Merge branch 'enhancement/clean_deps' into 'master'

Enhancement/clean deps

See merge request !16

.gitlab-ci.yml

@@ -58,11 +58,15 @@ test_py_tools_ds_install:
     - conda create -y -q --name py_tools_ds_testinstall python=3
     - source activate py_tools_ds_testinstall
 
+    # update conda and python
+    - conda update -n base -c defaults conda
+#    - conda update -c conda-forge python
+
       # 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 gdal scikit-image pyproj rasterio shapely geopandas
+    - conda install --yes -q -c conda-forge numpy gdal pyproj shapely geopandas
 
     # run installer
     - python setup.py install
@@ -130,7 +134,7 @@ deploy_anaconda:
   script:
     - source /root/miniconda3/bin/activate
     - source activate ci_env
-    - conda install -y -q conda-build anaconda-client
+    - conda install -y -q conda-build conda-build-all anaconda-client
     - yum install -y patch # https://stackoverflow.com/questions/40392161/building-conda-skeleton-from-pypi-package-throws-error
     # - conda skeleton pypi py_tools_ds --output-dir public/conda.recipe/py_tools_ds # create recipe
     - conda config --set anaconda_upload yes  # enable auto-upload to anaconda

README.rst

@@ -62,7 +62,7 @@ Using conda_, the recommended approach is:
     # create virtual environment for py_tools_ds, this is optional
     conda create -y -q --name py_tools_ds python=3
     source activate py_tools_ds
-    conda install -c conda-forge numpy gdal scikit-image pyproj rasterio shapely pandas
+    conda install -c conda-forge numpy gdal pyproj shapely scikit-image pandas
 
  Then install py_tools_ds using the pip installer:
 

conda_recipe/meta.yaml

@@ -22,13 +22,10 @@ requirements:
     - sphinx-argparse
   run:
     - python
-    - pyqt
     - numpy
     - gdal
-    - scikit-image
-    - rasterio
     - pyproj
-    - lxml
+    - scikit-image
     - geopandas
     - six
     - spectral

py_tools_ds/geo/raster/reproject.py

@@ -24,6 +24,7 @@
 import numpy as np
 import warnings
 import multiprocessing
+from pkgutil import find_loader
 
 # custom
 try:
@@ -44,9 +45,9 @@ from ...compatibility.gdal import get_gdal_func
 __author__ = "Daniel Scheffler"
 
 
-def warp_ndarray_OLD(ndarray, in_gt, in_prj, out_prj, out_gt=None, outRowsCols=None, outUL=None, out_res=None,
-                     out_extent=None, out_dtype=None, rsp_alg=0, in_nodata=None, out_nodata=None,
-                     outExtent_within=True):  # pragma: no cover
+def warp_ndarray_rasterio(ndarray, in_gt, in_prj, out_prj, out_gt=None, outRowsCols=None, outUL=None, out_res=None,
+                          out_extent=None, out_dtype=None, rsp_alg=0, in_nodata=None, out_nodata=None,
+                          outExtent_within=True):  # pragma: no cover
     """Reproject / warp a numpy array with given geo information to target coordinate system.
 
     :param ndarray:             numpy.ndarray [rows,cols,bands]
@@ -71,6 +72,11 @@ def warp_ndarray_OLD(ndarray, in_gt, in_prj, out_prj, out_gt=None, outRowsCols=N
     :return out_gt:             warped gdal GeoTransform
     :return out_prj:            warped projection as WKT string
     """
+
+    if not find_loader('rasterio'):
+        raise ImportError('This function requires rasterio. You need to install it manually '
+                          '(conda install -c conda-forge rasterio). It is not automatically installed.')
+
     # NOTE: rasterio seems to increase the number of objects with static TLS
     #       There is a maximum number and if this is exceeded an ImportError is raised:
     #       ImportError: dlopen: cannot load any more object with static TLS

py_tools_ds/version.py

@@ -19,5 +19,5 @@
 # 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__ = '0.14.24'
-__versionalias__ = '20200107_01'
+__version__ = '0.14.25'
+__versionalias__ = '20200108_01'

requirements.txt

@@ -3,9 +3,8 @@ kealib  # fix for libkea.so.1.4.7: cannot open shared object file: No such file
 numpy
 shapely
 six
-rasterio
+scikit-image
 pandas
 geopandas
-scikit-image
 pyproj
 spectral

setup.py

@@ -36,8 +36,7 @@ version = {}
 with open("py_tools_ds/version.py") as version_file:
     exec(version_file.read(), version)
 
-requirements = ['gdal', 'numpy', 'shapely', 'six', 'rasterio', 'pandas', 'geopandas',
-                'scikit-image', 'pyproj', 'spectral']
+requirements = ['gdal', 'numpy', 'shapely', 'six', 'pandas', 'scikit-image', 'geopandas', 'pyproj', 'spectral']
 setup_requirements = []  # TODO(danschef): put setup requirements (distutils extensions, etc.) here
 test_requirements = requirements + ["coverage", "nose", "nose2", "nose-htmloutput", "rednose"]
 
@@ -69,8 +68,10 @@ setup(
         'Programming Language :: Python :: 3.5',
         'Programming Language :: Python :: 3.6',
         'Programming Language :: Python :: 3.7',
+        'Programming Language :: Python :: 3.8',
     ],
     test_suite='tests',
     tests_require=test_requirements,
-    setup_requires=setup_requirements
+    setup_requires=setup_requirements,
+    extras_require={'rio_reproject': ["rasterio"]}
 )

tests/CI_docker/context/environment_py_tools_ds.yml

@@ -5,20 +5,14 @@ channels: &id1
 
 dependencies:
   - python=3.*.*
-  - pyqt
+  - pip  # avoids that conda uses the wrong pip
   - numpy
   - gdal
   - conda-forge::libgdal  # force to use conda-forge for libgdal to avoid package version incompatiblies due to mixed channels (libkea.so.1.4.7: cannot open shared object file: No such file or directory)
   # - kealib    # fix for libkea.so.1.4.7: cannot open shared object file: No such file or directory (not needed as long as libgdal and gdal are conda-forge packages)
-  - scikit-image
-  - rasterio
   - pyproj
-  - lxml
+  - scikit-image
   - geopandas
-  - ipython
-  - conda-build  # for conda deployment
-  - conda-build-all
-  - anaconda-client # for conda upload
   - pip:
     - sphinx-argparse
     - six

tests/CI_docker/context/py_tools_ds_ci.docker

@@ -6,7 +6,9 @@ RUN yum update -y && \
 COPY *.yml /root/
 
 # update the ci_env environment (that already contains all packages installed via 'docker_pyenvs' repo)
+# -> also include packages for conda deployment and upload
 RUN /bin/bash -i -c "\
     source /root/miniconda3/bin/activate ; \
     source activate ci_env; \
-    conda env update -n ci_env -f /root/environment_py_tools_ds.yml"
+    conda env update -n ci_env -f /root/environment_py_tools_ds.yml ; \
+    conda install -c conda-forge conda-build conda-build-all anaconda-client"