From d4d247f75d9ab432ad3cef8af2e4048fe2de626f Mon Sep 17 00:00:00 2001 From: Katy Barnhart Date: Mon, 16 Sep 2019 17:09:29 -0600 Subject: [PATCH 1/7] fix: typo in bibliography file --- joss/paper.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/joss/paper.md b/joss/paper.md index e218092..f7c076e 100644 --- a/joss/paper.md +++ b/joss/paper.md @@ -31,7 +31,7 @@ affiliations: - name: University of Colorado at Boulder, Institute for Arctic and Alpine Research index: 4 date: 4 September 2019 -bibliography: papers.bib +bibliography: paper.bib --- # Summary From 38207e49c20aa91bf81135590a56923f5fa1a4c8 Mon Sep 17 00:00:00 2001 From: Katy Barnhart Date: Mon, 16 Sep 2019 17:23:19 -0600 Subject: [PATCH 2/7] fix: updating author names --- joss/paper.bib | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/joss/paper.bib b/joss/paper.bib index 83502a4..cb15f84 100644 --- a/joss/paper.bib +++ b/joss/paper.bib @@ -62,7 +62,7 @@ @Article{club2017geomorphometric } @article{mudd2014statistical, - author = {Mudd, Simon M. and Attal, Mikaël and Milodowski, David T. and Grieve, Stuart W. D. and Valters, Declan A.}, + author = {Mudd, S. M. and Attal, M. and Milodowski, D. T. and Grieve, S. W. D. and Valters, D. A.}, title = {A statistical framework to quantify spatial variation in channel gradients using the integral method of channel profile analysis}, journal = {Journal of Geophysical Research: Earth Surface}, volume = {119}, @@ -89,6 +89,7 @@ @Article{schwanghart2014topo @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", From a958931de216aff560fe3b8dfa653aefa6dda439 Mon Sep 17 00:00:00 2001 From: Katy Barnhart Date: Mon, 16 Sep 2019 17:23:31 -0600 Subject: [PATCH 3/7] fix: adding missing references --- joss/paper.bib | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/joss/paper.bib b/joss/paper.bib index cb15f84..f712acc 100644 --- a/joss/paper.bib +++ b/joss/paper.bib @@ -100,3 +100,14 @@ @article{schwanghart2010topo doi = "https://doi.org/10.1016/j.envsoft.2009.12.002", url = "http://www.sciencedirect.com/science/article/pii/S1364815209003053" } + +@Article{ perron2013integral, + author = {Perron, J Taylor and Royden, Leigh}, + journal = {Earth Surface Processes and Landforms}, + number = {6}, + pages = {570--576}, + publisher = {Wiley Online Library}, + title = {An integral approach to bedrock river profile analysis}, + volume = {38}, + year = {2013} + } From f78c0b5ddbfc08a7f2f08ec811103a9363e69ba5 Mon Sep 17 00:00:00 2001 From: Katy Barnhart Date: Mon, 16 Sep 2019 17:26:19 -0600 Subject: [PATCH 4/7] fix: updating dakota reference --- joss/paper.bib | 17 +++++------------ joss/paper.md | 2 +- 2 files changed, 6 insertions(+), 13 deletions(-) diff --git a/joss/paper.bib b/joss/paper.bib index f712acc..c0fe942 100644 --- a/joss/paper.bib +++ b/joss/paper.bib @@ -22,18 +22,11 @@ @Article{barnhart2019terrain DOI = {10.5194/gmd-12-1267-2019} } -@Article{adams2017dakotatheory, - address = {Albuquerque, NM}, - author = {B.M. Adams and L.E. Bauman and W.J. Bohnhoff and K.R. - Dalbey and M.S. Ebeida and J.P. Eddy and M.S. Eldred and - P.D. Hough and K.T. Hu and J.D. Jakeman and J.A. Stephens - and L.P. Swiler and D.M. Vigil and T.M. Wildey}, - journal = {Sandia Technical Report SAND2014-4253}, - title = {Dakota, A Multilevel Parallel Object-Oriented Framework - for Design Optimization, Parameter Estimation, Uncertainty - Quantification, and Sensitivity Analysis: Version 6.6 - Theory Manual}, - year = {2017} +@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}, + 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}, + year = {2019} } diff --git a/joss/paper.md b/joss/paper.md index f7c076e..819d2ca 100644 --- a/joss/paper.md +++ b/joss/paper.md @@ -48,7 +48,7 @@ Umami is a package for calculating objective functions or objective function com Umami offers two primary classes: a [`Residual`](https://umami.readthedocs.io/en/latest/umami.residual.html#Residual) which represents the difference between model and data, and a [`Metric`](https://umami.readthedocs.io/en/latest/umami.metric.html) -which is a calculated value on either model or data. The set of currently supported calculations are found in the [`umami.calculations`](https://umami.readthedocs.io/en/latest/umami.calculations.html) submodule. Both the `Metric` and `Residual` classes are designed to be fully specified through a YAML-style input-file or python Dictionary interface. Many different calculations can be accomplished through parameter specification. This supports reproducible analysis and systematic variation in metric construction. For example, when used with `terrainbento` one input file can describe the model run, and one input file can describe the model assessment or model-data comparison. This streamlines model analysis