Merge branch 'master' into feature/implement_operators

# Conflicts:
#	geoarray/baseclasses.py

.gitlab-ci.yml

@@ -2,12 +2,6 @@ before_script:
   - git lfs pull
 
 
-# Advise GitLab that these environment vars should be loaded from the Variables config.
-variables:
-    PYPI_USER: SECURE
-    PYPI_PASSWORD: SECURE
-
-
 stages:
   - test
   - deploy
@@ -17,12 +11,13 @@ stages:
 test_geoarray:
   stage: test
   script:
-    - source /root/miniconda3/bin/activate
-    - export GDAL_DATA=/root/miniconda3/share/gdal
-    - export PYTHONPATH=$PYTHONPATH:/root  # /root <- directory needed later
-    - export LD_LIBRARY_PATH=/root/anaconda3/lib:$LD_LIBRARY_PATH # /root <- directory needed later
-    # update in-house dependencies
-    - pip install py_tools_ds>=0.9.0
+    - source /root/miniconda3/bin/activate ci_env
+
+    # update py_tools_ds
+    - pip install -U py_tools_ds -q
+
+    - pip install parameterized -q  # TODO remove as soon as CI runner is rebuilt
+
     # run tests
     - make nosetests
     - make docs
@@ -38,10 +33,7 @@ test_geoarray:
 test_styles:
   stage: test
   script:
-    - source /root/miniconda3/bin/activate
-    - export GDAL_DATA=/root/miniconda3/share/gdal
-    - export PYTHONPATH=$PYTHONPATH:/root  # /root <- directory needed later
-    - pip install "pycodestyle>=2.0.0,!=2.4.0"  # TODO remove as soon as docker runner is recreated
+    - source /root/miniconda3/bin/activate ci_env
     - make lint
   artifacts:
     paths:
@@ -51,17 +43,37 @@ test_styles:
     when: always
 
 
+test_urls:
+  stage: test
+  script:
+    - source /root/miniconda3/bin/activate ci_env
+    - pip install -U urlchecker
+    - make urlcheck
+  when: always
+
+
 test_geoarray_install:
   stage: test
   script:
     - source /root/miniconda3/bin/activate
-    - export GDAL_DATA=/root/miniconda3/share/gdal
-    - conda create -y -q --name geoarray python=3
-    - source activate geoarray
-     # resolve some requirements with conda
-    - conda install --yes -q -c conda-forge numpy scikit-image matplotlib geopandas gdal rasterio pyproj basemap shapely
+
+      # update conda and python
+    - conda update -n base -c conda-forge conda
+#    - conda update -c conda-forge python
+
+    # create test environment
+    - conda create -y -q -c conda-forge --name geoarray_testinstall python=3
+    - conda activate geoarray_testinstall
+
+    # avoid package incompatibilities due to usage of wrong channels
+#    - conda config --set channel_priority strict  # otherwise gdal or libgdal may be installed from defaults channel
+
+    # resolve some requirements with conda
+    - conda install --yes -q -c conda-forge numpy scikit-image matplotlib geopandas gdal pyproj cartopy shapely
+
     # run installer
     - python setup.py install
+
     # test if its importable
     - cd ..
     - pwd
@@ -83,12 +95,16 @@ pages:  # this job must be called 'pages' to advise GitLab to upload content to
     - mkdir -p public/doc
     - mkdir -p public/coverage
     - mkdir -p public/nosetests_reports
+
     # Copy over the docs
     - cp -r docs/_build/html/* public/doc/
+
     # Copy over the coverage reports
     - cp -r htmlcov/* public/coverage/
+
     # Copy over the nosetests reports
     - cp nosetests.* public/nosetests_reports/
+
     # Check if everything is working great
     - ls -al public
     - ls -al public/doc
@@ -106,22 +122,12 @@ deploy_pypi:
   stage: deploy
   dependencies:
     - test_geoarray
-  script:   # Configure the PyPI credentials, then push the package, and cleanup the creds.
-    - source /root/miniconda3/bin/activate
-    - printf "[distutils]\nindex-servers =\n    pypi\n\n" >> ~/.pypirc
-    - printf "[pypi]\n""repository:"" https://upload.pypi.org/legacy/\n" >> ~/.pypirc
-    - printf "username= ${PYPI_USER}\n" >> ~/.pypirc
-    - printf "password= ${PYPI_PASSWORD}\n" >> ~/.pypirc
-    - python setup.py check sdist upload -r pypi  # This will fail if your creds are bad.
-    - echo "" > ~/.pypirc && rm ~/.pypirc  # If the above fails, this won't run.
+  script:
+    - source /root/miniconda3/bin/activate ci_env
+    - pip install -U twine
+    - python setup.py sdist
+    - twine upload dist/*  # requires creds as environment variables
   only:
     - /^v\d+\.\d+\.\d+([abc]\d*)?$/  # PEP-440 compliant version (tags)
   except:
     - dev
-
-
-cleanup_pypirc:
-   stage: cleanup
-   when: always   # this is important; run even if preceding stages failed.
-   script:
-    - rm -vf ~/.pypirc  # we don't want to leave these around, but GitLab may clean up anyway.

