From df96c26e750992c96757889df889b89beced6599 Mon Sep 17 00:00:00 2001
From: Josef Kemetmueller <josef.kemetmueller@gmail.com>
Date: Sun, 3 Sep 2017 08:58:44 +0000
Subject: [PATCH 1/9] pythonPackages.shapely: Fix search for libc

This should fix the search for libc's free method on both linux and
darwin.
---
 pkgs/top-level/python-packages.nix | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index bb5aef27f13..d37c7bef7e1 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -21672,8 +21672,11 @@ in {
       export LANG="en_US.UTF-8";
     '';
 
-    patchPhase = ''
-      sed -i "s|_lgeos = load_dll('geos_c', fallbacks=.*)|_lgeos = load_dll('geos_c', fallbacks=['${pkgs.geos}/lib/libgeos_c.so'])|" shapely/geos.py
+    patchPhase = let
+      libc = if stdenv.isDarwin then "libc.dylib" else "libc.so.6";
+    in ''
+      sed -i "s|_lgeos = load_dll('geos_c', fallbacks=.*)|_lgeos = load_dll('geos_c', fallbacks=['${pkgs.geos}/lib/libgeos_c.${sharedLibraryExtension}'])|" shapely/geos.py
+      sed -i "s|free = load_dll('c').free|free = load_dll('c', fallbacks=['${stdenv.cc.libc}/lib/${libc}']).free|" shapely/geos.py
     '';
 
     # tests/test_voctorized fails because the vectorized extension is not
@@ -21684,6 +21687,7 @@ in {
 
     meta = {
       description = "Geometric objects, predicates, and operations";
+      maintainers = with maintainers; [ knedlsepp ];
       homepage = "https://pypi.python.org/pypi/Shapely/";
     };
   };

From d25edeb3ee26d8bab17ede29555f23ee92f559da Mon Sep 17 00:00:00 2001
From: Josef Kemetmueller <josef.kemetmueller@gmail.com>
Date: Sun, 3 Sep 2017 09:01:33 +0000
Subject: [PATCH 2/9] pythonPackages.click-plugins: init at 1.0.3

---
 .../python-modules/click-plugins/default.nix  | 29 +++++++++++++++++++
 pkgs/top-level/python-packages.nix            |  2 ++
 2 files changed, 31 insertions(+)
 create mode 100644 pkgs/development/python-modules/click-plugins/default.nix

diff --git a/pkgs/development/python-modules/click-plugins/default.nix b/pkgs/development/python-modules/click-plugins/default.nix
new file mode 100644
index 00000000000..3ae8537c6c0
--- /dev/null
+++ b/pkgs/development/python-modules/click-plugins/default.nix
@@ -0,0 +1,29 @@
+{ stdenv, buildPythonPackage, fetchPypi,
+  click, pytest
+}:
+
+buildPythonPackage rec {
+  pname = "click-plugins";
+  version = "1.0.3";
+  name = "${pname}-${version}";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1ifphgaw5mmcdnqd0qfnmrbm62q3k6p573aff4cxgpyjxmz5xk3s";
+  };
+
+  propagatedBuildInputs = [
+    click
+  ];
+
+  checkInputs = [
+    pytest
+  ];
+
+  meta = with stdenv.lib; {
+    description = "An extension module for click to enable registering CLI commands";
+    homepage = https://github.com/click-contrib/click-plugins;
+    license = licenses.bsd3;
+    maintainers = with maintainers; [ knedlsepp ];
+  };
+}
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index d37c7bef7e1..f9599beddc2 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -3042,6 +3042,8 @@ in {
     };
   };
 
+  click-plugins = callPackage ../development/python-modules/click-plugins {};
+
   click-threading = buildPythonPackage rec {
     version = "0.4.2";
     name = "click-threading-${version}";

From 4d70d536183c01a54b083db0309157ce522ea86a Mon Sep 17 00:00:00 2001
From: Josef Kemetmueller <josef.kemetmueller@gmail.com>
Date: Sun, 3 Sep 2017 09:02:28 +0000
Subject: [PATCH 3/9] pythonPackages.cligq: init at 0.4.0

