proj: 6.3.1 -> 7.2.1 and related updates

pkgs/development/libraries/proj/default.nix

@@ -1,21 +1,21 @@
-{ lib, stdenv, fetchFromGitHub, pkg-config, sqlite, autoreconfHook }:
+{ lib, stdenv, fetchFromGitHub, pkg-config, sqlite, autoreconfHook, libtiff, curl }:
 
 stdenv.mkDerivation rec {
   pname = "proj";
-  version = "6.3.1";
+  version = "7.2.1";
 
   src = fetchFromGitHub {
     owner = "OSGeo";
     repo = "PROJ";
     rev = version;
-    sha256 = "1ildcp57qsa01kvv2qxd05nqw5mg0wfkksiv9l138dbhp0s7rkxp";
+    sha256 = "0mymvfvs8xggl4axvlj7kc1ksd9g94kaz6w1vdv0x2y5mqk93gx9";
   };
 
   outputs = [ "out" "dev"];
 
   nativeBuildInputs = [ pkg-config autoreconfHook ];
 
-  buildInputs = [ sqlite ];
+  buildInputs = [ sqlite libtiff curl ];
 
   doCheck = stdenv.is64bit;
 

pkgs/development/python-modules/basemap/default.nix

@@ -1,6 +1,7 @@
 { lib
 , buildPythonPackage
 , fetchFromGitHub
+, pythonAtLeast
 , numpy
 , matplotlib
 , pillow
@@ -43,6 +44,7 @@ buildPythonPackage rec {
       http://matplotlib.github.com/basemap/users/examples.html for examples of what it can do.
     '';
     license = with licenses; [ mit gpl2 ];
+    broken = pythonAtLeast "3.9";
   };
 
 }

pkgs/development/python-modules/cartopy/default.nix

@@ -1,10 +1,9 @@
-{ buildPythonPackage, lib, fetchPypi
-, pytest_4, filelock, mock, pep8
-, cython, isPy27
+{ buildPythonPackage, lib, fetchPypi, fetchpatch
+, pytestCheckHook, filelock, mock, pep8
+, cython
 , six, pyshp, shapely, geos, numpy
 , gdal, pillow, matplotlib, pyepsg, pykdtree, scipy, owslib, fiona
-, xvfb_run
-, proj_5 # see https://github.com/SciTools/cartopy/pull/1252 for status on proj 6 support
+, proj
 }:
 
 buildPythonPackage rec {
@@ -17,28 +16,16 @@ buildPythonPackage rec {
     sha256 = "0d24fk0cbp29gmkysrwq05vry13swmwi3vx3cpcy04c0ixz33ykz";
   };
 
-  checkInputs = [ filelock mock pytest_4 pep8 ];
-
-  # several tests require network connectivity: we disable them.
-  # also py2.7's tk is over-eager in trying to open an x display,
-  # so give it xvfb
-  checkPhase = let
-    maybeXvfbRun = lib.optionalString isPy27 "${xvfb_run}/bin/xvfb-run";
-  in ''
-    export HOME=$(mktemp -d)
-    ${maybeXvfbRun} pytest --pyargs cartopy \
-      -m "not network and not natural_earth" \
-      -k "not test_nightshade_image and not background_img"
-  '';
-
-  nativeBuildInputs = [
-    cython
-    geos # for geos-config
-    proj_5
+  patches = [
+    # Fix numpy-1.20 compatibility.  Will be part of 0.19.
+    (fetchpatch {
+      url = "https://github.com/SciTools/cartopy/commit/e663bbbef07989a5f8484a8f36ea9c07e61d14ce.patch";
+      sha256 = "061kbjgzkc3apaz6sxy00pkgy3n9dxcgps5wzj4rglb5iy86n2kq";
+    })
   ];
 
   buildInputs = [
-    geos proj_5
+    geos proj
   ];
 
   propagatedBuildInputs = [
@@ -49,12 +36,28 @@ buildPythonPackage rec {
     gdal pillow matplotlib pyepsg pykdtree scipy fiona owslib
   ];
 
+  checkInputs = [ pytestCheckHook filelock mock pep8 ];
+
+  pytestFlagsArray = [
+    "--pyargs" "cartopy"
+    "-m" "'not network and not natural_earth'"
+  ];
+
+  disabledTests = [
+    "test_nightshade_image"
+    "background_img"
+  ];
+
+  nativeBuildInputs = [
+    cython
+    geos # for geos-config
+    proj
+  ];
+
   meta = with lib; {
     description = "Process geospatial data to create maps and perform analyses";
     license = licenses.lgpl3;
     homepage = "https://scitools.org.uk/cartopy/docs/latest/";
     maintainers = with maintainers; [ mredaelli ];
-    # following tests fail: test_eccentric_globe and test_ellipse_globe
-    broken = true;
   };
 }

