├── .gitignore
├── AUTHORS.rst
├── CHANGELOG.rst
├── CONTRIBUTING.rst
├── LICENSE
├── Makefile
├── README.rst
├── data
    ├── inputs
    │   ├── parameters_wolock.csv
    │   ├── timeseries_wolock.csv
    │   └── twi_wolock.csv
    ├── modelconfig.ini
    └── outputs
    │   ├── flow_duration_curve.png
    │   ├── flow_duration_curved_observed_vs_predicted.png
    │   ├── flow_observed.png
    │   ├── flow_observed_vs_flow_predicted.png
    │   ├── flow_predicted.png
    │   ├── output.csv
    │   ├── pet.png
    │   ├── precip_minus_pet.png
    │   ├── precipitation.png
    │   ├── report.html
    │   ├── saturation_deficit_avgs.png
    │   └── temperature.png
├── docs
    ├── Makefile
    ├── authors.rst
    ├── changelog.rst
    ├── code.rst
    ├── conf.py
    ├── contributing.rst
    ├── index.rst
    ├── installation.rst
    ├── lant-to-wolock-conversion-table.rst
    ├── make.bat
    ├── overview.rst
    ├── readme.rst
    ├── tutorial.rst
    └── usage.rst
├── requirements.txt
├── setup.py
├── tests
    ├── __init__.py
    ├── conftest.py
    ├── test_hydrocalcs.py
    ├── test_modelconfigfile.py
    ├── test_parametersfile.py
    ├── test_timeseriesfile.py
    ├── test_topmodel.py
    ├── test_twifile.py
    └── testdata
    │   ├── timeseries_wolock.csv
    │   └── twi_wolock.csv
└── topmodelpy
    ├── __init__.py
    ├── cli.py
    ├── exceptions.py
    ├── hydrocalcs.py
    ├── main.py
    ├── modelconfigfile.py
    ├── parametersfile.py
    ├── plots.py
    ├── report.py
    ├── templates
        └── report_template.html
    ├── timeseriesfile.py
    ├── topmodel.py
    ├── twifile.py
    └── utils.py


/.gitignore:
--------------------------------------------------------------------------------
 1 | # Byte-compiled / optimized / DLL files
 2 | .cache/
 3 | __pycache__/
 4 | *.py[cod]
 5 | *$py.class
 6 | *.py.swp
 7 | .pytest_cache/
 8 | 
 9 | # Sphinx documentation
10 | docs/_build
11 | 
12 | # Distribution / packaging
13 | *.egg-info/
14 | 
15 | # Virtual environment
16 | venv/
17 | 


--------------------------------------------------------------------------------
/AUTHORS.rst:
--------------------------------------------------------------------------------
 1 | Authors
 2 | =======
 3 | 
 4 | Development Leads
 5 | -----------------
 6 | 
 7 | - Jeremiah Lant <jlant@usgs.gov>
 8 | 
 9 | Core Developers
10 | ---------------
11 | 
12 | - name <email>
13 | 
14 | Contributors
15 | ------------
16 | 
17 | - name <email>
18 | 


--------------------------------------------------------------------------------
/CHANGELOG.rst:
--------------------------------------------------------------------------------
1 | Changelog
2 | =========
3 | 
4 | Version 0.1.0
5 | --------------------
6 | (bugfix | feature added | etc, released on yyyy-mm-dd)
7 | 
8 | - Add information about changes; i.e 'first release of topmodelpy'
9 | 


--------------------------------------------------------------------------------
/CONTRIBUTING.rst:
--------------------------------------------------------------------------------
  1 | Contributing
  2 | ============
  3 | 
  4 | Contributions are welcome, and they are greatly appreciated! Every
  5 | little bit helps, and credit will always be given.
  6 | 
  7 | You can contribute in many ways:
  8 | 
  9 | Types of Contributions
 10 | ----------------------
 11 | 
 12 | Report Bugs
 13 | ~~~~~~~~~~~
 14 | 
 15 | Report bugs to Jeremiah Lant at jlant@usgs.gov or on the issues page of
 16 | the respective online repository where topmodelpy is hosted.
 17 | 
 18 | If you are reporting a bug, please include:
 19 | 
 20 | * Your operating system name and version.
 21 | * Any details about your local setup that might be helpful in troubleshooting.
 22 | * Detailed steps to reproduce the bug.
 23 | 
 24 | Fix Bugs
 25 | ~~~~~~~~
 26 | 
 27 | Look through the issues page of the respective online repository where topmodelpy is hosted for bugs.
 28 | Anything tagged with "bug" is open to whoever wants to implement it.
 29 | 
 30 | Implement Features
 31 | ~~~~~~~~~~~~~~~~~~
 32 | 
 33 | Look through the issues page of the respective online repository where topmodelpy is hosted for features.
 34 | Anything tagged with "feature" is open to whoever wants to implement it.
 35 | 
 36 | Write Documentation
 37 | ~~~~~~~~~~~~~~~~~~~
 38 | 
 39 | topmodelpy could always use more documentation, whether as part of the
 40 | official topmodelpy docs or in docstrings.
 41 | 
 42 | Submit Feedback
 43 | ~~~~~~~~~~~~~~~
 44 | 
 45 | The best way to send feedback is to file an issue at jlant@usgs.gov or on the issues page of
 46 | the respective online repository where topmodelpy is hosted.
 47 | 
 48 | If you are proposing a feature:
 49 | 
 50 | * Explain in detail how it would work.
 51 | * Keep the scope as narrow as possible, to make it easier to implement.
 52 | * Remember that this is a volunteer-driven project, and that contributions
 53 |   are welcome :)
 54 | 
 55 | Get Started!
 56 | ------------
 57 | 
 58 | Ready to contribute? Here's how to set up `topmodelpy` for local development.
 59 | 
 60 | 1. Fork the `topmodelpy` repo.
 61 | 2. Clone your fork locally::
 62 | 
 63 |     $ git clone <remote url to your forked version of topmodelpy>
 64 | 
 65 | 3. Install your local copy into a virtual environment using virtualenv_ or conda_.
 66 | If you have virtualenvwrapper_ installed, this is how you set up your fork for local development::
 67 | 
 68 |     $ mkvirtualenv topmodelpy
 69 |     $ cd topmodelpy/
 70 |     $ python setup.py develop
 71 | 
 72 | If you have conda_ installed, this is how you set up your fork for local development on Linux or Mac OS X::
 73 | 
 74 |     $ conda create --name topmodelpy
 75 |     $ source activate topmodelpy
 76 |     $ cd <your-path-to-topmodelpy-project/
 77 |     $ python setup.py develop
 78 | 
 79 | If you have conda_ installed, this is how you set up your fork for local development on Windows::
 80 | 
 81 |     > conda create --name topmodelpy
 82 |     > activate topmodelpy
 83 |     > cd <your-path-to-topmodelpy-project/
 84 |     > python setup.py develop
 85 | 
 86 | 4. Create a branch for local development::
 87 | 
 88 |     $ git checkout -b name-of-your-bugfix-or-feature
 89 | 
 90 |    Now you can make your changes locally.
 91 | 
 92 | 5. When you're done making changes, check that your changes pass flake8_ and the tests, including testing other Python versions with tox_::
 93 | 
 94 |     $ flake8 topmodelpy tests
 95 |     $ py.test
 96 |     $ tox
 97 | 
 98 |    To get flake8 and tox, just pip install them into your virtualenv.
 99 | 
100 | 6. Commit your changes and push your branch to the respective online repository where topmodelpy is hosted::
101 | 
102 |     $ git add .
103 |     $ git commit -m "Your detailed description of your changes."
104 |     $ git push origin name-of-your-bugfix-or-feature
105 | 
106 | 7. Submit a pull request through the respective online repository website where topmodelpy is hosted.
107 | 
108 | Pull Request Guidelines
109 | -----------------------
110 | 
111 | Before you submit a pull request, check that it meets these guidelines:
112 | 
113 | 1. The pull request should include tests.
114 | 2. If the pull request adds functionality, the docs should be updated. Put
115 |    your new functionality into a function with a docstring, and add the
116 |    feature to the list in README.rst.
117 | 3. The pull request should work for Python 2.6, 2.7, 3.3, and 3.4.
118 | 
119 | Tips
120 | ----
121 | 
122 | To run a subset of tests::
123 | 
124 |     $ py.test tests/test_<your-awesome-module>.py
125 | 
126 | 
127 | .. _virtualenv: https://virtualenv.pypa.io/en/latest/
128 | .. _conda: http://conda.pydata.org/
129 | .. _virtualenvwrapper: http://virtualenvwrapper.readthedocs.io/en/latest/
130 | .. _flake8: https://flake8.readthedocs.io/en/latest/
131 | .. _tox: http://tox.readthedocs.io/en/latest/
132 | 


--------------------------------------------------------------------------------
/LICENSE:
--------------------------------------------------------------------------------
 1 | License
 2 | -------
 3 | 
 4 | This software is licensed under CC0 1.0 (http://creativecommons.org/publicdomain/zero/1.0/) and is in the public domain 
 5 | because it contains materials that originally came from the U.S. Geological Survey (USGS), an agency of the United 
 6 | States Department of Interior. For more information, see the official USGS copyright policy 
 7 | (http://www2.usgs.gov/visual-id/credit_usgs.html#copyright/).
 8 | 
 9 | 
10 | Disclaimer
11 | ----------
12 | 
13 | This software is preliminary or provisional and is subject to revision. It is being provided to meet the need for timely
14 | best science. The software has not received final approval by the U.S. Geological Survey (USGS). No warranty, expressed 
15 | or implied, is made by the USGS or the U.S. Government as to the functionality of the software and related material nor 
16 | shall the fact of release constitute any such warranty. The software is provided on the condition that neither the USGS 
17 | nor the U.S. Government shall be held liable for any damages resulting from the authorized or unauthorized use of the 
18 | software.
19 | 
20 | The USGS provides no warranty, expressed or implied, as to the correctness of the furnished software or the suitability 
21 | for any purpose. The software has been tested, but as with any complex software, there could be undetected errors. Users
22 | who find errors are requested to report them to the USGS.
23 | 
24 | References to non-USGS products, trade names, and (or) services are provided for information purposes only and do not
25 | constitute endorsement or warranty, express or implied, by the USGS, U.S. Department of Interior, or U.S. Government, as
26 | to their suitability, content, usefulness, functioning, completeness, or accuracy.
27 | 
28 | Although this program has been used by the USGS, no warranty, expressed or implied, is made by the USGS or the United
29 | States Government as to the accuracy and functioning of the program and related program material nor shall the fact of
30 | distribution constitute any such warranty, and no responsibility is assumed by the USGS in connection therewith.
31 | 
32 | This software is provided "AS IS."


--------------------------------------------------------------------------------
/Makefile:
--------------------------------------------------------------------------------
 1 | .PHONY: clean clean-pyc
 2 | 
 3 | help:
 4 | 	@echo "clean - remove all test and Python artifacts"
 5 | 	@echo "clean-pyc - remove Python file artifacts"
 6 | 
 7 | clean: clean-pyc 
 8 | 
 9 | clean-pyc:
10 | 	find . -name '*.pyc' -exec rm -f {} \;
11 | 	find . -name '*.pyo' -exec rm -f {} \;
12 | 	find . -name '*~' -exec rm -f {} \;
13 | 	find . -name '__pycache__' -exec rm -fr {} \;
14 | 
15 | 
16 | 


--------------------------------------------------------------------------------
/README.rst:
--------------------------------------------------------------------------------
  1 | .. image:: https://upload.wikimedia.org/wikipedia/commons/thumb/1/1c/USGS_logo_green.svg/320px-USGS_logo_green.svg.png
  2 |         :target: http://www.usgs.gov/
  3 |         :alt: U.S. Geological Survey logo
  4 | 
  5 | topmodelpy
  6 | ===============================
  7 | 
  8 | *topmodelpy* is a rainfall-runoff model that predicts the amount of water
  9 | flow in rivers. *topmodelpy* is a command line application written in Python
 10 | using Click_, and is a complete conversion of the original rainfall-runoff
 11 | model, called Topmodel, from Fortran to Python. The specific version of 
 12 | Topmodel that *topmodelpy* is based on is the version by David Wolock, 
 13 | U.S. Geological Survey. Please see report below for more details: 
 14 | 
 15 |         Wolock, D.M., "Simulating the variable-source-area concept of
 16 |         streamflow generation with the watershed model Topmodel", U.S. Geological
 17 |         Survey, Water-Resources Investigations Report 93-4124, 1993.
 18 | 
 19 | 
 20 | Features
 21 | --------
 22 | 
 23 | * Written entirely in Python for ease of use and model extension.
 24 | 
 25 | 
 26 | Example
 27 | -------
 28 | 
 29 | Add a short example
 30 | 
 31 | ::
 32 | 
 33 |     show some example code here
 34 | 
 35 | 
 36 | Documentation
 37 | -------------
 38 | 
 39 | Add a link to the project and code documenation site.
 40 | 
 41 | 
 42 | Tests
 43 | -----
 44 | 
 45 | A suite of tests were built using `pytest <http://pytest.org/latest/>`_.
 46 | 
 47 | To run the test suite, from the command line in the project's root directory::
 48 | 
 49 |     $ py.test tests/
 50 | 
 51 | 
 52 | 
 53 | Requirements
 54 | ------------
 55 | 
 56 | Add requirements and code dependencies.
 57 | 
 58 | 
 59 | Installation
 60 | ------------
 61 | 
 62 | To install topmodelpy from source:
 63 | 
 64 | 1. Check that you have Python_ installed::
 65 | 
 66 |     $ python --version
 67 | 
 68 | If you do not have Python_ installed, please download the latest version from `Python's download page`_
 69 | 
 70 | 2. Download topmodelpy from the repository and extract to a directory of your choice.
 71 | 
 72 |    Or, if you have git_ installed you can clone the project::
 73 | 
 74 |     $ git clone <remote url to topmodelpy>
 75 | 
 76 | 3. Navigate to the project's root directory where the setup script called `setup.py` is located::
 77 | 
 78 |     $ cd topmodelpy/
 79 | 
 80 | | The `setup.py` is a Python file that contains information regarding the installation of a Python module/package, and
 81 | | usually specifies that the module/package has been packaged and distributed with the standard Python distribution
 82 | | package called Distutils_.
 83 | 
 84 | 4. Run `setup.py` with the `install` command::
 85 | 
 86 |     $ python setup.py install
 87 | 
 88 | topmodelpy will now be installed to the standard location for third-party Python modules on your
 89 | computer platform.
 90 | 
 91 | For more information regarding installing third-party Python modules, please see `Installing Python Modules`_
 92 | For a description of how installation works including where the module will be installed on your computer platform,
 93 | please see `How Installation Works`_.
 94 | 
 95 | 
 96 | License
 97 | -------
 98 | 
 99 | This software is licensed under `CC0 1.0`_ and is in the `public domain`_ because it contains materials that originally
100 | came from the `U.S. Geological Survey (USGS)`_, an agency of the `United States Department of Interior`_. For more
101 | information, see the `official USGS copyright policy`_.
102 | 
103 | .. image:: http://i.creativecommons.org/p/zero/1.0/88x31.png
104 |         :target: http://creativecommons.org/publicdomain/zero/1.0/
105 |         :alt: Creative Commons logo
106 | 
107 | 
108 | Disclaimer
109 | ----------
110 | 
111 | This software is preliminary or provisional and is subject to revision. It is being provided to meet the need for timely
112 | best science. The software has not received final approval by the U.S. Geological Survey (USGS). No warranty, expressed
113 | or implied, is made by the USGS or the U.S. Government as to the functionality of the software and related material nor
114 | shall the fact of release constitute any such warranty. The software is provided on the condition that neither the USGS
115 | nor the U.S. Government shall be held liable for any damages resulting from the authorized or unauthorized use of the
116 | software.
117 | 
118 | The USGS provides no warranty, expressed or implied, as to the correctness of the furnished software or the suitability
119 | for any purpose. The software has been tested, but as with any complex software, there could be undetected errors. Users
120 | who find errors are requested to report them to the USGS.
121 | 
122 | References to non-USGS products, trade names, and (or) services are provided for information purposes only and do not
123 | constitute endorsement or warranty, express or implied, by the USGS, U.S. Department of Interior, or U.S. Government, as
124 | to their suitability, content, usefulness, functioning, completeness, or accuracy.
125 | 
126 | Although this program has been used by the USGS, no warranty, expressed or implied, is made by the USGS or the United
127 | States Government as to the accuracy and functioning of the program and related program material nor shall the fact of
128 | distribution constitute any such warranty, and no responsibility is assumed by the USGS in connection therewith.
129 | 
130 | This software is provided "AS IS."
131 | 
132 | 
133 | Author
134 | ------
135 | 
136 | Jeremiah Lant <jlant@usgs.gov>
137 | 
138 | 
139 | .. _Python: https://www.python.org/
140 | .. _pytest: http://pytest.org/latest/
141 | .. _Click: https://click.palletsprojects.com/
142 | .. _Sphinx: http://sphinx-doc.org/
143 | .. _public domain: https://en.wikipedia.org/wiki/Public_domain
144 | .. _CC0 1.0: http://creativecommons.org/publicdomain/zero/1.0/
145 | .. _U.S. Geological Survey: https://www.usgs.gov/
146 | .. _USGS: https://www.usgs.gov/
147 | .. _U.S. Geological Survey (USGS): https://www.usgs.gov/
148 | .. _United States Department of Interior: https://www.doi.gov/
149 | .. _official USGS copyright policy: http://www.usgs.gov/visual-id/credit_usgs.html#copyright/
150 | .. _U.S. Geological Survey (USGS) Software User Rights Notice: http://water.usgs.gov/software/help/notice/
151 | .. _Python's download page: https://www.python.org/downloads/
152 | .. _git: https://git-scm.com/
153 | .. _Distutils: https://docs.python.org/3/library/distutils.html
154 | .. _Installing Python Modules: https://docs.python.org/3.5/install/
155 | .. _How Installation Works: https://docs.python.org/3.5/install/#how-installation-works
156 | 


