Release3.2.13 (#725)

.flake8

@@ -0,0 +1,30 @@
+[flake8]
+exclude =
+    .git,
+    __pycache__,
+    build,
+    dist
+ignore =
+    # https://flake8.pycqa.org/en/latest/user/error-codes.html
+    F401, # 'module' imported but unused
+    # https://pycodestyle.readthedocs.io/en/latest/intro.html#error-codes
+    E121, # continuation line under-indented for hanging indent
+    E122, # continuation line missing indentation or outdented
+    E126, # continuation line over-indented for hanging indent
+    E127, # continuation line over-indented for visual indent
+    E128, # continuation line under-indented for visual indent
+    E221, # multiple spaces before operator
+    E222, # multiple spaces after operator
+    E226, # missing whitespace around arithmetic operator
+    E231, # missing whitespace after ','
+    E241, # multiple spaces after ','
+    E402, # module level import not at top of file
+    E501, # line too long (> 79 characters)
+    E722, # do not use bare 'except'
+    W291, # trailing whitespace
+    W292, # no newline at end of file
+    W293, # blank line contains whitespace
+    W391, # blank line at end of file
+    W503, # line break before binary operator
+    W504  # line break after binary operator
+statistics = True

.travis.yml

@@ -6,20 +6,21 @@ services:
 - xvfb
 matrix:
   include:
-  - env: TVER=PY27
+  - env: RUN_TYPE=test
     python: 2.7
-  - env: TVER=PY35
+  - env: RUN_TYPE=test
     python: 3.5
-  - env: TVER=PY36
+  - env: RUN_TYPE=test
     python: 3.6
-  - env: TVER=PY37
+  - env: RUN_TYPE=test
     python: 3.7
-  - env: TVER=PY37N
+  - env: RUN_TYPE=misc
     python: 3.7
-  - env: TVER=PY37D
-    python: 3.7-dev
-  allow_failures:
-  - env: TVER=PY37D
+# - env: RUN_TYPE=test
+#   python: 3.8-dev
+# allow_failures:
+# - env: RUN_TYPE=test
+#   python: 3.8-dev
 cache:
   pip: true
   directories:
@@ -32,57 +33,18 @@ addons:
     packages:
     - gfortran-8
     - g++-8
-    - python-pip
     - libhdf5-serial-dev
     - netcdf-bin
     - libnetcdf-dev
     - gdal-bin
     - libgdal-dev
 env:
   global:
-  - NO_NET=1
-install:
-- if [[ ! -d "$HOME/.local/bin" ]]; then mkdir "$HOME/.local/bin"; fi
-- export PATH="$HOME/.local/bin:$PATH"
-- ln -fs /usr/bin/gfortran-8 "$HOME/.local/bin/gfortran" && gfortran --version
-- ls -l /usr/bin/gfortran-8
-- ln -fs /usr/bin/gcc-8 "$HOME/.local/bin/gcc" && gcc --version
-- ls -l /usr/bin/gcc-8
-- ln -fs /usr/bin/g++-8 "$HOME/.local/bin/g++" && g++ --version
-- ls -l /usr/bin/g++-8
-- export CXX="g++"
-- if [[ $TRAVIS_PYTHON_VERSION == 2.7 ]]; then pip install -r requirements27.travis.txt;
-  echo requests version1; python -c "import requests; print(requests.__version__)";
-  else pip install -r requirements.travis.txt; fi
-- pip install https://github.com/modflowpy/pymake/zipball/master
-- pip install --upgrade jupyter
-- pip install nbconvert
-- pip install nose-timer
-- pip install coveralls
-- pip install pylint
-script:
-- export PYTHONPATH=$PYTHONPATH:.
-- echo python path; python -c "from __future__ import print_function; import sys;
-  print(sys.path)"
-- python -c "import os; is_travis = 'TRAVIS' in os.environ; print('TRAVIS {}'.format(is_travis))"
-- echo flopy version; python -c "from __future__ import print_function; import flopy;
-  print(flopy.__version__)"
-- echo numpy version; python -c "import numpy; print(numpy.version.version)"
-- echo pandas version; python -c "import pandas as pd; print(pd.__version__)"
-- echo pyshp; python -c "import shapefile; print(shapefile.__version__)"
-- echo nosetests version; nosetests --version
-- echo jupyter version; jupyter --version
-- echo jupyter runtime directory; jupyter --runtime-dir
-- echo pylint version; pylint --version
-- nosetests -v build_exes.py --with-id --with-timer -w ./autotest
-- if [[ $TVER == PY37N ]]; then nosetests -v autotest_scripts.py --with-id --with-timer
-  -w ./autotest --with-coverage --cover-package=flopy; nosetests -v autotest_notebooks.py
-  --with-id --with-timer -w ./autotest --with-coverage --cover-package=flopy; else
-  nosetests -v --with-id --with-timer -w ./autotest --with-coverage --cover-package=flopy;
-  fi
-after_success:
-- coveralls
-- if [[ $TRAVIS_PYTHON_VERSION == 3.5 ]]; then pylint --errors-only ./flopy; fi
+  - PYTHONPATH=$PYTHONPATH:.
+install: ./travis/install.sh
+before_script: ./travis/before_script.sh
+script: ./travis/script.sh
+after_success: coveralls
 notifications:
   slack:
     secure: 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

