Merge pull request #59 from wpreimes/develop

Allow subsets from non-binary masks

.gitignore

@@ -39,3 +39,6 @@ docs/_rst/*
 docs/_build/*
 cover/*
 MANIFEST
+
+# ignore local scripts
+local_scripts/*

.travis.yml

@@ -1,21 +1,31 @@
+dist: xenial
 language: python
 sudo: false
 notifications:
   email: false
 python:
   # We don't actually use the Travis Python, but this keeps it organized.
   - "2.7"
-  - "3.5"
   - "3.6"
+  - "3.7"
+env:
+  - PINNED=true # use fixed dependencies
+  - PINNED=false # use latest dependencies
+matrix:
+  exclude:
+    - python: "3.7"
+      env: PINNED=true
 install:
   # You may want to periodically update this, although the conda update
   # conda line below will keep everything up-to-date.  We do this
   # conditionally because it saves us some downloading if the version is
   # the same.
   - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
       wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh;
+      pinned_yml=environment_pinned_py2.yml;
     else
       wget http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+      pinned_yml=environment_pinned_py3.yml;
     fi
   - bash miniconda.sh -b -p $HOME/miniconda
   - export PATH="$HOME/miniconda/bin:$PATH"
@@ -26,10 +36,21 @@ install:
   - conda info -a
 
   - conda create -n pygeogrids python=${TRAVIS_PYTHON_VERSION}
+
+  - if $PINNED; then
+        conda env update -f $pinned_yml -n pygeogrids;
+    else
+        conda env update -f environment.yml -n pygeogrids;
+    fi
+
   - source activate pygeogrids
-  - conda env update -f environment.yml
   - python setup.py install
 
+  - conda list
+  - pip list
+  - which pip
+  - which python
+
 script:
   - python setup.py test
 after_success:

environment.yml

@@ -3,19 +3,13 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-- gdal=2.1.0
-- geos=3.5.0
-- geotiff=1.4.1
-- hdf4=4.2.12=1
-- hdf5=1.8.17=2
-- jbig=2.1
-- kealib=1.4.6
-- libnetcdf=4.4.1
-- libgdal=2.1.0
-- mkl=11.3.3=0
-- netcdf4=1.2.4
-- numpy=1.11.0
-- proj4=4.9.2
-- pyproj=1.9
-- pytest=2.9.1
-- pykdtree==1.1.1
+- gdal=2.4.1
+- geos
+- proj4
+- numpy
+- pandas
+- netcdf4
+- hdf5
+- pyproj
+- pykdtree
+- pytest

environment_pinned_py2.yml

@@ -0,0 +1,113 @@
+name: pygeogrids
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - atomicwrites=1.3.0
+  - attrs=19.1.0
+  - backports=1.0
+  - boost-cpp=1.70.0
+  - bzip2=1.0.8
+  - ca-certificates=2019.6.16
+  - cairo=1.16.0
+  - certifi=2019.6.16
+  - cfitsio=3.470
+  - cftime=1.0.3.4
+  - configparser=3.7.3
+  - contextlib2=0.5.5
+  - curl=7.65.3
+  - expat=2.2.5
+  - fontconfig=2.13.1
+  - freetype=2.10.0
+  - freexl=1.0.5
+  - funcsigs=1.0.2
+  - gdal=2.4.1
+  - geos=3.7.2
+  - geotiff=1.4.3
+  - gettext=0.19.8.1
+  - giflib=5.1.7
+  - glib=2.58.3
+  - hdf4=4.2.13
+  - hdf5=1.10.5
+  - icu=58.2
+  - importlib_metadata=0.18
+  - jpeg=9c
+  - json-c=0.13.1
+  - kealib=1.4.10
+  - krb5=1.16.3
+  - libblas=3.8.0
+  - libcblas=3.8.0
+  - libcurl=7.65.3
+  - libdap4=3.20.2
+  - libedit=3.1.20170329
+  - libffi=3.2.1
+  - libgcc-ng=9.1.0
+  - libgdal=2.4.1
+  - libgfortran-ng=7.3.0
+  - libiconv=1.15
+  - libkml=1.3.0
+  - liblapack=3.8.0
+  - libnetcdf=4.6.2
+  - libopenblas=0.3.6
+  - libpng=1.6.37
+  - libpq=11.4
+  - libspatialite=4.3.0a
+  - libssh2=1.8.2
+  - libstdcxx-ng=9.1.0
+  - libtiff=4.0.10
+  - libuuid=2.32.1
+  - libxcb=1.13
+  - libxml2=2.9.9
+  - lz4-c=1.8.3
+  - more-itertools=5.0.0
+  - ncurses=6.1
+  - netcdf4=1.5.1.2
+  - numpy=1.16.4
+  - openjpeg=2.3.1
+  - openssl=1.1.1c
+  - packaging=19.0
+  - pandas=0.24.2
+  - pathlib2=2.3.4
+  - pcre=8.41
+  - pip=19.2.1
+  - pixman=0.38.0
+  - pluggy=0.12.0
+  - poppler=0.67.0
+  - poppler-data=0.4.9
+  - postgresql=11.4
+  - proj4=5.2.0
+  - pthread-stubs=0.4
+  - py=1.8.0
+  - pykdtree=1.3.1
+  - pyparsing=2.4.2
+  - pyproj=1.9.6
+  - pytest=4.6.4
+  - python=2.7.15
+  - python-dateutil=2.8.0
+  - pytz=2019.2
+  - readline=8.0
+  - scandir=1.10.0
+  - setuptools=41.0.1
+  - six=1.12.0
+  - sqlite=3.29.0
+  - tk=8.6.9
+  - tzcode=2019a
+  - wcwidth=0.1.7
+  - wheel=0.33.4
+  - xerces-c=3.2.2
+  - xorg-kbproto=1.0.7
+  - xorg-libice=1.0.10
+  - xorg-libsm=1.2.3
+  - xorg-libx11=1.6.8
+  - xorg-libxau=1.0.9
+  - xorg-libxdmcp=1.1.3
+  - xorg-libxext=1.3.4
+  - xorg-libxrender=0.9.10
+  - xorg-renderproto=0.11.1
+  - xorg-xextproto=7.3.0
+  - xorg-xproto=7.0.31
+  - xz=5.2.4
+  - zipp=0.5.2
+  - zlib=1.2.11
+  - zstd=1.4.0