.travis.yml

-# Config file for automatic testing at travis-ci.org
-# This file will be regenerated if you run travis_pypi_setup.py
-
-language: python
-python: 3.5
-
-env:
-  - TOXENV=py35
-  - TOXENV=py34
-  - TOXENV=py33
-  - TOXENV=py27
-  - TOXENV=py26
-  - TOXENV=pypy
-
-# command to install dependencies, e.g. pip install -r requirements.txt --use-mirrors
-install: pip install -U tox
-
-# command to run tests, e.g. python setup.py test
-script: tox -e ${TOXENV}
-
-

CONTRIBUTING.rst

@@ -15,7 +15,7 @@ Types of Contributions
 Report Bugs
 ~~~~~~~~~~~
 
-Report bugs at https://gitext.gfz-potsdam.de/danschef/geoarray/issues.
+Report bugs at https://git.gfz-potsdam.de/danschef/geoarray/issues.
 
 If you are reporting a bug, please include:
 
@@ -45,7 +45,7 @@ articles, and such.
 Submit Feedback
 ~~~~~~~~~~~~~~~
 
-The best way to send feedback is to file an issue at https://gitext.gfz-potsdam.de/danschef/geoarray/issues.
+The best way to send feedback is to file an issue at https://git.gfz-potsdam.de/danschef/geoarray/issues.
 
 If you are proposing a feature:
 
@@ -62,7 +62,7 @@ Ready to contribute? Here's how to set up `geoarray` for local development.
 1. Fork the `geoarray` repo on GitHub.
 2. Clone your fork locally::
 
-    $ git clone https://gitext.gfz-potsdam.de/danschef/geoarray.git
+    $ git clone https://git.gfz-potsdam.de/danschef/geoarray.git
 
 3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development::
 

MANIFEST.in

@@ -6,7 +6,7 @@ include HISTORY.rst
 include LICENSE
 include README.rst
 
-recursive-include tests *
+recursive-exclude tests *
 recursive-exclude * __pycache__
 recursive-exclude * *.py[co]
 

Makefile

@@ -42,9 +42,10 @@ clean-pyc: ## remove Python file artifacts
 	find . -name '__pycache__' -exec rm -fr {} +
 
 clean-test: ## remove test and coverage artifacts
-	coverage erase
+	## don't call coverage erase here because make install calls make clean which calls make clean-test
+	## -> since make install should run without the test requirements we can't use coverage erase here
 	rm -fr .tox/
-	rm -f .coverage
+	rm -fr .coverage.*
 	rm -fr htmlcov/
 	rm -fr nosetests.html
 	rm -fr nosetests.xml
@@ -54,6 +55,9 @@ lint: ## check style with flake8
 	pycodestyle geoarray --exclude="*.ipynb,*.ipynb*" --max-line-length=120 > ./tests/linting/pycodestyle.log
 	-pydocstyle geoarray > ./tests/linting/pydocstyle.log
 
+urlcheck: ## check for dead URLs
+	urlchecker check . --file-types .py,.rst,.md,.json
+
 test: ## run tests quickly with the default Python
 	python setup.py test
 
@@ -86,9 +90,8 @@ docs: ## generate Sphinx HTML documentation, including API docs
 servedocs: docs ## compile the docs watching for changes
 	watchmedo shell-command -p '*.rst' -c '$(MAKE) -C docs html' -R -D .
 
-release: clean ## package and upload a release
-	python setup.py sdist upload
-	python setup.py bdist_wheel upload
+release: dist ## package and upload a release
+	twine upload dist/*
 
 dist: clean ## builds source and wheel package
 	python setup.py sdist

README.rst

@@ -5,76 +5,102 @@ geoarray
 
 Fast Python interface for geodata - either on disk or in memory.
 
+The geoarray package facilitates reading and writing of all GDAL compatible image file formats
+and provides functions for geospatial processing.
 
-* Free software: GNU General Public License v3
-* Documentation: http://danschef.gitext.gfz-potsdam.de/geoarray/doc/
+
+* Free software: GNU General Public License v3 or later (GPLv3+)
+* Documentation: https://danschef.git-pages.gfz-potsdam.de/geoarray/doc/
 
 
 Status
 ------
 
-.. .. image:: https://img.shields.io/travis/danschef/geoarray.svg
-        :target: https://travis-ci.org/danschef/geoarray
-
-.. .. image:: https://readthedocs.org/projects/geoarray/badge/?version=latest
-        :target: https://geoarray.readthedocs.io/en/latest/?badge=latest
-        :alt: Documentation Status
-
-.. .. image:: https://pyup.io/repos/github/danschef/geoarray/shield.svg
-     :target: https://pyup.io/repos/github/danschef/geoarray/
-     :alt: Updates
-
-.. image:: https://gitext.gfz-potsdam.de/danschef/geoarray/badges/master/build.svg
-        :target: https://gitext.gfz-potsdam.de/danschef/geoarray/commits/master
-.. image:: https://gitext.gfz-potsdam.de/danschef/geoarray/badges/master/coverage.svg
-        :target: http://danschef.gitext.gfz-potsdam.de/geoarray/coverage/
+.. image:: https://git.gfz-potsdam.de/danschef/geoarray/badges/master/pipeline.svg
+        :target: https://git.gfz-potsdam.de/danschef/geoarray/commits/master
+.. image:: https://git.gfz-potsdam.de/danschef/geoarray/badges/master/coverage.svg
+        :target: https://danschef.git-pages.gfz-potsdam.de/geoarray/coverage/
 .. image:: https://img.shields.io/pypi/v/geoarray.svg
         :target: https://pypi.python.org/pypi/geoarray
+.. image:: https://img.shields.io/conda/vn/conda-forge/geoarray.svg
+        :target: https://anaconda.org/conda-forge/geoarray
 .. image:: https://img.shields.io/pypi/l/geoarray.svg
-        :target: https://gitext.gfz-potsdam.de/danschef/geoarray/blob/master/LICENSE
+        :target: https://git.gfz-potsdam.de/danschef/geoarray/blob/master/LICENSE
 .. image:: https://img.shields.io/pypi/pyversions/geoarray.svg
         :target: https://img.shields.io/pypi/pyversions/geoarray.svg
+.. image:: https://img.shields.io/pypi/dm/geoarray.svg
+        :target: https://pypi.python.org/pypi/geoarray
 
 
 See also the latest coverage_ report and the nosetests_ HTML report.
 
 
-Features
---------
+Features and usage
+------------------
 
-* TODO
+* There is an example notebook that shows how to use geoarray: here_.
 
 
 Installation
 ------------
-geoarray depends on some open source packages which are usually installed without problems by the automatic install
-routine. However, for some projects, we strongly recommend resolving the dependency before the automatic installer
-is run. This approach avoids problems with conflicting versions of the same software.
-Using conda_, the recommended approach is:
 
- .. code-block:: console
+Using Anaconda or Miniconda (recommended)
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Using conda_ (latest version recommended), geoarray is installed as follows:
+
+
+1. Create virtual environment for geoarray (optional but recommended):
+
+   .. code-block:: bash
+
+    $ conda create -c conda-forge --name geoarray python=3
+    $ conda activate geoarray
+
+
+2. Then install geoarray itself:
+
+   .. code-block:: bash
+
+    $ conda install -c conda-forge geoarray
+
+
+This is the preferred method to install geoarray, as it always installs the most recent stable release and
+automatically resolves all the dependencies.
+
+
+Using pip (not recommended)
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-    # create virtual environment for geoarray, this is optional
-    conda create -y -q --name geoarray python=3
-    source activate geoarray
-    conda install -y -q -c conda-forge numpy gdal scikit-image matplotlib pandas rasterio pyproj basemap shapely geopandas
-    conda install --yes -c ioam bokeh holoviews  # optional
+There is also a `pip`_ installer for geoarray. However, please note that geoarray depends on some
+open source packages that may cause problems when installed with pip. Therefore, we strongly recommend
+to resolve the following dependencies before the pip installer is run:
 
+    * cartopy
+    * gdal >=2.1.0
+    * geopandas
+    * holoviews  # optional, in case you want to use interactive plotting
+    * matplotlib
+    * numpy
+    * pandas
+    * pyproj >2.2.0
+    * scikit-image
+    * shapely
 
-To install geoarray, use the pip installer:
+Then, the pip installer can be run by:
 
-.. code-block:: console
+   .. code-block:: bash
 
-    pip install geoarray
+    $ pip install geoarray
 
+If you don't have `pip`_ installed, this `Python installation guide`_ can guide you through the process.
 
-* Or clone the repository via GIT and update the PATH environment variable:
 
-.. code-block:: console
+History / Changelog
+-------------------
 
-    cd /your/installation/folder
-    git clone https://gitext.gfz-potsdam.de/danschef/geoarray.git
-    PATH=$PATH:~/path/to/your/installation/folder/geoarray
+You can find the protocol of recent changes in the geoarray package
+`here <https://git.gfz-potsdam.de/danschef/geoarray/-/blob/master/HISTORY.rst>`__.
 
 
 Credits
@@ -84,6 +110,9 @@ This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypack
 
 .. _Cookiecutter: https://github.com/audreyr/cookiecutter
 .. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage
-.. _coverage: http://danschef.gitext.gfz-potsdam.de/geoarray/coverage/
-.. _nosetests: http://danschef.gitext.gfz-potsdam.de/geoarray/nosetests_reports/nosetests.html
+.. _coverage: https://danschef.git-pages.gfz-potsdam.de/geoarray/coverage/
+.. _nosetests: https://danschef.git-pages.gfz-potsdam.de/geoarray/nosetests_reports/nosetests.html
 .. _conda: https://conda.io/docs/
+.. _here: https://git.gfz-potsdam.de/danschef/geoarray/-/blob/master/examples/notebooks/features_and_usage.ipynb
+.. _pip: https://pip.pypa.io
+.. _Python installation guide: http://docs.python-guide.org/en/latest/starting/installation/

docs/installation.rst

@@ -32,13 +32,13 @@ You can either clone the public repository:
 
 .. code-block:: console
 
-    $ git clone https://gitext.gfz-potsdam.de/danschef/geoarray.git
+    $ git clone https://git.gfz-potsdam.de/danschef/geoarray.git
 
 Or download the `tarball`_:
 
 .. code-block:: console
 
-    $ curl  -OL https://gitext.gfz-potsdam.de/danschef/geoarray/repository/archive.tar.gz?ref=master
+    $ curl  -OL https://git.gfz-potsdam.de/danschef/geoarray/repository/archive.tar.gz?ref=master
 
 Once you have a copy of the source, you can install it with:
 
@@ -47,5 +47,5 @@ Once you have a copy of the source, you can install it with:
     $ python setup.py install
 
 
-.. _GitLab repo: https://gitext.gfz-potsdam.de/danschef/geoarray
-.. _tarball: https://gitext.gfz-potsdam.de/danschef/geoarray/repository/archive.tar.gz?ref=master
+.. _GitLab repo: https://git.gfz-potsdam.de/danschef/geoarray
+.. _tarball: https://git.gfz-potsdam.de/danschef/geoarray/repository/archive.tar.gz?ref=master

geoarray/__init__.py

 # -*- coding: utf-8 -*-
 
+# geoarray, A fast Python interface for image geodata - either on disk or in memory.
+#
+# Copyright (C) 2019  Daniel Scheffler (GFZ Potsdam, daniel.scheffler@gfz-potsdam.de)
+#
+# This software was developed within the context of the GeoMultiSens project funded
+# by the German Federal Ministry of Education and Research
+# (project grant code: 01 IS 14 010 A-C).
+#
+# This program is free software: you can redistribute it and/or modify it under
+# the terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 import os
 if 'MPLBACKEND' not in os.environ:
     os.environ['MPLBACKEND'] = 'Agg'

geoarray/masks.py

 # -*- coding: utf-8 -*-
 
+# geoarray, A fast Python interface for image geodata - either on disk or in memory.
+#
+# Copyright (C) 2019  Daniel Scheffler (GFZ Potsdam, daniel.scheffler@gfz-potsdam.de)
+#
+# This software was developed within the context of the GeoMultiSens project funded
+# by the German Federal Ministry of Education and Research
+# (project grant code: 01 IS 14 010 A-C).
+#
+# This program is free software: you can redistribute it and/or modify it under
+# the terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 import numpy as np
 
 # internal imports
@@ -17,7 +38,7 @@ class BadDataMask(GeoArray):
         if self.is_inmem:
             # validate input data - before converting to bool
             self._validate_array_values(self.arr)
-            self.arr = self.arr.astype(np.bool)
+            self.arr = self.arr.astype(bool)
 
             # del self._mask_baddata, self.mask_baddata # TODO delete property (requires deleter)
 
@@ -29,7 +50,7 @@ class BadDataMask(GeoArray):
     def arr(self, ndarray):
         assert isinstance(ndarray, np.ndarray), "'arr' can only be set to a numpy array!"
         self._validate_array_values(ndarray)
-        self._arr = ndarray.astype(np.bool)
+        self._arr = ndarray.astype(bool)
 
     def _validate_array_values(self, maskarray):
         pixelVals_in_mask = sorted(list(np.unique(maskarray)))
@@ -50,7 +71,7 @@ class NoDataMask(GeoArray):
         if self.is_inmem:
             # validate input data - before converting to bool
             self._validate_array_values(self.arr)
-            self.arr = self.arr.astype(np.bool)
+            self.arr = self.arr.astype(bool)
 
             # del self._mask_nodata, self.mask_nodata # TODO delete property (requires deleter)
             # TODO disk-mode: init must check the numbers of bands, and ideally also the pixel values in mask
@@ -63,7 +84,7 @@ class NoDataMask(GeoArray):
     def arr(self, ndarray):
         assert isinstance(ndarray, np.ndarray), "'arr' can only be set to a numpy array!"
         self._validate_array_values(ndarray)
-        self._arr = ndarray.astype(np.bool)
+        self._arr = ndarray.astype(bool)
 
     def _validate_array_values(self, maskarray):
         pixelVals_in_mask = sorted(list(np.unique(maskarray)))

geoarray/metadata.py

 # -*- coding: utf-8 -*-
 
+# geoarray, A fast Python interface for image geodata - either on disk or in memory.
+#
+# Copyright (C) 2019  Daniel Scheffler (GFZ Potsdam, daniel.scheffler@gfz-potsdam.de)
+#
+# This software was developed within the context of the GeoMultiSens project funded
+# by the German Federal Ministry of Education and Research
+# (project grant code: 01 IS 14 010 A-C).
+#
+# This program is free software: you can redistribute it and/or modify it under
+# the terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# This program is distributed in the hope that it will be useful, but WITHOUT