Merge master into staging-next

pkgs/development/python-modules/acme-tiny/default.nix

@@ -3,11 +3,11 @@
 
 buildPythonPackage rec {
   pname = "acme-tiny";
-  version = "4.0.4";
+  version = "4.1.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0vqlmvk34jgvgx3qdsh50q7m4aiy02786jyjjcq45dcws7a4f9f1";
+    sha256 = "0jmg525n4n98hwy3hf303jbnq23z79sqwgliji9j7qcnph47gkgq";
   };
 
   patchPhase = ''

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

@@ -1,9 +1,10 @@
 { buildPythonPackage, lib, fetchPypi
 , pytest, filelock, mock, pep8
 , cython, isPy27
-, six, pyshp, shapely, geos, proj, numpy
+, 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
 }:
 
 buildPythonPackage rec {
@@ -27,17 +28,17 @@ buildPythonPackage rec {
     export HOME=$(mktemp -d)
     ${maybeXvfbRun} pytest --pyargs cartopy \
       -m "not network and not natural_earth" \
-      -k "not test_nightshade_image"
+      -k "not test_nightshade_image and not background_img"
   '';
 
   nativeBuildInputs = [
     cython
     geos # for geos-config
-    proj
+    proj_5
   ];
 
   buildInputs = [
-    geos proj
+    geos proj_5
   ];
 
   propagatedBuildInputs = [

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

@@ -1,7 +1,7 @@
 { stdenv, buildPythonPackage, fetchPypi, isPy3k, pythonOlder
 , attrs, click, cligj, click-plugins, six, munch, enum34
 , pytest, boto3, mock
-, gdal
+, gdal_2 # can't bump to 3 yet, https://github.com/Toblerity/Fiona/issues/745
 }:
 
 buildPythonPackage rec {
@@ -16,11 +16,11 @@ buildPythonPackage rec {
   CXXFLAGS = stdenv.lib.optionalString stdenv.cc.isClang "-std=c++11";
 
   nativeBuildInputs = [
-    gdal # for gdal-config
+    gdal_2 # for gdal-config
   ];
 
   buildInputs = [
-    gdal
+    gdal_2
   ];
 
   propagatedBuildInputs = [

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

@@ -0,0 +1,47 @@
+diff a/pyproj/datadir.py b/pyproj/datadir.py
+--- a/pyproj/datadir.py
++++ b/pyproj/datadir.py
+@@ -52,6 +52,7 @@ def get_data_dir():
+     str: The valid data directory.
+
+     """
++    return "@proj@/share/proj"
+     # to avoid re-validating
+     global _VALIDATED_PROJ_DATA
+     if _VALIDATED_PROJ_DATA is not None:
+diff a/setup.py b/setup.py
+--- a/setup.py
++++ b/setup.py
+@@ -16,7 +16,7 @@ INTERNAL_PROJ_DIR = os.path.join(CURRENT_FILE_PATH, "pyproj", BASE_INTERNAL_PROJ
+
+ def check_proj_version(proj_dir):
+     """checks that the PROJ library meets the minimum version"""
+-    proj = os.path.join(proj_dir, "bin", "proj")
++    proj = "@proj@/bin/proj"
+     proj_ver_bytes = subprocess.check_output(proj, stderr=subprocess.STDOUT)
+     proj_ver_bytes = (proj_ver_bytes.decode("ascii").split()[1]).strip(",")
+     proj_version = parse_version(proj_ver_bytes)
+@@ -33,6 +33,7 @@ def get_proj_dir():
+     """
+     This function finds the base PROJ directory.
+     """
++    return "@proj@"
+     proj_dir = os.environ.get("PROJ_DIR")
+     if proj_dir is None and os.path.exists(INTERNAL_PROJ_DIR):
+         proj_dir = INTERNAL_PROJ_DIR
+@@ -56,6 +57,7 @@ def get_proj_libdirs(proj_dir):
+     """
+     This function finds the library directories
+     """
++    return ["@proj@/lib"]
+     proj_libdir = os.environ.get("PROJ_LIBDIR")
+     libdirs = []
+     if proj_libdir is None:
+@@ -77,6 +79,7 @@ def get_proj_incdirs(proj_dir):
+     """
+     This function finds the include directories
+     """
++    return ["@proj@/include"]
+     proj_incdir = os.environ.get("PROJ_INCDIR")
+     incdirs = []
+     if proj_incdir is None:

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

@@ -1,38 +1,49 @@
-{ lib
-, buildPythonPackage
-, fetchFromGitHub
-, python
-, nose2
+{ lib, buildPythonPackage, fetchPypi, python, pkgs, pythonOlder, substituteAll
+, aenum
 , cython
-, proj ? null
+, pytest
+, mock
+, numpy
 }:
 