--------------------------------------------------------------------------------
/data/inputs/parameters_wolock.csv:
--------------------------------------------------------------------------------
 1 | name,value,units,description
 2 | scaling_parameter,10,millimeters,controls the rate of decline of transmissivity in the soil profile
 3 | saturated_hydraulic_conductivity,150,millimeters/day,saturated hydraulic conductivity of the C horizon of the soil
 4 | macropore_fraction,0.2,fraction,fraction of precipitation that can bypass the unsaturated subsurface zone and move directly into the saturated subsurface zone
 5 | soil_depth_total,1,mm,total soil depth - could be 90 cm for tile depth
 6 | soil_depth_ab_horizon,0.5,mm,soil depth of AB horizon - 25% thickness
 7 | field_capacity_fraction,0.2,fraction,fraction of soil moisture or water content in the soil after excess water has drained away
 8 | latitude,40.5,degrees,mean latitude of basin
 9 | basin_area_total,3.07,square kilometers,total basin area
10 | impervious_area_fraction,0.3,fraction,fraction of impervious area of basin
11 | snowmelt_temperature_cutoff,32,degrees fahrenheit,temperature cutoff for snowpack accumulation and snowmelt
12 | snowmelt_rate_coeff,0.06,1/degrees fahrenheit,used to control rate of snow melt
13 | snowmelt_rate_coeff_with_rain,0.007,inches per degree fahrenheit,used to control rate of snow melt when raining
14 | channel_length_max,1.98,kilometers,maximum channel length
15 | channel_velocity_avg,10,kilometers/day,average channel velocity
16 | flow_initial,1,millimeters/day,initial river flow
17 | 


