{"action":"created","comment":{"url":"https://api.github.com/repos/metoppv/improver/pulls/comments/121905658","pull_request_review_id":43970874,"id":121905658,"diff_hunk":"@@ -0,0 +1,305 @@\n+# -*- coding: utf-8 -*-\n+# -----------------------------------------------------------------------------\n+# (C) British Crown Copyright 2017 Met Office.\n+# All rights reserved.\n+#\n+# Redistribution and use in source and binary forms, with or without\n+# modification, are permitted provided that the following conditions are met:\n+#\n+# * Redistributions of source code must retain the above copyright notice, this\n+#   list of conditions and the following disclaimer.\n+#\n+# * Redistributions in binary form must reproduce the above copyright notice,\n+#   this list of conditions and the following disclaimer in the documentation\n+#   and/or other materials provided with the distribution.\n+#\n+# * Neither the name of the copyright holder nor the names of its\n+#   contributors may be used to endorse or promote products derived from\n+#   this software without specific prior written permission.\n+#\n+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS \"AS IS\"\n+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE\n+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE\n+# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE\n+# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR\n+# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF\n+# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS\n+# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN\n+# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)\n+# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE\n+# POSSIBILITY OF SUCH DAMAGE.\n+\"\"\"Unit tests for the nbhood.Kernels plugin.\"\"\"\n+\n+\n+import unittest\n+\n+from iris.cube import Cube\n+from iris.tests import IrisTest\n+import numpy as np\n+\n+from improver.nbhood import Kernels\n+from improver.tests.test_nbhood_neighbourhoodprocessing import (\n+    SINGLE_POINT_RANGE_2_CENTROID_FLAT, SINGLE_POINT_RANGE_3_CENTROID,\n+    SINGLE_POINT_RANGE_5_CENTROID, set_up_cube, set_up_cube_lat_long)\n+\n+\n+class Test_circular(IrisTest):\n+\n+    \"\"\"Test neighbourhood processing plugin on the OS National Grid.\"\"\"\n+\n+    RADIUS_IN_KM = 6.3  # Gives 3 grid cells worth.\n+    KERNEL_METHOD = \"circular\"\n+\n+    def test_basic(self):\n+        \"\"\"Test that the plugin returns an iris.cube.Cube.\"\"\"\n+        cube = set_up_cube(\n+            zero_point_indices=((0, 0, 2, 2),), num_time_points=1,\n+            num_grid_points=5)\n+        ranges = (2, 2)\n+        result = Kernels.circular(cube, ranges, unweighted_mode=True)\n+        self.assertIsInstance(result, Cube)\n+\n+    def test_single_point(self):\n+        \"\"\"Test behaviour for a single non-zero grid cell.\"\"\"\n+        cube = set_up_cube()\n+        expected = np.ones_like(cube.data)\n+        for index, slice_ in enumerate(SINGLE_POINT_RANGE_3_CENTROID):\n+            expected[0][0][5 + index][5:10] = slice_\n+        ranges = (3, 3)\n+        result = Kernels.circular(cube, ranges, unweighted_mode=False)\n+        self.assertArrayAlmostEqual(result.data, expected)\n+\n+    def test_single_point_flat(self):\n+        \"\"\"Test behaviour for a single non-zero grid cell, flat weighting.\n+\n+        Note that this gives one more grid cell range than weighted! As the\n+        affected area is one grid cell more in each direction, an equivalent\n+        range of 2 was chosen for this test.\n+\n+        \"\"\"\n+        cube = set_up_cube()\n+        expected = np.ones_like(cube.data)\n+        for index, slice_ in enumerate(SINGLE_POINT_RANGE_2_CENTROID_FLAT):\n+            expected[0][0][5 + index][5:10] = slice_\n+        radius_in_km = 4.2  # Equivalent to a range of 2.\n+        ranges = (2, 2)\n+        result = Kernels.circular(cube, ranges, unweighted_mode=True)\n+        self.assertArrayAlmostEqual(result.data, expected)\n+\n+    def test_multi_point_multitimes(self):\n+        \"\"\"Test behaviour for points over multiple times.\"\"\"\n+        cube = set_up_cube(\n+            zero_point_indices=[(0, 0, 10, 10), (0, 1, 7, 7)],\n+            num_time_points=2\n+        )\n+        expected = np.ones_like(cube.data)\n+        for index, slice_ in enumerate(SINGLE_POINT_RANGE_3_CENTROID):\n+            expected[0][0][8 + index][8:13] = slice_\n+        for index, slice_ in enumerate(SINGLE_POINT_RANGE_3_CENTROID):\n+            expected[0][1][5 + index][5:10] = slice_\n+        ranges = (3, 3)\n+        result = Kernels.circular(cube, ranges, unweighted_mode=False)\n+        self.assertArrayAlmostEqual(result.data, expected)\n+\n+    def test_single_point_lat_long(self):\n+        \"\"\"Test behaviour for a single grid cell on lat long grid.