pkgs/development/python-modules/pyproj/001.proj.patch

@@ -1,62 +1,56 @@
 diff -Nur a/pyproj/datadir.py b/pyproj/datadir.py
---- a/pyproj/datadir.py	2020-03-24 12:53:39.417440608 +0100
-+++ b/pyproj/datadir.py	2020-03-24 12:56:19.870089479 +0100
-@@ -66,9 +66,7 @@
+--- a/pyproj/datadir.py	2021-04-10 18:26:52.829018483 +0100
++++ b/pyproj/datadir.py	2021-04-10 18:44:59.155190614 +0100
+@@ -70,7 +70,7 @@
      if _VALIDATED_PROJ_DATA is not None:
          return _VALIDATED_PROJ_DATA
      global _USER_PROJ_DATA
--    internal_datadir = os.path.join(
--        os.path.dirname(os.path.abspath(__file__)), "proj_dir", "share", "proj"
--    )
-+    internal_datadir = "@proj@/share/proj"
+-    internal_datadir = Path(__file__).absolute().parent / "proj_dir" / "share" / "proj"
++    internal_datadir = Path("@proj@/share/proj")
      proj_lib_dirs = os.environ.get("PROJ_LIB", "")
-     prefix_datadir = os.path.join(sys.prefix, "share", "proj")
+     prefix_datadir = Path(sys.prefix, "share", "proj")
 
 diff -Nur a/setup.py b/setup.py
---- a/setup.py	2020-03-24 12:53:39.415440624 +0100
-+++ b/setup.py	2020-03-24 12:52:05.311232522 +0100
+--- a/setup.py	2021-04-10 18:26:52.817018512 +0100
++++ b/setup.py	2021-04-10 18:46:01.652324424 +0100
 @@ -11,7 +11,7 @@
- PROJ_MIN_VERSION = parse_version("6.2.0")
- CURRENT_FILE_PATH = os.path.dirname(os.path.abspath(__file__))
- BASE_INTERNAL_PROJ_DIR = "proj_dir"
--INTERNAL_PROJ_DIR = os.path.join(CURRENT_FILE_PATH, "pyproj", BASE_INTERNAL_PROJ_DIR)
-+INTERNAL_PROJ_DIR = "@proj@"
+ PROJ_MIN_VERSION = parse_version("7.2.0")
+ CURRENT_FILE_PATH = Path(__file__).absolute().parent
+ BASE_INTERNAL_PROJ_DIR = Path("proj_dir")
+-INTERNAL_PROJ_DIR = CURRENT_FILE_PATH / "pyproj" / BASE_INTERNAL_PROJ_DIR
++INTERNAL_PROJ_DIR = Path("@proj@")
 
 
- def check_proj_version(proj_dir):
-@@ -146,7 +146,7 @@
+ def get_proj_version(proj_dir: Path) -> str:
+@@ -150,7 +150,7 @@
      # By default we'll try to get options PROJ_DIR or the local version of proj
      proj_dir = get_proj_dir()
      library_dirs = get_proj_libdirs(proj_dir)
 -    include_dirs = get_proj_incdirs(proj_dir)
-+    include_dirs = get_proj_incdirs("@projdev@")
++    include_dirs = get_proj_incdirs(Path("@projdev@"))
 
-     # setup extension options
-     ext_options = {
+     proj_version = get_proj_version(proj_dir)
+     check_proj_version(proj_version)
 diff -Nur a/test/conftest.py b/test/conftest.py
---- a/test/conftest.py	2020-03-24 12:53:39.417440608 +0100
-+++ b/test/conftest.py	2020-03-24 23:16:47.373972786 +0100
-@@ -1,6 +1,7 @@
- import os
- import shutil
- import tempfile
+--- a/test/conftest.py	2021-04-10 18:26:52.831018478 +0100
++++ b/test/conftest.py	2021-04-10 18:37:01.605682432 +0100
+@@ -2,6 +2,7 @@
+ from contextlib import contextmanager
+ from distutils.version import LooseVersion
+ from pathlib import Path
 +import stat
 
- import pytest
-
-@@ -17,6 +18,15 @@
-     with tempfile.TemporaryDirectory() as tmpdir:
-         tmp_data_dir = os.path.join(tmpdir, "proj")
-         shutil.copytree(data_dir, tmp_data_dir)
-+
-+        # Data copied from the nix store is readonly (causes cleanup problem).
-+        # Make it writable.
-+        for r, d, files in os.walk(tmp_data_dir):
-+            os.chmod(r, os.stat(r).st_mode | stat.S_IWUSR)
-+            for f in files:
-+                fpath = os.path.join(r, f)
-+                os.chmod(fpath, os.stat(fpath).st_mode | stat.S_IWUSR)
-+
-         try:
-             os.remove(os.path.join(str(tmp_data_dir), "ntv2_0.gsb"))
-         except OSError:
+ import pyproj
+ from pyproj.datadir import get_data_dir, get_user_data_dir, set_data_dir
+diff -Nur a/test/test_cli.py b/test/test_cli.py
+--- a/test/test_cli.py	2021-04-10 18:26:52.831018478 +0100
++++ b/test/test_cli.py	2021-04-10 22:17:04.665088162 +0100
+@@ -14,7 +14,7 @@
+ from test.conftest import grids_available, proj_env, tmp_chdir
+
+ PYPROJ_CLI_ENDPONTS = pytest.mark.parametrize(
+-    "input_command", [["pyproj"], [sys.executable, "-m", "pyproj"]]
++    "input_command", [[sys.executable, "-m", "pyproj"]]
+ )
+
+

