I. #143 linting tests, remove pgp.testing
Remove pgp.testing from fisheries_io.py. Updating history Lots of test linting
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Doug
parent
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27
HISTORY.rst
27
HISTORY.rst
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@ -1,19 +1,26 @@
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.. :changelog:
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Unreleased Changes (3.9)
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------------------------
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* Migrating over to GDAL 3 from GDAL 2.
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* Updating requirements to reflect GDAL version >= 3.
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* Updating crop production tests that varied slightly due to GDAL 3
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differences in handling spatial references.
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* Adding function in utils.py to handle InVEST coordindate transformations.
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* Adding tests for new coordinate transformation function in utils.py.
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* General
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* Migrating over to GDAL 3 from GDAL 2.
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* Updating requirements to reflect GDAL version >= 3.
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* Updating crop production tests that varied slightly due to GDAL 3
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differences in handling spatial references.
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* Adding function in utils.py to handle InVEST coordindate transformations.
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* Adding tests for new coordinate transformation function in utils.py.
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* Making InVEST compatible with Pygeoprocessing 2.0 by updating:
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* ``convolve_2d`` keyword ``ignore_nodata`` to ``ignore_nodata_and_edges``.
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* ``get_raster_info`` / ``get_vector_info`` keyword ``projection`` to
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``projection_wkt``.
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* Updating InVEST tests that were dependent on the removed ``pgp.testing``
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module.
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Unreleased Changes
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------------------
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* SDR's compiled core now defines its own ``SQRT2`` instead of relying on an
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available standard C library definition. This new definition helps to avoid
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some compiler issues on Windows.
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* sdr
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* SDR's compiled core now defines its own ``SQRT2`` instead of relying on an
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available standard C library definition. This new definition helps to avoid
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some compiler issues on Windows.
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3.8.2 (2020-05-15)
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------------------
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@ -5,11 +5,11 @@ The Fisheries IO module contains functions for handling inputs and outputs
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import logging
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import os
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import csv
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import math
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import numpy
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from osgeo import ogr
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from osgeo import gdal
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import pygeoprocessing.testing
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from .. import reporting
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from .. import utils
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@ -271,9 +271,8 @@ def read_population_csv(args, path):
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"Region vector shapes do not match. %s" % path)
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# Check that information is correct
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assert pygeoprocessing.testing.isclose(
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pop_dict['Larvaldispersal'].sum(), 1), (
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"The Larvaldisperal vector does not sum exactly to one.. %s" % path)
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assert math.isclose(pop_dict['Larvaldispersal'].sum(), 1), (
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f"The Larvaldisperal vector does not sum exactly to one.. {path}")
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# Check that certain attributes have fraction elements
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Frac_Vectors = ['Survnaturalfrac', 'Vulnfishing',
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@ -13,8 +13,8 @@ import numpy
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def make_simple_raster(base_raster_path, fill_val, nodata_val):
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"""Create a 10x10 raster on designated path with fill value.
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Parameters:
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raster_path (str): the raster path for making the new raster.
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Args:
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base_raster_path (str): the raster path for making the new raster.
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fill_val (int): the value used for filling the raster.
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nodata_val (int or None): for defining a band's nodata value.
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@ -50,7 +50,7 @@ def make_simple_raster(base_raster_path, fill_val, nodata_val):
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def assert_raster_equal_value(base_raster_path, val_to_compare):
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"""Assert that the entire output raster has the same value as specified.
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Parameters:
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Args:
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base_raster_path (str): the filepath of the raster to be asserted.
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val_to_compare (float): the value to be filled in the array to compare.
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@ -70,7 +70,7 @@ def assert_raster_equal_value(base_raster_path, val_to_compare):
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def make_pools_csv(pools_csv_path):
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"""Create a carbon pools csv file with simplified land cover types.
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Parameters:
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Args:
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pools_csv_path (str): the path of carbon pool csv.
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Returns:
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@ -1,9 +1,10 @@
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"""Module for Testing the InVEST cli framework."""
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import sys
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import os
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import shutil
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import tempfile
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import unittest
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from unittest.mock import patch
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import unittest.mock
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import contextlib
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import json
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@ -24,6 +25,7 @@ def redirect_stdout():
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class CLIHeadlessTests(unittest.TestCase):
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"""Headless Tests for CLI."""
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def setUp(self):
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"""Use a temporary workspace for all tests in this class."""
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self.workspace_dir = tempfile.mkdtemp()
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@ -149,9 +151,8 @@ class CLIHeadlessTests(unittest.TestCase):
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os.path.dirname(__file__), '..', 'data', 'invest-test-data',
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'coastal_blue_carbon', 'cbc_galveston_bay.invs.json')
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with unittest.mock.patch(
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'natcap.invest.coastal_blue_carbon.coastal_blue_carbon.execute',
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return_value=None) as patched_model:
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targ = 'natcap.invest.coastal_blue_carbon.coastal_blue_carbon.execute'
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with unittest.mock.patch(targ, return_value=None) as patched_model:
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cli.main([
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'run',
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'cbc', # uses an alias
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@ -6,7 +6,6 @@ import shutil
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import csv
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import logging
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import tempfile
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import functools
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import copy
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import pprint
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@ -74,7 +73,7 @@ NODATA_INT = -9999
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def _read_array(raster_path):
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""""Read raster as array."""
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"""Read raster as array."""
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ds = gdal.Open(raster_path)
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band = ds.GetRasterBand(1)
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a = band.ReadAsArray()
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@ -98,7 +97,7 @@ def _create_workspace():
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def _get_args(workspace, num_transitions=2, valuation=True):
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"""Create and return arguments for CBC main model.
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Parameters:
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Args:
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workspace(string): A path to a folder on disk. Generated inputs will
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be saved to this directory.
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num_transitions=2 (int): The number of transitions to synthesize.
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@ -112,7 +111,7 @@ def _get_args(workspace, num_transitions=2, valuation=True):
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band_matrices_two = numpy.ones((2, 2)) * 2
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band_matrices_with_nodata = numpy.ones((2, 2))
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band_matrices_with_nodata[0][0] = NODATA_INT
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srs = osr.SpatialReference()
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srs.ImportFromEPSG(3157)
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projection_wkt = srs.ExportToWkt()
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@ -131,15 +130,15 @@ def _get_args(workspace, num_transitions=2, valuation=True):
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carbon_pool_transient_list)
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raster_0_path = os.path.join(workspace, 'raster_0.tif')
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pygeoprocessing.numpy_array_to_raster(
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band_matrices, NODATA_INT, (100, -100), origin, projection_wkt,
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band_matrices, NODATA_INT, (100, -100), origin, projection_wkt,
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raster_0_path)
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raster_1_path = os.path.join(workspace, 'raster_1.tif')
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pygeoprocessing.numpy_array_to_raster(
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band_matrices_with_nodata, NODATA_INT, (100, -100), origin,
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band_matrices_with_nodata, NODATA_INT, (100, -100), origin,
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projection_wkt, raster_1_path)
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raster_2_path = os.path.join(workspace, 'raster_2.tif')
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pygeoprocessing.numpy_array_to_raster(
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band_matrices_two, NODATA_INT, (100, -100), origin,
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band_matrices_two, NODATA_INT, (100, -100), origin,
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projection_wkt, raster_2_path)
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possible_transitions = [raster_1_path, raster_2_path]
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@ -153,7 +152,8 @@ def _get_args(workspace, num_transitions=2, valuation=True):
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'lulc_baseline_map_uri': raster_0_path,
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'lulc_baseline_year': 1995,
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'lulc_transition_maps_list': possible_transitions[:num_transitions+1],
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'lulc_transition_years_list': possible_transition_years[:num_transitions+1],
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'lulc_transition_years_list': possible_transition_years[
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:num_transitions+1],
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'analysis_year': 2010,
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'carbon_pool_initial_uri': carbon_pool_initial_path,
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'carbon_pool_transient_uri': carbon_pool_transient_path,
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@ -199,27 +199,27 @@ def _get_preprocessor_args(args_choice, workspace):
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raster_0_path = os.path.join(workspace, 'raster_0.tif')
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pygeoprocessing.numpy_array_to_raster(
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band_matrices_ones, NODATA_INT, (100, -100), origin, projection_wkt,
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band_matrices_ones, NODATA_INT, (100, -100), origin, projection_wkt,
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raster_0_path)
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raster_1_path = os.path.join(workspace, 'raster_1.tif')
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pygeoprocessing.numpy_array_to_raster(
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band_matrices_ones, NODATA_INT, (100, -100), origin, projection_wkt,
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band_matrices_ones, NODATA_INT, (100, -100), origin, projection_wkt,
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raster_1_path)
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raster_2_path = os.path.join(workspace, 'raster_2.tif')
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pygeoprocessing.numpy_array_to_raster(
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band_matrices_ones, NODATA_INT, (100, -100), origin, projection_wkt,
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band_matrices_ones, NODATA_INT, (100, -100), origin, projection_wkt,
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raster_2_path)
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raster_3_path = os.path.join(workspace, 'raster_3.tif')
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pygeoprocessing.numpy_array_to_raster(
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band_matrices_zeros, NODATA_INT, (100, -100), origin, projection_wkt,
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band_matrices_zeros, NODATA_INT, (100, -100), origin, projection_wkt,
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raster_3_path)
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raster_4_path = os.path.join(workspace, 'raster_4.tif')
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pygeoprocessing.numpy_array_to_raster(
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band_matrices_zeros, NODATA_INT, (100, -100), origin, projection_wkt,
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band_matrices_zeros, NODATA_INT, (100, -100), origin, projection_wkt,
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raster_4_path)
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raster_nodata_path = os.path.join(workspace, 'raster_4.tif')
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pygeoprocessing.numpy_array_to_raster(
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band_matrices_nodata, NODATA_INT, (100, -100), origin, projection_wkt,
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band_matrices_nodata, NODATA_INT, (100, -100), origin, projection_wkt,
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raster_nodata_path)
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args = {
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@ -240,14 +240,16 @@ def _get_preprocessor_args(args_choice, workspace):
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'workspace_dir': os.path.join(workspace, 'workspace'),
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'results_suffix': 'test',
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'lulc_lookup_uri': lulc_lookup_path,
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'lulc_snapshot_list': [raster_0_path, raster_nodata_path, raster_3_path]
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'lulc_snapshot_list': [
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raster_0_path, raster_nodata_path, raster_3_path]
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}
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args4 = {
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'workspace_dir': os.path.join(workspace, 'workspace'),
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'results_suffix': 'test',
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'lulc_lookup_uri': lulc_lookup_path,
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'lulc_snapshot_list': [raster_0_path, raster_nodata_path, raster_4_path]
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'lulc_snapshot_list': [
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raster_0_path, raster_nodata_path, raster_4_path]
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}
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if args_choice == 1:
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@ -274,9 +276,8 @@ class TestPreprocessor(unittest.TestCase):
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def test_create_carbon_pool_transient_table_template(self):
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"""Coastal Blue Carbon: Test creation of transient table template."""