--------------------------------------------------------------------------------
/data/inputs/timeseries_wolock.csv:
--------------------------------------------------------------------------------
  1 | date, temperature (celsius),precipitation (mm/day),pet (mm/day),flow_observed (mm/day)
  2 | 1980-01-22,-1.9,2.5,0.39,1.18
  3 | 1980-01-23,-0.3,0,0.44,1.02
  4 | 1980-01-24,-1.1,0,0.42,0.66
  5 | 1980-01-25,-6.1,0,0.31,0.5
  6 | 1980-01-26,-4.7,0,0.34,0.46
  7 | 1980-01-27,-4.4,0,0.35,0.4
  8 | 1980-01-28,-3.3,0,0.37,0.39
  9 | 1980-01-29,-3.1,0,0.38,0.33
 10 | 1980-01-30,-4.2,0,0.36,0.28
 11 | 1980-01-31,-5.6,0,0.33,0.24
 12 | 1980-02-01,-7.2,0,0.3,0.19
 13 | 1980-02-02,-9.4,0,0.27,0.2
 14 | 1980-02-03,-9.4,0,0.27,0.21
 15 | 1980-02-04,-7.2,0,0.31,0.24
 16 | 1980-02-05,-6.4,0,0.33,0.27
 17 | 1980-02-06,-5.6,0,0.34,0.28
 18 | 1980-02-07,-6.7,0,0.33,0.24
 19 | 1980-02-08,-2.2,0,0.43,0.25
 20 | 1980-02-09,-1.9,0,0.44,0.31
 21 | 1980-02-10,-3.6,0,0.4,0.32
 22 | 1980-02-11,-4.4,0,0.39,0.28
 23 | 1980-02-12,-3.1,2.5,0.42,0.27
 24 | 1980-02-13,-4.2,0,0.4,0.24
 25 | 1980-02-14,-3.6,0,0.41,0.29
 26 | 1980-02-15,-1.1,0,0.49,1.1
 27 | 1980-02-16,0.3,12.7,0.54,1.26
 28 | 1980-02-17,-4.4,0,0.41,0.64
 29 | 1980-02-18,-7.8,0,0.33,0.34
 30 | 1980-02-19,-5.3,0,0.39,0.79
 31 | 1980-02-20,0,0,0.54,1.02
 32 | 1980-02-21,1.1,0,0.59,0.87
 33 | 1980-02-22,5.8,10.2,0.79,1.97
 34 | 1980-02-23,0.6,0,0.58,1.42
 35 | 1980-02-24,4.4,0,0.74,0.78
 36 | 1980-02-25,3.9,0,0.72,0.58
 37 | 1980-02-26,1.1,0,0.61,0.43
 38 | 1980-02-27,-5.6,0,0.41,0.34
 39 | 1980-02-28,-5.6,0,0.41,0.34
 40 | 1980-02-29,-3.6,0,0.47,0.28
 41 | 1980-03-01,-11.4,0,0.29,0.24
 42 | 1980-03-02,-9.4,0,0.33,0.24
 43 | 1980-03-03,-6.9,0,0.39,0.24
 44 | 1980-03-04,-3.6,0,0.48,0.01
 45 | 1980-03-05,1.1,2.5,0.65,0.28
 46 | 1980-03-06,3.9,0,0.78,0.32
 47 | 1980-03-07,1.9,0,0.69,0.23
 48 | 1980-03-08,5,7.6,0.84,1.02
 49 | 1980-03-09,9.7,0,1.14,1.73
 50 | 1980-03-10,3.3,17.8,0.77,3.31
 51 | 1980-03-11,4.4,2.5,0.83,7.87
 52 | 1980-03-12,-1.7,0,0.57,1.89
 53 | 1980-03-13,-2.2,0,0.56,1.1
 54 | 1980-03-14,-2.5,15.2,0.56,2.05
 55 | 1980-03-15,1.1,0,0.7,3.07
 56 | 1980-03-16,-0.8,0,0.63,4.88
 57 | 1980-03-17,1.7,7.6,0.74,10.23
 58 | 1980-03-18,7.2,5.1,1.05,11.02
 59 | 1980-03-19,2.5,0,0.79,2.52
 60 | 1980-03-20,4.4,0,0.89,1.57
 61 | 1980-03-21,6.1,58.4,1,41.72
 62 | 1980-03-22,6.7,2.5,1.05,10.23
 63 | 1980-03-23,1.1,0,0.74,3.38
 64 | 1980-03-24,5.3,15.2,0.97,3.15
 65 | 1980-03-25,6.1,7.6,1.03,16.53
 66 | 1980-03-26,2.2,0,0.81,2.68
 67 | 1980-03-27,4.4,0,0.94,1.57
 68 | 1980-03-28,6.1,0,1.05,1.18
 69 | 1980-03-29,6.1,20.3,1.06,9.45
 70 | 1980-03-30,8.1,0,1.21,4.8
 71 | 1980-03-31,7.2,38.1,1.15,20.47
 72 | 1980-04-01,1.9,0,0.84,15.74
 73 | 1980-04-02,5.8,0,1.07,3.38
 74 | 1980-04-03,7.2,0,1.18,1.89
 75 | 1980-04-04,10.8,17.8,1.49,8.66
 76 | 1980-04-05,11.7,0,1.58,2.76
 77 | 1980-04-06,7.5,0,1.23,1.42
 78 | 1980-04-07,10.3,0,1.47,1.02
 79 | 1980-04-08,12.8,0,1.73,0.87
 80 | 1980-04-09,14.2,50.8,1.9,24.4
 81 | 1980-04-10,10.6,0,1.53,8.66
 82 | 1980-04-11,13.9,0,1.89,2.44
 83 | 1980-04-12,10.6,0,1.55,1.65
 84 | 1980-04-13,15.3,0,2.09,1.26
 85 | 1980-04-14,11.9,10.2,1.71,3.54
 86 | 1980-04-15,11.7,2.5,1.7,4.09
 87 | 1980-04-16,8.9,0,1.44,1.34
 88 | 1980-04-17,2.5,0,0.97,0.87
 89 | 1980-04-18,6.7,0,1.27,0.72
 90 | 1980-04-19,9.7,0,1.54,0.57
 91 | 1980-04-20,11.9,0,1.77,0.53
 92 | 1980-04-21,16.4,0,2.36,0.5
 93 | 1980-04-22,12.8,0,1.9,0.43
 94 | 1980-04-23,8.3,0,1.45,0.37
 95 | 1980-04-24,13.9,0,2.06,0.32
 96 | 1980-04-25,15.6,0,2.3,0.31
 97 | 1980-04-26,14.2,0,2.12,0.3
 98 | 1980-04-27,12.2,10.2,1.89,0.87
 99 | 1980-04-28,10,53.3,1.66,25.98
100 | 1980-04-29,8.6,17.8,1.53,17.32
101 | 1980-04-30,10,2.5,1.68,3.7
102 | 1980-05-01,12.2,0,1.93,2.28
103 | 1980-05-02,14.7,0,2.27,1.26
104 | 1980-05-03,13.9,0,2.17,0.94
105 | 1980-05-04,17.2,0,2.68,0.68
106 | 1980-05-05,15.3,2.5,2.39,0.57
107 | 1980-05-06,19.7,0,3.16,0.49
108 | 1980-05-07,20.8,5.1,3.4,0.68
109 | 1980-05-08,17.2,7.6,2.74,2.83
110 | 1980-05-09,8.3,0,1.58,0.79
111 | 1980-05-10,8.1,0,1.57,0.49
112 | 1980-05-11,11.9,0,2,0.43
113 | 1980-05-12,14.2,12.7,2.32,1.34
114 | 1980-05-13,18.1,12.7,2.96,4.8
115 | 1980-05-14,20.3,0,3.41,1.18
116 | 1980-05-15,15,0,2.47,0.57
117 | 1980-05-16,11.4,0,1.98,0.56
118 | 1980-05-17,14.4,0,2.4,0.43
119 | 1980-05-18,16.1,2.5,2.68,0.76
120 | 1980-05-19,14.4,2.5,2.42,0.37
121 | 1980-05-20,20,2.5,3.44,0.27
122 | 1980-05-21,17.5,12.7,2.96,1.97
123 | 1980-05-22,12.8,0,2.22,0.72
124 | 1980-05-23,19.7,0,3.42,0.41
125 | 1980-05-24,22.8,0,4.15,0.35
126 | 1980-05-25,22.2,0,4.02,0.34
127 | 1980-05-26,19.2,0,3.35,0.24
128 | 1980-05-27,15.3,0,2.64,0.17
129 | 1980-05-28,15.8,0,2.73,0.23
130 | 1980-05-29,17.2,0,2.98,0.12
131 | 1980-05-30,16.4,0,2.85,0.12
132 | 1980-05-31,18.3,0,3.21,0.17
133 | 1980-06-01,20.3,0,3.65,0.17
134 | 1980-06-02,21.7,10.2,3.99,0.68
135 | 1980-06-03,21.9,5.1,4.05,0.54
136 | 1980-06-04,21.9,0,4.06,0.23
137 | 1980-06-05,15.8,0,2.79,0.12
138 | 1980-06-06,16.1,0,2.85,0.09
139 | 1980-06-07,17.8,0,3.17,0.24
140 | 1980-06-08,21.7,2.5,4.04,0.27
141 | 1980-06-09,15,10.2,2.67,0.74
142 | 1980-06-10,13.1,0,2.38,0.57
143 | 1980-06-11,10.8,0,2.07,0.2
144 | 1980-06-12,12.5,2.5,2.3,0.12
145 | 1980-06-13,15,2.5,2.69,0.09
146 | 1980-06-14,16.9,0,3.03,0.08
147 | 1980-06-15,19.2,0,3.5,0.08
148 | 1980-06-16,21.4,0,4.01,0.19
149 | 1980-06-17,16.9,0,3.04,0.07
150 | 1980-06-18,17.5,0,3.15,0.03
151 | 1980-06-19,16.7,0,3,0.22
152 | 1980-06-20,18.3,0,3.31,0.24
153 | 1980-06-21,17.8,0,3.21,0.09
154 | 1980-06-22,19.4,0,3.55,0.02
155 | 1980-06-23,20.6,0,3.82,0.01
156 | 1980-06-24,22.5,0,4.3,0.01
157 | 1980-06-25,23.9,0,4.69,0
158 | 1980-06-26,24.2,0,4.77,0
159 | 1980-06-27,23.3,2.5,4.51,0.14
160 | 1980-06-28,25.3,0,5.1,0.11
161 | 1980-06-29,22.8,25.4,4.37,0.55
162 | 1980-06-30,23.6,15.2,4.58,2.68
163 | 1980-07-01,19.7,0,3.59,0.54
164 | 1980-07-02,21.7,0,4.06,0.21
165 | 1980-07-03,23.3,0,4.48,0.17
166 | 1980-07-04,21.7,0,4.05,0.13
167 | 1980-07-05,23.3,10.2,4.47,0.61
168 | 1980-07-06,23.1,0,4.4,0.87
169 | 1980-07-07,17.2,0,3.05,0.19
170 | 1980-07-08,19.2,0,3.44,0.17
171 | 1980-07-09,22.5,0,4.21,0.13
172 | 1980-07-10,24.4,0,4.73,0.11
173 | 1980-07-11,25,0,4.9,0.1
174 | 1980-07-12,24.4,0,4.71,0.18
175 | 1980-07-13,20,0,3.57,0.09
176 | 1980-07-14,21.7,0,3.96,0.06
177 | 1980-07-15,23.3,0,4.36,0.12
178 | 1980-07-16,25.6,0,5.01,0.11
179 | 1980-07-17,28.6,2.5,6.02,0.12
180 | 1980-07-18,25.6,0,4.98,0.07
181 | 1980-07-19,25.8,0,5.02,0.06
182 | 1980-07-20,26.9,0,5.36,0.04
183 | 1980-07-21,31.1,0,6.93,0.06
184 | 1980-07-22,30,10.2,6.45,0.39
185 | 1980-07-23,28.1,15.2,5.71,3.23
186 | 1980-07-24,22.8,0,4.09,0.4
187 | 1980-07-25,21.9,0,3.86,0.24
188 | 1980-07-26,23.9,0,4.35,0.14
189 | 1980-07-27,25.8,0,4.87,0.1
190 | 1980-07-28,26.7,0,5.13,0.08
191 | 1980-07-29,25.8,20.3,4.83,1.57
192 | 1980-07-30,21.9,0,3.77,0.34
193 | 1980-07-31,23.6,0,4.17,0.17
194 | 1980-08-01,24.7,0,4.45,0.15
195 | 1980-08-02,25.6,7.6,4.68,0.13
196 | 1980-08-03,26.4,0,4.89,0.37
197 | 1980-08-04,27.2,2.5,5.12,0.13
198 | 1980-08-05,27.2,0,5.09,0.66
199 | 1980-08-06,28.1,0,5.35,0.49
200 | 1980-08-07,25.6,0,4.56,0.17
201 | 1980-08-08,26.7,0,4.86,0.13
202 | 1980-08-09,28.6,0,5.43,0.11
203 | 1980-08-10,25.8,0,4.54,0.09
204 | 1980-08-11,24.7,5.1,4.22,0.08
205 | 1980-08-12,26.7,0,4.75,0.17
206 | 1980-08-13,23.3,0,3.83,0.11
207 | 1980-08-14,22.5,0,3.62,0.08
208 | 1980-08-15,23.3,2.5,3.78,0.41
209 | 1980-08-16,21.1,0,3.28,0.17
210 | 1980-08-17,18.1,0,2.71,0.08
211 | 1980-08-18,20.6,0,3.14,0.06
212 | 1980-08-19,22.2,0,3.45,0.07
213 | 1980-08-20,23.6,0,3.74,0.15
214 | 1980-08-21,21.9,0,3.34,0.04
215 | 1980-08-22,22.2,0,3.38,0.04
216 | 1980-08-23,21.7,0,3.26,0.06
217 | 1980-08-24,23.1,0,3.53,0.08
218 | 1980-08-25,23.9,2.5,3.69,0.05
219 | 1980-08-26,25.3,0,4,0.04
220 | 1980-08-27,25.6,0,4.04,0.02
221 | 1980-08-28,26.1,0,4.14,0.02
222 | 1980-08-29,26.4,0,4.19,0.02
223 | 1980-08-30,23.9,0,3.57,0.02
224 | 1980-08-31,26.7,0,4.21,0.02
225 | 1980-09-01,27.2,0,4.32,0.02
226 | 1980-09-02,28.6,0,4.68,0.02
227 | 1980-09-03,27.2,0,4.26,0.01
228 | 1980-09-04,22.8,0,3.22,0.01
229 | 1980-09-05,24.2,0,3.49,0.01
230 | 1980-09-06,22.5,0,3.12,0.02
231 | 1980-09-07,24.2,0,3.44,0.01
232 | 1980-09-08,19.4,0,2.53,0.01
233 | 1980-09-09,19.4,0,2.52,0.01
234 | 1980-09-10,20.6,0,2.69,0.01
235 | 1980-09-11,16.9,0,2.12,0.01
236 | 1980-09-12,18.1,0,2.27,0.01
237 | 1980-09-13,20,0,2.54,0.01
238 | 1980-09-14,21.7,2.5,2.8,0.01
239 | 1980-09-15,22.5,0,2.92,0.02
240 | 1980-09-16,17.5,0,2.12,0.02
241 | 1980-09-17,17.2,25.4,2.07,0.53
242 | 1980-09-18,21.9,22.9,2.75,1.89
243 | 1980-09-19,15.8,0,1.87,0.13
244 | 1980-09-20,16.9,0,1.99,0.09
245 | 1980-09-21,18.9,0,2.23,0.09
246 | 1980-09-22,25,0,3.23,0.09
247 | 1980-09-23,26.4,0,3.5,0.06
248 | 1980-09-24,20.3,0,2.38,0.06
249 | 1980-09-25,16.4,7.6,1.85,0.09
250 | 1980-09-26,13.9,7.6,1.57,0.13
251 | 1980-09-27,14.2,0,1.59,0.04
252 | 1980-09-28,10.3,0,1.24,0.04
253 | 1980-09-29,13.3,0,1.48,0.04
254 | 1980-09-30,14.4,0,1.57,0.05
255 | 1980-10-01,18.1,0,1.96,0.06
256 | 1980-10-02,19.4,20.3,2.11,0.42
257 | 1980-10-03,18.1,10.2,1.93,0.44
258 | 1980-10-04,13.3,0,1.42,1.5
259 | 1980-10-05,11.9,0,1.29,0.28
260 | 1980-10-06,11.7,0,1.27,0.17
261 | 1980-10-07,11.4,0,1.24,0.12
262 | 1980-10-08,10.6,0,1.17,0.1
263 | 1980-10-09,13.1,0,1.35,0.1
264 | 1980-10-10,11.9,0,1.24,0.07
265 | 1980-10-11,10.3,0,1.12,0.11
266 | 1980-10-12,10.6,0,1.13,0.21
267 | 1980-10-13,10,0,1.08,0.19
268 | 1980-10-14,8.3,0,0.96,0.16
269 | 1980-10-15,9.2,0,1.01,0.15
270 | 1980-10-16,10.8,0,1.11,0.15
271 | 1980-10-17,15,0,1.43,0.15
272 | 1980-10-18,17.5,10.2,1.65,0.77
273 | 1980-10-19,19.2,0,1.82,0.46
274 | 1980-10-20,12.2,0,1.17,0.22
275 | 1980-10-21,9.7,0,0.99,0.17
276 | 1980-10-22,10.3,0,1.02,0.17
277 | 1980-10-23,6.9,0,0.82,0.13
278 | 1980-10-24,5,0,0.72,0.07
279 | 1980-10-25,6.7,55.9,0.8,14.17
280 | 1980-10-26,11.7,0,1.08,1.97
281 | 1980-10-27,6.1,0,0.76,0.54
282 | 1980-10-28,7.2,2.5,0.81,0.49
283 | 1980-10-29,6.7,0,0.78,0.28
284 | 1980-10-30,4.4,0,0.67,0.2
285 | 1980-10-31,3.3,0,0.62,0.17
286 | 1980-11-01,5.6,0,0.71,0.17
287 | 1980-11-02,5.8,0,0.71,0.12
288 | 1980-11-03,1.9,0,0.55,0.08
289 | 1980-11-04,3.6,7.6,0.61,0.52
290 | 1980-11-05,7.2,0,0.76,0.31
291 | 1980-11-06,3.6,0,0.6,0.13
292 | 1980-11-07,2.2,0,0.55,0.12
293 | 1980-11-08,12.2,0,1.01,0.16
294 | 1980-11-09,7.5,7.6,0.75,0.79
295 | 1980-11-10,5.8,2.5,0.67,0.46
296 | 1980-11-11,5,0,0.63,0.23
297 | 1980-11-12,2.5,0,0.54,0.11
298 | 1980-11-13,4.4,0,0.6,0.06
299 | 1980-11-14,8.3,0,0.76,0.06
300 | 1980-11-15,11.4,0,0.92,0.06
301 | 1980-11-16,5,0,0.61,0.08
302 | 1980-11-17,-0.6,0,0.43,0.06
303 | 1980-11-18,-1.7,22.9,0.4,3.46
304 | 1980-11-19,1.4,0,0.48,0.87
305 | 1980-11-20,-1.1,0,0.41,0.46
306 | 1980-11-21,0.3,0,0.45,0.35
307 | 1980-11-22,1.1,2.5,0.47,0.27
308 | 1980-11-23,1.9,0,0.49,0.23
309 | 1980-11-24,2.8,35.6,0.51,8.66
310 | 1980-11-25,8.3,0,0.71,3.78
311 | 1980-11-26,4.4,0,0.56,1.26
312 | 1980-11-27,2.2,0,0.48,0.87
313 | 1980-11-28,1.7,10.2,0.47,2.99
314 | 1980-11-29,3.9,0,0.53,1.65
315 | 1980-11-30,2.5,0,0.49,0.94
316 | 1980-12-01,3.1,0,0.5,0.72
317 | 1980-12-02,5,0,0.56,0.65
318 | 1980-12-03,8.1,0,0.68,0.68
319 | 1980-12-04,-1.9,0,0.36,0.31
320 | 1980-12-05,-2.5,0,0.35,0.31
321 | 1980-12-06,-0.8,0,0.39,0.32
322 | 1980-12-07,2.5,0,0.47,0.31
323 | 1980-12-08,4.4,0,0.53,0.32
324 | 1980-12-09,10.6,0,0.78,0.32
325 | 1980-12-10,4.7,0,0.54,0.37
326 | 1980-12-11,1.4,0,0.44,0.28
327 | 1980-12-12,-4.4,0,0.31,0.26
328 | 1980-12-13,-0.3,0,0.39,0.26
329 | 1980-12-14,0.6,0,0.41,0.23
330 | 1980-12-15,-3.6,0,0.32,0.15
331 | 1980-12-16,-4.4,2.5,0.3,0.32
332 | 1980-12-17,-3.3,2.5,0.33,0.26
333 | 1980-12-18,-6.4,0,0.27,0.2
334 | 1980-12-19,-2.2,0,0.35,0.2
335 | 1980-12-20,-5.6,0,0.28,0.11
336 | 1980-12-21,-10.6,0,0.21,0.09
337 | 1980-12-22,-10.3,0,0.21,0.09
338 | 1980-12-23,-8.9,0,0.23,0.11
339 | 1980-12-24,-5,0,0.29,0.13
340 | 1980-12-25,-9.4,0,0.22,0.24
341 | 1980-12-26,-17.8,0,0.13,0.02
342 | 1980-12-27,-13.1,0,0.18,0.02
343 | 1980-12-28,-9.2,2.5,0.23,0.02
344 | 1980-12-29,0.3,0,0.41,0.03
345 | 1980-12-30,5.8,0,0.57,0.03
346 | 1980-12-31,-3.9,0,0.32,0.03
347 | 1981-01-01,-7.8,0,0.25,0.02
348 | 1981-01-02,-4.4,0,0.31,0.02
349 | 1981-01-03,-5.8,0,0.28,0.02
350 | 1981-01-04,-13.3,0,0.18,0.02
351 | 1981-01-05,-15.6,0,0.15,0.02