README.md

@@ -1,11 +1,12 @@
 
 <img src="https://raw.githubusercontent.com/modflowpy/flopy/master/examples/images/flopy3.png" alt="flopy3" style="width:50;height:20">
 
-### Version 3.2.12
+### Version 3.2.13
 [![Build Status](https://travis-ci.org/modflowpy/flopy.svg?branch=master)](https://travis-ci.org/modflowpy/flopy)
 [![PyPI Version](https://img.shields.io/pypi/v/flopy.png)](https://pypi.python.org/pypi/flopy)
 [![Coverage Status](https://coveralls.io/repos/github/modflowpy/flopy/badge.svg?branch=master)](https://coveralls.io/github/modflowpy/flopy?branch=master)
-[![Codacy Badge](https://api.codacy.com/project/badge/Grade/b23a5edd021b4aa19e947545ab49e577)](https://www.codacy.com/app/jdhughes-usgs/flopy?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=modflowpy/flopy&amp;utm_campaign=Badge_Grade)
+[![Codacy Badge](https://api.codacy.com/project/badge/Grade/b23a5edd021b4aa19e947545ab49e577)](https://www.codacy.com/app/jdhughes-usgs/flopy?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=modflowpy/flopy&amp;utm_campaign=Badge_Grade)[![Binder](https://aws-uswest2-binder.pangeo.io/badge_logo.svg)](https://aws-uswest2-binder.pangeo.io/v2/gh/modflowpy/flopy.git/master)
+
 
 Introduction
 -----------------------------------------------
@@ -111,7 +112,7 @@ Installation
 
 **Python versions:**
 
-FloPy requires **Python** 2.7 or **Python** 3.3 (or higher)
+FloPy requires **Python** 2.7 or **Python** 3.5 (or higher). **<span style="color:red" style="text-decoration:underline">Support for Python versions < 3.5 will be dropped in the next version of FloPy (version 3.3.0)</span>**
 
