0.2.1 release (#21)

* doc fix * Update issue templates * link to reference doc * add .gitattributes files * add support for using spatially enabled dataframes (arcgis) * add notebook * update notebook * updates * bump version * fix bug where coverage may not have demand_col when used in MCLP (#16) * Fix build badge * pin all python dependencies for CI (#17) * Update dependencies (#20) * fix empty geometry issue * update dependencies * bump version * bump arcgis version
apulverizer · Aug 29, 2020 · abb52ac · abb52ac
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diff --git a/Dockerfile b/Dockerfile
@@ -24,10 +24,11 @@ RUN apt-get update -y && apt-get install -y \
 USER allagash
 WORKDIR $HOME
 
+# Copy in environment file
+COPY --chown=allagash:allagash ci-environment.yml ci-environment.yml
+
 # Configure conda env
-RUN conda create -n allagash python=3.7 \
-    && conda install -c esri --name allagash -y geopandas=0.4.1 jupyter=1.0.0 matplotlib=3.1.1 pytest=5.0.1 arcgis=1.6.2 shapely=1.6.4 \
-    && /opt/conda/envs/allagash/bin/pip install pulp==1.6.10 nbval==0.9.2 \
+RUN conda env create -f ci-environment.yml \
     && /opt/conda/envs/allagash/bin/pip install allagash --no-deps \
     && conda clean -a -f -y
 

diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-# Allagash [![build status](https://github.com/apulverizer/allagash/workflows/build/badge.svg)](https://github.com/apulverizer/allagash/actions)
+# Allagash [![build status](https://github.com/apulverizer/allagash/workflows/Build/badge.svg)](https://github.com/apulverizer/allagash/actions)
 A spatial optimization library for covering problems. Full documentation is available [here](https://apulverizer.github.io/allagash)
 
 ### Running Locally
@@ -45,4 +45,4 @@ If you'd like to mount a directory of local data/files into the container, you c
 You can build a docker container that will run the tests (mounted into the container)
 
 1. `docker build . --file build.Dockerfile --tag apulverizer/allagash:build`
-2. `docker run --user=allagash -v $PWD/tests:/home/allagash/tests -v $PWD/src-doc:/home/allagash/src-doc apulverizer/allagash:build /bin/bash -c "py.test --nbval"`
+2. `docker run --user=allagash -v $PWD/tests:/home/allagash/tests -v $PWD/src-doc:/home/allagash/src-doc apulverizer/allagash:build /bin/bash -c "py.test --nbval"`
diff --git a/build.Dockerfile b/build.Dockerfile
@@ -24,11 +24,11 @@ RUN apt-get update -y && apt-get install -y \
 USER allagash
 WORKDIR $HOME
 
-COPY --chown=allagash:allagash environment.yml environment.yml
+COPY --chown=allagash:allagash ci-environment.yml ci-environment.yml
 COPY --chown=allagash:allagash src src
 
 # Configure conda env
-RUN conda env create -f environment.yml \
+RUN conda env create -f ci-environment.yml \
     && cd src \
     && /opt/conda/envs/allagash/bin/python setup.py sdist bdist_wheel \
     && /opt/conda/envs/allagash/bin/pip install allagash --no-deps --find-links dist \