352 | 1981-01-06,-7.8,0,0.25,0.02
353 | 1981-01-07,-5.3,2.5,0.29,0.03
354 | 1981-01-08,-6.4,0,0.28,0.03
355 | 1981-01-09,-15,0,0.16,0.03
356 | 1981-01-10,-13.9,0,0.17,0.03
357 | 1981-01-11,-11.7,0,0.2,0.02
358 | 1981-01-12,-16.1,0,0.15,0.02
359 | 1981-01-13,-18.3,0,0.14,0.02
360 | 1981-01-14,-15.6,0,0.16,0.02
361 | 1981-01-15,-5,0,0.31,0.02
362 | 1981-01-16,-2.5,0,0.37,0.02
363 | 1981-01-17,-5,0,0.32,0.02
364 | 1981-01-18,-10.3,0,0.23,0.02
365 | 1981-01-19,-6.4,0,0.29,0.02
366 | 1981-01-20,1.7,0,0.48,0.02
367 | 1981-01-21,-0.3,0,0.43,0.02
368 | 1981-01-22,-5.6,0,0.31,0.02
369 | 1981-01-23,-3.6,0,0.35,0.02
370 | 1981-01-24,1.7,0,0.5,0.02
371 | 1981-01-25,-0.3,0,0.44,0.02
372 | 1981-01-26,1.9,0,0.51,0.02
373 | 1981-01-27,2.8,0,0.54,0.02
374 | 1981-01-28,2.2,0,0.53,0.02
375 | 1981-01-29,1.1,0,0.49,0.02
376 | 1981-01-30,-4.4,0,0.35,0.02
377 | 1981-01-31,-7.5,0,0.29,0.02
378 | 1981-02-01,-4.7,2.5,0.35,0.03
379 | 1981-02-02,-0.8,35.6,0.45,11.02
380 | 1981-02-03,1.4,0,0.52,5.35
381 | 1981-02-04,-9.2,0,0.27,2.83
382 | 1981-02-05,-7.8,0,0.3,1.89
383 | 1981-02-06,-10.3,0,0.26,1.5
384 | 1981-02-07,-4.2,0,0.38,0.87
385 | 1981-02-08,-0.8,5.1,0.47,2.99
386 | 1981-02-09,-0.3,0,0.49,11.02
387 | 1981-02-10,-5.6,0,0.36,5.59
388 | 1981-02-11,3.3,22.9,0.62,13.38
389 | 1981-02-12,4.2,0,0.66,11.81
390 | 1981-02-13,-8.1,0,0.31,7.24
391 | 1981-02-14,-6.1,0,0.36,3.86
392 | 1981-02-15,-2.8,0,0.44,2.13
393 | 1981-02-16,0.3,0,0.54,1.18
394 | 1981-02-17,3.9,0,0.68,0.59
395 | 1981-02-18,8.9,0,0.93,0.32
396 | 1981-02-19,11.7,5.1,1.11,0.23
397 | 1981-02-20,11.9,22.9,1.14,14.17
398 | 1981-02-21,10,2.5,1.02,10.23
399 | 1981-02-22,11.4,2.5,1.12,9.45
400 | 1981-02-23,7.8,20.3,0.9,11.02
401 | 1981-02-24,6.1,2.5,0.82,14.17
402 | 1981-02-25,8.1,0,0.94,7.87
403 | 1981-02-26,5,0,0.78,5.98
404 | 1981-02-27,4.4,0,0.76,3.46
405 | 1981-02-28,3.6,0,0.72,2.28
406 | 1981-03-01,1.9,0,0.66,2.6
407 | 1981-03-02,3.3,0,0.72,1.73
408 | 1981-03-03,2.2,0,0.68,1.1
409 | 1981-03-04,-3.6,0,0.48,0.68
410 | 1981-03-05,-1.4,2.5,0.55,0.79
411 | 1981-03-06,-1.7,0,0.55,0.94
412 | 1981-03-07,0.3,0,0.62,1.18
413 | 1981-03-08,1.7,0,0.69,2.6
414 | 1981-03-09,5,0,0.85,2.91
415 | 1981-03-10,4.2,0,0.81,1.73
416 | 1981-03-11,2.8,2.5,0.75,0.94
417 | 1981-03-12,-0.8,0,0.61,0.87
418 | 1981-03-13,2.2,0,0.74,0.71
419 | 1981-03-14,5.6,0,0.92,0.54
420 | 1981-03-15,-1.9,0,0.58,0.41
421 | 1981-03-16,4.2,2.5,0.85,0.56
422 | 1981-03-17,1.7,0,0.74,0.4
423 | 1981-03-18,-3.3,0,0.55,0.3
424 | 1981-03-19,-3.1,0,0.56,0.3
425 | 1981-03-20,-3.6,0,0.54,0.28
426 | 1981-03-21,-3.1,0,0.56,0.26
427 | 1981-03-22,1.9,0,0.78,0.23
428 | 1981-03-23,4.7,0,0.93,0.24
429 | 1981-03-24,2.8,0,0.83,0.22
430 | 1981-03-25,5.3,0,0.98,0.2
431 | 1981-03-26,2.5,0,0.83,0.18
432 | 1981-03-27,5,0,0.98,0.23
433 | 1981-03-28,6.7,0,1.09,0.14
434 | 1981-03-29,8.9,0,1.26,0.16
435 | 1981-03-30,13.9,10.2,1.74,0.76
436 | 1981-03-31,13.9,10.2,1.75,0.76
437 | 1981-04-01,14.7,15.2,1.85,1.73
438 | 1981-04-02,14.2,0,1.81,1.97
439 | 1981-04-03,9.2,0,1.33,0.79
440 | 1981-04-04,14.7,0,1.89,0.58
441 | 1981-04-05,18.6,12.7,2.43,1.34
442 | 1981-04-06,12.8,0,1.71,1.97
443 | 1981-04-07,4.4,0,1.02,1.02
444 | 1981-04-08,8.6,0,1.33,0.61
445 | 1981-04-09,13.9,0,1.86,0.54
446 | 1981-04-10,12.2,0,1.69,0.46
447 | 1981-04-11,12.5,2.5,1.73,0.4
448 | 1981-04-12,15.6,7.6,2.12,0.61
449 | 1981-04-13,8.1,2.5,1.34,0.54
450 | 1981-04-14,8.3,20.3,1.36,6.06
451 | 1981-04-15,6.9,0,1.26,3.86
452 | 1981-04-16,3.1,0,1,1.89
453 | 1981-04-17,9.4,0,1.49,0.87
454 | 1981-04-18,12.8,0,1.85,0.72
455 | 1981-04-19,15.3,0,2.18,0.53
456 | 1981-04-20,12.5,0,1.84,0.46
457 | 1981-04-21,6.1,0,1.25,0.32
458 | 1981-04-22,3.3,0,1.05,0.29
459 | 1981-04-23,8.9,7.6,1.5,0.68
460 | 1981-04-24,10,2.5,1.62,1.42
461 | 1981-04-25,12.5,0,1.9,1.18
462 | 1981-04-26,6.7,0,1.33,1.26
463 | 1981-04-27,10.6,0,1.71,1.26
464 | 1981-04-28,12.5,0,1.93,1.5
465 | 1981-04-29,15.6,0,2.36,1.73
466 | 1981-04-30,15.3,0,2.33,1.1
467 | 1981-05-01,12.2,5.1,1.93,1.02
468 | 1981-05-02,13.9,12.7,2.16,5.27
469 | 1981-05-03,10.6,0,1.77,3.23
470 | 1981-05-04,13.6,0,2.14,1.97
471 | 1981-05-05,17.8,0,2.79,1.57
472 | 1981-05-06,15.8,0,2.48,1.42
473 | 1981-05-07,12.5,0,2.03,0.94
474 | 1981-05-08,11.4,0,1.91,0.76
475 | 1981-05-09,11.1,0,1.88,0.54
476 | 1981-05-10,12.2,0,2.03,0.39
477 | 1981-05-11,16.4,63.5,2.64,18.11
478 | 1981-05-12,16.4,0,2.66,10.23
479 | 1981-05-13,13.1,0,2.17,2.28
480 | 1981-05-14,14.2,0,2.34,1.34
481 | 1981-05-15,17.5,25.4,2.88,4.8
482 | 1981-05-16,19.4,0,3.26,6.22
483 | 1981-05-17,13.6,0,2.28,1.73
484 | 1981-05-18,13.6,0,2.29,1.18
485 | 1981-05-19,13.3,0,2.26,0.87
486 | 1981-05-20,11.7,0,2.06,0.73
487 | 1981-05-21,14.2,0,2.41,0.61
488 | 1981-05-22,15,0,2.54,0.5
489 | 1981-05-23,17.2,0,2.92,0.41
490 | 1981-05-24,16.9,0,2.88,0.31
491 | 1981-05-25,20.3,0,3.57,0.27
492 | 1981-05-26,22.2,0,4.03,0.2
493 | 1981-05-27,23.1,0,4.28,0.21
494 | 1981-05-28,23.6,0,4.42,0.18
495 | 1981-05-29,21.7,0,3.95,0.25
496 | 1981-05-30,19.7,0,3.5,0.16
497 | 1981-05-31,23.3,0,4.38,0.16
498 | 1981-06-01,17.8,0,3.12,0.02
499 | 1981-06-02,18.1,22.9,3.19,2.76
500 | 1981-06-03,15.3,5.1,2.69,0.64
501 | 1981-06-04,17.2,0,3.03,0.79
502 | 1981-06-05,21.4,0,3.94,0.3
503 | 1981-06-06,22.5,0,4.23,0.24
504 | 1981-06-07,21.1,0,3.89,0.18
505 | 1981-06-08,17.2,0,3.06,0.05
506 | 1981-06-09,20,2.5,3.65,0.59
507 | 1981-06-10,21.9,0,4.11,0.31
508 | 1981-06-11,17.5,0,3.13,0.2
509 | 1981-06-12,20.6,0,3.8,0.03
510 | 1981-06-13,22.2,0,4.2,0.01
511 | 1981-06-14,22.2,17.8,4.21,2.13
512 | 1981-06-15,17.2,2.5,3.09,0.79
513 | 1981-06-16,22.8,0,4.37,0.28
514 | 1981-06-17,27.8,0,5.97,0.18
515 | 1981-06-18,20,0,3.68,0.12
516 | 1981-06-19,21.4,0,4.02,0.1
517 | 1981-06-20,21.9,7.6,4.14,0.7
518 | 1981-06-21,21.1,0,3.94,0.27
519 | 1981-06-22,23.3,2.5,4.52,0.61
520 | 1981-06-23,24.7,0,4.93,0.2
521 | 1981-06-24,19.4,0,3.55,0.13
522 | 1981-06-25,20.8,20.3,3.87,2.76
523 | 1981-06-26,22.8,0,4.38,1.34
524 | 1981-06-27,16.4,0,2.94,0.29
525 | 1981-06-28,19.4,0,3.54,0.17
526 | 1981-06-29,20.8,0,3.86,0.13
527 | 1981-06-30,22.5,0,4.28,0.12
528 | 1981-07-01,22.8,7.6,4.36,0.43
529 | 1981-07-02,23.9,0,4.66,0.24
530 | 1981-07-03,23.9,0,4.65,0.13
531 | 1981-07-04,25,43.2,4.97,7.16
532 | 1981-07-05,21.1,2.5,3.9,3.23
533 | 1981-07-06,22.2,0,4.16,0.87
534 | 1981-07-07,24.2,0,4.7,0.54
535 | 1981-07-08,26.1,0,5.28,0.39
536 | 1981-07-09,26.9,0,5.54,0.28
537 | 1981-07-10,28.6,0,6.14,0.25
538 | 1981-07-11,23.9,0,4.58,0.28
539 | 1981-07-12,25.6,0,5.07,0.13
540 | 1981-07-13,26.7,15.2,5.41,1.81
541 | 1981-07-14,26.1,0,5.2,0.7
542 | 1981-07-15,21.1,0,3.8,0.13
543 | 1981-07-16,20.6,0,3.68,0.13
544 | 1981-07-17,21.7,0,3.92,0.1
545 | 1981-07-18,23.6,0,4.4,0.09
546 | 1981-07-19,25.3,0,4.87,0.07
547 | 1981-07-20,25.8,25.4,5.01,2.13
548 | 1981-07-21,24.4,7.6,4.57,4.33
549 | 1981-07-22,24.4,0,4.56,0.54
550 | 1981-07-23,20.8,0,3.63,0.2
551 | 1981-07-24,20,0,3.44,0.13
552 | 1981-07-25,20.6,0,3.56,0.1
553 | 1981-07-26,21.9,0,3.84,0.09
554 | 1981-07-27,25.3,22.9,4.72,5.75
555 | 1981-07-28,22.2,0,3.88,0.51
556 | 1981-07-29,20.8,5.1,3.54,0.79
557 | 1981-07-30,19.4,0,3.23,0.17
558 | 1981-07-31,20.3,0,3.4,0.13
559 | 1981-08-01,21.1,0,3.56,0.1
560 | 1981-08-02,21.9,0,3.72,0.08
561 | 1981-08-03,22.8,0,3.91,0.06
562 | 1981-08-04,22.2,0,3.75,0.06
563 | 1981-08-05,24.7,10.2,4.36,2.44
564 | 1981-08-06,23.3,0,3.98,0.19
565 | 1981-08-07,21.9,0,3.63,0.1
566 | 1981-08-08,23.1,15.2,3.88,3.07
567 | 1981-08-09,20,0,3.19,0.79
568 | 1981-08-10,23.6,0,3.96,0.18
569 | 1981-08-11,24.4,0,4.14,0.12
570 | 1981-08-12,25,0,4.28,0.37
571 | 1981-08-13,20.6,0,3.24,0.17
572 | 1981-08-14,22.2,0,3.55,0.11
573 | 1981-08-15,23.9,0,3.92,0.1
574 | 1981-08-16,24.7,0,4.1,0.12
575 | 1981-08-17,20.3,0,3.1,0.08
576 | 1981-08-18,16.9,0,2.5,0.03
577 | 1981-08-19,18.9,0,2.81,0
578 | 1981-08-20,20.3,0,3.04,0
579 | 1981-08-21,18.3,0,2.67,0
580 | 1981-08-22,20.3,0,3.01,0
581 | 1981-08-23,18.1,0,2.61,0
582 | 1981-08-24,20,0,2.91,0
583 | 1981-08-25,19.7,0,2.84,0
584 | 1981-08-26,20,0,2.88,0
585 | 1981-08-27,20,0,2.86,0
586 | 1981-08-28,22.5,0,3.31,0
587 | 1981-08-29,22.5,0,3.29,0
588 | 1981-08-30,23.9,2.5,3.57,0.02
589 | 1981-08-31,23.1,0,3.37,0.13
590 | 1981-09-01,21.9,0,3.11,0.09
591 | 1981-09-02,22.8,0,3.26,0.09
592 | 1981-09-03,20.3,0,2.78,0.07
593 | 1981-09-04,19.7,0,2.66,0.06
594 | 1981-09-05,18.6,0,2.46,0.06
595 | 1981-09-06,20.6,0,2.77,0.03
596 | 1981-09-07,20.8,0,2.78,0.03
597 | 1981-09-08,20.6,20.3,2.73,4.33
598 | 1981-09-09,19.2,0,2.48,1.89
599 | 1981-09-10,15,0,1.9,0.15
600 | 1981-09-11,15.8,0,1.98,0.12
601 | 1981-09-12,20.6,0,2.65,0.12
602 | 1981-09-13,20.8,0,2.67,0.09
603 | 1981-09-14,20.3,0,2.56,0.08
604 | 1981-09-15,23.6,12.7,3.12,0.51
605 | 1981-09-16,17.2,17.8,2.08,9.45
606 | 1981-09-17,15.3,0,1.84,1.1
607 | 1981-09-18,16.7,0,1.99,3.54
608 | 1981-09-19,16.1,0,1.9,0.79
609 | 1981-09-20,14.2,0,1.68,0.37
610 | 1981-09-21,14.2,0,1.67,0.25
611 | 1981-09-22,14.2,0,1.65,0.28
612 | 1981-09-23,16.7,0,1.92,0.33
613 | 1981-09-24,12.5,0,1.47,0.13
614 | 1981-09-25,11.9,0,1.4,0.09
615 | 1981-09-26,14.4,0,1.62,0.09
616 | 1981-09-27,15.8,0,1.76,0.09
617 | 1981-09-28,18.9,0,2.11,0.09
618 | 1981-09-29,10.6,0,1.25,0.09
619 | 1981-09-30,10,0,1.2,0.06
620 | 1981-10-01,10,10.2,1.19,0.02
621 | 1981-10-02,12.2,5.1,1.35,3.15
622 | 1981-10-03,10.6,0,1.21,0.32
623 | 1981-10-04,7.8,0,1.01,0.13
624 | 1981-10-05,9.4,0,1.11,0.14
625 | 1981-10-06,15.3,10.2,1.59,0.42
626 | 1981-10-07,14.4,0,1.49,1.1
627 | 1981-10-08,11.7,0,1.25,0.18
628 | 1981-10-09,8.3,0,1,0.1
629 | 1981-10-10,8.3,0,0.99,0.05
630 | 1981-10-11,7.5,0,0.94,0.03
631 | 1981-10-12,8.1,0,0.97,0.01
632 | 1981-10-13,5,0,0.79,0
633 | 1981-10-14,6.9,0,0.88,0
634 | 1981-10-15,8.9,0,0.99,0
635 | 1981-10-16,8.3,0,0.95,0
636 | 1981-10-17,11.7,0,1.16,0
637 | 1981-10-18,8.9,20.3,0.97,2.6
638 | 1981-10-19,9.4,0,0.99,1.57
639 | 1981-10-20,3.9,0,0.7,0.28
640 | 1981-10-21,5.6,0,0.77,0.17
641 | 1981-10-22,10.3,0,1.02,0.14
642 | 1981-10-23,12.5,15.2,1.16,1.5
643 | 1981-10-24,7.8,0,0.86,1.34
644 | 1981-10-25,4.2,0,0.69,0.39
645 | 1981-10-26,6.9,10.2,0.8,2.36
646 | 1981-10-27,12.8,33,1.15,11.02
647 | 1981-10-28,15.3,0,1.33,5.51
648 | 1981-10-29,10.8,0,1,1.18
649 | 1981-10-30,6.9,0,0.78,0.68
650 | 1981-10-31,7.5,0,0.8,0.5
651 | 1981-11-01,8.3,0,0.84,0.41
652 | 1981-11-02,9.2,0,0.88,0.35
653 | 1981-11-03,12.2,0,1.05,0.28
654 | 1981-11-04,9.2,0,0.86,0.26
655 | 1981-11-05,10.8,0,0.95,0.24
656 | 1981-11-06,10.3,12.7,0.91,2.6
657 | 1981-11-07,8.6,0,0.82,0.61
658 | 1981-11-08,6.4,0,0.71,0.43
659 | 1981-11-09,6.9,0,0.72,0.39
660 | 1981-11-10,7.8,0,0.76,0.35
661 | 1981-11-11,3.3,0,0.57,0.3
662 | 1981-11-12,5.6,0,0.65,0.28
663 | 1981-11-13,2.5,0,0.54,0.24
664 | 1981-11-14,3.9,0,0.58,0.24
665 | 1981-11-15,10,10.2,0.84,0.87
666 | 1981-11-16,9.7,0,0.82,1.34
667 | 1981-11-17,5.8,0,0.64,0.57
668 | 1981-11-18,6.1,2.5,0.65,0.51
669 | 1981-11-19,9.4,0,0.79,0.39
670 | 1981-11-20,10.3,15.2,0.83,1.42
671 | 1981-11-21,7.8,2.5,0.71,0.76
672 | 1981-11-22,5,5.1,0.59,0.51
673 | 1981-11-23,3.1,0,0.52,0.43
674 | 1981-11-24,-1.9,0,0.38,0.38
675 | 1981-11-25,-0.8,0,0.41,0.35
676 | 1981-11-26,-1.1,0,0.4,0.29
677 | 1981-11-27,0.3,0,0.43,0.31
678 | 1981-11-28,6.9,0,0.65,0.31
679 | 1981-11-29,2.5,0,0.49,0.26
680 | 1981-11-30,2.8,0,0.5,0.19
681 | 1981-12-01,-1.7,22.9,0.37,3.86
682 | 1981-12-02,2.2,20.3,0.47,13.38
683 | 1981-12-03,6.1,0,0.6,1.89
684 | 1981-12-04,3.1,0,0.5,1.02
685 | 1981-12-05,3.9,0,0.52,0.71
686 | 1981-12-06,2.8,0,0.48,0.53
687 | 1981-12-07,0.8,0,0.43,0.43
688 | 1981-12-08,3.9,5.1,0.52,0.87
689 | 1981-12-09,1.9,0,0.46,0.55
690 | 1981-12-10,-2.5,7.6,0.34,0.36
691 | 1981-12-11,-1.9,0,0.36,0.28
692 | 1981-12-12,0.3,0,0.41,0.25
693 | 1981-12-13,-2.2,2.5,0.35,0.21
694 | 1981-12-14,-2.8,15.2,0.34,0.47
695 | 1981-12-15,-2.5,35.6,0.34,20.47
696 | 1981-12-16,1.4,2.5,0.43,14.17
697 | 1981-12-17,-1.7,0,0.36,4.09
698 | 1981-12-18,-3.1,0,0.33,2.36
699 | 1981-12-19,-5.6,0,0.28,1.5
700 | 1981-12-20,-7.8,0,0.24,1.02
701 | 1981-12-21,-9.2,0,0.23,0.79
702 | 1981-12-22,-7.8,0,0.24,0.76
703 | 1981-12-23,1.1,5.1,0.43,5.35
704 | 1981-12-24,3.9,0,0.51,3.07
705 | 1981-12-25,1.1,0,0.43,1.81
706 | 1981-12-26,-3.1,0,0.33,1.18
707 | 1981-12-27,-1.9,2.5,0.35,1.81
708 | 1981-12-28,-0.3,0,0.39,1.81
709 | 1981-12-29,1.9,0,0.45,1.34
710 | 1981-12-30,-1.1,0,0.38,0.94
711 | 1981-12-31,-2.8,0,0.34,0.74
712 | 


