Merge pull request #356 from GeoscienceAustralia/release0.6.0

Release 0.6.0

Author: Matt Garthwaite

.github/workflows/build.yml

@@ -1,31 +1,38 @@
 name: PyRate CI
 
-on: [push, pull_request]
+
+on:
+  pull_request:
+    branches:
+      - 'master'
+  push:
+    branches:
+      - '**'
 
 jobs:
   build:
-    runs-on: ubuntu-16.04
+    if: ${{ ! (contains(github.event.head_commit.message, 'ci skip') || contains(github.event.head_commit.message, 'skip ci'))}}
+    runs-on: ubuntu-18.04
     name: Python ${{ matrix.python }}
-    if: "!(contains(github.event.head_commit.message, '[skip ci]') || contains(github.event.pull_request.head_commit.message, '[ci skip]'))"
     strategy:
       matrix:
         include:
           - build: 1
-            python-version: "3.6"
-            GDALVERSION: "3.0.2"
-            PROJVERSION: "6.1.1"
-          - build: 2
             python-version: "3.7"
             GDALVERSION: "3.0.2"
             PROJVERSION: "6.2.1"
-          - build: 3
+          - build: 2
             python-version: "3.7"
             GDALVERSION: "3.0.4"
             PROJVERSION: "6.1.1"
-          - build: 4
+          - build: 3
             python-version: "3.8"
             GDALVERSION: "3.0.4"
             PROJVERSION: "6.1.1"
+          - build: 4
+            python-version: "3.9"
+            GDALVERSION: "3.0.4"
+            PROJVERSION: "6.3.2"
 
     env:
       PIP_WHEEL_DIR: "/home/runner/.cache/pip/wheels"
@@ -36,6 +43,7 @@ jobs:
       PROJINST: "/home/runner/gdalinstall"
       PROJBUILD: "/home/runner/projbuild"
       PROJVERSION: ${{ matrix.PROJVERSION }}
+      PYTHONVERSION: ${{ matrix.python-version }}
 
     steps:
       - uses: actions/checkout@v2
@@ -44,35 +52,57 @@ jobs:
         with:
           path: |
             /home/runner/gdalinstall
-          key: ${{ runner.os }}-GDAL-${{ matrix.GDALVERSION }}-proj-${{ matrix.PROJVERSION }}
+          key: ${{ runner.os }}-cache-GDAL-${{ matrix.GDALVERSION }}-proj-${{ matrix.PROJVERSION }}
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v2
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Install packages
-        run: sudo apt-get install libhdf5-serial-dev libgdal-dev libatlas-dev libatlas-base-dev gfortran openmpi-bin libopenmpi-dev
-      - run: python -m pip install -U pip
-      - run: python -m pip install wheel
+      - name: Common set up ${{ matrix.python-version }}
+        run: |
+          sudo apt update
+          sudo apt upgrade
+          python -m pip install -U pip wheel
+      - 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
+      - name: Install packages except openmpi libraries
+        if: env.PYTHONVERSION == '3.9'
+        run: sudo apt install libhdf5-serial-dev libnetcdf13 libatlas-base-dev gfortran
       - name: Install proj ${{matrix.PROJVERSION}}
         run: |
           echo "PATH=$GDALINST/gdal-$GDALVERSION/bin:$PATH" >> $GITHUB_ENV
           echo "LD_LIBRARY_PATH=$GDALINST/gdal-$GDALVERSION/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV
           source ./scripts/ci_proj_install.sh
       - name: Install GDAL ${{matrix.GDALVERSION}}
         run: |
-          source ./scripts/ci_gdal_install.sh
           echo "GDAL_DATA=$GDALINST/gdal-$GDALVERSION/share/gdal" >> $GITHUB_ENV
           echo "PROJ_LIB=$GDALINST/gdal-$GDALVERSION/share/proj" >> $GITHUB_ENV
-      - name: Install PyRate
+          echo "LDFLAGS=-L$GDALINST/gdal-$GDALVERSION/lib -Wl,-rpath,$GDALINST/gdal-$GDALVERSION/lib" >> $GITHUB_ENV
+          source ./scripts/ci_gdal_install.sh
+      - name: Python ${{ matrix.python-version }} with MPI
+        if: env.PYTHONVERSION != '3.9'
         run: |
-          sed -i '/^GDAL/d' requirements.txt
-          pip install -r requirements.txt -r requirements-dev.txt -r requirements-test.txt
-          pip install GDAL==$(gdal-config --version)
           python setup.py install
           rm -rf Py_Rate.egg-info  # remove the local egg
-          echo "PYTHONPATH=$PYRATEPATH:$PYTHONPATH" >> $GITHUB_ENV
+          echo "PYTHONPATH=$(pwd):$PYTHONPATH" >> $GITHUB_ENV
           chmod 444 tests/test_data/small_test/tif/geo_070709-070813_unw.tif  # makes the file readonly, used in a test
-      - name: Test PyRate
+          pip install -r requirements-dev.txt -r requirements-test.txt
+      - name: Python ${{ matrix.python-version }} without MPI
+        if: env.PYTHONVERSION == '3.9'
+        run: |
+          python setup.py install
+          rm -rf Py_Rate.egg-info  # remove the local egg
+          echo "PYTHONPATH=$(pwd):$PYTHONPATH" >> $GITHUB_ENV
+          chmod 444 tests/test_data/small_test/tif/geo_070709-070813_unw.tif  # makes the file readonly, used in a test
+          pip install -r requirements-test.txt
+      - name: Test Pyrate in Python ${{ matrix.python-version }} with MPI
+        if: env.PYTHONVERSION != '3.9'
         run: |
           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"
+      - 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"

.travis.yml

@@ -24,21 +24,25 @@ Dependencies
 
 The following system dependencies are required by PyRate:
 
-- `Python <https://www.python.org/downloads/>`_, versions 3.6, 3.7 or 3.8.
+- `Python <https://www.python.org/downloads/>`_, versions 3.7, 3.8 or 3.9.
 - `GDAL <https://gdal.org/download.html>`_, versions 3.0.2 or 3.0.4
+
+The following optional dependency is required for MPI processing capability:
+
 - `Open MPI <https://www.open-mpi.org/software/ompi/v4.0/>`_, versions 2.1.6, 3.0.4, 3.1.4 or 4.0.2
 
 The versions of each package stated above have been tested to work using `GitHub Actions <https://github.com/GeoscienceAustralia/PyRate/actions>`_ continuous integration testing.
 