---
 .../python-modules/cligj/default.nix          | 25 +++++++++++++++++++
 pkgs/top-level/python-packages.nix            |  2 ++
 2 files changed, 27 insertions(+)
 create mode 100644 pkgs/development/python-modules/cligj/default.nix

diff --git a/pkgs/development/python-modules/cligj/default.nix b/pkgs/development/python-modules/cligj/default.nix
new file mode 100644
index 00000000000..12b597f3698
--- /dev/null
+++ b/pkgs/development/python-modules/cligj/default.nix
@@ -0,0 +1,25 @@
+{ stdenv, buildPythonPackage, fetchPypi,
+  click
+}:
+
+buildPythonPackage rec {
+  pname = "cligj";
+  version = "0.4.0";
+  name = "${pname}-${version}";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0m1zic66nay2rymfa9krd3jfpyajxjnbmzw7c2q764aw9ychgb8j";
+  };
+
+  propagatedBuildInputs = [
+    click
+  ];
+
+  meta = with stdenv.lib; {
+    description = "Click params for commmand line interfaces to GeoJSON";
+    homepage = https://github.com/mapbox/cligj;
+    license = licenses.bsd3;
+    maintainers = with maintainers; [ knedlsepp ];
+  };
+}
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index f9599beddc2..eaad744c8bf 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -3071,6 +3071,8 @@ in {
     };
   };
 
+  cligj = callPackage ../development/python-modules/cligj { };
+
   clepy = buildPythonPackage rec {
     name = "clepy-0.3.20";
 

From f039bb6b4ec5778a95068f36cd3eedf0bed98cf8 Mon Sep 17 00:00:00 2001
From: Josef Kemetmueller <josef.kemetmueller@gmail.com>
Date: Sun, 3 Sep 2017 09:04:34 +0000
Subject: [PATCH 4/9] pythonPackages.descartes: init at 1.1.0

---
 .../python-modules/descartes/default.nix      | 26 +++++++++++++++++++
 pkgs/top-level/python-packages.nix            |  2 ++
 2 files changed, 28 insertions(+)
 create mode 100644 pkgs/development/python-modules/descartes/default.nix

diff --git a/pkgs/development/python-modules/descartes/default.nix b/pkgs/development/python-modules/descartes/default.nix
new file mode 100644
index 00000000000..1407dd3d204
--- /dev/null
+++ b/pkgs/development/python-modules/descartes/default.nix
@@ -0,0 +1,26 @@
+{ stdenv, buildPythonPackage, fetchPypi,
+  matplotlib, shapely
+}:
+
+buildPythonPackage rec {
+  pname = "descartes";
+  version = "1.1.0";
+  name = "${pname}-${version}";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0nq36w9ylvfwmwn5qd9c8fsp2jzsqpmy4xcr6pzxcpmg8qhm0nhk";
+  };
+
+  propagatedBuildInputs = [
+    matplotlib
+    shapely
+  ];
+
+  meta = with stdenv.lib; {
+    description = "Python library to use Shapely or GeoJSON objects as matplotlib paths";
+    homepage = https://bitbucket.org/sgillies/descartes/;
+    license = licenses.bsd3;
+    maintainers = with maintainers; [ knedlsepp ];
+  };
+}
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index eaad744c8bf..ea0527d8cc2 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -8997,6 +8997,8 @@ in {
     };
   });
 
+  descartes = callPackage ../development/python-modules/descartes { };
+
   distutils_extra = buildPythonPackage rec {
     name = "distutils-extra-${version}";
     version = "2.39";

From aad9a691ab8905031c499f6cabd7284e596a079d Mon Sep 17 00:00:00 2001
From: Josef Kemetmueller <josef.kemetmueller@gmail.com>
Date: Sun, 3 Sep 2017 09:05:57 +0000
Subject: [PATCH 5/9] pythonPackages.fiona: init at 1.7.9