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/data/inputs/twi_wolock.csv:
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 1 | bin,twi,proportion,cells 
 2 | 1,11.6817837,0.003704784,0.370478397
 3 | 2,11.21175,0.005604416,0.560441613
 4 | 3,10.7417173,0.008413193,0.841319282
 5 | 4,10.2716837,0.012517415,1.2517415
 6 | 5,9.80165005,0.018429315,1.84293147
 7 | 6,9.33161736,0.026795687,2.67956872
 8 | 7,8.86158371,0.038372401,3.83724011
 9 | 8,8.39155006,0.053925101,5.39251007
10 | 9,7.9215169,0.073987022,7.3987022
11 | 10,7.45148373,0.098363318,9.83633175
12 | 11,6.98145008,0.125227734,12.5227734
13 | 12,6.51141691,0.149650559,14.9650559
14 | 13,6.04138327,0.161592662,16.1592662
15 | 14,5.5713501,0.14437668,14.437668
16 | 15,5.10131645,0.079039745,7.9039745
17 | 16,0,0,0
18 | 17,0,0,0
19 | 18,0,0,0
20 | 19,0,0,0
21 | 20,0,0,0
22 | 


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/data/modelconfig.ini:
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 1 | # Model configuration file
 2 | # ------------------------
 3 | # This file contains all the information necessary to complete a model run:
 4 | #     - location of input files
 5 | #     - model specific options/flags for various calculations
 6 | #     - location to write output files along with output format
 7 | #
 8 | # This data file is in the standard INI file format, more information
 9 | # can be found at https://en.wikipedia.org/wiki/INI_file
10 | #
11 | # This file contains different sections that group together common data
12 | # and/or options to make it easier for the user to find and edit. Each
13 | # section contains key-value pairs. For example:
14 | #
15 | #     [Section Name]
16 | #     key = value
17 | #
18 | # - Only edit the values, and DO NOT edit the sections or keys.
19 | #
20 | # - To use a value multiple times, use the following syntax:
21 | #      ${Section Name:key}
22 | #
23 | # -------------------------------------------------------------------------
24 | 
25 | # INPUTS
26 | # -------------------------------------------------------------------------
27 | [Inputs]
28 | # Input directory location, using for shortcut purposes
29 | input_dir = /home/jlant/jeremiah/projects/topmodelpy/data/inputs
30 | 
31 | # Model parameter data file (*.csv)
32 | parameters_file = ${Inputs:input_dir}/parameters_wolock.csv
33 | 
34 | # Climate timeseries data file(s) (*.csv)
35 | timeseries_file = ${Inputs:input_dir}/timeseries_wolock.csv
36 | 
37 | # Topographic wetness index (TWI) file(s) (*.csv)
38 | twi_file = ${Inputs:input_dir}/twi_wolock.csv
39 | 
40 | # OUTPUTS
41 | # -------------------------------------------------------------------------
42 | [Outputs]
43 | # Output directory location
44 | output_dir = /home/jlant/jeremiah/projects/topmodelpy/data/outputs
45 | 
46 | # Output filename for timeseries of main results (*.csv)
47 | output_filename = output.csv
48 | 
49 | # Output filename for timeseries of saturation deficit locals (*.csv)
50 | # Note: This file has the same number of columns as the number of twi bins
51 | output_filename_saturation_deficit_locals = output_saturation_deficit_locals.csv
52 | 
53 | # Output filename for timeseries of unsaturated zone storages (*.csv)
54 | # Note: This file has the same number of columns as the number of twi bins
55 | output_filename_unsaturated_zone_storages = output_unsaturated_zone_storages.csv
56 | 
57 | # Output filename for timeseries of unsaturated zone storages (*.csv)
58 | # Note: This file has the same number of columns as the number of twi bins
59 | output_filename_root_zone_storages = output_root_zone_storages.csv
60 | 
61 | # Output html report for timeseries of main results (*.html)
62 | output_report = report.html
63 | 
64 | # OPTIONS
65 | # -------------------------------------------------------------------------
66 | [Options]
67 | # Potential evapotranspiration (PET) calculation option, hamon only right now
68 | option_pet = hamon
69 | 
70 | # Snowmelt calculation, yes | no
71 | option_snowmelt = no
72 | 
73 | # Write output matrices of 
74 | #   saturation deficit local (mm)
75 | #   root zone storage (mm)
76 | #   unsaturated zone storage (mm)
77 | option_write_output_matrices = no
78 | 


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/data/outputs/flow_duration_curve.png:
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https://raw.githubusercontent.com/jlant/topmodelpy/77440b5c1fb066435fad78b8b95ba6e7157fb055/data/outputs/flow_duration_curve.png


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/data/outputs/flow_duration_curved_observed_vs_predicted.png:
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https://raw.githubusercontent.com/jlant/topmodelpy/77440b5c1fb066435fad78b8b95ba6e7157fb055/data/outputs/flow_duration_curved_observed_vs_predicted.png


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/data/outputs/flow_observed.png:
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https://raw.githubusercontent.com/jlant/topmodelpy/77440b5c1fb066435fad78b8b95ba6e7157fb055/data/outputs/flow_observed.png


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/data/outputs/flow_observed_vs_flow_predicted.png:
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https://raw.githubusercontent.com/jlant/topmodelpy/77440b5c1fb066435fad78b8b95ba6e7157fb055/data/outputs/flow_observed_vs_flow_predicted.png


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/data/outputs/flow_predicted.png:
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https://raw.githubusercontent.com/jlant/topmodelpy/77440b5c1fb066435fad78b8b95ba6e7157fb055/data/outputs/flow_predicted.png


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/data/outputs/pet.png:
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https://raw.githubusercontent.com/jlant/topmodelpy/77440b5c1fb066435fad78b8b95ba6e7157fb055/data/outputs/pet.png


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/data/outputs/precip_minus_pet.png:
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/docs/Makefile:
--------------------------------------------------------------------------------
  1 | # Makefile for Sphinx documentation
  2 | #
  3 | 
  4 | # You can set these variables from the command line.
  5 | SPHINXOPTS    =
  6 | SPHINXBUILD   = sphinx-build
  7 | PAPER         =
  8 | BUILDDIR      = _build
  9 | 
 10 | # User-friendly check for sphinx-build
 11 | ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
 12 | $(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
 13 | endif
 14 | 
 15 | # Internal variables.
 16 | PAPEROPT_a4     = -D latex_paper_size=a4
 17 | PAPEROPT_letter = -D latex_paper_size=letter
 18 | ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
 19 | # the i18n builder cannot share the environment and doctrees with the others
 20 | I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
 21 | 
 22 | .PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest coverage gettext
 23 | 
 24 | help:
 25 | 	@echo "Please use \`make <target>' where <target> is one of"
 26 | 	@echo "  html       to make standalone HTML files"
 27 | 	@echo "  dirhtml    to make HTML files named index.html in directories"
 28 | 	@echo "  singlehtml to make a single large HTML file"
 29 | 	@echo "  pickle     to make pickle files"
 30 | 	@echo "  json       to make JSON files"
 31 | 	@echo "  htmlhelp   to make HTML files and a HTML help project"
 32 | 	@echo "  qthelp     to make HTML files and a qthelp project"
 33 | 	@echo "  applehelp  to make an Apple Help Book"
 34 | 	@echo "  devhelp    to make HTML files and a Devhelp project"
 35 | 	@echo "  epub       to make an epub"
 36 | 	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
 37 | 	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
 38 | 	@echo "  latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
 39 | 	@echo "  text       to make text files"
 40 | 	@echo "  man        to make manual pages"
 41 | 	@echo "  texinfo    to make Texinfo files"
 42 | 	@echo "  info       to make Texinfo files and run them through makeinfo"
 43 | 	@echo "  gettext    to make PO message catalogs"
 44 | 	@echo "  changes    to make an overview of all changed/added/deprecated items"
 45 | 	@echo "  xml        to make Docutils-native XML files"
 46 | 	@echo "  pseudoxml  to make pseudoxml-XML files for display purposes"
 47 | 	@echo "  linkcheck  to check all external links for integrity"
 48 | 	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
 49 | 	@echo "  coverage   to run coverage check of the documentation (if enabled)"
 50 | 
 51 | clean:
 52 | 	rm -rf $(BUILDDIR)/*
 53 | 
 54 | html:
 55 | 	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
 56 | 	@echo
 57 | 	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
 58 | 
 59 | dirhtml:
 60 | 	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
 61 | 	@echo
 62 | 	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
 63 | 
 64 | singlehtml:
 65 | 	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
 66 | 	@echo
 67 | 	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
 68 | 
 69 | pickle:
 70 | 	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
 71 | 	@echo
 72 | 	@echo "Build finished; now you can process the pickle files."
 73 | 
 74 | json:
 75 | 	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
 76 | 	@echo
 77 | 	@echo "Build finished; now you can process the JSON files."
 78 | 
 79 | htmlhelp:
 80 | 	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
 81 | 	@echo
 82 | 	@echo "Build finished; now you can run HTML Help Workshop with the" \
 83 | 	      ".hhp project file in $(BUILDDIR)/htmlhelp."
 84 | 
 85 | qthelp:
 86 | 	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
 87 | 	@echo
 88 | 	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
 89 | 	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
 90 | 	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/nwispy.qhcp"
 91 | 	@echo "To view the help file:"
 92 | 	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/nwispy.qhc"
 93 | 
 94 | applehelp:
 95 | 	$(SPHINXBUILD) -b applehelp $(ALLSPHINXOPTS) $(BUILDDIR)/applehelp
 96 | 	@echo
 97 | 	@echo "Build finished. The help book is in $(BUILDDIR)/applehelp."
 98 | 	@echo "N.B. You won't be able to view it unless you put it in" \
 99 | 	      "~/Library/Documentation/Help or install it in your application" \
100 | 	      "bundle."
101 | 
102 | devhelp:
103 | 	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
104 | 	@echo
105 | 	@echo "Build finished."
106 | 	@echo "To view the help file:"
107 | 	@echo "# mkdir -p $$HOME/.local/share/devhelp/nwispy"
108 | 	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/nwispy"
109 | 	@echo "# devhelp"
110 | 
111 | epub:
112 | 	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
113 | 	@echo
114 | 	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
115 | 
116 | latex:
117 | 	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
118 | 	@echo
119 | 	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
120 | 	@echo "Run \`make' in that directory to run these through (pdf)latex" \
121 | 	      "(use \`make latexpdf' here to do that automatically)."
122 | 
123 | latexpdf:
124 | 	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
125 | 	@echo "Running LaTeX files through pdflatex..."
126 | 	$(MAKE) -C $(BUILDDIR)/latex all-pdf
127 | 	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
128 | 
129 | latexpdfja:
130 | 	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
131 | 	@echo "Running LaTeX files through platex and dvipdfmx..."
132 | 	$(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
133 | 	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
134 | 
135 | text:
136 | 	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
137 | 	@echo
138 | 	@echo "Build finished. The text files are in $(BUILDDIR)/text."
139 | 
140 | man:
141 | 	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
142 | 	@echo
143 | 	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
144 | 
145 | texinfo:
146 | 	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
147 | 	@echo
148 | 	@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
149 | 	@echo "Run \`make' in that directory to run these through makeinfo" \
150 | 	      "(use \`make info' here to do that automatically)."
151 | 
152 | info:
153 | 	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
154 | 	@echo "Running Texinfo files through makeinfo..."
155 | 	make -C $(BUILDDIR)/texinfo info
156 | 	@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
157 | 
158 | gettext:
159 | 	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
160 | 	@echo
161 | 	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
162 | 
163 | changes:
164 | 	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
165 | 	@echo
166 | 	@echo "The overview file is in $(BUILDDIR)/changes."
167 | 
168 | linkcheck:
169 | 	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
170 | 	@echo
171 | 	@echo "Link check complete; look for any errors in the above output " \
172 | 	      "or in $(BUILDDIR)/linkcheck/output.txt."
173 | 
174 | doctest:
175 | 	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
176 | 	@echo "Testing of doctests in the sources finished, look at the " \
177 | 	      "results in $(BUILDDIR)/doctest/output.txt."
178 | 
179 | coverage:
180 | 	$(SPHINXBUILD) -b coverage $(ALLSPHINXOPTS) $(BUILDDIR)/coverage
181 | 	@echo "Testing of coverage in the sources finished, look at the " \
182 | 	      "results in $(BUILDDIR)/coverage/python.txt."
183 | 
184 | xml:
185 | 	$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
186 | 	@echo
187 | 	@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
188 | 
189 | pseudoxml:
190 | 	$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
191 | 	@echo
192 | 	@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."
193 | 


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/docs/authors.rst:
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1 | .. include:: ../AUTHORS.rst
2 | 


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/docs/changelog.rst:
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1 | .. include:: ../CHANGELOG.rst
2 | 


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/docs/code.rst:
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1 | Code documentation
2 | ==================
3 | 
4 | .. automodule:: topmodelpy.topmodelpy
5 |    :members:
6 | 


