Merge branch 'master' into sed-flux-dep

HUGE code update. Tests pass. The sed_flux_dep eroder is 100% ported
from the 2016 master, so may be troublesome with existing drivers from
2014.

# Conflicts:
#	.gitignore
#	landlab/components/stream_power/examples/drive_sp_params_storms.txt
#	landlab/components/stream_power/examples/perturb_sed_flux_dep.py
#	landlab/components/stream_power/examples/perturb_sp_driver.py
#	landlab/components/stream_power/examples/perturb_sp_storms.py
#	landlab/components/stream_power/examples/simple_sp_driver.py
#	landlab/components/stream_power/examples/test_sed_flux_dep.py
#	landlab/components/stream_power/sed_flux_dep_incision.py
#
landlab/components/transport_limited_fluvial/tl_fluvial_monodirectional_
v3.py
#	landlab/plot/channel_profile.py

.ci/appveyor/deploy_to_pypi.ps1

@@ -0,0 +1,12 @@
+if (($env:appveyor_repo_tag -eq "true") -and ($env:appveyor_repo_tag_name.StartsWith("v"))) {
+    write-output "Deploying to PyPI..."
+    Invoke-Expression "twine upload -u mcflugen -p $env:PYPI_PASS dist/*"
+    write-output "OK"
+} else {
+    write-output "Not deploying."
+    write-output "Is a tagged commit... $env:appveyor_repo_tag"
+    if (($env:appveyor_repo_tag -eq "true")) {
+      write-output "Tag name... $env:appveyor_repo_tag_name"
+    }
+    write-output "Branch name... $env:appveyor_repo_branch"
+}

.ci/appveyor/install-miniconda.ps1

@@ -0,0 +1,71 @@
+# Sample script to install anaconda under windows
+# Authors: Stuart Mumford
+# Borrwed from: Olivier Grisel and Kyle Kastner
+# License: BSD 3 clause
+
+$MINICONDA_URL = "http://repo.continuum.io/miniconda/"
+
+function DownloadMiniconda ($version, $platform_suffix) {
+    $webclient = New-Object System.Net.WebClient
+    $filename = "Miniconda-" + $version + "-Windows-" + $platform_suffix + ".exe"
+
+    $url = $MINICONDA_URL + $filename
+
+    $basedir = $pwd.Path + "\"
+    $filepath = $basedir + $filename
+    if (Test-Path $filename) {
+        Write-Host "Reusing" $filepath
+        return $filepath
+    }
+
+    # Download and retry up to 3 times in case of network transient errors.
+    Write-Host "Downloading" $filename "from" $url
+    $retry_attempts = 2
+    for($i=0; $i -lt $retry_attempts; $i++){
+        try {
+            $webclient.DownloadFile($url, $filepath)
+            break
+        }
+        Catch [Exception]{
+            Start-Sleep 1
+        }
+   }
+   if (Test-Path $filepath) {
+       Write-Host "File saved at" $filepath
+   } else {
+       # Retry once to get the error message if any at the last try
+       $webclient.DownloadFile($url, $filepath)
+   }
+   return $filepath
+}
+
+function InstallMiniconda ($python_version, $architecture, $python_home) {
+    Write-Host "Installing miniconda" $python_version "for" $architecture "bit architecture to" $python_home
+    if (Test-Path $python_home) {
+        Write-Host $python_home "already exists, skipping."
+        return $false
+    }
+    if ($architecture -eq "x86") {
+        $platform_suffix = "x86"
+    } else {
+        $platform_suffix = "x86_64"
+    }
+    $filepath = DownloadMiniconda $python_version $platform_suffix
+    Write-Host "Installing" $filepath "to" $python_home
+    $args = "/InstallationType=AllUsers /S /AddToPath=1 /RegisterPython=1 /D=" + $python_home
+    Write-Host $filepath $args
+    Start-Process -FilePath $filepath -ArgumentList $args -Wait -Passthru
+    #Start-Sleep -s 15
+    if (Test-Path C:\conda) {
+        Write-Host "Miniconda $python_version ($architecture) installation complete"
+    } else {
+        Write-Host "Failed to install Python in $python_home"
+        Exit 1
+    }
+}
+
+function main () {
+    InstallMiniconda $env:MINICONDA_VERSION $env:PLATFORM $env:PYTHON
+}
+
+main

