Merge pull request #243 from GeoscienceAustralia/release-0.4.0

0.4.0 (2019-10-29)

.gitignore

@@ -1,5 +1,8 @@
 !*docs/_build/html/404.html
-
+!*tests/test_data/merge/linrate.tif
+!*tests/test_data/small_test/gamma_obs/20060619-20061002_utm_unw.tif
+*data/*
+*out*
 *.pyo
 *.pyc
 .project
@@ -24,7 +27,7 @@ docs/_build/
 .cache/
 build/
 dist/
-out
+# out
 Py_Rate.egg-info
 
 # files generated during tests
@@ -33,3 +36,10 @@ Py_Rate.egg-info
 *tests/test_data/prepifg/tif/1_1rlks_4cr.tif
 *tests/test_data/prepifg/tif/1_2rlks_4cr.tif
 
+*tests/test_data/merge/colormap.txt
+*tests/test_data/merge/linrate.kml
+*tests/test_data/merge/linrate.png
+*tests/test_data/merge/linrate.png.aux.xml
+*tests/test_data/merge/linrate.tif.aux.xml
+
+*tests/test_data/small_test/gamma_obs/*.tif

.travis.yml

@@ -5,13 +5,16 @@ branches:
   - /.*-travis$/
   - master
 
+os: linux
+dist: bionic # Ubuntu 18.04
+
 language: python
+cache: pip
 
-python: 3.6
+python:
+  - "3.6"
+  - "3.7"
 
-os: linux
-
-dist: bionic # Ubuntu 18.04
 
 before_install:
   - sudo apt-get update
@@ -22,7 +25,8 @@ before_install:
   - export C_INCLUDE_PATH=$C_INCLUDE_PATH:/usr/include/gdal
   - export CPLUS_INCLUDE_PATH=$CPLUS_INCLUDE_PATH:/usr/include/gdal
   - pip install -U pip
-
+  - pip install codecov
+
 install:
   - pip install -r requirements-test.txt
   - pip install -r requirements-dev.txt
@@ -33,9 +37,35 @@ install:
 
 # command to run tests, e.g. python setup.py test
 script:
+  - pip install numpy==1.16.4
   - pytest --cov-report term-missing:skip-covered --cov=pyrate tests/
 
-# cache:
-#   - apt
-#   - pip
-#   - $HOME/.cache/pip
+after_success:
+  - codecov
+
+jobs:
+  include:
+    - stage: deploy
+      python: 3.6
+      script:
+        - pip install numpy==1.16.4
+        - cd docs && make html
+      deploy:
+        provider: pages
+        skip-cleanup: true
+        keep-history: true
+        verbose: true
+        on:
+          branch: master
+        github-token: $GITHUB_TOKEN
+        local-dir: docs/_build/html
+        project_name: PyRate
+        email: [email protected]
+        name: InSAR Team
+
+notifications:
+  email:
+    recipients:
+      - $SHEECE_EMAIL
+    on_success: never
+    on_failure: always

README.rst

@@ -9,12 +9,10 @@ Python tool for InSAR Rate and Time-series Estimation
    :target: https://coveralls.io/github/GeoscienceAustralia/PyRate?branch=master
 .. image:: https://img.shields.io/badge/License-Apache%202.0-blue.svg
    :target: https://opensource.org/licenses/Apache-2.0
-   :alt: License
-.. image:: https://img.shields.io/badge/python-3.6-blue.svg
-   :target: https://docs.python.org/3/whatsnew/3.6.html
-   :alt: Python 3.6 support
+.. image:: https://img.shields.io/pypi/pyversions/Py-Rate 
+   :target: https://pypi.org/project/Py-Rate/ 
 
-PyRate is a Python tool for estimating the average rate (velocity) and cumulative displacement time-series of surface movements for every pixel in a stack of geocoded unwrapped interferograms generated by Interferometric Synthetic Aperture Radar (InSAR) processing. PyRate currently supports input data in the GAMMA or ROI_PAC software formats.
+PyRate is a Python tool for estimating the average rate (velocity) and cumulative displacement time-series of surface movements for every pixel in a stack of geocoded unwrapped interferograms generated by Interferometric Synthetic Aperture Radar (InSAR) processing. PyRate uses a "Small Baseline Subset" (SBAS) processing strategy and currently supports input data in the GAMMA or ROI_PAC software formats.
 