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from natcap.invest.coastal_blue_carbon import preprocessor
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args = _get_preprocessor_args(1, self.workspace_dir)
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filepath = os.path.join(self.workspace_dir,
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'transient_temp.csv')
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filepath = os.path.join(
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self.workspace_dir, 'transient_temp.csv')
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code_to_lulc_dict = {1: 'one', 2: 'two', 3: 'three'}
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preprocessor._create_carbon_pool_transient_table_template(
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filepath, code_to_lulc_dict)
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@ -376,19 +377,19 @@ class TestPreprocessor(unittest.TestCase):
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from natcap.invest.coastal_blue_carbon import preprocessor
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args = _get_preprocessor_args(1, self.workspace_dir)
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OTHER_NODATA = -1
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srs = osr.SpatialReference()
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srs.ImportFromEPSG(3157)
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projection_wkt = srs.ExportToWkt()
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origin = (443723.127327877911739, 4956546.905980412848294)
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band_matrices_with_nodata = numpy.ones((2, 2)) * OTHER_NODATA
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raster_wrong_nodata = os.path.join(
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self.workspace_dir, 'raster_wrong_nodata.tif')
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pygeoprocessing.numpy_array_to_raster(
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band_matrices_with_nodata, OTHER_NODATA, (100, -100), origin,
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band_matrices_with_nodata, OTHER_NODATA, (100, -100), origin,
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projection_wkt, raster_wrong_nodata)
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args['lulc_snapshot_list'][0] = raster_wrong_nodata
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with self.assertRaises(ValueError):
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preprocessor.execute(args)
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@ -415,7 +416,7 @@ class TestPreprocessor(unittest.TestCase):
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raster_zeros = os.path.join(self.workspace_dir, 'raster_1.tif')
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pygeoprocessing.numpy_array_to_raster(
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band_matrices_zero, NODATA_INT, (100, -100), origin,
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band_matrices_zero, NODATA_INT, (100, -100), origin,
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projection_wkt, raster_zeros)
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args['lulc_snapshot_list'][0] = raster_zeros
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@ -443,7 +444,7 @@ class TestPreprocessor(unittest.TestCase):
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raster_zeros = os.path.join(self.workspace_dir, 'raster_1.tif')
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pygeoprocessing.numpy_array_to_raster(
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band_matrices_zero, NODATA_INT, (100, -100), origin,
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band_matrices_zero, NODATA_INT, (100, -100), origin,
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projection_wkt, raster_zeros)
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args['lulc_snapshot_list'][0] = raster_zeros
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@ -496,6 +497,7 @@ class TestIO(unittest.TestCase):
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self.args = _get_args(self.workspace_dir)
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def tearDown(self):
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"""Clean up workspace when finished."""
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shutil.rmtree(self.workspace_dir)
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def test_get_inputs(self):
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@ -629,7 +631,8 @@ class TestModel(unittest.TestCase):
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self.args['analysis_year'] = None
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self.args['lulc_baseline_year'] = 2000
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self.args['lulc_transition_maps_list'] = [self.args['lulc_transition_maps_list'][0]]
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self.args['lulc_transition_maps_list'] = [
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self.args['lulc_transition_maps_list'][0]]
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self.args['lulc_transition_years_list'] = [2005]
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cbc.execute(self.args)
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@ -714,7 +717,8 @@ class TestModel(unittest.TestCase):
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'price_table_uri': os.path.join(
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REGRESSION_DATA, 'inputs/Price_table_SCC3.csv'),
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'lulc_transition_matrix_uri': os.path.join(
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REGRESSION_DATA, 'outputs_preprocessor/transitions_sample.csv'),
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REGRESSION_DATA,
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'outputs_preprocessor/transitions_sample.csv'),
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'price': 10.0,
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'results_suffix': '150225'
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}
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@ -741,7 +745,8 @@ class TestModel(unittest.TestCase):
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# walk through all files in the workspace and assert that outputs have
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# the file suffix.
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non_suffixed_files = []
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for root_dir, dirnames, filenames in os.walk(self.args['workspace_dir']):
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for root_dir, dirnames, filenames in os.walk(
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self.args['workspace_dir']):
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for filename in filenames:
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if not filename.lower().endswith('.txt'): # ignore logfile
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basename, extension = os.path.splitext(filename)
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@ -778,10 +783,13 @@ class TestModel(unittest.TestCase):
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class CBCRefactorTest(unittest.TestCase):
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"""CBC Refactor Tests."""
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def setUp(self):
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"""Create a temporary workspace."""
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self.workspace_dir = tempfile.mkdtemp()
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def tearDown(self):
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"""Remove temporary workspace when done."""
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shutil.rmtree(self.workspace_dir)
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@staticmethod
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@ -792,15 +800,15 @@ class CBCRefactorTest(unittest.TestCase):
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workspace (string): The path to the workspace directory on disk.
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Files will be saved to this location.
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transition_tuples (list or None): A list of tuples, where the first
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element of the tuple is a numpy matrix of the transition values,
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and the second element of the tuple is the year of the transition.
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Provided years must be in chronological order.
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element of the tuple is a numpy matrix of the transition
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values, and the second element of the tuple is the year of the
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transition. Provided years must be in chronological order.
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If ``None``, the transition parameters will be ignored.
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analysis_year (int or None): The year of the final analysis. If
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provided, it must be greater than the last year within the
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transition tuples (unless ``transition_tuples`` is None, in which
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case ``analysis_year`` can be anything greater than 2000, the
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baseline year).
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transition tuples (unless ``transition_tuples`` is None, in
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which case ``analysis_year`` can be anything greater than 2000,
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the baseline year).
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Returns:
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A dict of the model arguments.
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@ -810,12 +818,12 @@ class CBCRefactorTest(unittest.TestCase):
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args = {
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'workspace_dir': workspace,
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'lulc_lookup_uri': os.path.join(workspace, 'lulc_lookup.csv'),
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'lulc_transition_matrix_uri': os.path.join(workspace,
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'transition_matrix.csv'),
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'carbon_pool_initial_uri': os.path.join(workspace,
|
||||
'carbon_pool_initial.csv'),
|
||||
'carbon_pool_transient_uri': os.path.join(workspace,
|
||||
'carbon_pool_transient.csv'),
|
||||
'lulc_transition_matrix_uri': os.path.join(
|
||||
workspace, 'transition_matrix.csv'),
|
||||
'carbon_pool_initial_uri': os.path.join(
|
||||
workspace, 'carbon_pool_initial.csv'),
|
||||
'carbon_pool_transient_uri': os.path.join(
|
||||
workspace, 'carbon_pool_transient.csv'),
|
||||
'lulc_baseline_map_uri': os.path.join(workspace, 'lulc.tif'),
|
||||
'lulc_baseline_year': 2000,
|
||||
'do_economic_analysis': False,
|
||||
|
|
@ -831,12 +839,11 @@ class CBCRefactorTest(unittest.TestCase):
|
|||
args['carbon_pool_transient_uri'],
|
||||
carbon_pool_transient_list)
|
||||
|
||||
|
||||
srs = osr.SpatialReference()
|
||||
srs.ImportFromEPSG(3157)
|
||||
projection_wkt = srs.ExportToWkt()
|
||||
origin = (443723.127327877911739, 4956546.905980412848294)
|
||||
|
||||
|
||||
known_matrix_size = None
|
||||
if transition_tuples:
|
||||
args['lulc_transition_maps_list'] = []
|
||||
|
|
@ -847,7 +854,7 @@ class CBCRefactorTest(unittest.TestCase):
|
|||
filename = os.path.join(
|
||||
workspace, 'transition_%s.tif' % transition_year)
|
||||
pygeoprocessing.numpy_array_to_raster(
|
||||
band_matrix, -1, (100, -100), origin, projection_wkt,
|
||||
band_matrix, -1, (100, -100), origin, projection_wkt,
|
||||
filename)
|
||||
|
||||
args['lulc_transition_maps_list'].append(filename)
|
||||
|
|
@ -856,7 +863,7 @@ class CBCRefactorTest(unittest.TestCase):
|
|||
# Make the lulc
|
||||
lulc_shape = (10, 10) if not known_matrix_size else known_matrix_size
|
||||
pygeoprocessing.numpy_array_to_raster(
|
||||
numpy.ones(lulc_shape), -1, (100, -100), origin, projection_wkt,
|
||||
numpy.ones(lulc_shape), -1, (100, -100), origin, projection_wkt,
|
||||
args['lulc_baseline_map_uri'])
|
||||
|
||||
if analysis_year:
|
||||
|
|
@ -990,7 +997,8 @@ class CBCValidationTests(unittest.TestCase):
|
|||
from natcap.invest.coastal_blue_carbon import coastal_blue_carbon
|
||||
from natcap.invest import validation
|
||||
|
||||
validation_errors = coastal_blue_carbon.validate({}) # empty args dict.
|
||||
# empty args dict.
|
||||
validation_errors = coastal_blue_carbon.validate({})
|
||||
invalid_keys = validation.get_invalid_keys(validation_errors)
|
||||
expected_missing_keys = set(self.base_required_keys)
|
||||
self.assertEqual(invalid_keys, expected_missing_keys)
|
||||
|
|
|
|||
|
|
@ -10,7 +10,8 @@ from osgeo import gdal, osr, ogr
|
|||
import numpy.testing
|
||||
import pandas.testing
|
||||
import pygeoprocessing
|
||||
from shapely.geometry import Point, Polygon, MultiPolygon, LineString, MultiLineString
|
||||
from shapely.geometry import Point, Polygon, MultiPolygon
|
||||
from shapely.geometry import LineString, MultiLineString
|
||||
import shapely.wkb
|
||||
import taskgraph
|
||||
|
||||
|
|
@ -100,7 +101,8 @@ class CoastalVulnerabilityTests(unittest.TestCase):
|
|||
# add the max_fetch_distance to the bounding box so we can use
|
||||
# the clipped raster in the fetch-ray-depth routine.
|
||||
model_resolution = 5000
|
||||
fetch_buffer = max_fetch_distance + model_resolution # add the model resolution, to be safe
|
||||
# add the model resolution, to be safe
|
||||
fetch_buffer = max_fetch_distance + model_resolution
|
||||
aoi_bounding_box[0] -= fetch_buffer
|
||||
aoi_bounding_box[1] -= fetch_buffer
|
||||
aoi_bounding_box[2] += fetch_buffer
|
||||
|
|
@ -279,7 +281,8 @@ class CoastalVulnerabilityTests(unittest.TestCase):
|
|||
def test_invalid_habitats_outside_search_radius(self):
|
||||
"""CV: test habitat search when no valid habitat within range."""