diff --git a/ci-environment.yml b/ci-environment.yml
@@ -0,0 +1,216 @@
+name: allagash
+channels:
+  - esri
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - alabaster=0.7.12
+  - arcgis=1.8.2
+  - argon2-cffi=20.1.0
+  - attrs=20.1.0
+  - babel=2.8.0
+  - backcall=0.2.0
+  - blas=1.0
+  - bleach=3.1.5
+  - blinker=1.4
+  - brotlipy=0.7.0
+  - bzip2=1.0.8
+  - ca-certificates=2020.7.22
+  - cairo=1.14.12
+  - certifi=2020.6.20
+  - cffi=1.14.2
+  - cfitsio=3.470
+  - chardet=3.0.4
+  - click=7.1.2
+  - click-plugins=1.1.1
+  - cligj=0.5.0
+  - cmarkgfm=0.4.2
+  - cryptography=3.0
+  - curl=7.67.0
+  - cycler=0.10.0
+  - dbus=1.13.16
+  - decorator=4.4.2
+  - defusedxml=0.6.0
+  - descartes=1.1.0
+  - docutils=0.16
+  - entrypoints=0.3
+  - expat=2.2.9
+  - fiona=1.8.13.post1
+  - fontconfig=2.13.0
+  - freetype=2.10.2
+  - freexl=1.0.5
+  - future=0.18.2
+  - gdal=3.0.2
+  - geopandas=0.8.1
+  - geos=3.8.0
+  - geotiff=1.5.1
+  - giflib=5.1.4
+  - glib=2.65.0
+  - gst-plugins-base=1.14.0
+  - gstreamer=1.14.0
+  - hdf4=4.2.13
+  - hdf5=1.10.4
+  - icu=58.2
+  - idna=2.10
+  - imagesize=1.2.0
+  - importlib-metadata=1.7.0
+  - importlib_metadata=1.7.0
+  - iniconfig=1.0.1
+  - intel-openmp=2020.2
+  - ipykernel=5.3.4
+  - ipython=7.17.0
+  - ipython_genutils=0.2.0
+  - ipywidgets=7.5.1
+  - jedi=0.17.2
+  - jeepney=0.4.3
+  - jinja2=2.11.2
+  - jpeg=9b
+  - json-c=0.13.1
+  - jsonschema=3.2.0
+  - jupyter=1.0.0
+  - jupyter_client=6.1.6
+  - jupyter_console=6.1.0
+  - jupyter_core=4.6.3
+  - kealib=1.4.7
+  - keyring=21.3.1
+  - kiwisolver=1.2.0
+  - krb5=1.16.4
+  - lcms2=2.11
+  - ld_impl_linux-64=2.33.1
+  - lerc=2.2
+  - libboost=1.67.0
+  - libcurl=7.67.0
+  - libdap4=3.19.1
+  - libedit=3.1.20191231
+  - libffi=3.3
+  - libgcc-ng=9.1.0
+  - libgdal=3.0.2
+  - libgfortran-ng=7.3.0
+  - libkml=1.3.0
+  - libnetcdf=4.6.1
+  - libpng=1.6.37
+  - libpq=11.5
+  - libsodium=1.0.18
+  - libspatialindex=1.9.3
+  - libspatialite=4.3.0a
+  - libssh2=1.9.0
+  - libstdcxx-ng=9.1.0
+  - libtiff=4.1.0
+  - libuuid=1.0.3
+  - libxcb=1.14
+  - libxml2=2.9.10
+  - lz4-c=1.8.1.2
+  - markupsafe=1.1.1
+  - matplotlib=3.3.1
+  - matplotlib-base=3.3.1
+  - mistune=0.8.4
+  - mkl=2020.2
+  - mkl-service=2.3.0
+  - mkl_fft=1.1.0
+  - mkl_random=1.1.1
+  - more-itertools=8.4.0
+  - munch=2.5.0
+  - nbconvert=5.6.1
+  - nbformat=5.0.7
+  - conda-forge::nbsphinx=0.7.1
+  - ncurses=6.2
+  - notebook=6.1.1
+  - ntlm-auth=1.5.0
+  - numpy=1.19.1
+  - numpy-base=1.19.1
+  - oauthlib=3.1.0
+  - olefile=0.46
+  - openjpeg=2.3.0
+  - openssl=1.1.1g
+  - packaging=20.4
+  - pandas=1.1.1
+  - pandoc=2.10.1
+  - pandocfilters=1.4.2
+  - parso=0.7.0
+  - pcre=8.44
+  - pexpect=4.8.0
+  - pickleshare=0.7.5
+  - pillow=7.2.0
+  - pip=20.2.2
+  - pixman=0.40.0
+  - pkginfo=1.5.0.1
+  - pluggy=0.13.1
+  - poppler=0.65.0
+  - poppler-data=0.4.9
+  - postgresql=11.5
+  - proj=6.2.1
+  - prometheus_client=0.8.0
+  - prompt-toolkit=3.0.6
+  - prompt_toolkit=3.0.6
+  - ptyprocess=0.6.0
+  - py=1.9.0
+  - pycparser=2.20
+  - pygments=2.6.1
+  - pyjwt=1.7.1
+  - pykerberos=1.2.1
+  - pyopenssl=19.1.0
+  - pyparsing=2.4.7
+  - pyproj=2.6.1.post1
+  - pyqt=5.9.2
+  - pyrsistent=0.16.0
+  - pyshp=2.1.0
+  - pysocks=1.7.1
+  - pytest=6.0.1
+  - python=3.7.7
+  - python-dateutil=2.8.1
+  - pytz=2020.1
+  - pyzmq=19.0.1
+  - qt=5.9.7
+  - qtconsole=4.7.6
+  - qtpy=1.9.0
+  - readline=8.0
+  - readme_renderer=24.0
+  - requests=2.24.0
+  - requests-kerberos=0.12.0
+  - requests-oauthlib=1.3.0
+  - requests-toolbelt=0.9.1
+  - requests_ntlm=1.1.0
+  - rtree=0.9.4
+  - secretstorage=3.1.2
+  - send2trash=1.5.0
+  - setuptools=41.0.1