---
 .../python-modules/fiona/default.nix          | 41 +++++++++++++++++++
 pkgs/top-level/python-packages.nix            |  2 +
 2 files changed, 43 insertions(+)
 create mode 100644 pkgs/development/python-modules/fiona/default.nix

diff --git a/pkgs/development/python-modules/fiona/default.nix b/pkgs/development/python-modules/fiona/default.nix
new file mode 100644
index 00000000000..42e8e423bdd
--- /dev/null
+++ b/pkgs/development/python-modules/fiona/default.nix
@@ -0,0 +1,41 @@
+{ stdenv, buildPythonPackage, fetchPypi,
+  six, cligj, munch, click-plugins, enum34, pytest, nose,
+  gdal
+}:
+
+buildPythonPackage rec {
+  pname = "Fiona";
+  version = "1.7.9";
+  name = "${pname}-${version}";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1fmdgpfnifaqfqwkfiwkpk19wmpi9avmh8a7jqylqi578jvp3fwi";
+  };
+
+  buildInputs = [
+    gdal
+  ];
+
+  propagatedBuildInputs = [
+    six
+    cligj
+    munch
+    click-plugins
+    enum34
+  ];
+
+  checkInputs = [
+    pytest
+    nose
+  ];
+
+  doCheck = false;
+
+  meta = with stdenv.lib; {
+    description = "OGR's neat, nimble, no-nonsense API for Python";
+    homepage = http://toblerity.org/fiona/;
+    license = licenses.bsd3;
+    maintainers = with maintainers; [ knedlsepp ];
+  };
+}
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index ea0527d8cc2..80dcfa5662f 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -9917,6 +9917,8 @@ in {
     };
   };
 
+  fiona = callPackage ../development/python-modules/fiona { gdal = pkgs.gdal; };
+
   flake8 = callPackage ../development/python-modules/flake8 { };
 
   flake8-blind-except = callPackage ../development/python-modules/flake8-blind-except { };

From 05ac3f95209ed3b233191c9ffe6123c542726259 Mon Sep 17 00:00:00 2001
From: Josef Kemetmueller <josef.kemetmueller@gmail.com>
Date: Sun, 3 Sep 2017 09:06:33 +0000
Subject: [PATCH 6/9] pythonPackages.geopandas: init at 0.3.0

---
 .../python-modules/geopandas/default.nix      | 28 +++++++++++++++++++
 pkgs/top-level/python-packages.nix            |  2 ++
 2 files changed, 30 insertions(+)
 create mode 100644 pkgs/development/python-modules/geopandas/default.nix

diff --git a/pkgs/development/python-modules/geopandas/default.nix b/pkgs/development/python-modules/geopandas/default.nix
new file mode 100644
index 00000000000..c048f9d01ed
--- /dev/null
+++ b/pkgs/development/python-modules/geopandas/default.nix
@@ -0,0 +1,28 @@
+{ stdenv, buildPythonPackage, fetchPypi,
+  pandas, shapely, fiona, descartes, pyproj }:
+
+buildPythonPackage rec {
+  pname = "geopandas";
+  version = "0.3.0";
+  name = "${pname}-${version}";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "02wj58aqyq1nr0axz2vci72zvpkmalrj570lrndqqvai7qmb6fz6";
+  };
+
+  propagatedBuildInputs = [
+    pandas
+    shapely
+    fiona
+    descartes
+    pyproj
+  ];
+
+  meta = with stdenv.lib; {
+    description = "Python geospatial data analysis framework";
+    homepage = https://geopandas.org;
+    license = licenses.bsd3;
+    maintainers = with maintainers; [ knedlsepp ];
+  };
+}
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 80dcfa5662f..1b7c2746830 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -10725,6 +10725,8 @@ in {
 
   };
 
+  geopandas = callPackage ../development/python-modules/geopandas { };
+
   gevent-websocket = buildPythonPackage rec {
     name = "gevent-websocket-0.9.3";
 

From 1dbe68a5e8d52a70d815671023566058a14c70fc Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=B6rg=20Thalheim?= <joerg@thalheim.io>
Date: Tue, 5 Sep 2017 08:20:30 +0100
Subject: [PATCH 7/9] python.pkgs.geopandas: fix tests