 The PyRate project started in 2012 as a partial Python translation of "Pirate", a Matlab tool developed by the University of Leeds and the Guangdong University of Technology.
 

docs/_templates/layout.html

@@ -5,7 +5,7 @@
 {% endblock %}
 
 {% block footer %}
-<p>asdasdasd</p>
+<p>placeHolderText</p>
         <!-- your html code here -->
 {{ super() }}
 {% endblock %}

docs/algorithm.rst

@@ -1,5 +1,5 @@
 Algorithm Module
 ================
 
-.. automodule:: pyrate.algorithm
+.. automodule:: pyrate.core.algorithm
    :members:

docs/aps.rst

@@ -1,5 +1,5 @@
 Atmospheric Phase Screen Module
 ===============================
 
-.. automodule:: pyrate.aps
+.. automodule:: pyrate.core.aps
    :members:

docs/authors.rst

@@ -27,3 +27,4 @@ Thanks to `all the contributors`_ who helped in building this project.
 * Brenainn Moushall (GA)
 * Vanessa Newey (GA)
 * Garrick Paskos (GA)
+* Nahidul Samrat (GA)

docs/conf.py

@@ -1,29 +1,11 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
-#
-# PyRate documentation build configuration file, created by
-# sphinx-quickstart on Fri Mar  3 10:07:59 2017.
-#
-# This file is execfile()d with the current directory set to its
-# containing dir.
-#
-# Note that not all possible configuration values are present in this
-# autogenerated file.
-#
-# All configuration values have a default; values that are commented out
-# serve to show the default.
-
-# If extensions (or modules to document with autodoc) are in another directory,
-# add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
-#
 import os
-# import sys
-# sys.path.insert(0, os.path.abspath('.'))
 import datetime
 import sphinx_rtd_theme
-from pyrate import __version__
 
+
+__version__ = "0.4.0"
 # -- General configuration ------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
@@ -39,6 +21,7 @@
               'sphinx.ext.githubpages',
               'sphinx.ext.mathjax',
               'sphinx.ext.autosummary',
+              'sphinx.ext.napoleon',
               'matplotlib.sphinxext.plot_directive',
               'IPython.sphinxext.ipython_console_highlighting',
               'IPython.sphinxext.ipython_directive',
@@ -69,9 +52,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = __version__
+version = "0.4.0"
 # The full version, including alpha/beta/rc tags.
-release = __version__
+release = "0.4.0"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -207,5 +190,6 @@
 linkcheck_ignore = [r'http://localhost:\d+/',
                     'https://github.com/Nekroze/PyRate/fork']
 
+
 def setup(app):
-    app.add_stylesheet('css/custom.css')
+    app.add_stylesheet('css/custom.css')

docs/config.rst

@@ -1,5 +1,5 @@
 Config Module
 =============
 
-.. automodule:: pyrate.config
+.. automodule:: pyrate.core.config
    :members:

docs/covariance.rst

@@ -1,5 +1,5 @@
 Covariance Module
 =====================
 
-.. automodule:: pyrate.covariance
+.. automodule:: pyrate.core.covariance
    :members:

docs/gamma.rst

@@ -1,5 +1,5 @@
 GAMMA Module
 ============
 
-.. automodule:: pyrate.gamma
+.. automodule:: pyrate.core.gamma
    :members:

docs/gdal_python.rst

@@ -1,5 +1,5 @@
 GDAL-Python Bindings Module
 ===========================
 
-.. automodule:: pyrate.gdal_python
-   :members:
+.. automodule:: pyrate.core.gdal_python
+   :members:

docs/history.rst

@@ -2,12 +2,39 @@
 
 Release History
 ===============
+0.4.0 (2019-09-24)
+-----------------------
+Added
++++++
+- Python 3.7 support.
+- Optional 'conv2tif' step.
+- Building of docs integrated with Travis CI.
+- Coherence masking, view coherence masking section in 'input_parameters.conf'
+  for options.
+- Input parameter validation.
+- SLC and coherence file lists for file discovery.
+
+Changed
++++++++
+- 'linrate' step has been renamed to 'process'.
+- 'postprocess' step has been renamed to 'merge'
+- 'converttogeotiff' step has been renamed to 'conv2tif'
+- CLI structure: config files now need to provided with '-f' flag.
+- Reduced console output, default verbosity setting is now INFO.
+- Restructure of code layout, src modules now in 'core' directory and scripts
+  at top level.
+
+Removed
++++++++
+- Unused luigi code.
+- References to Matlab.
+
 0.3.0 (2019-07-26)
 -----------------------
 Added
 +++++
 - `apt_install.sh` in utils/ that lists Ubuntu/apt package requirements.
-- `load_modules.sh` in utils/ that sets up Raijin environment.
+- `load_modules.sh` in utils/ that sets up NCI Raijin HPC environment.
 
 Fixed
 +++++
@@ -41,4 +68,3 @@ Changed
 0.1.0 (2017-01-31)
 ------------------
 - First release on PyPI.
-

docs/hpc.rst

@@ -47,5 +47,5 @@ environment and reload the required modules:
 ::
 
     cd ~
-    source PyRateVM/bin/activate
+    source PyRateVenv/bin/activate
     source PyRate/utils/load_modules.sh