 
 **Dependencies:**
@@ -200,7 +201,11 @@ Additional dependencies to use optional FloPy helper methods are listed below.
 | `.loadtxt()` in `flopy.utils.flopyio` - ***used if available***                      | **pandas** >= 0.15                                 |
 | `.generate_classes()` in `flopy.mf6.utils`                                           | [**pymake**](https://github.com/modflowpy/pymake)  |
 | `.intersect()` in `flopy.discretization.VertexGrid`                                  | **matplotlib** >= 1.4                              |
-
+| `GridIntersect()` in `flopy.utils.gridintersect`                                     | **shapely**                                        |
+| `GridIntersect().plot_polygon()` in `flopy.utils.gridintersect`                      | **shapely** and **descartes**                      |
+| `Raster()` in `flopy.utils.Raster`                                                   | **rasterio**, **affine**, and **scipy**            |
+| `Raster().sample_polygon()` in `flopy.utils.Raster`                                  | **shapely**                                        |
+| `Raster().crop()` in `flopy.utils.Raster`                                            | **shapely**                                        |
 
 How to Cite
 -----------------------------------------------
@@ -211,7 +216,7 @@ How to Cite
 
 ##### ***Software/Code citation for FloPy:***
 
-[Bakker, M., Post, V., Langevin, C.D., Hughes, J.D., White, J.T., Starn, J.J., and Fienen, M.N., 2019, FloPy v3.2.12: U.S. Geological Survey Software Release, 31 May 2019, http://dx.doi.org/10.5066/F7BK19FH](http://dx.doi.org/10.5066/F7BK19FH)
+[Bakker, M., Post, V., Langevin, C.D., Hughes, J.D., White, J.T., Starn, J.J., and Fienen, M.N., 2019, FloPy v3.2.13: U.S. Geological Survey Software Release, 17 November 2019, http://dx.doi.org/10.5066/F7BK19FH](http://dx.doi.org/10.5066/F7BK19FH)
 
 
 MODFLOW Resources

autotest/t003_test.py

@@ -112,7 +112,7 @@ def test_load_nam_mt_nonexistant_file():
     test_loadoc_nstpfail()
     test_load_nam_mf_nonexistant_file()
     test_load_nam_mt_nonexistant_file()
-    # test_loadoc_lenfail()
-    # test_loadfreyberg()
-    # test_loadoahu()
-    # test_loadtwrip()
+    test_loadoc_lenfail()
+    test_loadfreyberg()
+    test_loadoahu()
+    test_loadtwrip()

autotest/t004_test_utilarray.py

@@ -685,8 +685,21 @@ def test_mflist():
     sp_data = {0: [[1, 1, 1, 1.0], [1, 1, 2, 2.0], [1, 1, 3, 3.0]],
                1: [1, 2, 4, 4.0]}
     wel = flopy.modflow.ModflowWel(ml, stress_period_data=sp_data)
-    m4ds = ml.wel.stress_period_data.masked_4D_arrays
+    spd = wel.stress_period_data
+
+    # verify dataframe can be cast when spd.data.keys() != to ml.nper
+    # verify that dataframe is cast correctly by recreating spd.data items
+    df = wel.stress_period_data.get_dataframe()
+    for per, data in spd.data.items():
+        fluxcol = 'flux{}'.format(per)
+        dfper = df.dropna(subset=[fluxcol], axis=0).copy()
+        dfper.rename(columns={fluxcol: 'flux'}, inplace=True)
+        dfdata = dfper[['k', 'i', 'j', 'flux']].to_records(index=False)
+        dfdata = dfdata.astype(data.dtype)
+        errmsg = 'data not equal:\n  {}\n  {}'.format(dfdata, data)
+        assert np.array_equal(dfdata, data), errmsg
 
+    m4ds = ml.wel.stress_period_data.masked_4D_arrays
     sp_data = flopy.utils.MfList.masked4D_arrays_to_stress_period_data \
         (flopy.modflow.ModflowWel.get_default_dtype(), m4ds)
     assert np.array_equal(sp_data[0], ml.wel.stress_period_data[0])
@@ -782,7 +795,7 @@ def test_util3d_reset():
     # test_util2d_external_fixed_nomodelws()
     # test_util2d_external_fixed_path_nomodelws()
     # test_transient2d()
-    #test_transient3d()
+    # test_transient3d()
     # test_util2d()
     # test_util3d()
     # test_how()