+  - shapely=1.6.4
+  - sip=4.19.8
+  - six=1.15.0
+  - snowballstemmer=2.0.0
+  - sphinx=3.2.1
+  - sphinxcontrib-applehelp=1.0.2
+  - sphinxcontrib-devhelp=1.0.2
+  - sphinxcontrib-htmlhelp=1.0.3
+  - sphinxcontrib-jsmath=1.0.1
+  - sphinxcontrib-qthelp=1.0.3
+  - sphinxcontrib-serializinghtml=1.1.4
+  - sqlite=3.33.0
+  - tbb=2018.0.5
+  - terminado=0.8.3
+  - testpath=0.4.4
+  - tiledb=1.6.3
+  - tk=8.6.10
+  - toml=0.10.1
+  - tornado=6.0.4
+  - tqdm=4.48.2
+  - traitlets=4.3.3
+  - twine=2.0.0
+  - tzcode=2020a
+  - urllib3=1.25.10
+  - wcwidth=0.2.5
+  - webencodings=0.5.1
+  - wheel=0.35.1
+  - widgetsnbextension=3.5.1
+  - xerces-c=3.2.2
+  - xz=5.2.5
+  - zeromq=4.3.2
+  - zipp=3.1.0
+  - zlib=1.2.11
+  - zstd=1.3.7
+  - pip:
+    - amply==0.1.2
+    - coverage==5.2.1
+    - nbval==0.9.6
+    - pulp==2.3
+    - sphinx-rtd-theme==0.4.3
diff --git a/environment.yml b/environment.yml
@@ -1,20 +1,22 @@
 name: allagash
 channels:
-  - defaults
   - esri
+  - defaults
 dependencies:
-  - arcgis=1.6.2
-  - shapely=1.6.4
-  - geopandas=0.4.1
-  - jupyter=1.0.0
-  - pip>=19.1.1
-  - pytest>=5.0.1
-  - python=3.7.4
-  - sphinx>=2.1
+  - arcgis>=1.8.2
+  - descartes>=1.1.0
+  - shapely==1.6.4
+  - geopandas>=0.8.1
+  - jupyter>=1.0.0
+  - pandoc>=2.2.3.2
+  - pip>=20.0.2
+  - pytest>=5.4.2
+  - python>=3.7
+  - sphinx>=3.0.3
   - conda-forge::nbsphinx>=0.4.2
-  - twine>=1.13.0
-  - conda-forge::setuptools>=41.2.0
+  - twine>=2.0.0
+  - setuptools>=41.0.1
   - pip:
-    - pulp==1.6.10
+    - pulp~=2.1
     - sphinx-rtd-theme~=0.4.3
-    - nbval~=0.9.2
+    - nbval~=0.9.5
diff --git a/src-doc/examples/LSCP.ipynb b/src-doc/examples/LSCP.ipynb
@@ -20,6 +20,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "import warnings\n",
+    "warnings.filterwarnings('ignore')\n",
     "import geopandas\n",
     "import matplotlib.pyplot as plt\n",
     "import pulp\n",
@@ -206,17 +208,8 @@
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
    "version": "3.7.4"
-  },
-  "pycharm": {
-   "stem_cell": {
-    "cell_type": "raw",
-    "metadata": {
-     "collapsed": false
-    },
-    "source": []
-   }
   }
  },
  "nbformat": 4,
  "nbformat_minor": 2
-}
+}
diff --git a/src-doc/examples/MCLP.ipynb b/src-doc/examples/MCLP.ipynb
@@ -20,6 +20,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "import warnings\n",
+    "warnings.filterwarnings('ignore')\n",
     "import geopandas\n",
     "import matplotlib.pyplot as plt\n",
     "import pulp\n",
@@ -206,17 +208,8 @@
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
    "version": "3.7.4"
-  },
-  "pycharm": {
-   "stem_cell": {
-    "cell_type": "raw",
-    "metadata": {
-     "collapsed": false
-    },
-    "source": []
-   }
   }
  },
  "nbformat": 4,
  "nbformat_minor": 2
-}
+}
diff --git a/src-doc/examples/Using ArcGIS.ipynb b/src-doc/examples/Using ArcGIS.ipynb
@@ -20,6 +20,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "import warnings\n",
+    "warnings.filterwarnings('ignore')\n",
     "from arcgis.features import GeoAccessor\n",
     "from arcgis.gis import GIS\n",
     "import pulp\n",
@@ -208,17 +210,8 @@
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
    "version": "3.7.4"
-  },
-  "pycharm": {
-   "stem_cell": {
-    "cell_type": "raw",
-    "metadata": {
-     "collapsed": false
-    },
-    "source": []
-   }
   }
  },
  "nbformat": 4,
  "nbformat_minor": 2
-}
+}
diff --git a/src/allagash/__init__.py b/src/allagash/__init__.py
@@ -1,4 +1,4 @@
 from .problem import Problem, UnboundedException, UndefinedException, InfeasibleException, NotSolvedException
 from .coverage import Coverage
 
-__version__ = "0.2.0"
+__version__ = "0.2.1"