environment_pinned_py3.yml

@@ -0,0 +1,108 @@
+name: pygeogrids
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - atomicwrites=1.3.0
+  - attrs=19.1.0
+  - boost-cpp=1.70.0
+  - bzip2=1.0.8
+  - ca-certificates=2019.6.16
+  - cairo=1.16.0
+  - certifi=2019.6.16
+  - cfitsio=3.470
+  - cftime=1.0.3.4
+  - curl=7.65.3
+  - expat=2.2.5
+  - fontconfig=2.13.1
+  - freetype=2.10.0
+  - freexl=1.0.5
+  - gdal=2.4.1
+  - geos=3.7.2
+  - geotiff=1.4.3
+  - gettext=0.19.8.1
+  - giflib=5.1.7
+  - glib=2.58.3
+  - hdf4=4.2.13
+  - hdf5=1.10.5
+  - icu=58.2
+  - importlib_metadata=0.18
+  - jpeg=9c
+  - json-c=0.13.1
+  - kealib=1.4.10
+  - krb5=1.16.3
+  - libblas=3.8.0
+  - libcblas=3.8.0
+  - libcurl=7.65.3
+  - libdap4=3.20.2
+  - libedit=3.1.20170329
+  - libffi=3.2.1
+  - libgcc-ng=9.1.0
+  - libgdal=2.4.1
+  - libgfortran-ng=7.3.0
+  - libiconv=1.15
+  - libkml=1.3.0
+  - liblapack=3.8.0
+  - libnetcdf=4.6.2
+  - libopenblas=0.3.6
+  - libpng=1.6.37
+  - libpq=11.4
+  - libspatialite=4.3.0a
+  - libssh2=1.8.2
+  - libstdcxx-ng=9.1.0
+  - libtiff=4.0.10
+  - libuuid=2.32.1
+  - libxcb=1.13
+  - libxml2=2.9.9
+  - lz4-c=1.8.3
+  - more-itertools=7.2.0
+  - ncurses=6.1
+  - netcdf4=1.5.1.2
+  - numpy=1.17.0
+  - openjpeg=2.3.1
+  - openssl=1.1.1c
+  - packaging=19.0
+  - pandas=0.25.0
+  - pcre=8.41
+  - pip=19.2.1
+  - pixman=0.38.0
+  - pluggy=0.12.0
+  - poppler=0.67.0
+  - poppler-data=0.4.9
+  - postgresql=11.4
+  - proj4=5.2.0
+  - pthread-stubs=0.4
+  - py=1.8.0
+  - pykdtree=1.3.1
+  - pyparsing=2.4.2
+  - pyproj=1.9.6
+  - pytest=5.0.1
+  - python=3.6.7
+  - python-dateutil=2.8.0
+  - pytz=2019.2
+  - readline=8.0
+  - setuptools=41.0.1
+  - six=1.12.0
+  - sqlite=3.29.0
+  - tk=8.6.9
+  - tzcode=2019a
+  - wcwidth=0.1.7
+  - wheel=0.33.4
+  - xerces-c=3.2.2
+  - xorg-kbproto=1.0.7
+  - xorg-libice=1.0.10
+  - xorg-libsm=1.2.3
+  - xorg-libx11=1.6.8
+  - xorg-libxau=1.0.9
+  - xorg-libxdmcp=1.1.3
+  - xorg-libxext=1.3.4
+  - xorg-libxrender=0.9.10
+  - xorg-renderproto=0.11.1
+  - xorg-xextproto=7.3.0
+  - xorg-xproto=7.0.31
+  - xz=5.2.4
+  - zipp=0.5.2
+  - zlib=1.2.11
+  - zstd=1.4.0
+

pygeogrids/grids.py

@@ -78,7 +78,7 @@ class BasicGrid(object):
     subset : numpy.array, optional
         if the active part of the array is only a subset of
         all the points then the subset array which is a index
-        into lon and lat can be given here
+        into lon and lat can be given here.
     setup_kdTree : boolean, optional
         if set (default) then the kdTree for nearest neighbour
         search will be built on initialization