Merge branch 'master' into release

TerrainBento · Aug 1, 2019 · 2b2ad53 · 2b2ad53
2 parents 1d5bad6 + 4a7754e
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diff --git a/.travis.yml b/.travis.yml
@@ -1,16 +1,41 @@
-env:
-  matrix:
-  - TRAVIS_PYTHON_VERSION="2.7" BUILD_DOCS=0 REPORT_TO_COVERALLS=0
-  - TRAVIS_PYTHON_VERSION="3.6" BUILD_DOCS=0 REPORT_TO_COVERALLS=0
-  - TRAVIS_PYTHON_VERSION="3.7" BUILD_DOCS=0 REPORT_TO_COVERALLS=0
-  global:
-  - CONDA_PREFIX=$HOME/miniconda
-  - MINICONDA_URL_BASE="https://repo.continuum.io/miniconda/Miniconda3-latest"
+language: generic
 os:
 - linux
 - osx
+env:
+  matrix:
+  - CONDA_ENV=3.7
+  - CONDA_ENV=3.6
+  global:
+  - MPLBACKEND=Agg
+  - secure: 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
 sudo: false
-filter_secrets: false
+jobs:
+  include:
+  - stage: lint
+    os: linux
+    script:
+    - pip install flake8
+    - make lint
+  - stage: docs
+    os: linux
+    install:
+    - conda env create --file docs/environment.yml
+    - conda activate terrainbento_docs
+    - pip install -e .
+    script:
+    - make -C docs clean html
+
+  - &deploy
+    stage: deploy
+    if: tag =~ v.*$
+    os: osx
+    env: CONDA_ENV=3.7
+    script:
+    - pip install twine wheel
+    - python setup.py bdist_wheel
+    - twine upload -u katybarnhart -p$TWINE_PASSWORD --verbose dist/*terrainbento*
+
 before_install:
 - |
   if [[ $TRAVIS_OS_NAME == "osx" ]]; then
@@ -19,60 +44,25 @@ before_install:
     rm -rf $(brew --cache)
   fi
 - |
-  if [[ "$TRAVIS_PYTHON_VERSION" == "3.7" && "$TRAVIS_OS_NAME" == "linux" && "$TRAVIS_EVENT_TYPE" == "push" ]]; then
-    REPORT_TO_COVERALLS=1
-  fi
-- |
-  if [[ "$TRAVIS_PYTHON_VERSION" == "3.7" && "$TRAVIS_OS_NAME" == "linux" ]]; then
-    BUILD_DOCS=1
-  fi
-
-install:
-- echo "Build on $TRAVIS_OS_NAME for Python $TRAVIS_PYTHON_VERSION, $TRAVIS_TAG"
+  mkdir -p $HOME/.matplotlib
+  echo "backend: Agg" > $HOME/.matplotlib/matplotlibrc
 - |
   if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then
-    OS="MacOSX-x86_64"
+    curl https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh > $HOME/miniconda.sh
   else
-    OS="Linux-x86_64"
+    curl https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh > $HOME/miniconda.sh
   fi
-- curl $MINICONDA_URL_BASE-$OS.sh > $HOME/minconda.sh
-- bash $HOME/minconda.sh -b -p $CONDA_PREFIX
-- export PATH="$CONDA_PREFIX/bin:$PATH"
+- bash $HOME/miniconda.sh -b -p $(pwd)/anaconda
+- export PATH="$(pwd)/anaconda/bin:$PATH"
 - hash -r
-- conda info
 - conda config --set always_yes yes --set changeps1 no
-- conda update conda
-- conda config --add channels conda-forge
-  # Useful for debugging any issues with conda
-- conda create -n test-environment python=$TRAVIS_PYTHON_VERSION
-- source activate test-environment
-- conda install -q curl
-- conda install -q libcurl
-- conda install -q coverage
-- conda install -q coveralls
-- conda install -q sphinx
-- conda install -q pytest
-- conda install -q pytest-cov
-- conda install -q flake8
-- pip install --upgrade pip
-- pip install codacy-coverage
+- conda create -n test_env python=$CONDA_ENV
+- source activate test_env
 - conda info -a && conda list
-- conda install --file=requirements.txt
-- python setup.py install
-
+install:
+- pip install numpy
+- pip install -e .
 script:
-- pytest --cov --cov-report=xml:$(pwd)/coverage.xml
-- |
-  if [[ "$REPORT_TO_COVERALLS" == "1" ]]; then
-    coveralls
-    export CODACY_PROJECT_TOKEN=$CODACITY_API_TOKEN
-    python-codacy-coverage -r coverage.xml
-  fi
-- make lint
-- |
- if [[ "$BUILD_DOCS" == "1" && "$TRAVIS_OS_NAME" == "linux" ]]; then
-   (cd docs && make html)
- fi
-
-virtualenv:
-  system_site_packages: false
+- pip install pytest pytest-cov pytest-datadir coveralls
+- pytest --cov-report=xml:$(pwd)/coverage.xml
+after_success: coveralls
diff --git a/README.md b/README.md
@@ -1,20 +1,26 @@
-| CI Status | Coverage | Docs | License | Health | Style | DOI |
-| --- | --- | --- | --- | --- | --- | --- |