.ci/appveyor/install.ps1

@@ -0,0 +1,97 @@
+# Sample script to install Miniconda under Windows
+# Authors: Olivier Grisel, Jonathan Helmus and Kyle Kastner, Robert McGibbon
+# License: CC0 1.0 Universal: http://creativecommons.org/publicdomain/zero/1.0/
+
+$MINICONDA_URL = "http://repo.continuum.io/miniconda/"
+
+
+function DownloadMiniconda ($python_version, $platform_suffix) {
+    $webclient = New-Object System.Net.WebClient
+    if ($python_version -match "3.4") {
+        $filename = "Miniconda3-3.5.5-Windows-" + $platform_suffix + ".exe"
+    } else {
+        $filename = "Miniconda-3.5.5-Windows-" + $platform_suffix + ".exe"
+    }
+    $url = $MINICONDA_URL + $filename
+
+    $basedir = $pwd.Path + "\"
+    $filepath = $basedir + $filename
+    if (Test-Path $filename) {
+        Write-Host "Reusing" $filepath
+        return $filepath
+    }
+
+    # Download and retry up to 3 times in case of network transient errors.
+    Write-Host "Downloading" $filename "from" $url
+    $retry_attempts = 2
+    for($i=0; $i -lt $retry_attempts; $i++){
+        try {
+            $webclient.DownloadFile($url, $filepath)
+            break
+        }
+        Catch [Exception]{
+            Start-Sleep 1
+        }
+   }
+   if (Test-Path $filepath) {
+       Write-Host "File saved at" $filepath
+   } else {
+       # Retry once to get the error message if any at the last try
+       $webclient.DownloadFile($url, $filepath)
+   }
+   return $filepath
+}
+
+
+function InstallMiniconda ($python_version, $architecture, $python_home) {
+    Write-Host "Installing Python" $python_version "for" $architecture "bit architecture to" $python_home
+    if (Test-Path $python_home) {
+        Write-Host $python_home "already exists, skipping."
+        return $false
+    }
+    if ($architecture -match "32") {
+        $platform_suffix = "x86"
+    } else {
+        $platform_suffix = "x86_64"
+    }
+
+    $filepath = DownloadMiniconda $python_version $platform_suffix
+    Write-Host "Installing" $filepath "to" $python_home
+    $install_log = $python_home + ".log"
+    $args = "/S /D=$python_home"
+    Write-Host $filepath $args
+    Start-Process -FilePath $filepath -ArgumentList $args -Wait -Passthru
+    if (Test-Path $python_home) {
+        Write-Host "Python $python_version ($architecture) installation complete"
+    } else {
+        Write-Host "Failed to install Python in $python_home"
+        Get-Content -Path $install_log
+        Exit 1
+    }
+}
+
+
+function InstallCondaPackages ($python_home, $spec) {
+    $conda_path = $python_home + "\Scripts\conda.exe"
+    $args = "install --yes " + $spec
+    Write-Host ("conda " + $args)
+    Start-Process -FilePath "$conda_path" -ArgumentList $args -Wait -Passthru
+}
+
+function UpdateConda ($python_home) {
+    $conda_path = $python_home + "\Scripts\conda.exe"
+    Write-Host "Updating conda..."
+    $args = "update --yes conda"
+    Write-Host $conda_path $args
+    Start-Process -FilePath "$conda_path" -ArgumentList $args -Wait -Passthru
+}
+
+
+function main () {
+    InstallMiniconda $env:PYTHON_VERSION $env:PYTHON_ARCH $env:PYTHON
+    UpdateConda $env:PYTHON
+    InstallCondaPackages $env:PYTHON "conda-build=1.4.0 pip jinja2 binstar"
+    InstallCondaPackages $env:PYTHON "conda-build=1.4.0 scipy>=0.12 numpy nose>=1.3 matplotlib netCDF4 sympy pandas cython>=0.22 wheel"
+}
+
+main