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/docs/conf.py:
--------------------------------------------------------------------------------
  1 | #!/usr/bin/env python
  2 | # -*- coding: utf-8 -*-
  3 | #
  4 | # topmodelpy documentation build configuration file, created by
  5 | # sphinx-quickstart on Tue Jul  9 22:26:36 2013.
  6 | #
  7 | # This file is execfile()d with the current directory set to its
  8 | # containing dir.
  9 | #
 10 | # Note that not all possible configuration values are present in this
 11 | # autogenerated file.
 12 | #
 13 | # All configuration values have a default; values that are commented out
 14 | # serve to show the default.
 15 | 
 16 | import sys
 17 | import os
 18 | 
 19 | # If extensions (or modules to document with autodoc) are in another
 20 | # directory, add these directories to sys.path here. If the directory is
 21 | # relative to the documentation root, use os.path.abspath to make it
 22 | # absolute, like shown here.
 23 | #sys.path.insert(0, os.path.abspath('.'))
 24 | 
 25 | # Get the project root dir, which is the parent dir of this
 26 | cwd = os.getcwd()
 27 | project_root = os.path.dirname(cwd)
 28 | 
 29 | # Insert the project root dir as the first element in the PYTHONPATH.
 30 | # This lets us ensure that the source package is imported, and that its
 31 | # version is used.
 32 | sys.path.insert(0, project_root)
 33 | 
 34 | import topmodelpy
 35 | 
 36 | # -- General configuration ---------------------------------------------
 37 | 
 38 | # If your documentation needs a minimal Sphinx version, state it here.
 39 | #needs_sphinx = '1.0'
 40 | 
 41 | # Add any Sphinx extension module names here, as strings. They can be
 42 | # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
 43 | extensions = ['sphinx.ext.autodoc', 'sphinx.ext.viewcode']
 44 | 
 45 | # Add any paths that contain templates here, relative to this directory.
 46 | templates_path = ['_templates']
 47 | 
 48 | # The suffix of source filenames.
 49 | source_suffix = '.rst'
 50 | 
 51 | # The encoding of source files.
 52 | #source_encoding = 'utf-8-sig'
 53 | 
 54 | # The master toctree document.
 55 | master_doc = 'index'
 56 | 
 57 | # General information about the project.
 58 | project = u'topmodelpy'
 59 | # copyright = u'2019, Jeremiah Lant'
 60 | 
 61 | # The version info for the project you're documenting, acts as replacement
 62 | # for |version| and |release|, also used in various other places throughout
 63 | # the built documents.
 64 | #
 65 | # The short X.Y version.
 66 | version = topmodelpy.__version__
 67 | # The full version, including alpha/beta/rc tags.
 68 | release = topmodelpy.__version__
 69 | 
 70 | # The language for content autogenerated by Sphinx. Refer to documentation
 71 | # for a list of supported languages.
 72 | #language = None
 73 | 
 74 | # There are two options for replacing |today|: either, you set today to
 75 | # some non-false value, then it is used:
 76 | #today = ''
 77 | # Else, today_fmt is used as the format for a strftime call.
 78 | #today_fmt = '%B %d, %Y'
 79 | 
 80 | # List of patterns, relative to source directory, that match files and
 81 | # directories to ignore when looking for source files.
 82 | exclude_patterns = ['_build']
 83 | 
 84 | # The reST default role (used for this markup: `text`) to use for all
 85 | # documents.
 86 | #default_role = None
 87 | 
 88 | # If true, '()' will be appended to :func: etc. cross-reference text.
 89 | #add_function_parentheses = True
 90 | 
 91 | # If true, the current module name will be prepended to all description
 92 | # unit titles (such as .. function::).
 93 | #add_module_names = True
 94 | 
 95 | # If true, sectionauthor and moduleauthor directives will be shown in the
 96 | # output. They are ignored by default.
 97 | #show_authors = False
 98 | 
 99 | # The name of the Pygments (syntax highlighting) style to use.
100 | pygments_style = 'sphinx'
101 | 
102 | # A list of ignored prefixes for module index sorting.
103 | #modindex_common_prefix = []
104 | 
105 | # If true, keep warnings as "system message" paragraphs in the built
106 | # documents.
107 | #keep_warnings = False
108 | 
109 | 
110 | # -- Options for HTML output -------------------------------------------
111 | 
112 | # The theme to use for HTML and HTML Help pages.  See the documentation for
113 | # a list of builtin themes.
114 | html_theme = 'alabaster'
115 | 
116 | # Theme options are theme-specific and customize the look and feel of a
117 | # theme further.  For a list of options available for each theme, see the
118 | # documentation.
119 | #html_theme_options = {}
120 | 
121 | # Add any paths that contain custom themes here, relative to this directory.
122 | #html_theme_path = []
123 | 
124 | # The name for this set of Sphinx documents.  If None, it defaults to
125 | # "<project> v<release> documentation".
126 | #html_title = None
127 | 
128 | # A shorter title for the navigation bar.  Default is the same as
129 | # html_title.
130 | #html_short_title = None
131 | 
132 | # The name of an image file (relative to this directory) to place at the
133 | # top of the sidebar.
134 | #html_logo = None
135 | 
136 | # The name of an image file (within the static path) to use as favicon
137 | # of the docs.  This file should be a Windows icon file (.ico) being
138 | # 16x16 or 32x32 pixels large.
139 | #html_favicon = None
140 | 
141 | # Add any paths that contain custom static files (such as style sheets)
142 | # here, relative to this directory. They are copied after the builtin
143 | # static files, so a file named "default.css" will overwrite the builtin
144 | # "default.css".
145 | #html_static_path = ['_static']
146 | 
147 | # If not '', a 'Last updated on:' timestamp is inserted at every page
148 | # bottom, using the given strftime format.
149 | #html_last_updated_fmt = '%b %d, %Y'
150 | 
151 | # If true, SmartyPants will be used to convert quotes and dashes to
152 | # typographically correct entities.
153 | #html_use_smartypants = True
154 | 
155 | # Custom sidebar templates, maps document names to template names.
156 | #html_sidebars = {}
157 | 
158 | # Additional templates that should be rendered to pages, maps page names
159 | # to template names.
160 | #html_additional_pages = {}
161 | 
162 | # If false, no module index is generated.
163 | #html_domain_indices = True
164 | 
165 | # If false, no index is generated.
166 | #html_use_index = True
167 | 
168 | # If true, the index is split into individual pages for each letter.
169 | #html_split_index = False
170 | 
171 | # If true, links to the reST sources are added to the pages.
172 | #html_show_sourcelink = True
173 | 
174 | # If true, "Created using Sphinx" is shown in the HTML footer.
175 | # Default is True.
176 | #html_show_sphinx = True
177 | 
178 | # If true, "(C) Copyright ..." is shown in the HTML footer.
179 | # Default is True.
180 | html_show_copyright = False
181 | 
182 | # If true, an OpenSearch description file will be output, and all pages
183 | # will contain a <link> tag referring to it.  The value of this option
184 | # must be the base URL from which the finished HTML is served.
185 | #html_use_opensearch = ''
186 | 
187 | # This is the file name suffix for HTML files (e.g. ".xhtml").
188 | #html_file_suffix = None
189 | 
190 | # Output file base name for HTML help builder.
191 | htmlhelp_basename = 'topmodelpydoc'
192 | 
193 | 
194 | # -- Options for LaTeX output ------------------------------------------
195 | 
196 | latex_elements = {
197 |     # The paper size ('letterpaper' or 'a4paper').
198 |     #'papersize': 'letterpaper',
199 | 
200 |     # The font size ('10pt', '11pt' or '12pt').
201 |     #'pointsize': '10pt',
202 | 
203 |     # Additional stuff for the LaTeX preamble.
204 |     #'preamble': '',
205 | }
206 | 
207 | # Grouping the document tree into LaTeX files. List of tuples
208 | # (source start file, target name, title, author, documentclass
209 | # [howto/manual]).
210 | latex_documents = [
211 |     ('index', 'topmodelpy.tex',
212 |      u'topmodelpy Documentation',
213 |      u'Jeremiah Lant', 'manual'),
214 | ]
215 | 
216 | # The name of an image file (relative to this directory) to place at
217 | # the top of the title page.
218 | #latex_logo = None
219 | 
220 | # For "manual" documents, if this is true, then toplevel headings
221 | # are parts, not chapters.
222 | #latex_use_parts = False
223 | 
224 | # If true, show page references after internal links.
225 | #latex_show_pagerefs = False
226 | 
227 | # If true, show URL addresses after external links.
228 | #latex_show_urls = False
229 | 
230 | # Documents to append as an appendix to all manuals.
231 | #latex_appendices = []
232 | 
233 | # If false, no module index is generated.
234 | #latex_domain_indices = True
235 | 
236 | 
237 | # -- Options for manual page output ------------------------------------
238 | 
239 | # One entry per manual page. List of tuples
240 | # (source start file, name, description, authors, manual section).
241 | man_pages = [
242 |     ('index', 'topmodelpy',
243 |      u'topmodelpy Documentation',
244 |      [u'Jeremiah Lant'], 1)
245 | ]
246 | 
247 | # If true, show URL addresses after external links.
248 | #man_show_urls = False
249 | 
250 | 
251 | # -- Options for Texinfo output ----------------------------------------
252 | 
253 | # Grouping the document tree into Texinfo files. List of tuples
254 | # (source start file, target name, title, author,
255 | #  dir menu entry, description, category)
256 | texinfo_documents = [
257 |     ('index', 'topmodelpy',
258 |      u'topmodelpy Documentation',
259 |      u'Jeremiah Lant',
260 |      'topmodelpy',
261 |      'One line description of project.',
262 |      'Miscellaneous'),
263 | ]
264 | 
265 | # Documents to append as an appendix to all manuals.
266 | #texinfo_appendices = []
267 | 
268 | # If false, no module index is generated.
269 | #texinfo_domain_indices = True
270 | 
271 | # How to display URL addresses: 'footnote', 'no', or 'inline'.
272 | #texinfo_show_urls = 'footnote'
273 | 
274 | # If true, do not generate a @detailmenu in the "Top" node's menu.
275 | #texinfo_no_detailmenu = False
276 | 


--------------------------------------------------------------------------------
/docs/contributing.rst:
--------------------------------------------------------------------------------
1 | .. include:: ../CONTRIBUTING.rst
2 | 


--------------------------------------------------------------------------------
/docs/index.rst:
--------------------------------------------------------------------------------
 1 | .. documentation master file, created by
 2 |    sphinx-quickstart
 3 |    You can adapt this file completely to your liking, but it should at least
 4 |    contain the root `toctree` directive.
 5 | 
 6 | Welcome to topmodelpy's documentation!
 7 | ===========================================================
 8 | 
 9 | topmodelpy is a command line interface for a rainfall-runoff model, 
10 | called Topmodel, that predicts the amount of water flow in rivers.
11 | 
12 | 
13 | Basics
14 | -------
15 | 
16 | .. toctree::
17 |    :maxdepth: 2
18 | 
19 |    readme
20 |    overview
21 |    installation
22 |    usage
23 |    tutorial
24 | 
25 | Code Documentation
26 | ------------------
27 | 
28 | .. toctree::
29 |    :maxdepth: 2
30 | 
31 |    code
32 | 
33 | Project Info
34 | ------------
35 | 
36 | .. toctree::
37 |    :maxdepth: 2
38 | 
39 |    contributing
40 |    authors
41 |    changelog
42 | 
43 | 
44 | 
45 | Index
46 | -----
47 | 
48 | * :ref:`genindex`
49 | * :ref:`modindex`
50 | * :ref:`search`
51 | 


--------------------------------------------------------------------------------
/docs/installation.rst:
--------------------------------------------------------------------------------
 1 | Installation
 2 | ============
 3 | 
 4 | To install topmodelpy from source:
 5 | 
 6 | 1. Check that you have Python_ installed::
 7 | 
 8 |     $ python --version
 9 | 
10 | If you do not have Python_ installed, please download the latest version from `Python's download page`_
11 | 
12 | 2. Download topmodelpy from the repository and extract to a directory of your choice.
13 | 
14 |    Or, if you have git_ installed you can clone the project::
15 | 
16 |     $ git clone <remote url to topmodelpy>
17 | 
18 | 3. Navigate to the project's root directory where the setup script called `setup.py` is located::
19 | 
20 |     $ cd topmodelpy/
21 | 
22 | | The `setup.py` is a Python file that contains information regarding the installation of a Python module/package, and 
23 | | usually specifies that the module/package has been packaged and distributed with the standard Python distribution package 
24 | | called Distutils_.
25 | 
26 | 4. Run `setup.py` with the `install` command::
27 | 
28 |     $ python setup.py install
29 | 
30 | topmodelpy will now be installed to the standard location for third-party Python modules on your computer platform.
31 | 
32 | For more information regarding installing third-party Python modules, please see `Installing Python Modules`_ 
33 | For a description of how installation works including where the module will be installed on your computer platform, please see `How Installation Works`_.
34 | 
35 | 
36 | .. _Python: https://www.python.org/
37 | .. _Python's download page: https://www.python.org/downloads/
38 | .. _git: https://git-scm.com/
39 | .. _Distutils: https://docs.python.org/3/library/distutils.html
40 | .. _Installing Python Modules: https://docs.python.org/3.5/install/
41 | .. _How Installation Works: https://docs.python.org/3.5/install/#how-installation-works
42 | 


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/docs/lant-to-wolock-conversion-table.rst:
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 1 | Table 1. Lookup table between variable names used in this code versus variable
 2 | names used in Wolock's Fortran code.
 3 | 
 4 | ==========================================     =====================     ================================================================     ============================   =======================
 5 | Lant Python Code                               Wolock Fortran Code       Definition                                                           Units                          Notes
 6 | ==========================================     =====================     ================================================================     ============================   =======================
 7 | timestep_daily_fraction                        DT                        Fraction of a daily timestep                                         fraction                                             
 8 | scaling_parameter                              SZM                       Scaling parameter based on soil properties                           millimeters                                             
 9 | saturated_hydraulic_conductivity               CONMEAN                   Saturated hydraulic conductivity of the C horizon of the soil        millimeters/day                                           
10 | macropore_fraction                             PMAC                      Fraction of precipitation bypassing the soil zone                    fraction                                             
11 | soil_depth_total                               ZTOT                      Total soil depth (zone AB + zone C)                                  meters                                                
12 | soil_depth_ab_horizon                          ZAB                       Depth of AB horizon                                                  meters                                               
13 | field_capacity_fraction                        THFC                      Field capacity of soil                                               fraction                                             
14 | latitude                                       XLAT                      Latitude                                                             degrees                                                
15 | basin_area_total                               ATOT                      Total watershed area                                                 square kilometers                                    
16 | impervious_area_fraction                       PIMP                      Fraction of impervious area                                          fraction                                               
17 | snowmelt_temperature_cutoff                    TCUT                      Temperature cutoff for snowpack accumulation and snowmelt            degrees Fahrenheit                                     
18 | snowmelt_rate_coeff                            SNOPROP                   Snowmelt parameter                                                   inches/degree Fahrenheit                              
19 | snowmelt_rate_with_rain_coeff                  RAINPRO                   Rain-induced snowmelt parameter                                      1/degree Fahrenheit                                    
20 | channel_length_max                             DMAX                      Maximum channel length                                               kilometers                                           
21 | channel_velocity_avg                           SUBV                      Channel velocity                                                     kilometers/day                                        
22 | channel_travel_time                            NTW                       Channel travel time                                                  days
23 | flow_initial                                   Q0                        Initial flow                                                         millimeters/day                                        
24 | twi_values                                     ST                        ln(a/tanB) values                                                    ln(meters)                                             
25 | twi_saturated_areas                            AC                        Saturated land-surface area in watershed                             fraction                                              
26 | twi_mean                                       TL                        Mean of ln(a/tanB) distribution                                      ln(meters)                                             
27 | num_twi_increments                             NAC                       Number of twi increments or bins                                     ---                                                     
28 | precip                                         PP,P,PPT                  Precipitation rate                                                   millimeters/day                                       
29 | pet                                            PET                       Potential evapotranspiration rate                                    millimeters/day                millimeters in Wolock     
30 | precip_available                               PPTPET                    Precipiation - Potential evapotranspiration                          millimeters/day
31 | num_timesteps                                  NSTEPS                    Number of timesteps; number of precipitation data values             ---
32 | flow_predicted                                 QPRED                     Total predicted flow                                                 millimeters/day
33 | soil_depth_roots                               ZROOT                     Root-zone depth                                                      meters
34 | soil_depth_c_horizon                           ZAB                       Depth of AB horizon                                                  meters
35 | vertical_drainage_flux_initial                 U0                        Initial vertical drainage flux                                       millimeters/day                CONMEAN*TSTEP in Wolock
36 | transmissivity_saturated_max                   TRANS                     Maximum saturated transmissivity                                     square millimeters/day
37 | flow_subsurface_max                            SZQ                       Maximum subsurface flow rate                                         millimeters/day
38 | root_zone_storage_max                          SRMAX                     Maximum root-zone storage                                            millimeters
39 | saturation_deficit_avg                         S                         Watershed average saturation deficit                                 millimeters 
40 | vertical_drainage_flux                         UZ                        Vertical drainage flux; upper soil to saturated subsurface           millimeters/day
41 | unsaturated_zone_storage                       SUZ                       Soil water available for drainage                                    millimeters
42 | root_zone_storage                              SRZ                       Root zone storage                                                    millimeters
43 | saturation_deficit_local                       SD                        Saturation deficit at location x                                     millimeters
44 | precip_for_evaporation                         EPC                       The negative of precip minus pet                                     millimeters/day                -PPTPET in Wolock
45 | precip_for_recharge                            PP                        The positive of precip minus pet                                     millimeters/day                PPTPET in Wolock
46 | precip_excesses                                EX                        Precip in excess of pet and field capacity storage                   millimeters                    array
47 | precip_excess                                  PPEX                      Precip in excess of pet and field capacity storage                   millimeters                    float
48 | flow_predicted_overland                        QOF                       Predicted overland flow                                              millimeters/day
49 | flow_predicted_vertical_drainage_flux          QUZ                       Predicted vertical drainage flux                                     millimeters/day                units? (UZ*AC(IA))
50 | flow_predicted_subsurface                      QB                        Predicted subsurface flow                                            millimeters/day
51 | flow_predicted_impervious_area                 --                        Predicted impervious area flow                                       millimeters/day                in Lant
52 | flow_predicted_total                           QPRED                     Total predicted flow                                                 millimeters/day            
53 | flow_predicted_stream                          QQ                        Flow delivered to stream channel                                     millimeters/day
54 | ==========================================     =====================     ================================================================     ============================   =======================
55 | 


