Merge branch 'master' into release

.travis.yml

@@ -61,6 +61,6 @@ install:
 - pip install -e .
 script:
 - pip install pytest pytest-cov coveralls
-- pip install jupyter pandas plotnine holoviews terrainbento tqdm
+- pip install jupyter pandas plotnine holoviews terrainbento tqdm rasterio
 - pytest umami tests/ --doctest-modules --cov=umami --cov-report=xml:$(pwd)/coverage.xml -vvv
 after_success: coveralls

README.md

@@ -4,6 +4,7 @@
 [![Coverage Status](https://coveralls.io/repos/github/TerrainBento/umami/badge.svg?branch=master)](https://coveralls.io/github/TerrainBento/umami?branch=master)
 [![Anaconda-Server Badge](https://anaconda.org/conda-forge/umami/badges/installer/conda.svg)](https://conda.anaconda.org/conda-forge)
 [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/TerrainBento/umami/master?filepath=notebooks%2FWelcome.ipynb)
+[![status](https://joss.theoj.org/papers/1dea51d02def0ff3ef5108eb2a7af3a4/status.svg)](https://joss.theoj.org/papers/1dea51d02def0ff3ef5108eb2a7af3a4)
 
 # What is it?
 
@@ -91,18 +92,26 @@ Documentation is housed on [ReadTheDocs](https://umami.readthedocs.io).
 
 Umami uses Github Issue as a single point of contact for users and developers.
 To ask a question, report a bug, make a feature request, or to get in touch for
-any reason, please make
-[an Issue](https://github.com/TerrainBento/umami/issues).
+any reason, please make [an Issue](https://github.com/TerrainBento/umami/issues).
 
 # Contribute to umami
 
-All contributions are welcome.
+All contributions are welcome and appreciated. Feel free to:
+
+- Make [an issue](https://github.com/TerrainBento/umami/issues) to ask a
+  question. Your question will help others in the future.
+- Make [an issue](https://github.com/TerrainBento/umami/issues) to report a
+  bug or a potential improvement. We will work to fix it. If you have an idea
+  about how to fix it, please feel free to propose it, or make a Pull Request.  
+- [Fork the repository](https://help.github.com/en/articles/fork-a-repo), make
+  changes to the source code on a
+  [development branch](https://www.atlassian.com/git/tutorials/comparing-workflows/gitflow-workflow),
+  and submit a Pull Request to have your changes brought into the umami
+  repository. **No contribution to the code base or documentation is too small.**
 
 Contributors and maintainers to this project are are expected to abide the [Contributor Code of Conduct](https://github.com/TerrainBento/umami/blob/master/CODE_OF_CONDUCT.md).
 
 # Cite umami
+[![status](https://joss.theoj.org/papers/1dea51d02def0ff3ef5108eb2a7af3a4/status.svg)](https://joss.theoj.org/papers/1dea51d02def0ff3ef5108eb2a7af3a4)
 
-If you use umami in your research, please cite it.
-
-A Journal of Open Source Software submission is planned. When it is finalized,
-a link and citation will be found here.
+Umami is described by a Journal of Open Source Software paper. If you use umami in your research, please cite it. 

appveyor.yml

@@ -29,6 +29,8 @@ install:
   - cmd: conda config --set always_yes yes
   - cmd: pip install pytest
   - cmd: pip install jupyter pandas plotnine holoviews terrainbento tqdm
+  - cmd: conda install rasterio -c conda-forge
+  - cmd: conda install landlab -c conda-forge
   - cmd: conda info
   - cmd: conda list
 

binder/postBuild

@@ -9,5 +9,6 @@ conda install pandas
 conda install plotnine>=0.6.0
 conda install terrainbento>=1.10.1
 conda install tqdm
+conda install rasterio
 
 python setup.py install

environment-dev.yml

@@ -20,3 +20,5 @@ dependencies:
    - tqdm
    - plotnine>=0.6.0
    - terrainbento>=1.1
+   - gdal
+   - rasterio

