old_contents: # coding: utf-8
  #   This Python module is part of the PyRate software package.
  #
  #   Copyright 2020 Geoscience Australia
  #
  #   Licensed under the Apache License, Version 2.0 (the "License");
  #   you may not use this file except in compliance with the License.
  #   You may obtain a copy of the License at
  #
  #       http://www.apache.org/licenses/LICENSE-2.0
  #
  #   Unless required by applicable law or agreed to in writing, software
  #   distributed under the License is distributed on an "AS IS" BASIS,
  #   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  #   See the License for the specific language governing permissions and
  #   limitations under the License.
  """
  This Python module contains tests for the Merge step of PyRate.
  """
  import os
  from subprocess import check_call
  import itertools
  import pytest
  from pathlib import Path
  
  import pyrate.configuration
  from pyrate.merge import _create_png_from_tif
  from pyrate.core import config as cf
  from pyrate.merge import _merge_stack
  from pyrate.configuration import Configuration
  from tests.common import manipulate_test_conf
  
  
  @pytest.fixture
  def create_stack_output(tempdir, gamma_conf):
      tdir = Path(tempdir())
      params = manipulate_test_conf(gamma_conf, tdir)
      output_conf_file = tdir.joinpath('conf.cfg')
      output_conf = tdir.joinpath(output_conf_file)
      pyrate.configuration.write_config_file(params=params, output_conf_file=output_conf)
      check_call(f"pyrate conv2tif -f {output_conf}", shell=True)
      check_call(f"pyrate prepifg -f {output_conf}", shell=True)
      check_call(f"pyrate process -f {output_conf}", shell=True)
  
      params = Configuration(output_conf).__dict__
      return params, tdir
  
  
  @pytest.mark.slow
  def test_png_creation(create_stack_output):
      params, tdir = create_stack_output
  
      output_folder_path = params[cf.OUT_DIR]
  
      _merge_stack(params)
      _create_png_from_tif(output_folder_path)
  
      # check if color map is created
      for out_type in ['rate', 'error']:
          output_color_map_path = os.path.join(output_folder_path, f"colourmap_{out_type}.txt")
          assert Path(output_color_map_path).exists(), "Output color map file not found at: " + output_color_map_path
  
      # check if merged files are created
      for _type, output_type in itertools.product(["stack_rate", "stack_error"], ['.tif', '.png', '.kml']):
          output_image_path = os.path.join(output_folder_path, _type + output_type)
          print(f"checking {output_image_path}")
          assert Path(output_image_path).exists(), f"Output {output_type} file not found at {output_image_path}"
  
new_contents: # coding: utf-8
  #   This Python module is part of the PyRate software package.
  #
  #   Copyright 2020 Geoscience Australia
  #
  #   Licensed under the Apache License, Version 2.0 (the "License");
  #   you may not use this file except in compliance with the License.
  #   You may obtain a copy of the License at
  #
  #       http://www.apache.org/licenses/LICENSE-2.0
  #
  #   Unless required by applicable law or agreed to in writing, software
  #   distributed under the License is distributed on an "AS IS" BASIS,
  #   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  #   See the License for the specific language governing permissions and
  #   limitations under the License.
  """
  This Python module contains tests for the Merge step of PyRate.
  """
  import os
  from subprocess import check_call
  import itertools
  import pytest
  from pathlib import Path
  from pyrate.merge import create_png_and_kml_from_tif
  from pyrate.core import config as cf
  from pyrate.merge import _merge_stack, _merge_linrate
  from pyrate.configuration import Configuration, write_config_file
  from tests.common import manipulate_test_conf
  
  
  @pytest.fixture
  def create_merge_output(tempdir, gamma_conf):
      tdir = Path(tempdir())
      params = manipulate_test_conf(gamma_conf, tdir)
      print(params[cf.TIME_SERIES_CAL])
      output_conf_file = tdir.joinpath('conf.cfg')
      output_conf = tdir.joinpath(output_conf_file)
      write_config_file(params=params, output_conf_file=output_conf)
      check_call(f"pyrate conv2tif -f {output_conf}", shell=True)
      check_call(f"pyrate prepifg -f {output_conf}", shell=True)
      check_call(f"pyrate process -f {output_conf}", shell=True)
  
      params = Configuration(output_conf).__dict__
      _merge_stack(params)
      _merge_linrate(params)
      return params, tdir
  
  
  @pytest.mark.slow
  def test_file_creation(create_merge_output):
      params, tdir = create_merge_output
  
      # check if color map is created
      for ot in ['stack_rate', 'stack_error', 'linear_rate', 'linear_error', 'linear_rsquared']:
          create_png_and_kml_from_tif(params[cf.OUT_DIR], output_type=ot)
          output_color_map_path = os.path.join(params[cf.OUT_DIR], f"colourmap_{ot}.txt")
          assert Path(output_color_map_path).exists(), "Output color map file not found at: " + output_color_map_path
  
      # check if merged files are created
      for _type, ot in itertools.product(['stack_rate', 'stack_error', 'linear_rate',
                                          'linear_error', 'linear_rsquared'], ['.tif', '.png', '.kml']):
          output_image_path = os.path.join(params[cf.OUT_DIR], _type + ot)
          print(f"checking {output_image_path}")
          assert Path(output_image_path).exists(), f"Output {ot} file not found at {output_image_path}"
  
subject: fix merge tests