|
||||
workspace_dir = self.workspace_dir
|
||||
habitat_vector_path = os.path.join(workspace_dir, 'invalid_habitat.gpkg')
|
||||
habitat_vector_path = os.path.join(
|
||||
workspace_dir, 'invalid_habitat.gpkg')
|
||||
_ = make_vector_of_invalid_geoms(habitat_vector_path)
|
||||
|
||||
base_shore_point_vector_path = os.path.join(
|
||||
|
|
@ -287,7 +290,8 @@ class CoastalVulnerabilityTests(unittest.TestCase):
|
|||
search_radius = 1 # meter, we don't want to find any habitat.
|
||||
habitat_rank = 1
|
||||
habitat_id = 'foo'
|
||||
target_habitat_pickle_path = os.path.join(workspace_dir, 'target.pickle')
|
||||
target_habitat_pickle_path = os.path.join(
|
||||
workspace_dir, 'target.pickle')
|
||||
|
||||
coastal_vulnerability.search_for_habitat(
|
||||
base_shore_point_vector_path, search_radius, habitat_rank,
|
||||
|
|
@ -335,7 +339,7 @@ class CoastalVulnerabilityTests(unittest.TestCase):
|
|||
fields = {'shore_id': ogr.OFTInteger}
|
||||
attrs = [{'shore_id': 0}]
|
||||
pygeoprocessing.shapely_geometry_to_vector(
|
||||
point, simple_points_path, projection_wkt, 'GPKG',
|
||||
point, simple_points_path, projection_wkt, 'GPKG',
|
||||
fields=fields, attribute_list=attrs, ogr_geom_type=ogr.wkbPoint)
|
||||
target_pickle_path = os.path.join(
|
||||
workspace_dir, 'geomorphology.pickle')
|
||||
|
|
@ -375,7 +379,7 @@ class CoastalVulnerabilityTests(unittest.TestCase):
|
|||
target_surge_pickle_path, expected_raw_values_path)
|
||||
|
||||
def test_no_shelf_contour_near_aoi(self):
|
||||
"""CV: test ValueError raised if shelf contour is too far from shore."""
|
||||
"""CV: test ValueError raised if shelf contour too far from shore."""
|
||||
workspace_dir = self.workspace_dir
|
||||
base_shore_point_vector_path = os.path.join(
|
||||
INPUT_DATA, "wwiii_shore_points_5000m.gpkg")
|
||||
|
|
@ -390,7 +394,7 @@ class CoastalVulnerabilityTests(unittest.TestCase):
|
|||
(bbox[0] - 2e6, bbox[1] - 2e6),
|
||||
(bbox[0] - 2e6 - 100, bbox[1] - 2e6 - 100)])
|
||||
pygeoprocessing.shapely_geometry_to_vector(
|
||||
[line_a], shelf_contour_path, srs_wkt, 'GeoJSON',
|
||||
[line_a], shelf_contour_path, srs_wkt, 'GeoJSON',
|
||||
ogr_geom_type=ogr.wkbLineString)
|
||||
|
||||
target_surge_pickle_path = os.path.join(workspace_dir, 'surge.pickle')
|
||||
|
|
@ -418,8 +422,8 @@ class CoastalVulnerabilityTests(unittest.TestCase):
|
|||
# Make a shore point in center of AOI bbox
|
||||
shore_point_path = os.path.join(workspace_dir, 'shore_point.shp')
|
||||
pygeoprocessing.shapely_geometry_to_vector(
|
||||
geometries, shore_point_path, srs_wkt, 'GeoJSON',
|
||||
fields=fields, attribute_list=attributes,
|
||||
geometries, shore_point_path, srs_wkt, 'GeoJSON',
|
||||
fields=fields, attribute_list=attributes,
|
||||
ogr_geom_type=ogr.wkbPoint)
|
||||
|
||||
# Make surge line as diagonal of AOI bounding box
|
||||
|
|
@ -429,7 +433,7 @@ class CoastalVulnerabilityTests(unittest.TestCase):
|
|||
line_b = LineString([(bbox[0], bbox[1]), (bbox[2], bbox[3])])
|
||||
geometries = [MultiLineString([line_a, line_b])]
|
||||
pygeoprocessing.shapely_geometry_to_vector(
|
||||
geometries, shelf_contour_path, srs_wkt, 'GeoJSON',
|
||||
geometries, shelf_contour_path, srs_wkt, 'GeoJSON',
|
||||
ogr_geom_type=ogr.wkbMultiLineString)
|
||||
|
||||
target_surge_pickle_path = os.path.join(
|
||||
|
|
@ -482,7 +486,8 @@ class CoastalVulnerabilityTests(unittest.TestCase):
|
|||
expected_values_dict, invert_values=True)
|
||||
expected_rank_dict = {
|
||||
int(x[0]): int(x[1]) for x in expected_rank_dict.items()}
|
||||
# the dict items need sorting by FID to match the pre-sorted pickled items
|
||||
# the dict items need sorting by FID to match the pre-sorted pickled
|
||||
# items
|
||||
expected_ranks = [x[1] for x in sorted(expected_rank_dict.items())]
|
||||
|
||||
numpy.testing.assert_array_equal(
|
||||
|
|
@ -524,13 +529,15 @@ class CoastalVulnerabilityTests(unittest.TestCase):
|
|||
|
||||
# Make an SLR point vector
|
||||
slr_fieldname = 'Trend'
|
||||
slr_point_vector_path = os.path.join(workspace_dir, 'simple_points.shp')
|
||||
slr_point_vector_path = os.path.join(
|
||||
workspace_dir, 'simple_points.shp')
|
||||
out_driver = ogr.GetDriverByName('ESRI Shapefile')
|
||||
srs = osr.SpatialReference()
|
||||
srs.ImportFromEPSG(4326)
|
||||
shapely_feature = Point(-125.65, 49.0)
|
||||
out_vector = out_driver.CreateDataSource(slr_point_vector_path)
|
||||
layer_name = os.path.basename(os.path.splitext(slr_point_vector_path)[0])
|
||||
layer_name = os.path.basename(
|
||||
os.path.splitext(slr_point_vector_path)[0])
|
||||
out_layer = out_vector.CreateLayer(layer_name, srs=srs)
|
||||
field_defn = ogr.FieldDefn(slr_fieldname, ogr.OFTReal)
|
||||
out_layer.CreateField(field_defn)
|
||||
|
|
@ -565,11 +572,11 @@ class CoastalVulnerabilityTests(unittest.TestCase):
|
|||
projection_wkt = srs.ExportToWkt()
|
||||
shore_point_path = os.path.join(workspace_dir, 'shore_point.shp')
|
||||
fields = {'shore_id': ogr.OFTInteger}
|
||||
attributes=[{'shore_id': 0}]
|
||||
attributes = [{'shore_id': 0}]
|
||||
|
||||
pygeoprocessing.shapely_geometry_to_vector(
|
||||
[Point(0., 0.)], shore_point_path, projection_wkt, 'GeoJSON',
|
||||
fields=fields, attribute_list=attributes,
|
||||
[Point(0., 0.)], shore_point_path, projection_wkt, 'GeoJSON',
|
||||
fields=fields, attribute_list=attributes,
|
||||
ogr_geom_type=ogr.wkbPoint)
|
||||
|
||||
slr_point_vector_path = os.path.join(workspace_dir, 'slr_point.shp')
|
||||
|
|
@ -600,11 +607,11 @@ class CoastalVulnerabilityTests(unittest.TestCase):
|
|||
projection_wkt = srs.ExportToWkt()
|
||||
shore_point_path = os.path.join(workspace_dir, 'shore_point.shp')
|
||||
fields = {'shore_id': ogr.OFTInteger}
|
||||
attributes=[{'shore_id': 0}]
|
||||
attributes = [{'shore_id': 0}]
|
||||
|
||||
pygeoprocessing.shapely_geometry_to_vector(
|
||||
[Point(0., 0.)], shore_point_path, projection_wkt, 'GeoJSON',
|
||||
fields=fields, attribute_list=attributes,
|
||||
[Point(0., 0.)], shore_point_path, projection_wkt, 'GeoJSON',
|
||||
fields=fields, attribute_list=attributes,
|
||||
ogr_geom_type=ogr.wkbPoint)
|
||||
|
||||
slr_point_vector_path = os.path.join(workspace_dir, 'slr_point.shp')
|
||||
|
|
@ -623,7 +630,7 @@ class CoastalVulnerabilityTests(unittest.TestCase):
|
|||
self.assertTrue(expected_message in actual_message)
|
||||
|
||||
def test_long_aggregate_radius(self):
|
||||
"""CV: handle an unreasonably long search radius in raster aggregation."""
|
||||
"""CV: handle unreasonably long search radius in raster aggregation."""
|
||||
workspace_dir = self.workspace_dir
|
||||
raster_path = os.path.join(workspace_dir, 'simple_raster.tif')
|
||||
target_pickle_path = os.path.join(workspace_dir, 'target.pickle')
|
||||
|
|
@ -654,7 +661,7 @@ class CoastalVulnerabilityTests(unittest.TestCase):
|
|||
|
||||
geometries = [
|
||||
Point(0.1, -0.1), # pixel (0,0): kernel origin out of bounds
|
||||
Point(1.25, -1.25), # pixel (2,2): kernel origin & extent out of bounds
|
||||
Point(1.25, -1.25), # pixel (2,2): kernel origin & extent O.O.B
|
||||
Point(2.1, -2.1), # pixel (4,4): kernel extent out of bounds
|
||||
]
|
||||
fields = {'shore_id': ogr.OFTInteger}
|
||||
|
|
@ -662,8 +669,8 @@ class CoastalVulnerabilityTests(unittest.TestCase):
|
|||
# Make a vector proximate to the raster
|
||||
simple_points_path = os.path.join(workspace_dir, 'simple_points.shp')
|
||||
pygeoprocessing.shapely_geometry_to_vector(
|
||||
geometries, simple_points_path, projection_wkt, 'GeoJSON',
|
||||
fields=fields, attribute_list=attributes,
|
||||
geometries, simple_points_path, projection_wkt, 'GeoJSON',
|
||||
fields=fields, attribute_list=attributes,
|
||||
ogr_geom_type=ogr.wkbPoint)
|
||||
|
||||
coastal_vulnerability._aggregate_raster_values_in_radius(
|
||||
|
|
@ -679,7 +686,7 @@ class CoastalVulnerabilityTests(unittest.TestCase):
|
|||
list(actual_values.values()), expected_values, decimal=4)
|
||||
|
||||
def test_complete_run(self):
|
||||
"""CV: regression test for a complete run with all optional arguments."""