applications by making driver files more re-usable and by placing the code that accomplished calculations in the umami package rather than within the driver file. Umami also provides multiple output formats (YAML and Dakota), the latter of which is designed to interface with Sandia National Laboratory's Dakota package [@adams2017dakotatheory]. +which is a calculated value on either model or data. The set of currently supported calculations are found in the [`umami.calculations`](https://umami.readthedocs.io/en/latest/umami.calculations.html) submodule. Both the `Metric` and `Residual` classes are designed to be fully specified through a YAML-style input-file or python Dictionary interface. Many different calculations can be accomplished through parameter specification. This supports reproducible analysis and systematic variation in metric construction. For example, when used with `terrainbento` one input file can describe the model run, and one input file can describe the model assessment or model-data comparison. This streamlines model analysis applications by making driver files more re-usable and by placing the code that accomplished calculations in the umami package rather than within the driver file. Umami also provides multiple output formats (YAML and Dakota), the latter of which is designed to interface with Sandia National Laboratory's Dakota package [@adams2019dakota]. The novel contribution of the umami package is not primarily found in the specific calculations accomplished (e.g., some of them are as straightforward as the mean of a state variable). Instead it is the flexible and extensible nature of the input file format and the `Metric` and `Residual` classes. Additionally, the package can be extended through the addition of new calculation methods. From 653b09f83253109a4dd3791d7bafd835b8d3720f Mon Sep 17 00:00:00 2001 From: Katy Barnhart Date: Sun, 6 Oct 2019 12:32:18 -0600 Subject: [PATCH 5/7] fix: remove old notebook output cell contents --- notebooks/IntroductionToMetric.ipynb | 16 ++-------------- 1 file changed, 2 insertions(+), 14 deletions(-) diff --git a/notebooks/IntroductionToMetric.ipynb b/notebooks/IntroductionToMetric.ipynb index ed520e8..9d1843f 100644 --- a/notebooks/IntroductionToMetric.ipynb +++ b/notebooks/IntroductionToMetric.ipynb @@ -21,21 +21,9 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "ename": "ModuleNotFoundError", - "evalue": "No module named 'umami'", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mModuleNotFoundError\u001b[0m Traceback (most recent call last)", - "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[1;32m 4\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0mio\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mStringIO\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 5\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0mlandlab\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mRasterModelGrid\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mimshow_grid\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 6\u001b[0;31m \u001b[0;32mfrom\u001b[0m \u001b[0mumami\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mMetric\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 7\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0mumami\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcalculations\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0maggregate\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;31mModuleNotFoundError\u001b[0m: No module named 'umami'" - ] - } - ], + "outputs": [], "source": [ "import warnings\n", "warnings.filterwarnings('ignore')\n", From 5daf5b3ddd87cdc14b013155cfee3fe5fef0b31c Mon Sep 17 00:00:00 2001 From: Katy Barnhart Date: Mon, 7 Oct 2019 07:05:12 -0600 Subject: [PATCH 6/7] fix: relax python_requires --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index f7e1ca3..6fa3e8b 100644 --- a/setup.py +++ b/setup.py @@ -5,7 +5,7 @@ setup( name="umami", - python_requires=">=3.6", + python_requires=">=3", version=versioneer.get_version(), classifiers=[ "Intended Audience :: Science/Research", From 08e062df6fde43075eb5a3d88431c955e4112a4f Mon Sep 17 00:00:00 2001 From: Katy Barnhart Date: Mon, 7 Oct 2019 07:05:26 -0600 Subject: [PATCH 7/7] add more classifiers --- setup.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/setup.py b/setup.py index 6fa3e8b..d4c7540 100644 --- a/setup.py +++ b/setup.py @@ -11,6 +11,8 @@ "Intended Audience :: Science/Research", "License :: OSI Approved :: MIT License", "Operating System :: OS Independent", + "Programming Language :: Python :: 3.4", + "Programming Language :: Python :: 3.5", "Programming Language :: Python :: 3.6", "Programming Language :: Python :: 3.7", "Programming Language :: Python :: Implementation :: CPython",