-| [![Build Status](https://travis-ci.org/TerrainBento/terrainbento.svg?branch=master)](https://travis-ci.org/TerrainBento/terrainbento) [![Build status](https://ci.appveyor.com/api/projects/status/kwwpjifg8vrwe51x/branch/master?svg=true)](https://ci.appveyor.com/project/kbarnhart/terrainbento/branch/master) | [![Coverage Status](https://coveralls.io/repos/github/TerrainBento/terrainbento/badge.svg?branch=master)](https://coveralls.io/github/TerrainBento/terrainbento?branch=master) | [![Documentation Status](https://readthedocs.org/projects/terrainbento/badge/?version=latest)](http://terrainbento.readthedocs.io/en/latest/?badge=latest) | [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT) |[![Code Health](https://landscape.io/github/TerrainBento/terrainbento/master/landscape.svg?style=flat)](https://landscape.io/github/TerrainBento/terrainbento/master) [![Codacy Badge](https://api.codacy.com/project/badge/Grade/7fcb775a6c3044cda4429ed1c1dac2e8)](https://www.codacy.com/app/katy.barnhart/terrainbento?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=TerrainBento/terrainbento&amp;utm_campaign=Badge_Grade)| [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/ambv/black)| [![DOI](https://zenodo.org/badge/123941145.svg)](https://zenodo.org/badge/latestdoi/123941145)|
-
-| Name | Downloads | Version | Platforms |
-| --- | --- | --- | --- |
-| [![Conda Recipe](https://img.shields.io/badge/recipe-terrainbento-green.svg)](https://anaconda.org/conda-forge/terrainbento) | [![Conda Downloads](https://img.shields.io/conda/dn/conda-forge/terrainbento.svg)](https://anaconda.org/conda-forge/terrainbento) | [![Conda Version](https://img.shields.io/conda/vn/conda-forge/terrainbento.svg)](https://anaconda.org/conda-forge/terrainbento) | [![Conda Platforms](https://img.shields.io/conda/pn/conda-forge/terrainbento.svg)](https://anaconda.org/conda-forge/terrainbento) |
+| Thing | Badge |
+| :---: | :---: |
+| CI Status | [![Build Status](https://travis-ci.org/TerrainBento/terrainbento.svg?branch=master)](https://travis-ci.org/TerrainBento/terrainbento) [![Build status](https://ci.appveyor.com/api/projects/status/kwwpjifg8vrwe51x/branch/master?svg=true)](https://ci.appveyor.com/project/kbarnhart/terrainbento/branch/master) |
+| Coverage | [![Coverage Status](https://coveralls.io/repos/github/TerrainBento/terrainbento/badge.svg?branch=master)](https://coveralls.io/github/TerrainBento/terrainbento?branch=master) |
+| Docs | [![Documentation Status](https://readthedocs.org/projects/terrainbento/badge/?version=latest)](http://terrainbento.readthedocs.io/en/latest/?badge=latest) |
+| License | [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT) |
+| Health | [![Code Health](https://landscape.io/github/TerrainBento/terrainbento/master/landscape.svg?style=flat)](https://landscape.io/github/TerrainBento/terrainbento/master) [![Codacy Badge](https://api.codacy.com/project/badge/Grade/7fcb775a6c3044cda4429ed1c1dac2e8)](https://www.codacy.com/app/katy.barnhart/terrainbento?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=TerrainBento/terrainbento&amp;utm_campaign=Badge_Grade) |
+| Style | [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/ambv/black) |
+| DOI | [![DOI](https://zenodo.org/badge/123941145.svg)](https://zenodo.org/badge/latestdoi/123941145) |
+| Conda Recipe | [![Conda Recipe](https://img.shields.io/badge/recipe-terrainbento-green.svg)](https://anaconda.org/conda-forge/terrainbento) |
+| Downloads | [![Conda Downloads](https://img.shields.io/conda/dn/conda-forge/terrainbento.svg)](https://anaconda.org/conda-forge/terrainbento) |
+| Version | [![Conda Version](https://img.shields.io/conda/vn/conda-forge/terrainbento.svg)](https://anaconda.org/conda-forge/terrainbento) |
+| Platforms | [![Conda Platforms](https://img.shields.io/conda/pn/conda-forge/terrainbento.svg)](https://anaconda.org/conda-forge/terrainbento) |
+| Binder | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/TerrainBento/terrainbento/master?filepath=notebooks%2FWelcome_to_TerrainBento.ipynb) |
 