|
||||
"""CV: regression test for a complete run w/ all optional arguments."""
|
||||
args = CoastalVulnerabilityTests.generate_base_args(self.workspace_dir)
|
||||
# these optional args aren't included in base_args:
|
||||
args['geomorphology_vector_path'] = os.path.join(
|
||||
|
|
@ -703,10 +710,12 @@ class CoastalVulnerabilityTests(unittest.TestCase):
|
|||
# Also expect matching shore_id field in all tabular outputs:
|
||||
intermediate_csv = pandas.read_csv(
|
||||
os.path.join(
|
||||
args['workspace_dir'], 'intermediate/intermediate_exposure.csv'))
|
||||
args['workspace_dir'],
|
||||
'intermediate/intermediate_exposure.csv'))
|
||||
habitat_csv = pandas.read_csv(
|
||||
os.path.join(
|
||||
args['workspace_dir'], 'intermediate/habitats/habitat_protection.csv'))
|
||||
args['workspace_dir'],
|
||||
'intermediate/habitats/habitat_protection.csv'))
|
||||
pandas.testing.assert_series_equal(
|
||||
actual_values_df['shore_id'], intermediate_csv['shore_id'])
|
||||
pandas.testing.assert_series_equal(
|
||||
|
|
@ -723,12 +732,14 @@ class CoastalVulnerabilityTests(unittest.TestCase):
|
|||
|
||||
# Points with ranks for the final equation. Also includes a field
|
||||
# without the R_ prefix, which final equation should ignore.
|
||||
base_vector_path = os.path.join(REGRESSION_DATA, 'coastal_exposure.gpkg')
|
||||
base_vector_path = os.path.join(
|
||||
REGRESSION_DATA, 'coastal_exposure.gpkg')
|
||||
|
||||
# This input gets modified in place, so first copy to working dir
|
||||
# I'm using GPKG driver to copy because that driver may have problems
|
||||
# updating a file created by a different GPKG driver version, and the version
|
||||
# used is dependent on GDAL version. https://gdal.org/drivers/vector/gpkg.html
|
||||
# updating a file created by a different GPKG driver version, and the
|
||||
# version used is dependent on GDAL version.
|
||||
# https://gdal.org/drivers/vector/gpkg.html
|
||||
base_shore_point_vector = ogr.Open(base_vector_path)
|
||||
gpkg_driver = ogr.GetDriverByName('GPKG')
|
||||
gpkg_driver.CopyDataSource(
|
||||
|
|
@ -750,17 +761,23 @@ class CoastalVulnerabilityTests(unittest.TestCase):
|
|||
self.assertTrue(numpy.isnan(result))
|
||||
|
||||
def test_final_risk_calc_with_missing_data(self):
|
||||
"""CV: test missing data at feature propogates to empty field in output."""
|
||||
"""CV: test final risk calculation w/ missing data.
|
||||
|
||||
Test missing data at feature propogates to empty field in output.
|
||||
"""
|
||||
target_vector_path = os.path.join(self.workspace_dir, 'target.gpkg')
|
||||
target_csv_path = os.path.join(self.workspace_dir, 'target.csv')
|
||||
|
||||
# This gpkg has a feature with an empty field value for 'R_slr'
|
||||
# The function modifies the file in place, so copy to test workspace first.
|
||||
# The function modifies the file in place, so copy to test workspace
|
||||
# first.
|
||||
|
||||
# I'm using GPKG driver to copy because that driver may have problems
|
||||
# updating a file created by a different GPKG driver version, and the version
|
||||
# used is dependent on GDAL version. https://gdal.org/drivers/vector/gpkg.html
|
||||
base_vector_path = os.path.join(REGRESSION_DATA, 'test_missing_values.gpkg')
|
||||
# updating a file created by a different GPKG driver version, and the
|
||||
# version used is dependent on GDAL version.
|
||||
# https://gdal.org/drivers/vector/gpkg.html
|
||||
base_vector_path = os.path.join(
|
||||
REGRESSION_DATA, 'test_missing_values.gpkg')
|
||||
base_shore_point_vector = ogr.Open(base_vector_path)
|
||||
gpkg_driver = ogr.GetDriverByName('GPKG')
|
||||
gpkg_driver.CopyDataSource(
|
||||
|
|
@ -833,8 +850,8 @@ class CoastalVulnerabilityTests(unittest.TestCase):
|
|||
fields = {'shore_id': ogr.OFTInteger}
|
||||
attributes = [{'shore_id': 0}]
|
||||
pygeoprocessing.shapely_geometry_to_vector(
|
||||
[Point(0., 0.)], simple_points_path, projection_wkt, 'GeoJSON',
|
||||
fields=fields, attribute_list=attributes,
|
||||
[Point(0., 0.)], simple_points_path, projection_wkt, 'GeoJSON',
|
||||
fields=fields, attribute_list=attributes,
|
||||
ogr_geom_type=ogr.wkbPoint)
|
||||
|
||||
coastal_vulnerability._aggregate_raster_values_in_radius(
|
||||
|
|
@ -955,7 +972,7 @@ class CoastalVulnerabilityTests(unittest.TestCase):
|
|||
srs = osr.SpatialReference()
|
||||
srs.ImportFromEPSG(26910) # UTM Zone 10N
|
||||
wkt = srs.ExportToWkt()
|
||||
|
||||
|
||||
aoi_geometries = [Polygon([
|
||||
(-200, -200), (200, -200), (200, 200), (-200, 200), (-200, -200)])]
|
||||
pygeoprocessing.shapely_geometry_to_vector(
|
||||
|
|
@ -963,13 +980,13 @@ class CoastalVulnerabilityTests(unittest.TestCase):
|
|||
|
||||
landmass_path = os.path.join(workspace_dir, 'landmass.geojson')
|
||||
poly_a = Polygon([
|
||||
(-200, -200), (-100, -200), (-100, -100), (-200, -100),
|
||||
(-200, -200), (-100, -200), (-100, -100), (-200, -100),
|
||||
(-200, -200)])
|
||||
poly_b = Polygon([
|
||||
(100, 100), (200, 100), (200, 200), (100, 200), (100, 100)])
|
||||
landmass_geometries = [poly_a, poly_b, MultiPolygon([poly_a, poly_b])]
|
||||
pygeoprocessing.shapely_geometry_to_vector(
|
||||
landmass_geometries, landmass_path, wkt, 'GeoJSON',
|
||||
landmass_geometries, landmass_path, wkt, 'GeoJSON',
|
||||
ogr_geom_type=ogr.wkbUnknown)
|
||||
|
||||
args['aoi_vector_path'] = aoi_path
|
||||
|
|
@ -1054,11 +1071,11 @@ class CoastalVulnerabilityTests(unittest.TestCase):
|
|||
srs.ImportFromEPSG(26910) # UTM Zone 10N
|
||||
wkt = srs.ExportToWkt()
|
||||
poly_a = Polygon([
|
||||
(-200, -200), (-100, -200), (-100, -100), (-200, -100),
|
||||
(-200, -200), (-100, -200), (-100, -100), (-200, -100),
|
||||
(-200, -200)])
|
||||
poly_b = Polygon([
|
||||
(100, 100), (200, 100), (200, 200), (100, 200), (100, 100)])
|
||||
|
||||
|
||||
pygeoprocessing.shapely_geometry_to_vector(
|
||||
[poly_a, poly_b], aoi_path, wkt, 'GeoJSON')
|
||||
|
||||
|
|
@ -1096,20 +1113,21 @@ class CoastalVulnerabilityTests(unittest.TestCase):
|
|||
self.assertTrue(n_points == 6)
|
||||
|
||||
def test_no_wwiii_coverage(self):
|
||||
"""CV: test exception when shore points are outside max wwiii distance."""
|
||||
"""CV: test exception when shore points are outside max wwiii dist."""
|
||||
args = CoastalVulnerabilityTests.generate_base_args(self.workspace_dir)
|
||||
srs = osr.SpatialReference()
|
||||
srs.ImportFromEPSG(26910) # UTM Zone 10N
|
||||
projection_wkt = srs.ExportToWkt()
|
||||
|
||||
simple_points_path = os.path.join(self.workspace_dir, 'simple_points.shp')
|
||||
simple_points_path = os.path.join(
|
||||
self.workspace_dir, 'simple_points.shp')
|
||||
|
||||
fields = {'shore_id': ogr.OFTInteger}
|
||||
attributes = [{'shore_id': 0}]
|
||||
|
||||
pygeoprocessing.shapely_geometry_to_vector(
|
||||
[Point(0.0, 0.0)], simple_points_path, projection_wkt, 'GeoJSON',
|
||||
fields=fields, attribute_list=attributes,
|
||||
[Point(0.0, 0.0)], simple_points_path, projection_wkt, 'GeoJSON',
|
||||
fields=fields, attribute_list=attributes,
|
||||
ogr_geom_type=ogr.wkbPoint)
|
||||
|
||||
target_path = os.path.join(self.workspace_dir, 'target.gpkg')
|
||||
|
|
@ -1142,8 +1160,8 @@ class CoastalVulnerabilityTests(unittest.TestCase):
|
|||
attributes = [{'shore_id': 0}]
|
||||
|
||||
pygeoprocessing.shapely_geometry_to_vector(
|
||||
geometries, simple_points_path, projection_wkt, 'GeoJSON',
|
||||
fields=fields, attribute_list=attributes,
|
||||
geometries, simple_points_path, projection_wkt, 'GeoJSON',
|
||||
fields=fields, attribute_list=attributes,
|
||||
ogr_geom_type=ogr.wkbPoint)
|
||||
|
||||
target_path = os.path.join(workspace_dir, 'target.gpkg')
|
||||
|
|
@ -1278,7 +1296,8 @@ class CoastalVulnerabilityTests(unittest.TestCase):
|
|||
base_point_vector_path, base_raster_path, sample_distance,
|
||||
target_pickle_path, aggregation_mode)
|
||||
actual_message = str(cm.exception)
|
||||
expected_message = 'aggregation mode must be either "mean" or "density"'
|
||||
expected_message = ('aggregation mode must be either "mean" or '
|
||||
'"density"')
|
||||
self.assertTrue(actual_message == expected_message)
|
||||
|
||||
def test_invalid_habitat_table_paths(self):
|
||||
|
|
@ -1298,7 +1317,8 @@ class CoastalVulnerabilityTests(unittest.TestCase):
|
|||
def test_polygon_to_lines(self):
|
||||
"""CV: test a helper function that converts polygons to linestrings."""