---
 .../python-modules/geopandas/default.nix      | 22 +++++++++++++------
 1 file changed, 15 insertions(+), 7 deletions(-)

diff --git a/pkgs/development/python-modules/geopandas/default.nix b/pkgs/development/python-modules/geopandas/default.nix
index c048f9d01ed..f8f54e0e429 100644
--- a/pkgs/development/python-modules/geopandas/default.nix
+++ b/pkgs/development/python-modules/geopandas/default.nix
@@ -1,16 +1,24 @@
-{ stdenv, buildPythonPackage, fetchPypi,
-  pandas, shapely, fiona, descartes, pyproj }:
+{ stdenv, buildPythonPackage, fetchFromGitHub
+, pandas, shapely, fiona, descartes, pyproj
+, pytest }:
 
 buildPythonPackage rec {
-  pname = "geopandas";
+  name = "geopandas-${version}";
   version = "0.3.0";
-  name = "${pname}-${version}";
 
-  src = fetchPypi {
-    inherit pname version;
-    sha256 = "02wj58aqyq1nr0axz2vci72zvpkmalrj570lrndqqvai7qmb6fz6";
+  src = fetchFromGitHub {
+    owner = "geopandas";
+    repo = "geopandas";
+    rev = "v${version}";
+    sha256 = "0maafafr7sjjmlg2f19bizg06c8a5z5igmbcgq6kgmi7rklx8xxz";
   };
 
+  checkInputs = [ pytest ];
+
+  checkPhase = ''
+    py.test geopandas
+  '';
+
   propagatedBuildInputs = [
     pandas
     shapely

From 85011d70845f5705d6b06ba2a3c2a10eb352fcd7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=B6rg=20Thalheim?= <joerg@thalheim.io>
Date: Tue, 5 Sep 2017 08:38:02 +0100
Subject: [PATCH 8/9] python.pkgs.shapely: fix library extension

there was one dot too much
---
 .../python-modules/shapely/default.nix        | 44 +++++++++++++++++++
 pkgs/top-level/python-packages.nix            | 39 +---------------
 2 files changed, 45 insertions(+), 38 deletions(-)
 create mode 100644 pkgs/development/python-modules/shapely/default.nix

diff --git a/pkgs/development/python-modules/shapely/default.nix b/pkgs/development/python-modules/shapely/default.nix
new file mode 100644
index 00000000000..8b8b06f9a2c
--- /dev/null
+++ b/pkgs/development/python-modules/shapely/default.nix
@@ -0,0 +1,44 @@
+{ stdenv, buildPythonPackage, fetchPypi
+, geos, glibcLocales, pytest, cython, sharedLibraryExtension
+, numpy
+}:
+
+buildPythonPackage rec {
+  name = "${pname}-${version}";
+  pname = "Shapely";
+  version = "1.5.15";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0lfqxb3kpdn0g9zzlhzg79yc8iyy4fpsk0p5nd80gar1mmhr8pg7";
+  };
+
+  buildInputs = [ geos glibcLocales cython ];
+
+  checkInputs = [ pytest ];
+
+  propagatedBuildInputs = [ numpy ];
+
+  preConfigure = ''
+    export LANG="en_US.UTF-8";
+  '';
+
+  patchPhase = let
+    libc = if stdenv.isDarwin then "libc.dylib" else "libc.so.6";
+  in ''
+    sed -i "s|_lgeos = load_dll('geos_c', fallbacks=.*)|_lgeos = load_dll('geos_c', fallbacks=['${geos}/lib/libgeos_c${sharedLibraryExtension}'])|" shapely/geos.py
+    sed -i "s|free = load_dll('c').free|free = load_dll('c', fallbacks=['${stdenv.cc.libc}/lib/${stdenv.cc.libc}']).free|" shapely/geos.py
+  '';
+
+  # tests/test_voctorized fails because the vectorized extension is not
+  # available in when running tests
+  checkPhase = ''
+    py.test --ignore tests/test_vectorized.py
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Geometric objects, predicates, and operations";
+    maintainers = with maintainers; [ knedlsepp ];
+    homepage = "https://pypi.python.org/pypi/Shapely/";
+  };
+}
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 1b7c2746830..94dcfa32322 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -21665,44 +21665,7 @@ in {
     };
   };
 