 # terrainbento
 
 A modular landscape evolution modeling package built on top of the [Landlab Toolkit](http://landlab.github.io).
 
 terrainbento"s User Manual is located at our [Read The Docs page](http://terrainbento.readthedocs.io/).
 
-We recommend that you start with [this set of Jupyter notebooks](https://github.com/TerrainBento/examples_tests_and_tutorials) that introduce terrainbento .
+We recommend that you start with a set of Jupyter notebooks [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/TerrainBento/terrainbento/master?filepath=notebooks%2FWelcome_to_TerrainBento.ipynb) that introduce terrainbento and the model description paper [Barnhart et al. (2019)](https://doi.org/10.5194/gmd-12-1267-2019). The link above goes to a Binder instance, if you want the notebooks themselves clone the repo and navigate to the directory `notebooks`.
 
-A manuscript describing terrainbento is currently in discussion at GMD. The discussion paper can be found [here](https://www.geosci-model-dev-discuss.net/gmd-2018-204/).
 
 ## A quick example
 
@@ -32,9 +38,26 @@ params = {
               "step": 10,
               "stop": 1e5},
 
-    # Create the Grid.
-    "grid": {"grid": {"RasterModelGrid":[(200, 320), {"xy_spacing": 10}]},
-             "fields": {"at_node": {"topographic__elevation":{"random":[{"where":"CORE_NODE"}]}}}},
+    # Create the Grid
+    "grid": {
+        "RasterModelGrid": [
+            (200, 320),
+            {
+                "xy_spacing": 10
+            },
+            {
+                "fields": {
+                    "node": {
+                        "topographic__elevation": {
+                            "random": [{
+                                "where": "CORE_NODE"
+                            }]
+                        }
+                    }
+                }
+            },
+        ]
+    },
 
     # Set up Boundary Handlers
     "boundary_handlers":{"NotCoreNodeBaselevelHandler": {"modify_core_nodes": True,
@@ -88,37 +111,34 @@ with imageio.get_writer("terrainbento_example.gif", mode="I") as writer:
 
 Before installing terrainbento you will need a python distribution. We recommend that you use the [Anaconda python distribution](https://www.anaconda.com/download/). Unless you have a specific reason to want Python 2.7 we strongly suggest that you install Python 3.7 (or the current 3.* version provided by Anaconda).
 
+To install the release version of terrainbento (this is probably what you want) we support conda and pip package management.
+
 ### Using conda
-To install the release version of terrainbento (this is probably what you want) open a terminal and execute the following:
+Open a terminal and execute the following:
 
 ```
 conda config --add channels conda-forge
 conda install terrainbento
 ```
 
-### From source code
-
-To install the terrainbento source code version of terrainbento do the following:
-
-#### Option A: You already have landlab installed (either through conda or through the source code)
+### Using pip
+Open a terminal and execute the following:
 
 ```
-git clone https://github.com/TerrainBento/terrainbento.git
-cd terrainbento
-conda install --file=requirements.txt
-python setup.py install
+pip install terrainbento
 ```
 
