATH";
     in
       ''
         export HOME=$TMPDIR