Merge pull request #378 from GeoscienceAustralia/develop

Release 0.6.1
GeoscienceAustralia · Feb 24, 2022 · 791d01c · 791d01c
2 parents 8203989 + 1033836
commit 791d01c
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diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -61,7 +61,7 @@ jobs:
         run: |
           sudo apt update
           sudo apt upgrade
-          python -m pip install -U pip wheel
+          python -m pip install -U pip wheel setuptools==58.0
       - name: Install packages including openmpi
         if: env.PYTHONVERSION != '3.9'
         run: sudo apt install libhdf5-serial-dev libnetcdf13 libatlas-base-dev gfortran openmpi-bin libopenmpi-dev
@@ -101,8 +101,13 @@ jobs:
           pytest tests/ -m "slow"
           mpirun -n 3 pytest tests/test_shared.py -k test_tiles_split -s
           pytest --cov-config=.coveragerc --cov-report term-missing:skip-covered --cov=pyrate tests/ -m "not slow"
+        env:
+             OMP_NUM_THREADS: 1
       - name: Test Pyrate in Python ${{ matrix.python-version }} without MPI
         if: env.PYTHONVERSION == '3.9'
         run: |
           pytest tests/ -m "not mpi and slow"
           pytest --cov-config=.coveragerc --cov-report term-missing:skip-covered --cov=pyrate tests/ -m "not slow and not mpi"
+        env:
+             OMP_NUM_THREADS: 1
+
diff --git a/docs/_build/html/404.html b/docs/_build/html/404.html
@@ -374,7 +374,7 @@ <h1>
 
               <div role="contentinfo">
                 <p>
-                  &copy; Copyright 2021, Geoscience Australia
+                  &copy; Copyright 2022, Geoscience Australia
                 </p>
               </div>
               Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a

diff --git a/docs/history.rst b/docs/history.rst
@@ -3,6 +3,20 @@
 Release History
 ===============
 
+0.6.1 (2022-02-18)
+------------------
+Added
++++++
+- List generator in ``utils/listcreator.sh`` for easier input generation from GAMMA output to PyRate.
+
+Fixed
++++++
+- Fix wrong sign in Y-intercept output file.
+- Fix and simplify how user supplied reference pixel is validated and cropping issue.
+- Add metadata for reference pixel latitude and longitude to output files.
+- Fix non-determinism in unit tests that use array comparison by running them single threaded.
+
+
 0.6.0 (2021-10-18)
 ------------------
 Added

diff --git a/docs/usage.rst b/docs/usage.rst
@@ -20,7 +20,9 @@ To allow flexibility in the file types that can be processed, `PyRate` requires
 file lists to be provided. This allows `PyRate` to identify files of each
 type without relying on file extensions. The file path to these lists are 
 provided under ``ifgfilelist``, ``hdrfilelist``, ``cohfilelist`` and 
-``basefilelist`` keywords in the configuration file.
+``basefilelist`` keywords in the configuration file. These lists can be created manually 
+or generated using the script ``list_creator.sh`` located in the ``utils`` folder.
+This script may need to be slightly modified depending on the output paths of your input data.
 
 .. note::
 

diff --git a/pyrate/configuration.py b/pyrate/configuration.py
@@ -1,6 +1,6 @@
 #   This Python module is part of the PyRate software package.
 #
-#   Copyright 2021 Geoscience Australia
+#   Copyright 2022 Geoscience Australia
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.

diff --git a/pyrate/conv2tif.py b/pyrate/conv2tif.py
@@ -1,6 +1,6 @@
 #   This Python module is part of the PyRate software package.
 #
-#   Copyright 2021 Geoscience Australia
+#   Copyright 2022 Geoscience Australia
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.

diff --git a/pyrate/core/algorithm.py b/pyrate/core/algorithm.py
@@ -1,6 +1,6 @@
 #   This Python module is part of the PyRate software package.
 #
-#   Copyright 2021 Geoscience Australia
+#   Copyright 2022 Geoscience Australia
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.

diff --git a/pyrate/core/aps.py b/pyrate/core/aps.py
@@ -1,6 +1,6 @@
 #   This Python module is part of the PyRate software package.
 #
-#   Copyright 2021 Geoscience Australia
+#   Copyright 2022 Geoscience Australia
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.

diff --git a/pyrate/core/covariance.py b/pyrate/core/covariance.py
@@ -1,6 +1,6 @@
 #   This Python module is part of the PyRate software package.
 #
-#   Copyright 2021 Geoscience Australia
+#   Copyright 2022 Geoscience Australia
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.

diff --git a/pyrate/core/dem_error.py b/pyrate/core/dem_error.py
@@ -1,6 +1,6 @@
 #   This Python module is part of the PyRate software package.
 #
-#   Copyright 2021 Geoscience Australia
+#   Copyright 2022 Geoscience Australia
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.

diff --git a/pyrate/core/gamma.py b/pyrate/core/gamma.py
@@ -1,6 +1,6 @@
 #   This Python module is part of the PyRate software package.
 #
-#   Copyright 2021 Geoscience Australia
+#   Copyright 2022 Geoscience Australia
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.