-buildPythonPackage (rec {
+buildPythonPackage rec {
   pname = "pyproj";
-  version = "unstable-2018-11-13";
+  version = "2.2.1";
 
-  src = fetchFromGitHub {
-    owner = "jswhit";
-    repo = pname;
-    rev = "78540f5ff40da92160f80860416c91ee74b7643c";
-    sha256 = "1vq5smxmpdjxialxxglsfh48wx8kaq9sc5mqqxn4fgv1r5n1m3n9";
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0yigcxwmx5cczipf2mpmy2gq1dnl0635yjvjq86ay47j1j5fd2gc";
   };
 
-  buildInputs = [ cython ];
+  # force pyproj to use ${pkgs.proj}
+  patches = [
+    (substituteAll {
+      src = ./001.proj.patch;
+      proj = pkgs.proj;
+    })
+  ];
 
-  checkInputs = [ nose2 ];
+  buildInputs = [ cython pkgs.proj ];
 
+  propagatedBuildInputs = [
+    numpy
+  ] ++ lib.optional (pythonOlder "3.6") aenum;
+
+  checkInputs = [ pytest mock ];
+
+  # ignore rounding errors, and impure docgen
+  # datadir is ignored because it does the proj look up logic, which isn't relevant
   checkPhase = ''
-    runHook preCheck
-    pushd unittest  # changing directory should ensure we're importing the global pyproj
-    ${python.interpreter} test.py && ${python.interpreter} -c "import doctest, pyproj, sys; sys.exit(doctest.testmod(pyproj)[0])"
-    popd
-    runHook postCheck
+    pytest . -k 'not alternative_grid_name \
+                 and not transform_wgs84_to_alaska \
+                 and not repr' \
+            --ignore=test/test_doctest_wrapper.py \
+            --ignore=test/test_datadir.py
   '';
 
   meta = {
     description = "Python interface to PROJ.4 library";
-    homepage = https://github.com/jswhit/pyproj;
+    homepage = "https://github.com/jswhit/pyproj";
     license = with lib.licenses; [ isc ];
   };
-} // (if proj == null then {} else { PROJ_DIR = proj; }))
+}

pkgs/development/python-modules/sklearn-deap/default.nix

@@ -1,17 +1,25 @@
-{ stdenv, buildPythonPackage, fetchFromGitHub, numpy, scipy, deap, scikitlearn, python, isPy3k }:
+{ stdenv, buildPythonPackage, fetchFromGitHub, fetchpatch, numpy, scipy, deap, scikitlearn, python }:
 
 buildPythonPackage rec {
   pname = "sklearn-deap";
-  version = "0.2.2";
+  version = "0.2.3";
 
   # No tests in Pypi
   src = fetchFromGitHub {
     owner = "rsteca";
     repo = pname;
     rev = "${version}";
-    sha256 = "01ynmzxg181xhv2d7bs53zjvk9x2qpxix32sspq54mpigxh13ava";
+    sha256 = "1yqnmy8h08i2y6bb2s0a5nx9cwvyg45293whqh420c195gpzg1x3";
   };
 
+  patches = [
+    # Fix for newer versions of scikit-learn. See: https://github.com/rsteca/sklearn-deap/pull/62
+    (fetchpatch {
+      url = "https://github.com/rsteca/sklearn-deap/commit/3ae62990fc87f36b59382e7c4db3c74cf99ec3bf.patch";
+      sha256 = "1na6wf4v0dcmyz3pz8aiqkmv76d1iz3hi4iyfq9kfnycgzpv1kxk";
+    })
+  ];
+
   propagatedBuildInputs = [ numpy scipy deap scikitlearn ];
 
   checkPhase = ''
@@ -23,7 +31,6 @@ buildPythonPackage rec {
     homepage = https://github.com/rsteca/sklearn-deap;
     license = licenses.lgpl3;
     maintainers = with maintainers; [ psyanticy ];
-    broken = isPy3k; # https://github.com/rsteca/sklearn-deap/issues/65
   };
 }
 

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

@@ -0,0 +1,30 @@
+{ buildPythonPackage
+, lib
+, python
+, fetchPypi
+, msrest
+}:
+
+buildPythonPackage rec {
+  version = "0.1.25";
+  pname = "vsts";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "15sgwqa72ynpahj101r2kc15s3dnsafg5gqx0sz3hnqz29h925ys";
+  };
+
+  propagatedBuildInputs = [ msrest ];
+
+  # Tests are highly impure
+  checkPhase = ''
+    ${python.interpreter} -c 'import vsts.version; print(vsts.version.VERSION)'
+  '';
+
+  meta = with lib; {
+    description = "Python APIs for interacting with and managing Azure DevOps";
+    homepage = https://github.com/microsoft/azure-devops-python-api;
+    license = licenses.mit;
+    maintainers = with maintainers; [ jonringer ];
+  };
+}