-  shapely = buildPythonPackage rec {
-    name = "Shapely-${version}";
-    version = "1.5.15";
-
-    src = pkgs.fetchurl {
-      url = "mirror://pypi/S/Shapely/${name}.tar.gz";
-      sha256 = "0lfqxb3kpdn0g9zzlhzg79yc8iyy4fpsk0p5nd80gar1mmhr8pg7";
-    };
-
-    buildInputs = with self; [ pkgs.geos pkgs.glibcLocales pytest cython ];
-
-    propagatedBuildInputs = with self; [ numpy ];
-
-    preConfigure = ''
-      export LANG="en_US.UTF-8";
-    '';
-
-    patchPhase = let
-      libc = if stdenv.isDarwin then "libc.dylib" else "libc.so.6";
-    in ''
-      sed -i "s|_lgeos = load_dll('geos_c', fallbacks=.*)|_lgeos = load_dll('geos_c', fallbacks=['${pkgs.geos}/lib/libgeos_c.${sharedLibraryExtension}'])|" shapely/geos.py
-      sed -i "s|free = load_dll('c').free|free = load_dll('c', fallbacks=['${stdenv.cc.libc}/lib/${libc}']).free|" shapely/geos.py
-    '';
-
-    # tests/test_voctorized fails because the vectorized extension is not
-    # available in when running tests
-    checkPhase = ''
-      py.test --ignore tests/test_vectorized.py
-    '';
-
-    meta = {
-      description = "Geometric objects, predicates, and operations";
-      maintainers = with maintainers; [ knedlsepp ];
-      homepage = "https://pypi.python.org/pypi/Shapely/";
-    };
-  };
-
-
+  shapely = callPackage ../development/python-modules/shapely { };
 
   sopel = buildPythonPackage rec {
     name = "sopel-6.3.1";

From e1eb89e3e10f5cf6e438cdb9fb7da2df34a7da24 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=B6rg=20Thalheim?= <joerg@thalheim.io>
Date: Tue, 5 Sep 2017 08:42:53 +0100
Subject: [PATCH 9/9] python.pkgs.cligj: enable tests

---
 .../python-modules/cligj/default.nix           | 18 +++++++++++++-----
 1 file changed, 13 insertions(+), 5 deletions(-)

diff --git a/pkgs/development/python-modules/cligj/default.nix b/pkgs/development/python-modules/cligj/default.nix
index 12b597f3698..91b289e2ede 100644
--- a/pkgs/development/python-modules/cligj/default.nix
+++ b/pkgs/development/python-modules/cligj/default.nix
@@ -1,5 +1,5 @@
-{ stdenv, buildPythonPackage, fetchPypi,
-  click
+{ stdenv, buildPythonPackage, fetchFromGitHub
+, click, pytest, glibcLocales
 }:
 
 buildPythonPackage rec {
@@ -7,15 +7,23 @@ buildPythonPackage rec {
   version = "0.4.0";
   name = "${pname}-${version}";
 
-  src = fetchPypi {
-    inherit pname version;
-    sha256 = "0m1zic66nay2rymfa9krd3jfpyajxjnbmzw7c2q764aw9ychgb8j";
+  src = fetchFromGitHub {
+    owner = "mapbox";
+    repo = "cligj";
+    rev = version;
+    sha256 = "0fclxagxv23v75yiypb29a8sja23dakhvmx3blmxyhg2sci92sx8";
   };
 
   propagatedBuildInputs = [
     click
   ];
 
+  checkInputs = [ pytest glibcLocales ];
+
+  checkPhase = ''
+    LC_ALL=en_US.utf-8 pytest tests
+  '';
+
   meta = with stdenv.lib; {
     description = "Click params for commmand line interfaces to GeoJSON";
     homepage = https://github.com/mapbox/cligj;