joss/paper.bib

@@ -1,44 +1,41 @@
 @Article{hobley2017creative,
     AUTHOR = {Hobley, D. E. J. and Adams, J. M. and Nudurupati, S. S. and Hutton, E. W. H. and Gasparini, N. M. and Istanbulluoglu, E. and Tucker, G. E.},
-    TITLE = {Creative computing with Landlab: an open-source toolkit for building, coupling, and exploring two-dimensional numerical models of Earth-surface dynamics},
+    TITLE = {{Creative computing with Landlab: an open-source toolkit for building, coupling, and exploring two-dimensional numerical models of Earth-surface dynamics}},
     JOURNAL = {Earth Surface Dynamics},
     VOLUME = {5},
     YEAR = {2017},
     NUMBER = {1},
     PAGES = {21--46},
-    URL = {https://www.earth-surf-dynam.net/5/21/2017/},
     DOI = {10.5194/esurf-5-21-2017}
     }
 
 @Article{barnhart2019terrain,
     AUTHOR = {Barnhart, K. R. and Glade, R. C. and Shobe, C. M. and Tucker, G. E.},
-    TITLE = {Terrainbento 1.0: a Python package for multi-model analysis in long-term drainage basin evolution},
+    TITLE = {{Terrainbento 1.0: a Python package for multi-model analysis in long-term drainage basin evolution}},
     JOURNAL = {Geoscientific Model Development},
     VOLUME = {12},
     YEAR = {2019},
     NUMBER = {4},
     PAGES = {1267--1297},
-    URL = {https://www.geosci-model-dev.net/12/1267/2019/},
     DOI = {10.5194/gmd-12-1267-2019}
     }
 
 @article{adams2019dakota,
-    author = {Adams, Brian M and Eldred, Michael S and Geraci, Gianluca and Hooper, Russell W and Jakeman, John D and Maupin, Kathryn A and Monschk, Jason A and Rushdi, Ahmad A and Stephens, J Adam and Swiler, Laura P and Wildey, Timothy M and Bohnhoff, William J and Dalbey, Keith R and Ebeida, Mohamed S and Eddy, John P and Hough, Patricia D and Khalil, Mohammad and Hu, Kenneth T and Ridgway, Elliott M and Vigil, Dena M and Winokur, Justin G},
+    author = {Adams, B. M. and Eldred, S. and Geraci, G. and Hooper, R. W. and Jakeman, J. D. and Maupin, K. A. and Monschk, J. A. and Rushdi, A. A. and Stephens, J. A. and Swiler, L. P. and Wildey, T. M. and Bohnhoff, W. J. and Dalbey, K. R. and Ebeida, M. S. and Eddy, J. P. and Hough, P. D. and Khalil, M. and Hu, K. T. and Ridgway, E. M. and Vigil, D. M. and Winokur, J. G.},
     title = {{Dakota, A Multilevel Parallel Object-Oriented Framework for Design Optimization, Parameter Estimation, Uncertainty Quantification, and Sensitivity Analysis: Version 6.10 User{\textquoteright}s Manual}},
-    journal = {Sandia National Laboratories, Tech. Rep. SAND2014-4633},
+    journal = {{Sandia National Laboratories, Tech. Rep. SAND2014-4633}},
     year = {2019}
     }
 
 
 @Article{forte2019tak,
     AUTHOR = {Forte, A. M. and Whipple, K. X.},
-    TITLE = {Short communication: The Topographic Analysis Kit (TAK) for TopoToolbox},
+    TITLE = {{Short communication: The Topographic Analysis Kit (TAK) for TopoToolbox}},
     JOURNAL = {Earth Surface Dynamics},
     VOLUME = {7},
     YEAR = {2019},
     NUMBER = {1},
     PAGES = {87--95},
-    URL = {https://www.earth-surf-dynam.net/7/87/2019/},
     DOI = {10.5194/esurf-7-87-2019}
     }
 