\"\"\"\n+        cube = set_up_cube_lat_long()\n+        msg = \"Invalid grid: projection_x/y coords required\"\n+        expected = np.zeros_like(cube.data)\n+        ranges = (3, 3)\n+        with self.assertRaisesRegexp(ValueError, msg):\n+            Kernels.circular(cube, ranges, unweighted_mode=False)\n+\n+    def test_single_point_masked_to_null(self):\n+        \"\"\"Test behaviour with a masked non-zero point.\n+\n+        The behaviour here is not right, as the mask is ignored.\n+        This comes directly from the scipy.ndimage.correlate base\n+        behaviour.\n+\n+        \"\"\"\n+        cube = set_up_cube()\n+        expected = np.ones_like(cube.data)\n+        mask = np.zeros_like(cube.data)\n+        mask[0][0][7][7] = 1\n+        cube.data = np.ma.masked_array(cube.data, mask=mask)\n+        for time_index in range(len(expected)):\n+            for index, slice_ in enumerate(SINGLE_POINT_RANGE_3_CENTROID):\n+                expected[0][time_index][5 + index][5:10] = slice_\n+        ranges = (3, 3)\n+        result = Kernels.circular(cube, ranges, unweighted_mode=False)\n+        self.assertArrayAlmostEqual(result.data, expected)\n+\n+    def test_single_point_masked_other_point(self):\n+        \"\"\"Test behaviour with a non-zero point next to a masked point.\n+\n+        The behaviour here is not right, as the mask is ignored.\n+\n+        \"\"\"\n+        cube = set_up_cube()\n+        expected = np.ones_like(cube.data)\n+        mask = np.zeros_like(cube.data)\n+        mask[0][0][6][7] = 1\n+        cube.data = np.ma.masked_array(cube.data, mask=mask)\n+        for time_index in range(len(expected)):\n+            for index, slice_ in enumerate(SINGLE_POINT_RANGE_3_CENTROID):\n+                expected[0][time_index][5 + index][5:10] = slice_\n+        ranges = (3, 3)\n+        result = Kernels.circular(cube, ranges, unweighted_mode=False)\n+        self.assertArrayAlmostEqual(result.data, expected)\n+\n+    def test_single_point_range_1(self):\n+        \"\"\"Test behaviour with a non-zero point with unit range.\"\"\"\n+        cube = set_up_cube()\n+        expected = np.ones_like(cube.data)\n+        expected[0][0][7][7] = 0.0\n+        radius_in_km = 2.1  # Equivalent to a range of 1 grid cell.","path":"lib/improver/tests/test_nbhood_kernels.py","position":156,"original_position":156,"commit_id":"98073ff3a84f5abfd84affd7ca35b6c8effed65b","original_commit_id":"98073ff3a84f5abfd84affd7ca35b6c8effed65b","user":{"login":"codacy-bot","id":19940114,"avatar_url":"https://avatars2.githubusercontent.com/u/19940114?v=3","gravatar_id":"","url":"https://api.github.com/users/codacy-bot","html_url":"https://github.com/codacy-bot","followers_url":"https://api.github.com/users/codacy-bot/followers","following_url":"https://api.github.com/users/codacy-bot/following{/other_user}","gists_url":"https://api.github.com/users/codacy-bot/gists{/gist_id}","starred_url":"https://api.github.com/users/codacy-bot/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/codacy-bot/subscriptions","organizations_url":"https://api.github.com/users/codacy-bot/orgs","repos_url":"https://api.github.com/users/codacy-bot/repos","events_url":"https://api.github.com/users/codacy-bot/events{/privacy}","received_events_url":"https://api.github.com/users/codacy-bot/received_events","type":"User","site_admin":false},"body":"![Codacy](https://www.codacy.com/assets/images/favicon.png) Issue found: [Unused variable 'radius_in_km'](https://www.codacy.com/app/metoppv/improver/pullRequest?prid=709757)","created_at":"2017-06-14T10:01:09Z","updated_at":"2017-06-14T10:01:09Z","html_url":"https://github.com/metoppv/improver/pull/114#discussion_r121905658","pull_request_url":"https://api.github.com/repos/metoppv/improver/pulls/114","_links":{"self":{"href":"https://api.github.com/repos/metoppv/improver/pulls/comments/121905658"},"html":{"href":"https://github.com/metoppv/improver/pull/114#discussion_r121905658"},"pull_request":{"href":"https://api.github.com/repos/metoppv/improver/pulls/114"}}},"pull_request":{"url":"https://api.github.com/repos/metoppv/improver/pulls/114","id":125556014,"html_url":"https://github.com/metoppv/improver/pull/114","diff_url":"https://github.com/metoppv/improver/pull/114.diff","patch_url":"https://github.com/metoppv/improver/pull/114.patch","issue_url":"https://api.github.com/repos/metoppv/improver/issues/114","number":114,"state":"open","locked":false,"title":"Nbhood add up 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passed OK\r\n - [x] Added new tests for the new