|
||||
# Test a polygon with inner rings to cover all paths through function.
|
||||
donut_wkt = 'POLYGON ((35 10, 45 45, 15 40, 10 20, 35 10), (20 30, 35 35, 30 20, 20 30))'
|
||||
donut_wkt = ('POLYGON ((35 10, 45 45, 15 40, 10 20, 35 10), '
|
||||
'(20 30, 35 35, 30 20, 20 30))')
|
||||
geometry = ogr.CreateGeometryFromWkt(donut_wkt)
|
||||
shapely_geom = shapely.wkb.loads(geometry.ExportToWkb())
|
||||
line_list = coastal_vulnerability.polygon_to_lines(shapely_geom)
|
||||
|
|
@ -1359,7 +1379,8 @@ class CoastalVulnerabilityValidationTests(unittest.TestCase):
|
|||
from natcap.invest import coastal_vulnerability
|
||||
from natcap.invest import validation
|
||||
|
||||
validation_errors = coastal_vulnerability.validate({}) # empty args dict.
|
||||
# empty args dict.
|
||||
validation_errors = coastal_vulnerability.validate({})
|
||||
invalid_keys = validation.get_invalid_keys(validation_errors)
|
||||
expected_missing_keys = set(
|
||||
self.base_required_keys)
|
||||
|
|
@ -1498,8 +1519,9 @@ def make_vector_of_invalid_geoms(target_vector_path):
|
|||
assert not invalid_shared_edge_polygon.IsValid()
|
||||
|
||||
# 3: Dangling edge - fixed by buffer
|
||||
invalid_dangling_edge_polygon = ogr.CreateGeometryFromWkt(
|
||||
'POLYGON((100 100, 110 100, 115 105, 110 100, 110 110, 100 110, 100 100))')
|
||||
dangle_geom = ('POLYGON((100 100, 110 100, 115 105, 110 100, 110 110, '
|
||||
'100 110, 100 100))')
|
||||
invalid_dangling_edge_polygon = ogr.CreateGeometryFromWkt(dangle_geom)
|
||||
assert not invalid_dangling_edge_polygon.IsValid()
|
||||
|
||||
# One invalid geom that cannot be loaded by shapely or fixed by buffer
|
||||
|
|
|
|||
|
|
@ -319,7 +319,8 @@ class CropValidationTests(unittest.TestCase):
|
|||
from natcap.invest import crop_production_percentile
|
||||
from natcap.invest import validation
|
||||
|
||||
validation_errors = crop_production_percentile.validate({}) # empty args dict.
|
||||
# empty args dict.
|
||||
validation_errors = crop_production_percentile.validate({})
|
||||
invalid_keys = validation.get_invalid_keys(validation_errors)
|
||||
expected_missing_keys = set(self.base_required_keys)
|
||||
self.assertEqual(invalid_keys, expected_missing_keys)
|
||||
|
|
@ -329,7 +330,8 @@ class CropValidationTests(unittest.TestCase):
|
|||
from natcap.invest import crop_production_regression
|
||||
from natcap.invest import validation
|
||||
|
||||
validation_errors = crop_production_regression.validate({}) # empty args dict.
|
||||
# empty args dict.
|
||||
validation_errors = crop_production_regression.validate({})
|
||||
invalid_keys = validation.get_invalid_keys(validation_errors)
|
||||
expected_missing_keys = set(
|
||||
self.base_required_keys +
|
||||
|
|
|
|||
|
|
@ -1,3 +1,4 @@
|
|||
"""Testing Module for Datastack."""
|
||||
import os
|
||||
import unittest
|
||||
import tempfile
|
||||
|
|
@ -44,13 +45,13 @@ def _assert_vectors_equal(
|
|||
av, ev, decimal=tolerance_places)
|
||||
else:
|
||||
assert(ev is None)
|
||||
|
||||
|
||||
expected_geom = feature.GetGeometryRef()
|
||||
expected_geom_wkt = expected_geom.ExportToWkt()
|
||||
actual_geom = feature.GetGeometryRef()
|
||||
actual_geom_wkt = actual_geom.ExportToWkt()
|
||||
assert(expected_geom_wkt == actual_geom_wkt)
|
||||
|
||||
|
||||
feature = None
|
||||
actual_feature = None
|
||||
finally:
|
||||
|
|
@ -61,13 +62,17 @@ def _assert_vectors_equal(
|
|||
|
||||
|
||||
class DatastacksTest(unittest.TestCase):
|
||||
"""Test Datastack."""
|
||||
def setUp(self):
|
||||
"""Create temporary workspace."""
|
||||
self.workspace = tempfile.mkdtemp()
|
||||
|
||||
def tearDown(self):
|
||||
"""Remove temporary workspace."""
|
||||
shutil.rmtree(self.workspace)
|
||||
|
||||
def test_collect_simple_parameters(self):
|
||||
"""Datastack: test collect simple parameters."""
|
||||
from natcap.invest import datastack
|
||||
params = {
|
||||
'a': 1,
|
||||
|
|
@ -93,6 +98,7 @@ class DatastacksTest(unittest.TestCase):
|
|||
{'a': 1, 'b': 'hello there', 'c': 'plain bytestring', 'd': ''})
|
||||
|
||||
def test_collect_multipart_gdal_raster(self):
|
||||
"""Datastack: test collect multipart gdal raster."""
|
||||
from natcap.invest import datastack
|
||||
params = {
|
||||
'raster': os.path.join(DATA_DIR, 'dem'),
|
||||
|
|
@ -119,6 +125,7 @@ class DatastacksTest(unittest.TestCase):
|
|||
numpy.testing.assert_allclose(model_array, reg_array)
|
||||
|
||||
def test_collect_geotiff(self):
|
||||
"""Datastack: test collect geotiff."""
|
||||
# Necessary test, as this is proving to be an issue.
|
||||
from natcap.invest import datastack
|
||||
params = {
|
||||
|
|
@ -136,6 +143,7 @@ class DatastacksTest(unittest.TestCase):
|
|||
numpy.testing.assert_allclose(model_array, reg_array)
|
||||
|
||||
def test_collect_ogr_vector(self):
|
||||
"""Datastack: test collect ogr vector."""
|
||||
from natcap.invest import datastack
|
||||
source_vector_path = os.path.join(DATA_DIR, 'watersheds.shp')
|
||||
source_vector = ogr.Open(source_vector_path)
|
||||
|
|
@ -169,12 +177,13 @@ class DatastacksTest(unittest.TestCase):
|
|||
out_directory,
|
||||
datastack.DATASTACK_PARAMETER_FILENAME)))['args']
|
||||
_assert_vectors_equal(
|
||||
params['vector'],
|
||||
params['vector'],
|
||||
os.path.join(out_directory, archived_params['vector']))
|
||||
|
||||
self.assertEqual(len(archived_params), 1) # sanity check
|
||||
|
||||
def test_collect_ogr_table(self):
|
||||
"""Datastack: test collect ogr table."""
|
||||
from natcap.invest import datastack
|
||||
params = {
|
||||
'table': os.path.join(DATA_DIR, 'carbon_pools_samp.csv'),
|
||||
|
|
@ -193,14 +202,15 @@ class DatastacksTest(unittest.TestCase):
|
|||
open(os.path.join(
|
||||
out_directory,
|
||||
datastack.DATASTACK_PARAMETER_FILENAME)))['args']
|
||||
model_df = pandas.read_csv(params['table'])
|
||||
reg_df = pandas.read_csv(
|
||||
model_df = pandas.read_csv(params['table'])
|
||||
reg_df = pandas.read_csv(
|
||||
os.path.join(out_directory, archived_params['table']))
|
||||
pandas.testing.assert_frame_equal(model_df, reg_df)
|
||||
|
||||
self.assertEqual(len(archived_params), 1) # sanity check
|
||||
|
||||
def test_nonspatial_single_file(self):
|
||||
"""Datastack: test nonspatial single file."""
|
||||
from natcap.invest import datastack
|
||||
|
||||
params = {
|
||||
|
|
@ -222,13 +232,14 @@ class DatastacksTest(unittest.TestCase):
|
|||
open(os.path.join(out_directory,
|
||||
datastack.DATASTACK_PARAMETER_FILENAME)))['args']
|
||||
self.assertTrue(filecmp.cmp(
|
||||
params['some_file'],
|
||||
os.path.join(out_directory, archived_params['some_file']),
|
||||
params['some_file'],
|
||||
os.path.join(out_directory, archived_params['some_file']),
|
||||
shallow=False))
|
||||
|
||||
self.assertEqual(len(archived_params), 1) # sanity check
|
||||
|
||||
def test_data_dir(self):
|
||||
"""Datastack: test data directory."""
|
||||
from natcap.invest import datastack
|
||||
params = {
|
||||
'data_dir': os.path.join(self.workspace, 'data_dir')
|
||||
|
|
@ -261,7 +272,7 @@ class DatastacksTest(unittest.TestCase):
|
|||
self.assertEqual(len(archived_params), 1) # sanity check
|
||||
common_files = ['foo.txt', 'bar.txt', 'baz.txt', 'nested/nested.txt']
|
||||
matched_files, mismatch_files, error_files = filecmp.cmpfiles(
|
||||
params['data_dir'],
|
||||
params['data_dir'],
|
||||
os.path.join(out_directory, archived_params['data_dir']),
|
||||
common_files, shallow=False)
|
||||
if mismatch_files or error_files:
|
||||
|
|
@ -269,6 +280,7 @@ class DatastacksTest(unittest.TestCase):
|
|||
f' {mismatch_files} ; and the errors are {error_files}')
|
||||
|
||||
def test_list_of_inputs(self):
|
||||
"""Datastack: test list of inputs."""
|
||||
from natcap.invest import datastack
|
||||
params = {
|
||||
'file_list': [
|
||||
|
|
@ -292,8 +304,9 @@ class DatastacksTest(unittest.TestCase):
|
|||
archived_params = json.load(
|
||||
open(os.path.join(out_directory,
|
||||
datastack.DATASTACK_PARAMETER_FILENAME)))['args']
|
||||
archived_file_list = [
|
||||
os.path.join(out_directory, filename) for filename in archived_params['file_list']]
|
||||
archived_file_list = [
|
||||
os.path.join(out_directory, filename)
|
||||
for filename in archived_params['file_list']]
|
||||
|
||||
self.assertEqual(len(archived_params), 1) # sanity check
|
||||
for expected_file, archive_file in zip(
|
||||
|
|
@ -302,6 +315,7 @@ class DatastacksTest(unittest.TestCase):
|
|||
self.fail(f'File mismatch: {expected_file} != {archive_file}')
|
||||
|
||||
def test_duplicate_filepaths(self):
|
||||
"""Datastack: test duplicate filepaths."""