.ci/appveyor/run_with_env.cmd

@@ -0,0 +1,36 @@
+@echo off
+:: To build extensions for 64 bit Python 3, we need to configure environment
+:: variables to use the MSVC 2010 C++ compilers from GRMSDKX_EN_DVD.iso of:
+:: MS Windows SDK for Windows 7 and .NET Framework 4
+::
+:: More details at:
+:: https://github.com/cython/cython/wiki/64BitCythonExtensionsOnWindows
+::
+SET COMMAND_TO_RUN=%*
+SET WIN_SDK_ROOT=C:\Program Files\Microsoft SDKs\Windows
+SET MAJOR_PYTHON_VERSION="%PYTHON_VERSION:~0,1%"
+SET WINDOWS_SDK_VERSION="v7.0"
+IF %MAJOR_PYTHON_VERSION%=="3" (
+  SET WINDOWS_SDK_VERSION="v7.1"
+)
+ECHO Configuring Windows SDK %WINDOWS_SDK_VERSION%
+
+IF "%DISTUTILS_USE_SDK%"=="1" (
+
+    IF "%PLATFORM%"=="x64" (
+        ECHO Configuring Windows SDK %WINDOWS_SDK_VERSION% for Python %MAJOR_PYTHON_VERSION% on a 64 bit architecture
+        SET MSSdk=1
+        "%WIN_SDK_ROOT%\%WINDOWS_SDK_VERSION%\Setup\WindowsSdkVer.exe" -q -version:%WINDOWS_SDK_VERSION%
+        "%WIN_SDK_ROOT%\%WINDOWS_SDK_VERSION%\Bin\SetEnv.cmd" /x64 /release
+        ECHO Executing: %COMMAND_TO_RUN%
+        call %COMMAND_TO_RUN% || EXIT 1
+    ) ELSE (
+        ECHO Using default MSVC build environment for 32 bit architecture
+        ECHO Executing: %COMMAND_TO_RUN%
+        call %COMMAND_TO_RUN% || EXIT 1
+    )
+) ELSE (
+    ECHO Using default MSVC build environment
+    ECHO Executing: %COMMAND_TO_RUN%
+    call %COMMAND_TO_RUN% || EXIT 1
+)

.ci/travis/deploy_to_pypi.sh

@@ -0,0 +1,18 @@
+if [[ "$TRAVIS_TAG" == v* && "$TRAVIS_BRANCH" == "release" ]]; then
+  echo "Installing deployment requirements."
+  pip install twine wheel
+  if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then
+    echo "Creating a source distribution."
+    python setup.py sdist
+  else
+    echo "Creating a binary wheel distribution."
+    python setup.py bdist_wheel
+  fi
+  echo "Uploading to PyPI."
+  twine upload -u mcflugen -p$PYPI_PASS dist/*
+  echo "Done."
+else
+  echo "Not deploying."
+  echo "Tag is... $TRAVIS_TAG"
+  echo "Branch name is... $TRAVIS_BRANCH"
+fi

.travis/install_python.sh → .ci/travis/install_python.sh

@@ -5,17 +5,16 @@ if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then
 else
     OS="Linux-x86_64";
 fi
-sudo apt-get update 2> /dev/null || echo "No apt-get"
 if [[ "$TRAVIS_PYTHON_VERSION" == 2.* ]]; then
-      wget http://repo.continuum.io/miniconda/Miniconda-3.4.2-$OS.sh -O miniconda.sh;
+      wget http://repo.continuum.io/miniconda/Miniconda-latest-$OS.sh -O miniconda.sh;
 else
-      wget http://repo.continuum.io/miniconda/Miniconda3-3.4.2-$OS.sh -O miniconda.sh;
+      wget http://repo.continuum.io/miniconda/Miniconda3-latest-$OS.sh -O miniconda.sh;
 fi
 bash miniconda.sh -b -p $HOME/miniconda
 export PATH="$HOME/miniconda/bin:$PATH"
 hash -r
 conda config --set always_yes yes --set changeps1 no
-conda update conda
+# conda update conda
 conda info -a
 cat requirements.txt | grep -v numpydoc | xargs conda create -n test-env python=$TRAVIS_PYTHON_VERSION
 source activate test-env

.ci/travis/run_travis_test.sh

@@ -0,0 +1,15 @@
+#! /bin/bash
+
+PYTHON=${PYTHON:-python}
+
+run_test()
+{
+  mkdir -p _test
+  cd _test
+
+  INSTALLDIR=$($PYTHON -c "import os; import landlab; print(os.path.dirname(landlab.__file__))")
+
+  coverage run --source=$INSTALLDIR ../scripts/test-installed-landlab.py && (coverage report && cp .coverage ..)
+}
+
+run_test

.codeclimate.yml

@@ -0,0 +1,8 @@
+languages:
+  Python: true
+exclude_paths:
+- "docs/*"
+- "scripts/*"
+- "landlab/components/**/*"
+- "landlab/examples/*"
+- "landlab/**/test_*.py"

.gitignore

@@ -58,11 +58,25 @@ docs/_build/
 *.swp
 *.swo
 
-landlab/test.pdf
 test-results.xml
 
 *.gif
 
 *.p
 
+*.pdf
+!docs/**/*.pdf
+
 *.png
+!docs/**/*.png
+
+*.aux
+
+*.synctex.gz
+
+installfiles.txt
+
+# Ignore all .c files as, currently, they are all cython generated.
+*.c
+
+landlab/io/mysave.grid