--------------------------------------------------------------------------------
/docs/make.bat:
--------------------------------------------------------------------------------
  1 | @ECHO OFF
  2 | 
  3 | REM Command file for Sphinx documentation
  4 | 
  5 | if "%SPHINXBUILD%" == "" (
  6 | 	set SPHINXBUILD=sphinx-build
  7 | )
  8 | set BUILDDIR=_build
  9 | set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% .
 10 | set I18NSPHINXOPTS=%SPHINXOPTS% .
 11 | if NOT "%PAPER%" == "" (
 12 | 	set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS%
 13 | 	set I18NSPHINXOPTS=-D latex_paper_size=%PAPER% %I18NSPHINXOPTS%
 14 | )
 15 | 
 16 | if "%1" == "" goto help
 17 | 
 18 | if "%1" == "help" (
 19 | 	:help
 20 | 	echo.Please use `make ^<target^>` where ^<target^> is one of
 21 | 	echo.  html       to make standalone HTML files
 22 | 	echo.  dirhtml    to make HTML files named index.html in directories
 23 | 	echo.  singlehtml to make a single large HTML file
 24 | 	echo.  pickle     to make pickle files
 25 | 	echo.  json       to make JSON files
 26 | 	echo.  htmlhelp   to make HTML files and a HTML help project
 27 | 	echo.  qthelp     to make HTML files and a qthelp project
 28 | 	echo.  devhelp    to make HTML files and a Devhelp project
 29 | 	echo.  epub       to make an epub
 30 | 	echo.  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter
 31 | 	echo.  text       to make text files
 32 | 	echo.  man        to make manual pages
 33 | 	echo.  texinfo    to make Texinfo files
 34 | 	echo.  gettext    to make PO message catalogs
 35 | 	echo.  changes    to make an overview over all changed/added/deprecated items
 36 | 	echo.  xml        to make Docutils-native XML files
 37 | 	echo.  pseudoxml  to make pseudoxml-XML files for display purposes
 38 | 	echo.  linkcheck  to check all external links for integrity
 39 | 	echo.  doctest    to run all doctests embedded in the documentation if enabled
 40 | 	echo.  coverage   to run coverage check of the documentation if enabled
 41 | 	goto end
 42 | )
 43 | 
 44 | if "%1" == "clean" (
 45 | 	for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i
 46 | 	del /q /s %BUILDDIR%\*
 47 | 	goto end
 48 | )
 49 | 
 50 | 
 51 | REM Check if sphinx-build is available and fallback to Python version if any
 52 | %SPHINXBUILD% 2> nul
 53 | if errorlevel 9009 goto sphinx_python
 54 | goto sphinx_ok
 55 | 
 56 | :sphinx_python
 57 | 
 58 | set SPHINXBUILD=python -m sphinx.__init__
 59 | %SPHINXBUILD% 2> nul
 60 | if errorlevel 9009 (
 61 | 	echo.
 62 | 	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
 63 | 	echo.installed, then set the SPHINXBUILD environment variable to point
 64 | 	echo.to the full path of the 'sphinx-build' executable. Alternatively you
 65 | 	echo.may add the Sphinx directory to PATH.
 66 | 	echo.
 67 | 	echo.If you don't have Sphinx installed, grab it from
 68 | 	echo.http://sphinx-doc.org/
 69 | 	exit /b 1
 70 | )
 71 | 
 72 | :sphinx_ok
 73 | 
 74 | 
 75 | if "%1" == "html" (
 76 | 	%SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html
 77 | 	if errorlevel 1 exit /b 1
 78 | 	echo.
 79 | 	echo.Build finished. The HTML pages are in %BUILDDIR%/html.
 80 | 	goto end
 81 | )
 82 | 
 83 | if "%1" == "dirhtml" (
 84 | 	%SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml
 85 | 	if errorlevel 1 exit /b 1
 86 | 	echo.
 87 | 	echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml.
 88 | 	goto end
 89 | )
 90 | 
 91 | if "%1" == "singlehtml" (
 92 | 	%SPHINXBUILD% -b singlehtml %ALLSPHINXOPTS% %BUILDDIR%/singlehtml
 93 | 	if errorlevel 1 exit /b 1
 94 | 	echo.
 95 | 	echo.Build finished. The HTML pages are in %BUILDDIR%/singlehtml.
 96 | 	goto end
 97 | )
 98 | 
 99 | if "%1" == "pickle" (
100 | 	%SPHINXBUILD% -b pickle %ALLSPHINXOPTS% %BUILDDIR%/pickle
101 | 	if errorlevel 1 exit /b 1
102 | 	echo.
103 | 	echo.Build finished; now you can process the pickle files.
104 | 	goto end
105 | )
106 | 
107 | if "%1" == "json" (
108 | 	%SPHINXBUILD% -b json %ALLSPHINXOPTS% %BUILDDIR%/json
109 | 	if errorlevel 1 exit /b 1
110 | 	echo.
111 | 	echo.Build finished; now you can process the JSON files.
112 | 	goto end
113 | )
114 | 
115 | if "%1" == "htmlhelp" (
116 | 	%SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% %BUILDDIR%/htmlhelp
117 | 	if errorlevel 1 exit /b 1
118 | 	echo.
119 | 	echo.Build finished; now you can run HTML Help Workshop with the ^
120 | .hhp project file in %BUILDDIR%/htmlhelp.
121 | 	goto end
122 | )
123 | 
124 | if "%1" == "qthelp" (
125 | 	%SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% %BUILDDIR%/qthelp
126 | 	if errorlevel 1 exit /b 1
127 | 	echo.
128 | 	echo.Build finished; now you can run "qcollectiongenerator" with the ^
129 | .qhcp project file in %BUILDDIR%/qthelp, like this:
130 | 	echo.^> qcollectiongenerator %BUILDDIR%\qthelp\nwispy.qhcp
131 | 	echo.To view the help file:
132 | 	echo.^> assistant -collectionFile %BUILDDIR%\qthelp\nwispy.ghc
133 | 	goto end
134 | )
135 | 
136 | if "%1" == "devhelp" (
137 | 	%SPHINXBUILD% -b devhelp %ALLSPHINXOPTS% %BUILDDIR%/devhelp
138 | 	if errorlevel 1 exit /b 1
139 | 	echo.
140 | 	echo.Build finished.
141 | 	goto end
142 | )
143 | 
144 | if "%1" == "epub" (
145 | 	%SPHINXBUILD% -b epub %ALLSPHINXOPTS% %BUILDDIR%/epub
146 | 	if errorlevel 1 exit /b 1
147 | 	echo.
148 | 	echo.Build finished. The epub file is in %BUILDDIR%/epub.
149 | 	goto end
150 | )
151 | 
152 | if "%1" == "latex" (
153 | 	%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
154 | 	if errorlevel 1 exit /b 1
155 | 	echo.
156 | 	echo.Build finished; the LaTeX files are in %BUILDDIR%/latex.
157 | 	goto end
158 | )
159 | 
160 | if "%1" == "latexpdf" (
161 | 	%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
162 | 	cd %BUILDDIR%/latex
163 | 	make all-pdf
164 | 	cd %~dp0
165 | 	echo.
166 | 	echo.Build finished; the PDF files are in %BUILDDIR%/latex.
167 | 	goto end
168 | )
169 | 
170 | if "%1" == "latexpdfja" (
171 | 	%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
172 | 	cd %BUILDDIR%/latex
173 | 	make all-pdf-ja
174 | 	cd %~dp0
175 | 	echo.
176 | 	echo.Build finished; the PDF files are in %BUILDDIR%/latex.
177 | 	goto end
178 | )
179 | 
180 | if "%1" == "text" (
181 | 	%SPHINXBUILD% -b text %ALLSPHINXOPTS% %BUILDDIR%/text
182 | 	if errorlevel 1 exit /b 1
183 | 	echo.
184 | 	echo.Build finished. The text files are in %BUILDDIR%/text.
185 | 	goto end
186 | )
187 | 
188 | if "%1" == "man" (
189 | 	%SPHINXBUILD% -b man %ALLSPHINXOPTS% %BUILDDIR%/man
190 | 	if errorlevel 1 exit /b 1
191 | 	echo.
192 | 	echo.Build finished. The manual pages are in %BUILDDIR%/man.
193 | 	goto end
194 | )
195 | 
196 | if "%1" == "texinfo" (
197 | 	%SPHINXBUILD% -b texinfo %ALLSPHINXOPTS% %BUILDDIR%/texinfo
198 | 	if errorlevel 1 exit /b 1
199 | 	echo.
200 | 	echo.Build finished. The Texinfo files are in %BUILDDIR%/texinfo.
201 | 	goto end
202 | )
203 | 
204 | if "%1" == "gettext" (
205 | 	%SPHINXBUILD% -b gettext %I18NSPHINXOPTS% %BUILDDIR%/locale
206 | 	if errorlevel 1 exit /b 1
207 | 	echo.
208 | 	echo.Build finished. The message catalogs are in %BUILDDIR%/locale.
209 | 	goto end
210 | )
211 | 
212 | if "%1" == "changes" (
213 | 	%SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes
214 | 	if errorlevel 1 exit /b 1
215 | 	echo.
216 | 	echo.The overview file is in %BUILDDIR%/changes.
217 | 	goto end
218 | )
219 | 
220 | if "%1" == "linkcheck" (
221 | 	%SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% %BUILDDIR%/linkcheck
222 | 	if errorlevel 1 exit /b 1
223 | 	echo.
224 | 	echo.Link check complete; look for any errors in the above output ^
225 | or in %BUILDDIR%/linkcheck/output.txt.
226 | 	goto end
227 | )
228 | 
229 | if "%1" == "doctest" (
230 | 	%SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest
231 | 	if errorlevel 1 exit /b 1
232 | 	echo.
233 | 	echo.Testing of doctests in the sources finished, look at the ^
234 | results in %BUILDDIR%/doctest/output.txt.
235 | 	goto end
236 | )
237 | 
238 | if "%1" == "coverage" (
239 | 	%SPHINXBUILD% -b coverage %ALLSPHINXOPTS% %BUILDDIR%/coverage
240 | 	if errorlevel 1 exit /b 1
241 | 	echo.
242 | 	echo.Testing of coverage in the sources finished, look at the ^
243 | results in %BUILDDIR%/coverage/python.txt.
244 | 	goto end
245 | )
246 | 
247 | if "%1" == "xml" (
248 | 	%SPHINXBUILD% -b xml %ALLSPHINXOPTS% %BUILDDIR%/xml
249 | 	if errorlevel 1 exit /b 1
250 | 	echo.
251 | 	echo.Build finished. The XML files are in %BUILDDIR%/xml.
252 | 	goto end
253 | )
254 | 
255 | if "%1" == "pseudoxml" (
256 | 	%SPHINXBUILD% -b pseudoxml %ALLSPHINXOPTS% %BUILDDIR%/pseudoxml
257 | 	if errorlevel 1 exit /b 1
258 | 	echo.
259 | 	echo.Build finished. The pseudo-XML files are in %BUILDDIR%/pseudoxml.
260 | 	goto end
261 | )
262 | 
263 | :end
264 | 


--------------------------------------------------------------------------------
/docs/overview.rst:
--------------------------------------------------------------------------------
1 | Overview
2 | ========
3 | 
4 | Add an overview of the project.
5 | 


--------------------------------------------------------------------------------
/docs/readme.rst:
--------------------------------------------------------------------------------
1 | .. include:: ../README.rst
2 | 


--------------------------------------------------------------------------------
/docs/tutorial.rst:
--------------------------------------------------------------------------------
1 | Tutorial
2 | ========
3 | 
4 | Add a tutorial.
5 | 


--------------------------------------------------------------------------------
/docs/usage.rst:
--------------------------------------------------------------------------------
 1 | Usage
 2 | =====
 3 | 
 4 | Add details on how to use the project, i.e.
 5 | 
 6 | To use topmodelpy from the command line::
 7 | 
 8 |     $ topmodelpy --help
 9 | 
10 | or
11 | 
12 | To use topmodelpy in a project::
13 | 
14 |     import topmodelpy
15 | 


--------------------------------------------------------------------------------
/requirements.txt:
--------------------------------------------------------------------------------
 1 | atomicwrites==1.3.0
 2 | attrs==19.1.0
 3 | Click==7.0
 4 | cycler==0.10.0
 5 | entrypoints==0.3
 6 | flake8==3.7.7
 7 | Jinja2==2.10.1
 8 | kiwisolver==1.0.1
 9 | MarkupSafe==1.1.1
10 | matplotlib==3.0.3
11 | mccabe==0.6.1
12 | more-itertools==6.0.0
13 | mpld3==0.3
14 | numpy==1.16.2
15 | pandas==0.24.1
16 | pkg-resources==0.0.0
17 | pluggy==0.9.0
18 | py==1.8.0
19 | pycodestyle==2.5.0
20 | pyflakes==2.1.1
21 | pyparsing==2.3.1
22 | pytest==4.3.0
23 | python-dateutil==2.8.0
24 | pytz==2018.9
25 | scipy==1.2.1
26 | six==1.12.0
27 | -e git+git@github.com:jlant/topmodelpy.git@067cdea4d6bc272d24e224b4c12d36cef915899f#egg=topmodelpy
28 | 


--------------------------------------------------------------------------------
/setup.py:
--------------------------------------------------------------------------------
 1 | #!/usr/bin/env python
 2 | # -*- coding: utf-8 -*-
 3 | 
 4 | try:
 5 |     from setuptools import setup
 6 | except ImportError:
 7 |     from distutils.core import setup
 8 | 
 9 | 
10 | with open("README.rst") as readme_file:
11 |     readme = readme_file.read()
12 | 
13 | with open("CHANGELOG.rst") as changelog_file:
14 |     changelog = changelog_file.read()
15 | 
16 | with open("LICENSE") as license_file:
17 |     license = license_file.read()
18 | 
19 | 
20 | requirements = [
21 |     "click",
22 |     "numpy",
23 |     "pandas",
24 | ]
25 | 
26 | test_requirements = [
27 |     "pytest",
28 | ]
29 | 
30 | 
31 | setup(
32 |     name="topmodelpy",
33 |     version="0.1",
34 |     description=("A rainfall-runoff model that predicts the amount "
35 |                  "of water flow in rivers."),
36 |     long_description=readme + "\n\n" + changelog,
37 |     author="Jeremiah Lant",
38 |     author_email="jlant@usgs.gov",
39 |     url="",
40 |     packages=[
41 |         "topmodelpy",
42 |     ],
43 |     package_dir={"topmodelpy": "topmodelpy"},
44 |     entry_points={"console_scripts": ["topmodelpy = topmodelpy.cli:main"]},
45 |     include_package_data=True,
46 |     install_requires=requirements,
47 |     license=license,
48 |     zip_safe=False,
49 |     keywords="topmodelpy",
50 |     classifiers=[
51 |         "Development Status :: 2 - Pre-Alpha",
52 |         "Intended Audience :: Developers",
53 |         "License :: CC0 1.0 Universal (CC0 1.0) Public Domain Dedication",
54 |         "Natural Language :: English",
55 |         "Programming Language :: Python :: 3",
56 |         "Programming Language :: Python :: 3.3",
57 |         "Programming Language :: Python :: 3.4",
58 |         "Programming Language :: Python :: 3.5",
59 |         "Programming Language :: Python :: 3.6",
60 |     ],
61 |     test_suite="tests",
62 |     tests_require=test_requirements
63 | )
64 | 