|
||||
from natcap.invest import datastack
|
||||
params = {
|
||||
'foo': os.path.join(self.workspace, 'foo.txt'),
|
||||
|
|
@ -335,6 +349,7 @@ class DatastacksTest(unittest.TestCase):
|
|||
len(os.listdir(os.path.join(out_directory, 'data'))), 1)
|
||||
|
||||
def test_archive_extraction(self):
|
||||
"""Datastack: test archive extraction."""
|
||||
from natcap.invest import datastack
|
||||
params = {
|
||||
'blank': '',
|
||||
|
|
@ -378,7 +393,7 @@ class DatastacksTest(unittest.TestCase):
|
|||
numpy.testing.assert_allclose(model_array, reg_array)
|
||||
_assert_vectors_equal(
|
||||
archive_params['vector'], params['vector'])
|
||||
model_df = pandas.read_csv(archive_params['table'])
|
||||
model_df = pandas.read_csv(archive_params['table'])
|
||||
reg_df = pandas.read_csv(params['table'])
|
||||
pandas.testing.assert_frame_equal(model_df, reg_df)
|
||||
for key in ('blank', 'a', 'b', 'c'):
|
||||
|
|
@ -396,6 +411,7 @@ class DatastacksTest(unittest.TestCase):
|
|||
filecmp.cmp(expected_file, archive_file, shallow=False))
|
||||
|
||||
def test_nested_args_keys(self):
|
||||
"""Datastack: test nested argument keys."""
|
||||
from natcap.invest import datastack
|
||||
|
||||
params = {
|
||||
|
|
@ -412,6 +428,7 @@ class DatastacksTest(unittest.TestCase):
|
|||
self.assertEqual(archive_params, params)
|
||||
|
||||
def test_datastack_parameter_set(self):
|
||||
"""Datastack: test datastack parameter set."""
|
||||
from natcap.invest import datastack, __version__
|
||||
|
||||
params = {
|
||||
|
|
@ -455,6 +472,7 @@ class DatastacksTest(unittest.TestCase):
|
|||
self.assertEqual(callable_name, modelname)
|
||||
|
||||
def test_relative_parameter_set(self):
|
||||
"""Datastack: test relative parameter set."""
|
||||
from natcap.invest import datastack, __version__
|
||||
|
||||
params = {
|
||||
|
|
@ -566,6 +584,7 @@ class DatastacksTest(unittest.TestCase):
|
|||
params, 'sample_model', natcap.invest.__version__))
|
||||
|
||||
def test_get_datatack_info_parameter_set(self):
|
||||
"""Datastack: test get datastack info parameter set."""
|
||||
import natcap.invest
|
||||
from natcap.invest import datastack
|
||||
|
||||
|
|
@ -585,6 +604,7 @@ class DatastacksTest(unittest.TestCase):
|
|||
params, 'sample_model', natcap.invest.__version__))
|
||||
|
||||
def test_get_datastack_info_logfile_new_style(self):
|
||||
"""Datastack: test get datastack info logfile new style."""
|
||||
import natcap.invest
|
||||
from natcap.invest import datastack
|
||||
args = {
|
||||
|
|
@ -605,6 +625,7 @@ class DatastacksTest(unittest.TestCase):
|
|||
args, 'some_modelname', natcap.invest.__version__))
|
||||
|
||||
def test_get_datastack_info_logfile_iui_style(self):
|
||||
"""Datastack: test get datastack info logfile iui style."""
|
||||
from natcap.invest import datastack
|
||||
|
||||
logfile_path = os.path.join(self.workspace, 'logfile.txt')
|
||||
|
|
@ -701,16 +722,17 @@ class DatastacksTest(unittest.TestCase):
|
|||
extraction_path)
|
||||
|
||||
expected_args = {
|
||||
'windows_path': os.path.join(extraction_path, 'data',
|
||||
'filepath1.txt'),
|
||||
'linux_path': os.path.join(extraction_path, 'data',
|
||||
'filepath2.txt'),
|
||||
'windows_path': os.path.join(
|
||||
extraction_path, 'data', 'filepath1.txt'),
|
||||
'linux_path': os.path.join(
|
||||
extraction_path, 'data', 'filepath2.txt'),
|
||||
}
|
||||
self.maxDiff = None # show whole exception on failure
|
||||
self.assertEqual(extracted_args, expected_args)
|
||||
|
||||
|
||||
class UtilitiesTest(unittest.TestCase):
|
||||
"""Datastack Utilities Tests."""
|
||||
def test_print_args(self):
|
||||
"""Datastacks: verify that we format args correctly."""
|
||||
from natcap.invest.datastack import format_args_dict, __version__
|
||||
|
|
|
|||
|
|
@ -125,7 +125,6 @@ class DelineateItTests(unittest.TestCase):
|
|||
|
||||
def test_point_snapping(self):
|
||||
"""DelineateIt: test point snapping."""
|
||||
|
||||
from natcap.invest import delineateit
|
||||
|
||||
srs = osr.SpatialReference()
|
||||
|
|
@ -155,14 +154,14 @@ class DelineateItTests(unittest.TestCase):
|
|||
Point(13, -5),
|
||||
box(-2, -2, -1, -1), # Off the edge
|
||||
]
|
||||
fields={'foo': ogr.OFTInteger, 'bar': ogr.OFTString}
|
||||
attributes=[
|
||||
fields = {'foo': ogr.OFTInteger, 'bar': ogr.OFTString}
|
||||
attributes = [
|
||||
{'foo': 0, 'bar': 0.1}, {'foo': 1, 'bar': 1.1},
|
||||
{'foo': 2, 'bar': 2.1}, {'foo': 3, 'bar': 3.1},
|
||||
{'foo': 4, 'bar': 4.1}]
|
||||
pygeoprocessing.shapely_geometry_to_vector(
|
||||
source_features, source_points_path, wkt, 'GeoJSON',
|
||||
fields=fields, attribute_list=attributes,
|
||||
source_features, source_points_path, wkt, 'GeoJSON',
|
||||
fields=fields, attribute_list=attributes,
|
||||
ogr_geom_type=ogr.wkbUnknown)
|
||||
|
||||
snapped_points_path = os.path.join(self.workspace_dir,
|
||||
|
|
@ -256,7 +255,7 @@ class DelineateItTests(unittest.TestCase):
|
|||
dem_raster_path = os.path.join(self.workspace_dir, 'dem.tif')
|
||||
# byte datatype
|
||||
pygeoprocessing.numpy_array_to_raster(
|
||||
dem_matrix, 255, (2, -2), (2, -2), projection_wkt,
|
||||
dem_matrix, 255, (2, -2), (2, -2), projection_wkt,
|
||||
dem_raster_path)
|
||||
|
||||
# empty geometry
|
||||
|
|
@ -314,7 +313,8 @@ class DelineateItTests(unittest.TestCase):
|
|||
outflow_layer = None
|
||||
outflow_vector = None
|
||||
|
||||
target_vector_path = os.path.join(self.workspace_dir, 'checked_geometries.gpkg')
|
||||
target_vector_path = os.path.join(
|
||||
self.workspace_dir, 'checked_geometries.gpkg')
|
||||
with self.assertRaises(ValueError) as cm:
|
||||
delineateit.check_geometries(
|
||||
outflow_vector_path, dem_raster_path, target_vector_path,
|
||||
|
|
@ -335,7 +335,8 @@ class DelineateItTests(unittest.TestCase):
|
|||
|
||||
target_vector = gdal.OpenEx(target_vector_path, gdal.OF_VECTOR)
|
||||
target_layer = target_vector.GetLayer()
|
||||
self.assertEqual(target_layer.GetFeatureCount(), len(expected_geom_areas))
|
||||
self.assertEqual(
|
||||
target_layer.GetFeatureCount(), len(expected_geom_areas))
|
||||
|
||||
for feature in target_layer:
|
||||
geom = feature.GetGeometryRef()
|
||||
|
|
|
|||
|
|
@ -26,7 +26,7 @@ EXPECTED_FILE_LIST = [
|
|||
def _make_harvest_shp(workspace_dir):
|
||||
"""Within workspace, make an output folder with dummy Finfish_Harvest.shp.
|
||||
|
||||
Parameters:
|
||||
Args:
|
||||
workspace_dir: path to workspace for creating the output folder.
|
||||
"""
|
||||
output_path = os.path.join(workspace_dir, 'output')
|
||||
|
|
@ -35,6 +35,7 @@ def _make_harvest_shp(workspace_dir):
|
|||
with open(os.path.join(output_path, 'Finfish_Harvest.shp'), 'wb') as shp:
|
||||
shp.write(b'')
|
||||
|
||||
|
||||
def _assert_vectors_equal(
|
||||
actual_vector_path, expected_vector_path, tolerance_places=3):
|
||||
"""Assert fieldnames and values are equal with no respect to order."""
|
||||
|
|
@ -63,13 +64,13 @@ def _assert_vectors_equal(
|
|||
av, ev, decimal=tolerance_places)
|
||||
else:
|
||||
assert(ev is None)
|
||||
|
||||
|
||||
expected_geom = feature.GetGeometryRef()
|
||||
expected_geom_wkt = expected_geom.ExportToWkt()
|
||||
actual_geom = feature.GetGeometryRef()
|
||||
actual_geom_wkt = actual_geom.ExportToWkt()
|
||||
assert(expected_geom_wkt == actual_geom_wkt)
|
||||
|
||||
|
||||
feature = None
|
||||
actual_feature = None
|
||||
finally:
|
||||
|
|
@ -78,6 +79,7 @@ def _assert_vectors_equal(
|
|||
expected_layer = None
|
||||
expected_vector = None
|
||||
|
||||
|
||||
class FinfishTests(unittest.TestCase):
|
||||
"""Tests for Finfish Aquaculture."""
|
||||
|
||||
|
|
@ -93,7 +95,7 @@ class FinfishTests(unittest.TestCase):
|
|||
|
||||
@staticmethod
|
||||
def generate_base_args(workspace_dir):
|
||||
"""Generate an args list that is consistent for both regression tests"""
|
||||
"""Generate args list that is consistent for both regression tests."""
|
||||
args = {
|
||||
'farm_ID': 'FarmID',
|
||||
'farm_op_tbl': os.path.join(SAMPLE_DATA, 'Farm_Operations.csv'),
|
||||
|
|
@ -150,7 +152,7 @@ class FinfishTests(unittest.TestCase):
|
|||
def _test_same_files(base_path_list, directory_path):
|
||||
"""Assert files in `base_path_list` are in `directory_path`.