pkgs/development/python-modules/pyproj/default.nix

@@ -1,60 +1,94 @@
-{ lib, buildPythonPackage, fetchFromGitHub, python, pkgs, pythonOlder, isPy27, substituteAll
-, aenum
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, python
+, proj
+, pythonOlder
+, substituteAll
 , cython
 , pytestCheckHook
 , mock
+, certifi
 , numpy
 , shapely
+, pandas
+, xarray
 }:
 
 buildPythonPackage rec {
   pname = "pyproj";
-  version = "2.6.0";
-  disabled = isPy27;
+  version = "3.0.1";
+  disabled = pythonOlder "3.7";
 
   src = fetchFromGitHub {
     owner = "pyproj4";
     repo = "pyproj";
-    rev = "v${version}rel";
-    sha256 = "0fyggkbr3kp8mlq4c0r8sl5ah58bdg2mj4kzql9p3qyrkcdlgixh";
+    rev = version;
+    sha256 = "1q1i1235cp3k32dpb11r7krx5rpqwszb89mrx85rflc1z5acaj58";
   };
 
-  # force pyproj to use ${pkgs.proj}
+  # force pyproj to use ${proj}
   patches = [
     (substituteAll {
       src = ./001.proj.patch;
-      proj = pkgs.proj;
-      projdev = pkgs.proj.dev;
+      proj = proj;
+      projdev = proj.dev;
     })
   ];
 
-  buildInputs = [ cython pkgs.proj ];
+  nativeBuildInputs = [ cython ];
+  buildInputs = [ proj ];
 
   propagatedBuildInputs = [
-    numpy shapely
-  ] ++ lib.optional (pythonOlder "3.6") aenum;
+     certifi
+  ];
+
+  checkInputs = [
+    pytestCheckHook
+    mock
+    numpy
+    shapely
+    pandas
+    xarray
+  ];
 
-  checkInputs = [ pytestCheckHook mock ];
+  preCheck = ''
+    # We need to build extensions locally to run tests
+    ${python.interpreter} setup.py build_ext --inplace
+    cd test
+  '';
 
-  # prevent importing local directory
-  preCheck = "cd test";
-  pytestFlagsArray = [
-    "--ignore=test_doctest_wrapper.py"
-    "--ignore=test_datadir.py"
+  disabledTestPaths = [
+    "test_doctest_wrapper.py"
+    "test_datadir.py"
   ];
 
   disabledTests = [
-    "alternative_grid_name"
-    "transform_wgs84_to_alaska"
-    "transformer_group__unavailable"
-    "transform_group__missing_best"
-    "datum"
-    "repr"
+    # The following tests try to access network and end up with a URLError
+    "test__load_grid_geojson_old_file"
+    "test_get_transform_grid_list"
+    "test_get_transform_grid_list__area_of_use"
+    "test_get_transform_grid_list__bbox__antimeridian"
+    "test_get_transform_grid_list__bbox__out_of_bounds"
+    "test_get_transform_grid_list__contains"
+    "test_get_transform_grid_list__file"
+    "test_get_transform_grid_list__source_id"
+    "test_sync__area_of_use__list"
+    "test_sync__bbox__list"
+    "test_sync__bbox__list__exclude_world_coverage"
+    "test_sync__download_grids"
+    "test_sync__file__list"
+    "test_sync__source_id__list"
+    "test_sync_download"
+    "test_sync_download__directory"
+    "test_sync_download__system_directory"
+    "test_transformer_group__download_grids"
   ];
 
   meta = {
     description = "Python interface to PROJ.4 library";
-    homepage = "https://github.com/jswhit/pyproj";
+    homepage = "https://github.com/pyproj4/pyproj";
     license = with lib.licenses; [ isc ];
+    maintainers = with lib.maintainers; [ lsix ];
   };
 }

pkgs/top-level/aliases.nix

@@ -577,6 +577,7 @@ mapAliases ({
   ppl-address-book = throw "ppl-address-book deprecated on 2019-05-02: abandoned by upstream.";
   processing3 = processing; # added 2019-08-16
   procps-ng = procps; # added 2018-06-08
+  proj_5 = throw "Proj-5 has been removed from nixpkgs, use proj instead."; # added 2021-04-12
   prometheus-cups-exporter = throw "outdated and broken by design; removed by developer."; # added 2021-03-16
   pygmentex = texlive.bin.pygmentex; # added 2019-12-15
   pyload = throw "pyload has been removed from nixpkgs, as it was unmaintained."; # added 2021-03-21

pkgs/top-level/all-packages.nix

@@ -16843,8 +16843,6 @@ in
 
   proj = callPackage ../development/libraries/proj { };
 
-  proj_5 = callPackage ../development/libraries/proj/5.2.nix { };
-
   proj-datumgrid = callPackage ../development/libraries/proj-datumgrid { };
 
   proselint = callPackage ../tools/text/proselint {