 Python dependencies for PyRate are::
 
-    joblib==0.14.1
+    joblib==1.0.0
     mpi4py==3.0.3
-    networkx==2.4
-    numpy==1.18.3
-    pyproj==2.6.0
-    scipy==1.4.1
-    numexpr==2.7.1
+    networkx==2.5
+    numpy==1.19.4
+    pyproj==3.0.0
+    scipy==1.5.4
+    numexpr==2.7.2
+    nptyping==1.4.0
 
 Install
 -------

README.rst

@@ -374,7 +374,7 @@ <h1>
 
               <div role="contentinfo">
                 <p>
-                  &copy; Copyright 2020, Geoscience Australia
+                  &copy; Copyright 2021, Geoscience Australia
                 </p>
               </div>
               Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a

docs/PyRate_plot_screenshot.png

@@ -6,7 +6,7 @@ Development Lead
 ----------------
 
 `PyRate` has been developed by `Geoscience Australia <http://www.ga.gov.au>`__
-with assistance from the `National Computational Infrastructure <http://nci.org.au/>`__.
+with some initial assistance from the `National Computational Infrastructure <http://nci.org.au/>`__.
 
 Contact: `Geoscience Australia InSAR team <mailto:insar@ga.gov.au>`__
 
@@ -25,9 +25,11 @@ Thanks to `all the contributors`_ who helped to build the ship and raise the sai
 * Matt Garthwaite (GA)
 * Simon Knapp (GA)
 * Sarah Lawrie (GA)
+* Jonathan Mettes (GA)
 * Negin Moghaddam (GA)
 * Brenainn Moushall (GA)
 * Vanessa Newey (GA)
 * Chandrakanta Ojha (GA)
 * Garrick Paskos (GA)
 * Nahidul Samrat (GA)
+* Richard Taylor (GA)

docs/_build/html/404.html

@@ -5,7 +5,7 @@
 import sphinx_rtd_theme
 
 
-__version__ = "0.5.0"
+__version__ = "0.6.0"
 # -- General configuration ------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
@@ -25,7 +25,8 @@
               'matplotlib.sphinxext.plot_directive',
               'IPython.sphinxext.ipython_console_highlighting',
               'IPython.sphinxext.ipython_directive',
-              'sphinxcontrib.programoutput'
+              'sphinxcontrib.programoutput',
+              'm2r2'
               ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -52,9 +53,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = "0.4.0"
+version = __version__
 # The full version, including alpha/beta/rc tags.
-release = "0.4.0"
+release = __version__
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/authors.rst

@@ -0,0 +1,5 @@
+Configuration Module
+====================
+
+.. automodule:: pyrate.configuration
+   :members:

docs/conf.py

@@ -112,8 +112,8 @@ Before you submit a pull request, check that it meets these guidelines:
 1. The pull request should include tests that cover new functionality.
 2. If the pull request adds functionality, the documentation should be updated.
    Put your new functionality into a function with a docstring.
-3. The pull request should work for Python 3.6+.
+3. The pull request should work for Python 3.7+.
 
-   Check https://travis-ci.org/GeoscienceAustralia/PyRate
-   under pull requests for active pull requests or run the ``tox`` command and
+   Check https://github.com/GeoscienceAustralia/PyRate/actions
+   for active pull requests or run the ``tox`` command and
    make sure that the tests pass for all supported Python versions.

docs/config.rst

@@ -0,0 +1,5 @@
+DEM Error Correction Module
+===========================
+
+.. automodule:: pyrate.core.dem_error
+   :members:

docs/configuration.rst

@@ -4,17 +4,21 @@ Dependencies
 The following dependencies need to be on your system (or in your working
 environment) prior to `PyRate` installation:
 
-- Python_, versions 3.6, 3.7 or 3.8.
+- Python_, versions 3.7, 3.8 or 3.9.
 - GDAL_, versions 3.0.2 or 3.0.4
+
+The following optional dependency should be on your system if you want to make
+use of MPI processing:
+
 - `Open MPI`_, versions 2.1.6, 3.0.4, 3.1.4 or 4.0.2
 
 The versions of each package stated above have been tested to work using
-`Travis CI`_ continuous integration testing.
+`GitHub Actions`_ continuous integration testing.
 
 .. _Python: https://www.python.org/downloads/
 .. _GDAL: https://gdal.org/download.html
 .. _`Open MPI`: https://www.open-mpi.org/software/ompi/v4.0/
-.. _`Travis CI`: https://travis-ci.org/github/GeoscienceAustralia/PyRate
+.. _`GitHub Actions`: https://github.com/GeoscienceAustralia/PyRate/actions
 
 Other Python dependencies that will be installed are listed in
 ``PyRate/requirements.txt``.

docs/contributing.rst

@@ -0,0 +1,5 @@
+Geometry Module
+===============
+
+.. automodule:: pyrate.core.geometry
+   :members: