Added URL checker and corresponding CI job. Fixed dead links. Updated...

Added URL checker and corresponding CI job. Fixed dead links. Updated installation procedure documentation.
Signed-off-by: Daniel Scheffler <danschef@gfz-potsdam.de>

.gitlab-ci.yml

@@ -41,6 +41,15 @@ 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_sensormapgeo_install:
   stage: test
   script:

CONTRIBUTING.rst

@@ -15,7 +15,7 @@ Types of Contributions
 Report Bugs
 ~~~~~~~~~~~
 
-Report bugs at https://github.com/danschef/sensormapgeo/issues.
+Report bugs at https://gitext.gfz-potsdam.de/EnMAP/sensormapgeo/-/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://github.com/danschef/sensormapgeo/issues.
+The best way to send feedback is to file an issue at https://gitext.gfz-potsdam.de/EnMAP/sensormapgeo/-/issues.
 
 If you are proposing a feature:
 

HISTORY.rst

@@ -2,10 +2,13 @@
 History
 =======
 
-0.4.7 (coming soon)
--------------------
+0.4.7 (2020-12-10)
+------------------
 
 * Use 'conda activate' instead of deprecated 'source activate'.
+* Added URL checker and corresponding CI job.
+* Fixed dead links.
+* Updated installation procedure documentation.
 
 
 0.4.6 (2020-10-12)

Makefile

@@ -55,6 +55,9 @@ lint: ## check style with flake8
 	pycodestyle sensormapgeo --exclude="*.ipynb,*.ipynb*" --max-line-length=120 > ./tests/linting/pycodestyle.log
 	-pydocstyle sensormapgeo > ./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
 

README.rst

@@ -23,14 +23,6 @@ Status
         :target: https://gitext.gfz-potsdam.de/EnMAP/sensormapgeo/blob/master/LICENSE
 .. image:: https://img.shields.io/pypi/pyversions/sensormapgeo.svg
         :target: https://img.shields.io/pypi/pyversions/sensormapgeo.svg
-.. .. image:: https://img.shields.io/travis/EnMAP/sensormapgeo.svg
-        :target: https://travis-ci.org/EnMAP/sensormapgeo
-.. .. image:: https://readthedocs.org/projects/sensormapgeo/badge/?version=latest
-        :target: https://sensormapgeo.readthedocs.io/en/latest/?badge=latest
-        :alt: Documentation Status
-.. .. image:: https://pyup.io/repos/github/EnMAP/sensormapgeo/shield.svg
-     :target: https://pyup.io/repos/github/EnMAP/sensormapgeo/
-     :alt: Updates
 
 See also the latest coverage_ report and the nosetests_ HTML report.
 

docs/installation.rst

-.. highlight:: shell
+.. _installation:
 
 ============
 Installation
 ============
 
 
-Stable release
---------------
+Using Anaconda or Miniconda (recommended)
+-----------------------------------------
 
-To install sensormapgeo, run this command in your terminal:
+Using conda_ (latest version recommended), sensormapgeo is installed as follows:
 
-.. code-block:: console
 
-    $ pip install sensormapgeo
+1. Create virtual environment for sensormapgeo (optional but recommended):
 
-This is the preferred method to install sensormapgeo, as it will always install the most recent stable release.
+   .. code-block:: bash
 
-If you don't have `pip`_ installed, this `Python installation guide`_ can guide
-you through the process.
+    $ conda create -c conda-forge --name sensormapgeo python=3
+    $ conda activate sensormapgeo
 
-.. _pip: https://pip.pypa.io
-.. _Python installation guide: http://docs.python-guide.org/en/latest/starting/installation/
 
+2. Then install sensormapgeo itself:
 
-From sources
-------------
+   .. code-block:: bash
 
-The sources for sensormapgeo can be downloaded from the `Github repo`_.
+    $ conda install -c conda-forge sensormapgeo
 
-You can either clone the public repository:
 
-.. code-block:: console
+This is the preferred method to install sensormapgeo, as it always installs the most recent stable release and
+automatically resolves all the dependencies.
 
-    $ git clone git://github.com/danschef/sensormapgeo
 
-Or download the `tarball`_:
+Using pip (not recommended)
+---------------------------
 
-.. code-block:: console
+There is also a `pip`_ installer for sensormapgeo. However, please note that sensormapgeo 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:
 
-    $ curl -OJL https://github.com/danschef/sensormapgeo/tarball/master
 
-Once you have a copy of the source, you can install it with:
+    * _openmp_mutex=*=*llvm*
+    * geopandas
+    * gdal
+    * lxml
+    * numpy
+    * pyproj
+    * pyqt
+    * pyresample
+    * scikit-image
 
-.. code-block:: console
 
-    $ python setup.py install
+Then, the pip installer can be run by:
 
+   .. code-block:: bash
 
-.. _Github repo: https://github.com/danschef/sensormapgeo
-.. _tarball: https://github.com/danschef/sensormapgeo/tarball/master
+    $ pip install sensormapgeo
+
+If you don't have `pip`_ installed, this `Python installation guide`_ can guide
+you through the process.
+
+
+
+.. note::
+
+    sensormapgeo has been tested with Python 3.6+.,
+    i.e., should be fully compatible to all Python versions from 3.6 onwards.
+
+
+.. _pip: https://pip.pypa.io
+.. _Python installation guide: http://docs.python-guide.org/en/latest/starting/installation/
+.. _conda: https://conda.io/docs

sensormapgeo/transformer_2d.py

@@ -164,9 +164,9 @@ class SensorMapGeometryTransformer(object):
 
             out_res = (area_definition.pixel_size_x, area_definition.pixel_size_y)
             if tgt_res and tgt_res != out_res:
-                warnings.warn('With respect to the Lon/Lat arrays the pixel size was set to %s instead of the desired '
-                              '%s. Provide a target extent where the coordinates are multiples of the pixel sizes to '
-                              'avoid this.' % (str(out_res), str(tgt_res)), UserWarning)
+                warnings.warn(f'With respect to the Lon/Lat arrays the pixel size was set to {str(out_res)} instead of '
+                              f'the desired {str(tgt_res)}. Provide a target extent where the coordinates are '
+                              f'multiples of the pixel sizes to avoid this.', UserWarning)
 
         else:
             def raiseErr_if_empty(gdal_ds):
@@ -218,19 +218,17 @@ class SensorMapGeometryTransformer(object):
                 vrt.FlushCache()
                 del ds_data, vrt
 
-                subcall_with_output("gdalwarp '%s' '%s' "
-                                    '-geoloc '
-                                    '-t_srs EPSG:%d '
-                                    '-srcnodata 0 '
-                                    '-r near '
-                                    '-of ENVI '
-                                    '-dstnodata none '
-                                    '-et 0 '
-                                    '-overwrite '
-                                    '-te %s '
-                                    '%s' % (path_datavrt, path_data_out, tgt_epsg,
-                                            ' '.join([str(i) for i in tgt_extent]),
-                                            ' -tr %s %s' % tgt_res if tgt_res else '',),
+                subcall_with_output(f"gdalwarp '{path_datavrt}' '{path_data_out}' "
+                                    f'-geoloc '
+                                    f'-t_srs EPSG:{tgt_epsg} '
+                                    f'-srcnodata 0 '
+                                    f'-r near '
+                                    f'-of ENVI '
+                                    f'-dstnodata none '
+                                    f'-et 0 '
+                                    f'-overwrite '
+                                    f'-te {" ".join([str(i) for i in tgt_extent])} '
+                                    f'{f"-tr {tgt_res[0]} {tgt_res[1]}" if tgt_res else ""}',
                                     v=True)
 
                 # get output X/Y size
@@ -374,13 +372,12 @@ class SensorMapGeometryTransformer(object):
 
         # output validation
         if not data_mapgeo.shape[:2] == (self.area_definition.height, self.area_definition.width):
-            raise RuntimeError('The computed map geometry output does not have the expected number of rows/columns. '
-                               'Expected: %s; output: %s.'
-                               % (str((self.area_definition.height, self.area_definition.width)),
-                                  str(data_mapgeo.shape[:2])))
+            raise RuntimeError(f'The computed map geometry output does not have the expected number of rows/columns. '
+                               f'Expected: {str((self.area_definition.height, self.area_definition.width))}; '
+                               f'output: {str(data_mapgeo.shape[:2])}.')
         if data.ndim > 2 and data_mapgeo.ndim == 2:
-            raise RuntimeError('The computed map geometry output has only one band instead of the expected %d bands.'
-                               % data.shape[2])
+            raise RuntimeError(f'The computed map geometry output has only one band '
+                               f'instead of the expected {data.shape[2]} bands.')
 
         return data_mapgeo, out_gt, out_prj
 
@@ -402,13 +399,13 @@ class SensorMapGeometryTransformer(object):
 
         # output validation
         if not data_sensorgeo.shape[:2] == self.lats.shape[:2]:
-            raise RuntimeError('The computed sensor geometry output does not have the same X/Y dimension like the '
-                               'coordinates array. Coordinates array: %s; output array: %s.'
-                               % (self.lats.shape, data_sensorgeo.shape))
+            raise RuntimeError(f'The computed sensor geometry output does not have '
+                               f'the same X/Y dimension like the coordinates array. '
+                               f'Coordinates array: {self.lats.shape}; output array: {data_sensorgeo.shape}.')
 
         if data.ndim > 2 and data_sensorgeo.ndim == 2:
-            raise RuntimeError('The computed sensor geometry output has only one band instead of the expected %d bands.'
-                               % data.shape[2])
+            raise RuntimeError(f'The computed sensor geometry output has only one band '
+                               f'instead of the expected {data.shape[2]} bands.')
 
         return data_sensorgeo
 

sensormapgeo/version.py

@@ -22,6 +22,6 @@
 # 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/>.
 
-__version__ = '0.4.6'
-__versionalias__ = '20201012.01'
+__version__ = '0.4.7'
+__versionalias__ = '20201210.01'
 __author__ = 'Daniel Scheffler'

setup.py

@@ -41,7 +41,7 @@ requirements = ['numpy', 'gdal', 'pyresample>=1.11.0', 'py_tools_ds>=0.14.26', '
 
 setup_requirements = []
 
-test_requirements = ['coverage', 'nose', 'nose-htmloutput', 'rednose']
+test_requirements = ['coverage', 'nose', 'nose-htmloutput', 'rednose', 'urlchecker']
 
 setup(
     author="Daniel Scheffler",

tests/CI_docker/context/environment_sensormapgeo.yml

@@ -6,30 +6,24 @@ channels: &id1
 dependencies:
   - python=3.*.*
   - pip  # avoids that conda uses the wrong pip
-  - numpy
-  - gdal
-  - pyresample>=1.11.0
   - _openmp_mutex=*=*llvm* [Unix]  # fixes a deadlock (https://gitext.gfz-potsdam.de/EnMAP/sensormapgeo/-/issues/6)
+  - gdal
+  - numpy
+  - py_tools_ds>=0.14.26
   - pyproj>=2.2
-
-  # py_tools_ds
-  - pyqt
-  - scikit-image
-  - lxml
-  - geopandas
-  - ipython
+  - pyresample>=1.11.0
 
   - pip:
-    - py_tools_ds>=0.14.26
     - pebble
 
-    - sphinx-argparse
+    - coverage
     - flake8
-    - pycodestyle
-    - pylint
-    - pydocstyle
     - nose
     - nose2
     - nose-htmloutput
-    - coverage
+    - pycodestyle
+    - pydocstyle
+    - pylint
     - rednose
+    - sphinx-argparse
+    - urlchecker