@@ -50,7 +47,6 @@ @Article{club2017geomorphometric
     YEAR = {2017},
     NUMBER = {3},
     PAGES = {369--385},
-    URL = {https://www.earth-surf-dynam.net/5/369/2017/},
     DOI = {10.5194/esurf-5-369-2017}
     }
 
@@ -61,42 +57,38 @@ @article{mudd2014statistical
     volume = {119},
     number = {2},
     pages = {138-152},
-    keywords = {bedrock channels, topographic analysis, landscape evolution},
     doi = {10.1002/2013JF002981},
-    url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1002/2013JF002981},
     year = {2014}
     }
 
 
 @Article{schwanghart2014topo,
     AUTHOR = {Schwanghart, W. and Scherler, D.},
-    TITLE = {Short Communication: TopoToolbox 2 - a MATLAB-based software for topographic analysis and modeling in Earth surface sciences},
+    TITLE = {{Short Communication: TopoToolbox 2 - a MATLAB-based software for topographic analysis and modeling in Earth surface sciences}},
     JOURNAL = {Earth Surface Dynamics},
     VOLUME = {2},
     YEAR = {2014},
     NUMBER = {1},
     PAGES = {1--7},
-    URL = {https://www.earth-surf-dynam.net/2/1/2014/},
     DOI = {10.5194/esurf-2-1-2014}
     }
 
 
 @article{schwanghart2010topo,
-    author = "Schwanghart, W. and Kuhn, N. J.",
-    title = "TopoToolbox: A set of Matlab functions for topographic analysis",
-    journal = "Environmental Modelling & Software",
-    volume = "25",
-    number = "6",
-    pages = "770 - 781",
-    year = "2010",
-    issn = "1364-8152",
-    doi = "https://doi.org/10.1016/j.envsoft.2009.12.002",
-    url = "http://www.sciencedirect.com/science/article/pii/S1364815209003053"
+    author = {Schwanghart, W. and Kuhn, N. J.},
+    title = {{TopoToolbox: A set of Matlab functions for topographic analysis}},
+    journal = {{Environmental Modelling \& Software}},
+    volume = {25},
+    number = {6},
+    pages = {770 - 781},
+    year = {2010},
+    issn = {1364-8152},
+    doi = {https://doi.org/10.1016/j.envsoft.2009.12.002}
     }
 
 @Article{	  perron2013integral,
     author	= {Perron, J Taylor and Royden, Leigh},
-    journal	= {Earth Surface Processes and Landforms},
+    journal	= {{Earth Surface Processes and Landforms}},
     number	= {6},
     pages		= {570--576},
     publisher	= {Wiley Online Library},

notebooks/DiscretizedMisfit.ipynb

@@ -4,14 +4,14 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Part 4: Application using the Discretized Misfit calculation\n",
+    "# Part 5: Application using the Discretized Misfit calculation\n",
     "\n",
     "\n",
-    "By now, you should have looked through [Part 1](IntroductionToMetric.ipynb) and [Part 2](IntroductionToResidual.ipynb) of the introductory notebook series. These introduced the umami `Metric` and `Residual` classes. You should have also worked through [Part 3](ExampleApplication.ipynb), which provides an example application of umami. \n",
+    "By now, you should have looked through [Part 1](IntroductionToMetric.ipynb), [Part 2](IntroductionToResidual.ipynb) of the introductory notebook series, and [Part 3](OtherIO_options.ipynb) of the introductory notebook series. These introduced the umami `Metric` and `Residual` classes. You should have also worked through [Part 4](ExampleApplication.ipynb), which provides an example application of umami. \n",
     "\n",
     "## Scope\n",
     "\n",
-    "Similar to [Part 3](ExampleApplication.ipynb), this application will use umami alongside the [terrainbento](https://terrainbento.readthedocs.io/en/latest/) package. As in the prior example, we will define a \"synthetic truth\" model evaluation with a specific set of input parameters, and then do a grid search letting some of those parameters vary. In this way we will explore which statistics for model-data comparison do best at identifying the \"true\" parameters. \n",
+    "Similar to [Part 4](ExampleApplication.ipynb), this application will use umami alongside the [terrainbento](https://terrainbento.readthedocs.io/en/latest/) package. As in the prior example, we will define a \"synthetic truth\" model evaluation with a specific set of input parameters, and then do a grid search letting some of those parameters vary. In this way we will explore which statistics for model-data comparison do best at identifying the \"true\" parameters. \n",
     "\n",
     "This application focuses on the least intuitive of the umami calculations: the [`discretized_misfit`](https://umami.readthedocs.io/en/latest/umami.calculations.residual.discretized_misfit.html). \n",
     "\n",
@@ -477,7 +477,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.3"
+   "version": "3.7.4"
   }
  },
  "nbformat": 4,