feature(s)","created_at":"2017-06-14T09:59:48Z","updated_at":"2017-06-14T10:01:09Z","closed_at":null,"merged_at":null,"merge_commit_sha":"f205713fd5703694187ceb524460b30bea850fc8","assignee":{"login":"gavinevans","id":26933341,"avatar_url":"https://avatars0.githubusercontent.com/u/26933341?v=3","gravatar_id":"","url":"https://api.github.com/users/gavinevans","html_url":"https://github.com/gavinevans","followers_url":"https://api.github.com/users/gavinevans/followers","following_url":"https://api.github.com/users/gavinevans/following{/other_user}","gists_url":"https://api.github.com/users/gavinevans/gists{/gist_id}","starred_url":"https://api.github.com/users/gavinevans/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gavinevans/subscriptions","organizations_url":"https://api.github.com/users/gavinevans/orgs","repos_url":"https://api.github.com/users/gavinevans/repos","events_url":"https://api.github.com/users/gavinevans/events{/privacy}","received_events_url":"https://api.github.com/users/gavinevans/received_events","type":"User","site_admin":false},"assignees":[{"login":"gavinevans","id":26933341,"avatar_url":"https://avatars0.githubusercontent.com/u/26933341?v=3","gravatar_id":"","url":"https://api.github.com/users/gavinevans","html_url":"https://github.com/gavinevans","followers_url":"https://api.github.com/users/gavinevans/followers","following_url":"https://api.github.com/users/gavinevans/following{/other_user}","gists_url":"https://api.github.com/users/gavinevans/gists{/gist_id}","starred_url":"https://api.github.com/users/gavinevans/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gavinevans/subscriptions","organizations_url":"https://api.github.com/users/gavinevans/orgs","repos_url":"https://api.github.com/users/gavinevans/repos","events_url":"https://api.github.com/users/gavinevans/events{/privacy}","received_events_url":"https://api.github.com/users/gavinevans/received_events","type":"User","site_admin":false},{"login":"meabhnicguidhir","id":28393790,"avatar_url":"https://avatars0.githubusercontent.com/u/28393790?v=3","gravatar_id":"","url":"https://api.github.com/users/meabhnicguidhir","html_url":"https://github.com/meabhnicguidhir","followers_url":"https://api.github.com/users/meabhnicguidhir/followers","following_url":"https://api.github.com/users/meabhnicguidhir/following{/other_user}","gists_url":"https://api.github.com/users/meabhnicguidhir/gists{/gist_id}","starred_url":"https://api.github.com/users/meabhnicguidhir/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/meabhnicguidhir/subscriptions","organizations_url":"https://api.github.com/users/meabhnicguidhir/orgs","repos_url":"https://api.github.com/users/meabhnicguidhir/repos","events_url":"https://api.github.com/users/meabhnicguidhir/events{/privacy}","received_events_url":"https://api.github.com/users/meabhnicguidhir/received_events","type":"User","site_admin":false}],"requested_reviewers":[{"login":"MoseleyS","id":23079172,"avatar_url":"https://avatars3.githubusercontent.com/u/23079172?v=3","gravatar_id":"","url":"https://api.github.com/users/MoseleyS","html_url":"https://github.com/MoseleyS","followers_url":"https://api.github.com/users/MoseleyS/followers","following_url":"https://api.github.com/users/MoseleyS/following{/other_user}","gists_url":"https://api.github.com/users/MoseleyS/gists{/gist_id}","starred_url":"https://api.github.com/users/MoseleyS/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MoseleyS/subscriptions","organizations_url":"https://api.github.com/users/MoseleyS/orgs","repos_url":"https://api.github.com/users/MoseleyS/repos","events_url":"https://api.github.com/users/MoseleyS/events{/privacy}","received_events_url":"https://api.github.com/users/MoseleyS/received_events","type":"User","site_admin":false},{"login":"carolinejjones","id":28533631,"avatar_url":"https://avatars3.githubusercontent.com/u/28533631?v=3","gravatar_id":"","url":"https://api.github.com/users/carolinejjones","html_url":"https://github.com/carolinejjones","followers_url":"https://api.github.com/users/carolinejjones/followers","following_url":"https://api.github.com/users/carolinejjones/following{/other_user}","gists_url":"https://api.github.com/users/carolinejjones/gists{/gist_id}","starred_url":"https://api.github.com/users/carolinejjones/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/carolinejjones/subscriptions","organizations_url":"https://api.github.com/users/carolinejjones/orgs","repos_url":"https://api.github.com/users/carolinejjones/repos","events_url":"https://api.github.com/users/carolinejjones/events{/privacy}","received_events_url":"https://api.github.com/users/carolinejjones/received_events","type":"User","site_admin":false}],"milestone":{"url":"https://api.github.com/repos/metoppv/improver/milestones/2","html_url":"https://github.com/metoppv/improver/milestone/2","labels_url":"https://api.github.com/repos/met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