|
||||
|
||||
Parameters:
|
||||
Args:
|
||||
base_path_list (list): list of strings which are relative
|
||||
file paths.
|
||||
directory_path (string): a path to a directory whose contents will
|
||||
|
|
@ -205,7 +207,8 @@ class FinfishValidationTests(unittest.TestCase):
|
|||
from natcap.invest.finfish_aquaculture import finfish_aquaculture
|
||||
from natcap.invest import validation
|
||||
|
||||
validation_errors = finfish_aquaculture.validate({}) # empty args dict.
|
||||
# empty args dict.
|
||||
validation_errors = finfish_aquaculture.validate({})
|
||||
invalid_keys = validation.get_invalid_keys(validation_errors)
|
||||
expected_missing_keys = set(
|
||||
self.base_required_keys +
|
||||
|
|
|
|||
|
|
@ -30,7 +30,7 @@ class FisheriesSampleDataTests(unittest.TestCase):
|
|||
def get_harvest_info(workspace, filename='results_table.csv'):
|
||||
"""Extract final harvest info from the results CSV.
|
||||
|
||||
Parameters:
|
||||
Args:
|
||||
workspace (string): The path to the output workspace. The file
|
||||
*workspace*/output/results_table.csv must exist.
|
||||
|
||||
|
|
@ -73,16 +73,14 @@ class FisheriesSampleDataTests(unittest.TestCase):
|
|||
from natcap.invest.fisheries import fisheries
|
||||
args = {
|
||||
'alpha': 6050000.0,
|
||||
'aoi_vector_path': os.path.join(SAMPLE_DATA,
|
||||
'shapefile_galveston',
|
||||
'Galveston_Subregion.shp'),
|
||||
'aoi_vector_path': os.path.join(
|
||||
SAMPLE_DATA, 'shapefile_galveston', 'Galveston_Subregion.shp'),
|
||||
'beta': 4.14e-08,
|
||||
'do_batch': False,
|
||||
'harvest_units': 'Weight',
|
||||
'migr_cont': False,
|
||||
'population_csv_path': os.path.join(SAMPLE_DATA,
|
||||
'input_shrimp',
|
||||
'population_params.csv'),
|
||||
'population_csv_path': os.path.join(
|
||||
SAMPLE_DATA, 'input_shrimp', 'population_params.csv'),
|
||||
'population_type': 'Stage-Based',
|
||||
'recruitment_type': 'Fixed',
|
||||
'sexsp': 'No',
|
||||
|
|
@ -97,7 +95,8 @@ class FisheriesSampleDataTests(unittest.TestCase):
|
|||
}
|
||||
validation_warnings = fisheries.validate(args)
|
||||
self.assertEqual(len(validation_warnings), 1)
|
||||
self.assertTrue('required but has no value' in validation_warnings[0][1])
|
||||
self.assertTrue(
|
||||
'required but has no value' in validation_warnings[0][1])
|
||||
|
||||
def test_validation_batch(self):
|
||||
"""Fisheries: Batch parameters (full model validation)."""
|
||||
|
|
@ -106,18 +105,16 @@ class FisheriesSampleDataTests(unittest.TestCase):
|
|||
# enabled.
|
||||
args = {
|
||||
'alpha': 5.77e6,
|
||||
'aoi_vector_path': os.path.join(SAMPLE_DATA,
|
||||
'shapefile_belize',
|
||||
'Lob_Belize_Subregions.shp'),
|
||||
'aoi_vector_path': os.path.join(
|
||||
SAMPLE_DATA, 'shapefile_belize', 'Lob_Belize_Subregions.shp'),
|
||||
'beta': 2.885e6,
|
||||
'do_batch': False,
|
||||
'harvest_units': 'Weight',
|
||||
'migr_cont': True,
|
||||
'migration_dir': os.path.join(SAMPLE_DATA,
|
||||
'input_lobster', 'Migrations'),
|
||||
'population_csv_path': os.path.join(SAMPLE_DATA,
|
||||
'input_lobster',
|
||||
'population_params.csv'),
|
||||
'migration_dir': os.path.join(
|
||||
SAMPLE_DATA, 'input_lobster', 'Migrations'),
|
||||
'population_csv_path': os.path.join(
|
||||
SAMPLE_DATA, 'input_lobster', 'population_params.csv'),
|
||||
'population_type': 'Age-Based',
|
||||
'recruitment_type': 'Beverton-Holt',
|
||||
'sexsp': 'No',
|
||||
|
|
@ -169,7 +166,8 @@ class FisheriesSampleDataTests(unittest.TestCase):
|
|||
"""Fisheries: Validate AOI fields."""
|
||||
from natcap.invest.fisheries import fisheries
|
||||
|
||||
args = {'aoi_vector_path': os.path.join(self.workspace_dir, 'aoi.gpkg')}
|
||||
args = {
|
||||
'aoi_vector_path': os.path.join(self.workspace_dir, 'aoi.gpkg')}
|
||||
gpkg_driver = gdal.GetDriverByName('GPKG')
|
||||
vector = gpkg_driver.Create(
|
||||
args['aoi_vector_path'], 0, 0, 0, gdal.GDT_Unknown)
|
||||
|
|
@ -179,7 +177,8 @@ class FisheriesSampleDataTests(unittest.TestCase):
|
|||
layer = None
|
||||
vector = None
|
||||
|
||||
validation_warnings = fisheries.validate(args, limit_to='aoi_vector_path')
|
||||
validation_warnings = fisheries.validate(
|
||||
args, limit_to='aoi_vector_path')
|
||||
self.assertEqual(len(validation_warnings), 1)
|
||||
self.assertTrue('Fields are missing from the first layer' in
|
||||
validation_warnings[0][1])
|
||||
|
|
@ -200,16 +199,14 @@ class FisheriesSampleDataTests(unittest.TestCase):
|
|||
from natcap.invest.fisheries import fisheries
|
||||
args = {
|
||||
'alpha': 6050000.0,
|
||||
'aoi_vector_path': os.path.join(SAMPLE_DATA,
|
||||
'shapefile_galveston',
|
||||
'Galveston_Subregion.shp'),
|
||||
'aoi_vector_path': os.path.join(
|
||||
SAMPLE_DATA, 'shapefile_galveston', 'Galveston_Subregion.shp'),
|
||||
'beta': 4.14e-08,
|
||||
'do_batch': False,
|
||||
'harvest_units': 'Weight',
|
||||
'migr_cont': False,
|
||||
'population_csv_path': os.path.join(SAMPLE_DATA,
|
||||
'input_shrimp',
|
||||
'population_params.csv'),
|
||||
'population_csv_path': os.path.join(
|
||||
SAMPLE_DATA, 'input_shrimp', 'population_params.csv'),
|
||||
'population_type': 'Stage-Based',
|
||||
'recruitment_type': 'Fixed',
|
||||
'sexsp': 'No',
|
||||
|
|
@ -225,7 +222,8 @@ class FisheriesSampleDataTests(unittest.TestCase):
|
|||
fisheries.execute(args)
|
||||
final_timestep_data = FisheriesSampleDataTests.get_harvest_info(
|
||||
args['workspace_dir'], 'results_table_foo.csv')
|
||||
self.assertEqual(final_timestep_data['spawners'], '(fixed recruitment)')
|
||||
self.assertEqual(
|
||||
final_timestep_data['spawners'], '(fixed recruitment)')
|
||||
self.assertEqual(final_timestep_data['harvest'], 3120557.88)
|
||||
|
||||
def test_sampledata_lobster(self):
|
||||
|
|
@ -233,18 +231,16 @@ class FisheriesSampleDataTests(unittest.TestCase):
|
|||
from natcap.invest.fisheries import fisheries
|
||||
args = {
|
||||
'alpha': 5.77e6,
|
||||
'aoi_vector_path': os.path.join(SAMPLE_DATA,
|
||||
'shapefile_belize',
|
||||
'Lob_Belize_Subregions.shp'),
|
||||
'aoi_vector_path': os.path.join(
|
||||
SAMPLE_DATA, 'shapefile_belize', 'Lob_Belize_Subregions.shp'),
|
||||
'beta': 2.885e6,
|
||||
'do_batch': False,
|
||||
'harvest_units': 'Weight',
|
||||
'migr_cont': True,
|
||||
'migration_dir': os.path.join(SAMPLE_DATA,
|
||||
'input_lobster', 'Migrations'),
|
||||
'population_csv_path': os.path.join(SAMPLE_DATA,
|
||||
'input_lobster',
|
||||
'population_params.csv'),
|
||||
'migration_dir': os.path.join(
|
||||
SAMPLE_DATA, 'input_lobster', 'Migrations'),
|
||||
'population_csv_path': os.path.join(
|
||||
SAMPLE_DATA, 'input_lobster', 'population_params.csv'),
|
||||
'population_type': 'Age-Based',
|
||||
'recruitment_type': 'Beverton-Holt',
|
||||
'sexsp': 'No',
|
||||
|
|
@ -269,16 +265,14 @@ class FisheriesSampleDataTests(unittest.TestCase):
|
|||
from natcap.invest.fisheries import fisheries
|
||||
args = {
|
||||
'alpha': 6.05e6,
|
||||
'aoi_vector_path': os.path.join(SAMPLE_DATA,
|
||||
'shapefile_galveston',
|
||||
'Galveston_Subregion.shp'),
|
||||
'aoi_vector_path': os.path.join(
|
||||
SAMPLE_DATA, 'shapefile_galveston', 'Galveston_Subregion.shp'),
|
||||
'beta': 4.14e-08,
|
||||
'do_batch': False,
|
||||
'harvest_units': 'Individuals',
|
||||
'migr_cont': False,
|
||||
'population_csv_path': os.path.join(SAMPLE_DATA,
|
||||
'input_blue_crab',
|
||||
'population_params.csv'),
|
||||
'population_csv_path': os.path.join(
|
||||
SAMPLE_DATA, 'input_blue_crab', 'population_params.csv'),
|
||||
'population_type': 'Age-Based',
|
||||
'recruitment_type': 'Ricker',
|
||||
'sexsp': 'No',
|
||||
|
|
@ -301,15 +295,13 @@ class FisheriesSampleDataTests(unittest.TestCase):
|
|||
from natcap.invest.fisheries import fisheries
|
||||
args = {
|
||||
'alpha': 6.05e6,
|
||||
'aoi_vector_path': os.path.join(SAMPLE_DATA,
|
||||
'shapefile_galveston',
|
||||
'Galveston_Subregion.shp'),
|
||||
'aoi_vector_path': os.path.join(
|
||||
SAMPLE_DATA, 'shapefile_galveston', 'Galveston_Subregion.shp'),
|
||||
'beta': 4.14e-08,
|
||||
'do_batch': True,
|
||||
'harvest_units': 'Individuals',
|
||||
'migr_cont': False,
|
||||
'population_csv_dir': os.path.join(SAMPLE_DATA,
|
||||
'input_blue_crab'),
|
||||
'population_csv_dir': os.path.join(SAMPLE_DATA, 'input_blue_crab'),
|
||||
'population_type': 'Age-Based',
|
||||
'recruitment_type': 'Ricker',
|
||||
'sexsp': 'No',
|
||||
|
|
@ -332,16 +324,15 @@ class FisheriesSampleDataTests(unittest.TestCase):
|
|||
from natcap.invest.fisheries import fisheries
|
||||
args = {
|
||||
'alpha': 2e6,
|
||||
'aoi_vector_path': os.path.join(SAMPLE_DATA,
|
||||
'shapefile_hood_canal',
|
||||
'DC_HoodCanal_Subregions.shp'),
|
||||
'aoi_vector_path': os.path.join(
|
||||
SAMPLE_DATA, 'shapefile_hood_canal',
|
||||
'DC_HoodCanal_Subregions.shp'),
|
||||
'beta': 3.09e-7,
|
||||
'do_batch': False,
|
||||
'harvest_units': 'Individuals',
|
||||
'migr_cont': False,
|
||||
'population_csv_path': os.path.join(SAMPLE_DATA,
|
||||
'input_dungeness_crab',
|
||||
'population_params.csv'),
|
||||
'population_csv_path': os.path.join(
|
||||
SAMPLE_DATA, 'input_dungeness_crab', 'population_params.csv'),
|
||||
'population_type': 'Age-Based',
|
||||
'recruitment_type': 'Ricker',
|
||||
'sexsp': 'Yes',
|
||||
|
|
@ -361,12 +352,11 @@ class FisheriesSampleDataTests(unittest.TestCase):
|
|||
|
||||
@staticmethod
|
||||
def fecundity_args(workspace):
|
||||
"""
|
||||
Create a base set of args for the fecundity recruitment model.