notebooks/ExampleApplication.ipynb

@@ -4,9 +4,9 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Part 3: Example application\n",
+    "# Part 4: Example application\n",
     "\n",
-    "By now, you should have looked through [Part 1](IntroductionToMetric.ipynb) and [Part 2](IntroductionToResidual.ipynb) of the introductory notebook series. These introduced the umami `Metric` and `Residual` classes. \n",
+    "By now, you should have looked through [Part 1](IntroductionToMetric.ipynb), [Part 2](IntroductionToResidual.ipynb) of the introductory notebook series, and [Part 3](OtherIO_options.ipynb). These introduced the umami `Metric` and `Residual` classes. \n",
     "\n",
     "## Scope\n",
     "\n",
@@ -402,7 +402,7 @@
    "source": [
     "# Next steps\n",
     "\n",
-    "The next step is the final notebook in the four part introductory series: [Part 4: Application using the Discretized Misfit calculation](DiscretizedMisfit.ipynb)."
+    "The next step is the final notebook in the four part introductory series: [Part 5: Application using the Discretized Misfit calculation](DiscretizedMisfit.ipynb)."
    ]
   },
   {
@@ -429,7 +429,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.3"
+   "version": "3.7.4"
   }
  },
  "nbformat": 4,

notebooks/IntroductionToMetric.ipynb

@@ -6,7 +6,7 @@
    "source": [
     "# Part 1: Introduction to Umami and the `Metric` Class\n",
     "\n",
-    "Umami is a package for calculating metrics for use with for Earth surface dynamics models. This notebook is the first half of a two-part introduction to using umami.\n",
+    "Umami is a package for calculating metrics for use with for Earth surface dynamics models. This notebook is the first part of a three-part introduction to using umami.\n",
     "\n",
     "Umami was designed to work well with the [terrainbento](https://terrainbento.readthedocs.io/en/latest/) model package, as well as other models built using the [Landlab Toolkit](https://github.com/landlab/landlab). \n",
     "\n",
@@ -361,7 +361,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.3"
+   "version": "3.7.4"
   }
  },
  "nbformat": 4,

notebooks/IntroductionToResidual.ipynb

@@ -6,7 +6,7 @@
    "source": [
     "# Part 2: Introduction to Umami and the `Residual` Class\n",
     "\n",
-    "Umami is a package for calculating metrics for use with for Earth surface dynamics models. This notebook is the second half of a two-part introduction to using umami.\n",
+    "Umami is a package for calculating metrics for use with for Earth surface dynamics models. This notebook is the second notebook in a three-part introduction to using umami.\n",
     "\n",
     "## Scope of this tutorial\n",
     "\n",
@@ -278,8 +278,15 @@
    "source": [
     "# Next steps\n",
     "\n",
-    "Now that you have a sense for how the `Metric` and `Residual` classes are used, try the next notebook: [Part 3: Example application](ExampleApplication.ipynb)."
+    "Now that you have a sense for how the `Metric` and `Residual` classes are used, try the next notebook: [Part 3: Other IO options (using umami without Landlab or terrainbento)](OtherIO_options.ipynb)."
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
@@ -298,7 +305,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.3"
+   "version": "3.7.4"
   }
  },
  "nbformat": 4,