diff --git a/pyrate/core/gdal_python.py b/pyrate/core/gdal_python.py
@@ -1,6 +1,6 @@
 #   This Python module is part of the PyRate software package.
 #
-#   Copyright 2021 Geoscience Australia
+#   Copyright 2022 Geoscience Australia
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.

diff --git a/pyrate/core/geometry.py b/pyrate/core/geometry.py
@@ -1,6 +1,6 @@
 #   This Python module is part of the PyRate software package.
 #
-#   Copyright 2021 Geoscience Australia
+#   Copyright 2022 Geoscience Australia
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.

diff --git a/pyrate/core/ifgconstants.py b/pyrate/core/ifgconstants.py
@@ -1,6 +1,6 @@
 #   This Python module is part of the PyRate software package.
 #
-#   Copyright 2021 Geoscience Australia
+#   Copyright 2022 Geoscience Australia
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.

diff --git a/pyrate/core/logger.py b/pyrate/core/logger.py
@@ -1,6 +1,6 @@
 #   This Python module is part of the PyRate software package.
 #
-#   Copyright 2021 Geoscience Australia
+#   Copyright 2022 Geoscience Australia
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.

diff --git a/pyrate/core/mpiops.py b/pyrate/core/mpiops.py
@@ -1,6 +1,6 @@
 #   This Python module is part of the PyRate software package.
 #
-#   Copyright 2021 Geoscience Australia
+#   Copyright 2022 Geoscience Australia
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.

diff --git a/pyrate/core/mst.py b/pyrate/core/mst.py
@@ -1,6 +1,6 @@
 #   This Python module is part of the PyRate software package.
 #
-#   Copyright 2021 Geoscience Australia
+#   Copyright 2022 Geoscience Australia
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.

diff --git a/pyrate/core/orbital.py b/pyrate/core/orbital.py
@@ -1,6 +1,6 @@
 #   This Python module is part of the PyRate software package.
 #
-#   Copyright 2021 Geoscience Australia
+#   Copyright 2022 Geoscience Australia
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.

diff --git a/pyrate/core/phase_closure/closure_check.py b/pyrate/core/phase_closure/closure_check.py
@@ -1,6 +1,6 @@
 #   This Python module is part of the PyRate software package.
 #
-#   Copyright 2021 Geoscience Australia
+#   Copyright 2022 Geoscience Australia
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.

diff --git a/pyrate/core/phase_closure/collect_loops.py b/pyrate/core/phase_closure/collect_loops.py
@@ -1,6 +1,6 @@
 #   This Python module is part of the PyRate software package.
 #
-#   Copyright 2021 Geoscience Australia
+#   Copyright 2022 Geoscience Australia
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.

diff --git a/pyrate/core/phase_closure/mst_closure.py b/pyrate/core/phase_closure/mst_closure.py
@@ -1,6 +1,6 @@
 #   This Python module is part of the PyRate software package.
 #
-#   Copyright 2021 Geoscience Australia
+#   Copyright 2022 Geoscience Australia
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.

diff --git a/pyrate/core/phase_closure/plot_closure.py b/pyrate/core/phase_closure/plot_closure.py
@@ -1,6 +1,6 @@
 #   This Python module is part of the PyRate software package.
 #
-#   Copyright 2021 Geoscience Australia
+#   Copyright 2022 Geoscience Australia
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.

diff --git a/pyrate/core/phase_closure/sum_closure.py b/pyrate/core/phase_closure/sum_closure.py
@@ -1,6 +1,6 @@
 #   This Python module is part of the PyRate software package.
 #
-#   Copyright 2021 Geoscience Australia
+#   Copyright 2022 Geoscience Australia
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.

diff --git a/pyrate/core/prepifg_helper.py b/pyrate/core/prepifg_helper.py
@@ -1,6 +1,6 @@
 #   This Python module is part of the PyRate software package
 #
-#   Copyright 2021 Geoscience Australia
+#   Copyright 2022 Geoscience Australia
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.

diff --git a/pyrate/core/ref_phs_est.py b/pyrate/core/ref_phs_est.py
@@ -1,6 +1,6 @@
 #   This Python module is part of the PyRate software package.
 #
-#   Copyright 2021 Geoscience Australia
+#   Copyright 2022 Geoscience Australia
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.

diff --git a/pyrate/core/refpixel.py b/pyrate/core/refpixel.py
@@ -1,6 +1,6 @@
 #   This Python module is part of the PyRate software package.
 #
-#   Copyright 2021 Geoscience Australia
+#   Copyright 2022 Geoscience Australia
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.

diff --git a/pyrate/core/roipac.py b/pyrate/core/roipac.py
@@ -1,6 +1,6 @@
 #   This Python module is part of the PyRate software package.
 #
-#   Copyright 2021 Geoscience Australia
+#   Copyright 2022 Geoscience Australia
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.