-#### Option B: You do not have landlab installed
+### From source code
+
+To install the terrainbento source code version of terrainbento we recommend creating a conda environment for terrainbento.
 
 ```
-conda config --add channels conda-forge
-conda install landlab
 git clone https://github.com/TerrainBento/terrainbento.git
 cd terrainbento
-conda install --file=requirements.txt
+cconda env create -f environment-dev.yml
+conda activate terrainbento-dev
 python setup.py install
-```
+``` 
 
 #### A note to developers
 
@@ -127,4 +147,4 @@ If you plan to develop with terrainbento, please fork terrainbento, clone the fo
 
 ## How to cite
 
-A manuscript describing terrainbento is currently in discussion at GMD. The discussion paper can be found [here](https://www.geosci-model-dev-discuss.net/gmd-2018-204/).
+Barnhart, K. R., Glade, R. C., Shobe, C. M., and Tucker, G. E.: Terrainbento 1.0: a Python package for multi-model analysis in long-term drainage basin evolution, Geosci. Model Dev., 12, 1267-1297, https://doi.org/10.5194/gmd-12-1267-2019, 2019.
diff --git a/appveyor.yml b/appveyor.yml
@@ -1,19 +1,17 @@
 environment:
-
+  TWINE_PASSWORD:
+    secure: 7/AZVv0ovctfsb6fBFuC84eyDbvrPSwFlwtIR5RKvQ0=
   matrix:
 
     - TARGET_ARCH: x64
-      CONDA_PY: 27
-      CONDA_INSTALL_LOCN: C:\\Miniconda-x64
-      DISTUTILS_USE_SDK: 1
+      CONDA_NPY: 111
+      CONDA_INSTALL_LOCN: C:\\Miniconda37-x64
+      CONDA_PY: 3.7
 
     - TARGET_ARCH: x64
+      CONDA_NPY: 111
       CONDA_INSTALL_LOCN: C:\\Miniconda36-x64
-      CONDA_PY: 36
-
-    - TARGET_ARCH: x64
-      CONDA_INSTALL_LOCN: C:\\Miniconda37-x64
-      CONDA_PY: 37
+      CONDA_PY: 3.6
 
 platform:
   - x64
@@ -27,18 +25,20 @@ init:
 
 install:
   - cmd: call %CONDA_INSTALL_LOCN%\Scripts\activate.bat
-  - cmd: conda config --set always_yes yes
-  - cmd: conda update conda
+  - cmd: conda update --yes --quiet conda
   - cmd: set PYTHONUNBUFFERED=1
+  - cmd: conda config --set always_yes yes
+  - cmd: pip install twine pytest pytest-cov pytest-datadir
   - cmd: conda info
-  - cmd: conda config --add channels conda-forge
-  - cmd: pip install pytest
-  - cmd: conda config --set always_yes yes --set changeps1 no
-  - cmd: conda info -a && conda list
-  - cmd: conda install --file=requirements.txt
-  - cmd: python setup.py install
+  - cmd: conda list
 
 build: false
 
 test_script:
-  - cmd: pytest
+  - pip install numpy"
+  - pip install -e ."
+  - pytest -vvv
+
+artifacts:
+  # Archive the generated conda package in the ci.appveyor.com build report.
+  - path: 'dist\*'
diff --git a/docs/Makefile b/docs/Makefile
@@ -8,7 +8,7 @@ SPHINXAPIDOC  = sphinx-apidoc
 SPHINXPROJ    = terrainbento
 SOURCEDIR     = .
 BUILDDIR      = _build
-SPHINXEXCLUDE = $(shell find ../terrainbento/* -name tests -or -name examples)
+SPHINXEXCLUDE = $(shell find ../terrainbento/* -name tests)
 
 
 # Put it first so that "make" without argument is like "make help".

diff --git a/docs/conf.py b/docs/conf.py
@@ -67,15 +67,6 @@ def test():
     "yaml",
     "numpy",
     "numpy.testing",
-    "nose",
-    "nose.plugins",
-    "nose.plugins.base",
-    "doctests",
-    "Doctest",
-    "Tester",
-    "doctests.Doctest",
-    "test",
-    "bench",
     "xarray",
     "dask",
     "glob",

diff --git a/docs/environment.yml b/docs/environment.yml
@@ -0,0 +1,15 @@
+
+name: terrainbento_docs
+channels:
+  - conda-forge
+dependencies:
+- python==3.6
+- numpy
+- pandoc
+- pip
+- sphinx>=1.5.1
+- sphinx_rtd_theme
+- tornado
+- entrypoints
+- pip:
+    - sphinxcontrib_github_alt
diff --git a/environment-dev.yml b/environment-dev.yml
@@ -0,0 +1,19 @@
+name: terrainbento-dev
+ channels:
+   - conda-forge
+ dependencies:
+ - python
+ - black
+ - flake8
+ - isort
+ - pytest
+ - pytest-cov
+ - scipy
+ - numpy
+ - xarray
+ - dask
+ - landlab>=1.9
+ - jupyter
+ - holoviews
+ - pandas
+ - dask[complete]