.landscape.yaml

@@ -0,0 +1,7 @@
+ignore-patterns:
+  - ez_setup.py
+  - setup.py
+ignore-paths:
+  - docs
+strictness: veryhigh
+doc-warnings: True

.travis.yml

@@ -1,30 +1,50 @@
-language: python
-python:
-  - "2.6"
-  - "2.7"
-  - "3.3"
-  - "3.4"
+env:
+  matrix:
+  - TRAVIS_PYTHON_VERSION="2.6" NUMPY_VERSION="1.9"
+  - TRAVIS_PYTHON_VERSION="2.7" NUMPY_VERSION="1.9"
+  - TRAVIS_PYTHON_VERSION="2.7" NUMPY_VERSION="1.10"
+  - TRAVIS_PYTHON_VERSION="3.3" NUMPY_VERSION="1.9"
+  - TRAVIS_PYTHON_VERSION="3.4" NUMPY_VERSION="1.9"
+  - TRAVIS_PYTHON_VERSION="3.4" NUMPY_VERSION="1.10"
+  - TRAVIS_PYTHON_VERSION="3.5" NUMPY_VERSION="1.9"
+  - TRAVIS_PYTHON_VERSION="3.5" NUMPY_VERSION="1.10"
+  global:
+    secure: UxPkdFKl0xtk+H+98CNHSnYN8SJrEq5xJjLtPUPR+5UF5lLKL7godwrOdYeO0B0fXPi2Plw0vtoIID6H1AV4x+8QD/AgAizoWIh8KLim3E7rDX0v0M3WnUHctvYwt76mGCYvIGH6qR2Ziml37Ec6nz2aTuz0oex27P6dq0BKkXs=
 os:
-  - linux
-  - osx
-
+- linux
+- osx
+matrix:
+  allow_failures:
+  - os: osx
+    env: TRAVIS_PYTHON_VERSION="2.6" NUMPY_VERSION="1.9"
+sudo: false
 install:
-  - echo "Build on $TRAVIS_OS_NAME for Python $TRAVIS_PYTHON_VERSION"
-  - bash .travis/install_python.sh
-  - export PATH="$HOME/miniconda/bin:$PATH"
-  - source activate test-env
-  - pip install coveralls
-  - if [[ "$TRAVIS_PYTHON_VERSION" == 3.* ]]; then
-      bash .travis/convert_to_python_3.sh;
-    fi
-  - python setup.py install
-
-script: 
-  - (cd docs && make html)
-  - nosetests --with-coverage --cover-package=landlab
-
+- echo "Build on $TRAVIS_OS_NAME for Python $TRAVIS_PYTHON_VERSION"
+- bash .ci/travis/install_python.sh
+- export PATH="$HOME/miniconda/bin:$PATH"
+- source activate test-env
+- pip install coveralls
+- conda install numpy=$NUMPY_VERSION
+- conda install scipy
+- python setup.py install
+script:
+- if [[ "$TRAVIS_PYTHON_VERSION" == 2.7 ]]; then (cd docs && make html 2> /dev/null); fi
+- bash .ci/travis/run_travis_test.sh
 virtualenv:
   system_site_packages: false
-
 after_success:
-  coveralls
+  - bash .ci/travis/deploy_to_pypi.sh
+  - coveralls
+deploy:
+  provider: pypi
+  user: mcflugen
+  password:
+    secure: V15DceMv4DUmjgxToaxrP3KaQxsLbfrTkB1s6D8YNQZvYJiVvNlBpC1nF8yWbOt3IWJQSGjaQEnObd2ZhHe2Kq/H+QsEFyBKlYF7SNp35FyS5zLuf2qhnNhmzhqkspwBpiGe88c1PQPFzfqdIUQXp7ZAv6L8YRvNy2sbzvgxh6I=
+  on:
+    tags: true
+    branch: release
+    repo: landlab/landlab
+  distributions: sdist bdist_wheel
+notifications:
+  slack:
+    secure: gRKbqjPgp0ZcFtecHOwjLAFbzzBr2zyFrxk7OAS/cea/9U8bLQNA0jZs3ZHtAgR53gdnFlx/GI10d/KD9XMKU55gQkO4FSvfYMK7Xzs2tfnEa5flTqQKRfjB1oJ2fmb81yshUe+xKsXBoedP7SPYv2mutMOY8srKwUcuE0yGmAw=