diff --git a/pyrate/core/shared.py b/pyrate/core/shared.py
@@ -1,6 +1,6 @@
 #   This Python module is part of the PyRate software package.
 #
-#   Copyright 2021 Geoscience Australia
+#   Copyright 2022 Geoscience Australia
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.
@@ -40,11 +40,8 @@
 
 import pyrate.constants as C
 
-try:
-    from osgeo import osr, gdal
-    from osgeo.gdalconst import GA_Update, GA_ReadOnly
-except ImportError:
-    import gdal
+from osgeo import osr, gdal
+from osgeo.gdalconst import GA_Update, GA_ReadOnly
 
 from pyrate.core import ifgconstants as ifc, mpiops
 from pyrate.core.logger import pyratelogger as log

diff --git a/pyrate/core/stack.py b/pyrate/core/stack.py
@@ -1,6 +1,6 @@
 #   This Python module is part of the PyRate software package.
 #
-#   Copyright 2021 Geoscience Australia
+#   Copyright 2022 Geoscience Australia
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.

diff --git a/pyrate/core/timeseries.py b/pyrate/core/timeseries.py
@@ -1,6 +1,6 @@
 #   This Python module is part of the PyRate software package.
 #
-#   Copyright 2021 Geoscience Australia
+#   Copyright 2022 Geoscience Australia
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.

diff --git a/pyrate/correct.py b/pyrate/correct.py
@@ -1,6 +1,6 @@
 #   This Python module is part of the PyRate software package.
 #
-#   Copyright 2021 Geoscience Australia
+#   Copyright 2022 Geoscience Australia
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.

diff --git a/pyrate/default_parameters.py b/pyrate/default_parameters.py
@@ -1,6 +1,6 @@
 #   This Python module is part of the PyRate software package.
 #
-#   Copyright 2021 Geoscience Australia
+#   Copyright 2022 Geoscience Australia
 #
 #   Licensed under the Apache License,
 #   Version 2.0 (the "License");

diff --git a/pyrate/main.py b/pyrate/main.py
@@ -1,6 +1,6 @@
 #   This Python module is part of the PyRate software package.
 #
-#   Copyright 2021 Geoscience Australia
+#   Copyright 2022 Geoscience Australia
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.

diff --git a/pyrate/merge.py b/pyrate/merge.py
@@ -1,6 +1,6 @@
 #   This Python module is part of the PyRate software package.
 #
-#   Copyright 2021 Geoscience Australia
+#   Copyright 2022 Geoscience Australia
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.

diff --git a/pyrate/prepifg.py b/pyrate/prepifg.py
@@ -1,6 +1,6 @@
 #   This Python module is part of the PyRate software package.
 #
-#   Copyright 2021 Geoscience Australia
+#   Copyright 2022 Geoscience Australia
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.

diff --git a/scripts/plot_ifgs.py b/scripts/plot_ifgs.py
@@ -1,6 +1,6 @@
 #   This Python module is part of the PyRate software package.
 #
-#   Copyright 2021 Geoscience Australia
+#   Copyright 2022 Geoscience Australia
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.

diff --git a/setup.py b/setup.py
@@ -1,6 +1,6 @@
 #   This Python module is part of the PyRate software package.
 #
-#   Copyright 2021 Geoscience Australia
+#   Copyright 2022 Geoscience Australia
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.
@@ -20,7 +20,7 @@
 from subprocess import check_output, run
 import platform
 import setuptools
-__version__ = "0.6.0"
+__version__ = "0.6.1"
 
 # Get requirements (and dev requirements for testing) from requirements
 #  txt files. Also ensure we are using correct GDAL version.

diff --git a/tests/common.py b/tests/common.py
@@ -1,6 +1,6 @@
 #   This Python module is part of the PyRate software package.
 #
-#   Copyright 2021 Geoscience Australia
+#   Copyright 2022 Geoscience Australia
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.

diff --git a/tests/conftest.py b/tests/conftest.py
@@ -1,6 +1,6 @@
 #   This Python module is part of the PyRate software package.
 #
-#   Copyright 2021 Geoscience Australia
+#   Copyright 2022 Geoscience Australia
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.

diff --git a/tests/phase_closure/test_closure_check.py b/tests/phase_closure/test_closure_check.py
@@ -1,6 +1,6 @@
 #   This Python module is part of the PyRate software package.
 #
-#   Copyright 2021 Geoscience Australia
+#   Copyright 2022 Geoscience Australia
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.

diff --git a/tests/phase_closure/test_mst_closure.py b/tests/phase_closure/test_mst_closure.py
@@ -1,6 +1,6 @@
 #   This Python module is part of the PyRate software package.
 #
-#   Copyright 2021 Geoscience Australia
+#   Copyright 2022 Geoscience Australia
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.

diff --git a/tests/phase_closure/test_plot_closure.py b/tests/phase_closure/test_plot_closure.py
@@ -1,6 +1,6 @@
 #   This Python module is part of the PyRate software package.
 #
-#   Copyright 2021 Geoscience Australia
+#   Copyright 2022 Geoscience Australia
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.

diff --git a/tests/phase_closure/test_sum_closure.py b/tests/phase_closure/test_sum_closure.py
@@ -1,6 +1,6 @@
 #   This Python module is part of the PyRate software package.
 #
-#   Copyright 2021 Geoscience Australia
+#   Copyright 2022 Geoscience Australia
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.