|
||||
"""Create a base set of args for the fecundity recruitment model.
|
||||
|
||||
The AOI is located in Belize.
|
||||
|
||||
Parameters:
|
||||
Args:
|
||||
workspace (string): The path to the workspace on disk.
|
||||
|
||||
Returns:
|
||||
|
|
@ -374,15 +364,14 @@ class FisheriesSampleDataTests(unittest.TestCase):
|
|||
"""
|
||||
args = {
|
||||
'alpha': 5.77e6,
|
||||
'aoi_vector_path': os.path.join(SAMPLE_DATA,
|
||||
'shapefile_belize',
|
||||
'Lob_Belize_Subregions.shp'),
|
||||
'aoi_vector_path': os.path.join(
|
||||
SAMPLE_DATA, 'shapefile_belize', 'Lob_Belize_Subregions.shp'),
|
||||
'beta': 2.885e6,
|
||||
'do_batch': False,
|
||||
'harvest_units': 'Weight',
|
||||
'migr_cont': False,
|
||||
'population_csv_path': os.path.join(TEST_DATA,
|
||||
'sample_fecundity_params.csv'),
|
||||
'population_csv_path': os.path.join(
|
||||
TEST_DATA, 'sample_fecundity_params.csv'),
|
||||
'population_type': 'Age-Based',
|
||||
'recruitment_type': 'Fecundity',
|
||||
'sexsp': 'No',
|
||||
|
|
@ -397,10 +386,9 @@ class FisheriesSampleDataTests(unittest.TestCase):
|
|||
|
||||
@staticmethod
|
||||
def galveston_args(workspace):
|
||||
"""
|
||||
Create a base set of fecundity args for Galveston Bay.
|
||||
"""Create a base set of fecundity args for Galveston Bay.
|
||||
|
||||
Parameters:
|
||||
Args:
|
||||
workspace (string): The path to the workspace on disk.
|
||||
|
||||
Returns:
|
||||
|
|
@ -409,9 +397,8 @@ class FisheriesSampleDataTests(unittest.TestCase):
|
|||
args = FisheriesSampleDataTests.fecundity_args(workspace)
|
||||
args.update({
|
||||
'alpha': 6050000.0,
|
||||
'aoi_vector_path': os.path.join(SAMPLE_DATA,
|
||||
'shapefile_galveston',
|
||||
'Galveston_Subregion.shp'),
|
||||
'aoi_vector_path': os.path.join(
|
||||
SAMPLE_DATA, 'shapefile_galveston', 'Galveston_Subregion.shp'),
|
||||
'beta': 4.14e-08,
|
||||
'harvest_units': 'Individuals',
|
||||
'spawn_units': 'Individuals',
|
||||
|
|
@ -441,7 +428,7 @@ class FisheriesSampleDataTests(unittest.TestCase):
|
|||
# This doesn't model anything real, but it will produce outputs as
|
||||
# expected.
|
||||
'recruitment_func': lambda x: (numpy.ones((9,)),
|
||||
numpy.float64(100))
|
||||
numpy.float64(100))
|
||||
})
|
||||
|
||||
fisheries.execute(args)
|
||||
|
|
@ -495,9 +482,8 @@ class FisheriesSampleDataTests(unittest.TestCase):
|
|||
args = {
|
||||
'alpha': 6050000.0,
|
||||
'beta': 4.14e-08,
|
||||
'aoi_vector_path': os.path.join(SAMPLE_DATA,
|
||||
'shapefile_galveston',
|
||||
'Galveston_Subregion.shp'),
|
||||
'aoi_vector_path': os.path.join(
|
||||
SAMPLE_DATA, 'shapefile_galveston', 'Galveston_Subregion.shp'),
|
||||
'do_batch': False,
|
||||
'harvest_units': 'Weight',
|
||||
'migr_cont': False,
|
||||
|
|
@ -518,15 +504,17 @@ class FisheriesSampleDataTests(unittest.TestCase):
|
|||
fisheries.execute(args)
|
||||
final_timestep_data = FisheriesSampleDataTests.get_harvest_info(
|
||||
args['workspace_dir'], 'results_table_foo.csv')
|
||||
self.assertEqual(final_timestep_data['spawners'], '(fixed recruitment)')
|
||||
self.assertEqual(
|
||||
final_timestep_data['spawners'], '(fixed recruitment)')
|
||||
self.assertEqual(final_timestep_data['harvest'], 3120557.88)
|
||||
|
||||
# verify that two identical subregions were found.
|
||||
in_subregion = False
|
||||
subregions = {}
|
||||
harvest_table_path = os.path.join(self.workspace_dir, 'output',
|
||||
'results_table_foo.csv')
|
||||
with io.open(harvest_table_path, 'r', newline=os.linesep) as harvest_table:
|
||||
harvest_table_path = os.path.join(
|
||||
self.workspace_dir, 'output', 'results_table_foo.csv')
|
||||
with io.open(
|
||||
harvest_table_path, 'r', newline=os.linesep) as harvest_table:
|
||||
for line in harvest_table:
|
||||
if in_subregion:
|
||||
if line.lower().startswith('total'):
|
||||
|
|
@ -560,10 +548,10 @@ class FisheriesHSTTest(unittest.TestCase):
|
|||
args = {
|
||||
'gamma': 0.5,
|
||||
'hab_cont': False,
|
||||
'habitat_chg_csv_path': os.path.join(HST_INPUTS,
|
||||
'habitat_chg_params.csv'),
|
||||
'habitat_dep_csv_path': os.path.join(HST_INPUTS,
|
||||
'habitat_dep_params.csv'),
|
||||
'habitat_chg_csv_path': os.path.join(
|
||||
HST_INPUTS, 'habitat_chg_params.csv'),
|
||||
'habitat_dep_csv_path': os.path.join(
|
||||
HST_INPUTS, 'habitat_dep_params.csv'),
|
||||
'pop_cont': False,
|
||||
'population_csv_path': os.path.join(HST_INPUTS, 'pop_params.csv'),
|
||||
'sexsp': 'No',
|
||||
|
|
@ -572,7 +560,8 @@ class FisheriesHSTTest(unittest.TestCase):
|
|||
fisheries_hst.execute(args)
|
||||
|
||||
actual_values_df = pandas.read_csv(
|
||||
os.path.join(args['workspace_dir'], 'output', 'pop_params_modified.csv'))
|
||||
os.path.join(
|
||||
args['workspace_dir'], 'output', 'pop_params_modified.csv'))
|
||||
expected_values_df = pandas.read_csv(
|
||||
os.path.join(TEST_DATA, 'pop_params_modified.csv'))
|
||||
pandas.testing.assert_frame_equal(actual_values_df, expected_values_df)
|
||||
|
|
@ -583,13 +572,13 @@ class FisheriesHSTTest(unittest.TestCase):
|
|||
args = {
|
||||
'gamma': 0.5,
|
||||
'hab_cont': False,
|
||||
'habitat_chg_csv_path': os.path.join(HST_INPUTS,
|
||||
'habitat_chg_params.csv'),
|
||||
'habitat_dep_csv_path': os.path.join(HST_INPUTS,
|
||||
'habitat_dep_params.csv'),
|
||||
'habitat_chg_csv_path': os.path.join(
|
||||
HST_INPUTS, 'habitat_chg_params.csv'),
|
||||
'habitat_dep_csv_path': os.path.join(
|
||||
HST_INPUTS, 'habitat_dep_params.csv'),
|
||||
'pop_cont': False,
|
||||
'population_csv_path': os.path.join(TEST_DATA,
|
||||
'hst_pop_params_sexsp.csv'),
|
||||
'population_csv_path': os.path.join(
|
||||
TEST_DATA, 'hst_pop_params_sexsp.csv'),
|
||||
'sexsp': 'Yes',
|
||||
'workspace_dir': self.workspace_dir,
|
||||
}
|
||||
|
|
@ -597,7 +586,9 @@ class FisheriesHSTTest(unittest.TestCase):
|
|||
fisheries_hst.execute(args)
|
||||
|
||||
actual_values_df = pandas.read_csv(
|
||||
os.path.join(args['workspace_dir'], 'output', 'hst_pop_params_sexsp_modified.csv'))
|
||||
os.path.join(
|
||||
args['workspace_dir'], 'output',
|
||||
'hst_pop_params_sexsp_modified.csv'))
|
||||
expected_values_df = pandas.read_csv(
|
||||
os.path.join(TEST_DATA, 'hst_pop_params_sexsp_modified.csv'))
|
||||
pandas.testing.assert_frame_equal(actual_values_df, expected_values_df)
|
||||
|
|
|
|||
Loading…
Reference in New Issue