--------------------------------------------------------------------------------
/tests/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 | 


--------------------------------------------------------------------------------
/tests/conftest.py:
--------------------------------------------------------------------------------
  1 | """Test configurations and fixtures."""
  2 | 
  3 | from configparser import ConfigParser, ExtendedInterpolation
  4 | import os
  5 | import numpy as np
  6 | import pandas as pd
  7 | import pytest
  8 | from pathlib import Path
  9 | 
 10 | 
 11 | @pytest.fixture(scope="module")
 12 | def timeseries_wolock():
 13 |     """Return a Pandas dataframe of timeseries test data
 14 |     from Dave Wolock's Topmodel version. Test data contains
 15 |     input values along with model output values in a single file.
 16 |     """
 17 | 
 18 |     fname = os.path.join(os.path.dirname(__file__),
 19 |                          "testdata/timeseries_wolock.csv")
 20 |     data = pd.read_csv(fname,
 21 |                        names=["date",
 22 |                               "temperature",
 23 |                               "precipitation",
 24 |                               "pet",
 25 |                               "precip_minus_pet",
 26 |                               "flow_observed",
 27 |                               "flow_predicted"],
 28 |                        header=0)  # skip header
 29 | 
 30 |     return data
 31 | 
 32 | 
 33 | @pytest.fixture(scope="module")
 34 | def twi_wolock():
 35 |     """Return a Pandas dataframe of twi test data
 36 |     from Dave Wolock's Topmodel version"""
 37 | 
 38 |     fname = os.path.join(os.path.dirname(__file__),
 39 |                          "testdata/twi_wolock.csv")
 40 |     data = pd.read_csv(fname,
 41 |                        names=["bin",
 42 |                               "twi",
 43 |                               "proportion",
 44 |                               "cells"],
 45 |                        header=0)  # skip header
 46 | 
 47 |     return data
 48 | 
 49 | 
 50 | @pytest.fixture(scope="module")
 51 | def twi_weighted_mean_wolock():
 52 |     """Return the weighted mean of the twi test data
 53 |     from Dave Wolock's Topmodel version"""
 54 | 
 55 |     fname = os.path.join(os.path.dirname(__file__),
 56 |                          "testdata/twi_wolock.csv")
 57 |     data = pd.read_csv(fname,
 58 |                        names=["bin",
 59 |                               "twi",
 60 |                               "proportion",
 61 |                               "cells"],
 62 |                        header=0)  # skip header
 63 | 
 64 |     twi_weighted_mean = (
 65 |         np.sum(data["twi"].values * data["proportion"].values)
 66 |         / np.sum(data["proportion"].values)
 67 |     )
 68 | 
 69 |     return twi_weighted_mean
 70 | 
 71 | 
 72 | @pytest.fixture(scope="module")
 73 | def parameters_wolock():
 74 |     """Return a dictionary of parameter test data
 75 |     from Dave Wolock's Topmodel version"""
 76 | 
 77 |     data = {
 78 |         "scaling_parameter": 10,
 79 |         "saturated_hydraulic_conductivity": 150,
 80 |         "macropore_fraction": 0.2,
 81 |         "soil_depth_total": 1,
 82 |         "soil_depth_ab_horizon": 0.5,
 83 |         "field_capacity_fraction": 0.2,
 84 |         "latitude": 40.5,
 85 |         "basin_area_total": 3.07,
 86 |         "impervious_area_fraction": 0.3,
 87 |         "snowmelt_temperature_cutoff": 32,
 88 |         "snowmelt_rate_coeff": 0.06,
 89 |         "snowmelt_rate_coeff_with_rain": 0.007,
 90 |         "channel_length_max": 1.98,
 91 |         "channel_velocity_avg": 10,
 92 |         "flow_initial": 1
 93 |     }
 94 | 
 95 |     return data
 96 | 
 97 | 
 98 | @pytest.fixture(scope="module")
 99 | def modelconfig_obj():
100 |     config = ConfigParser(interpolation=ExtendedInterpolation())
101 |     config["Inputs"] = {
102 |         "input_dir": Path.cwd(),
103 |         "parameters_file": "${Inputs:input_dir}/parameters.csv",
104 |         "timeseries_file": "${Inputs:input_dir}/timeseries.csv",
105 |         "twi_file": "${Inputs:input_dir}/twi.csv",
106 |     }
107 | 
108 |     config["Outputs"] = {
109 |         "output_dir": Path.cwd(),
110 |     }
111 | 
112 |     config["Options"] = {
113 |         "option_pet": "hamon",
114 |         "option_snowmelt": "yes",
115 |     }
116 | 
117 |     return config
118 | 
119 | 
120 | @pytest.fixture(scope="module")
121 | def modelconfig_obj_invalid_sections():
122 |     return ConfigParser(interpolation=ExtendedInterpolation())
123 | 
124 | 
125 | @pytest.fixture(scope="module")
126 | def modelconfig_obj_invalid_filepath():
127 |     config = ConfigParser(interpolation=ExtendedInterpolation())
128 |     config["Inputs"] = {
129 |         "input_dir": Path.cwd(),
130 |         "parameters_file": "some/bad/filepath/",
131 |         "timeseries_file": "${Inputs:input_dir}/timeseries.csv",
132 |         "twi_file": "${Inputs:input_dir}/twi.csv",
133 |     }
134 | 
135 |     config["Outputs"] = {
136 |         "output_dir": "",
137 |     }
138 | 
139 |     config["Options"] = {
140 |         "option_pet": "hamon",
141 |         "option_snowmelt": "yes",
142 |     }
143 | 
144 |     return config
145 | 
146 | 
147 | @pytest.fixture(scope="module")
148 | def modelconfig_obj_invalid_options():
149 |     config = ConfigParser(interpolation=ExtendedInterpolation())
150 |     config["Inputs"] = {
151 |         "input_dir": Path.cwd(),
152 |         "parameters_file": "${Inputs:input_dir}/parameters.csv",
153 |         "timeseries_file": "${Inputs:input_dir}/timeseries.csv",
154 |         "twi_file": "${Inputs:input_dir}/twi.csv",
155 |     }
156 | 
157 |     config["Outputs"] = {
158 |         "output_dir": Path.cwd(),
159 |     }
160 | 
161 |     config["Options"] = {
162 |         "option_pet": "yes",
163 |         "option_snowmelt": "hello",
164 |     }
165 | 
166 |     return config
167 | 
168 | 
169 | @pytest.fixture(scope="module")
170 | def parameters_file():
171 |     return ("""name,value,units,description
172 | scaling_parameter,10,millimeters,a description
173 | saturated_hydraulic_conductivity,150,millimeters/day,a description
174 | macropore_fraction,0.2,fraction,a description
175 | soil_depth_total,1,meters,a description
176 | soil_depth_ab_horizon,0.7,meters,a description
177 | field_capacity_fraction,0.2,fraction,a description
178 | latitude,40.5,degrees,a description
179 | basin_area_total,3.5,square kilometers,a description
180 | impervious_area_fraction,0.3,fraction,a description
181 | snowmelt_temperature_cutoff,-32,degrees fahrenheit,a description
182 | snowmelt_rate_coeff,0.06,1/degrees fahrenheit,a description
183 | snowmelt_rate_coeff_with_rain,7E-3,inches per degree fahrenheit,a description
184 | channel_length_max,5,kilometers,a description
185 | channel_velocity_avg,19,kilometers/day,a description
186 | flow_initial,1,millimeters/day,a description
187 | """)
188 | 
189 | 
190 | @pytest.fixture(scope="module")
191 | def parameters_file_invalid_header():
192 |     return ("""names,val,unit,descr
193 | scaling_parameter,10,millimeters,a description
194 | saturated_hydraulic_conductivity,150,millimeters/day,a description
195 | macropore_fraction,0.2,fraction,a description
196 | soil_depth_total,1,meters,a description
197 | soil_depth_ab_horizon,0.7,meters,a description
198 | field_capacity_fraction,0.2,fraction,a description
199 | latitude,40.5,degrees,a description
200 | basin_area_total,3.5,square kilometers,a description
201 | impervious_area_fraction,0.3,fraction,a description
202 | snowmelt_temperature_cutoff,-32,degrees fahrenheit,a description
203 | snowmelt_rate_coeff,0.06,1/degrees fahrenheit,a description
204 | snowmelt_rate_coeff_with_rain,7E-3,inches per degree fahrenheit,a description
205 | channel_length_max,5,kilometers,a description
206 | channel_velocity_avg,19,kilometers/day,a description
207 | flow_initial,1,millimeters/day,a description
208 | """)
209 | 
210 | 
211 | @pytest.fixture(scope="module")
212 | def timeseries_file():
213 |     return ("""date,temperature (celsius),precipitation (mm/day),pet (mm/day),flow_observed (mm/day)
214 | 2019-01-01,1.0,2.0,3.0,4.0
215 | 2019-01-02,1.1,2.1,3.1,4.1
216 | 2019-01-03,1.2,2.2,3.2,4.2
217 | 2019-01-04,1.3,2.3,3.3,4.3
218 | 2019-01-05,1.4,2.4,3.4,4.4
219 | """)
220 | 
221 | 
222 | @pytest.fixture(scope="module")
223 | def timeseries_file_invalid_header():
224 |     return ("""date,temperature (fahrenheit),precipitation (mm/day),pet (mm/day),flow observed (mm/day)
225 | 2019-01-01,1.0,2.0,3.0,4.0
226 | 2019-01-02,1.1,2.1,3.1,4.1
227 | 2019-01-03,1.2,2.2,3.2,4.2
228 | 2019-01-04,1.3,2.3,3.3,4.3
229 | 2019-01-05,1.4,2.4,3.4,4.4
230 | """)
231 | 
232 | 
233 | @pytest.fixture(scope="module")
234 | def timeseries_file_missing_dates():
235 |     return ("""date,temperature (celsius),precipitation (mm/day),pet (mm/day),flow_observed (mm/day)
236 | 2019-01-01,1.0,2.0,3.0,4.0
237 | ,1.1,2.1,3.1,4.1
238 | 2019-01-03,1.2,2.2,3.2,4.2
239 | 2019-01-04,1.3,2.3,3.3,4.3
240 | ,1.4,2.4,3.4,4.4
241 | """)
242 | 
243 | 
244 | @pytest.fixture(scope="module")
245 | def timeseries_file_missing_values():
246 |     return ("""date,temperature (celsius),precipitation (mm/day),pet (mm/day),flow_observed (mm/day)
247 | 2019-01-01,1.0,2.0,3.0,
248 | 2019-01-02,1.1,2.1,3.1,4.1
249 | 2019-01-03,,2.2,3.2,4.2
250 | 2019-01-04,1.3,2.3,3.3,4.3
251 | 2019-01-05,1.4,2.4,3.4,4.4
252 | """)
253 | 
254 | 
255 | @pytest.fixture(scope="module")
256 | def timeseries_file_invalid_timestep():
257 |     return ("""date,temperature (celsius),precipitation (mm/day),pet (mm/day),flow_observed (mm/day)
258 | 2019-01-01,1.0,2.0,3.0,4.0
259 | 2019-02-01,1.1,2.1,3.1,4.1
260 | 2019-03-01,1,2.2,3.2,4.2
261 | 2019-04-01,1.3,2.3,3.3,4.3
262 | 2019-05-01,1.4,2.4,3.4,4.4
263 | """)
264 | 
265 | 
266 | @pytest.fixture(scope="module")
267 | def twi_file():
268 |     return ("""bin,twi,proportion,cells
269 | 1,0.02,0.10,10
270 | 2,0.03,0.15,15
271 | 3,0.04,0.25,25
272 | 4,0.05,0.30,30
273 | 5,0.06,0.20,20
274 | """)
275 | 
276 | 
277 | @pytest.fixture(scope="module")
278 | def twi_file_invalid_header():
279 |     return ("""bin,value,proportion,cells
280 | 1,0.02,0.10,10
281 | 2,0.03,0.15,15
282 | 3,0.04,0.25,25
283 | 4,0.05,0.30,30
284 | 5,0.06,0.20,20
285 | """)
286 | 
287 | 
288 | @pytest.fixture(scope="module")
289 | def twi_file_missing_values():
290 |     return ("""bin,twi,proportion,cells
291 | 1,0.02,0.10,
292 | 2,0.03,0.15,15
293 | 3,0.04,0.25,25
294 | 4,0.05,0.30,30
295 | 5,,0.20,20
296 | """)
297 | 
298 | 
299 | @pytest.fixture(scope="module")
300 | def twi_file_invalid_proportion():
301 |     return ("""bin,twi,proportion,cells
302 | 1,0.02,0.10,10
303 | 2,0.03,0.15,15
304 | 3,0.04,0.25,25
305 | 4,0.05,0.30,30
306 | 5,0.06,0.22,20
307 | """)
308 | 
309 | 
310 | @pytest.fixture(scope="module")
311 | def observed_data():
312 |     return np.array([55.7, 62.0, 65.5, 64.7, 61.1])
313 | 
314 | 
315 | @pytest.fixture(scope="module")
316 | def modeled_data():
317 |     return np.array([55.5, 62.1, 65.3, 64.4, 61.2])
318 | 


--------------------------------------------------------------------------------
/tests/test_hydrocalcs.py:
--------------------------------------------------------------------------------
 1 | """Tests for hydrocals module."""
 2 | 
 3 | from datetime import datetime
 4 | import numpy as np
 5 | 
 6 | from waterpy import hydrocalcs
 7 | 
 8 | 
 9 | def test_pet(parameters_wolock,
10 |              timeseries_wolock):
11 | 
12 |     dates = np.array(timeseries_wolock["date"].values,
13 |                      dtype=np.datetime64).astype(datetime)
14 |     actual = hydrocalcs.pet(
15 |         dates=dates,
16 |         temperatures=timeseries_wolock["temperature"].values,
17 |         latitude=parameters_wolock["latitude"],
18 |         method="hamon"
19 |     )
20 | 
21 |     # The absolute tolerance is set because the calculation done in waterpy
22 |     # is a little different than the calculation done in Wolock's version.
23 |     np.testing.assert_allclose(actual,
24 |                                timeseries_wolock["pet"].values,
25 |                                atol=1.5)
26 | 
27 | 
28 | def test_absolute_error(observed_data, modeled_data):
29 | 
30 |     expected = np.array([0.2, -0.1, 0.2, 0.3, -0.1])
31 |     actual = hydrocalcs.absolute_error(observed_data, modeled_data)
32 | 
33 |     np.testing.assert_allclose(actual, expected)
34 | 
35 | 
36 | def test_mean_squared_error(observed_data, modeled_data):
37 | 
38 |     expected = 0.038
39 |     actual = hydrocalcs.mean_squared_error(observed_data, modeled_data)
40 | 
41 |     np.testing.assert_allclose(actual, expected)
42 | 
43 | 
44 | def test_relative_error(observed_data, modeled_data):
45 | 
46 |     expected = np.array([0.00359066, -0.0016129, 0.00305344, 0.00463679, -0.00163666])
47 |     actual = hydrocalcs.relative_error(observed_data, modeled_data)
48 | 
49 |     np.testing.assert_allclose(actual, expected, atol=1e-8)
50 | 
51 | 
52 | def test_percent_error(observed_data, modeled_data):
53 | 
54 |     expected = np.array([0.359066, -0.16129, 0.305344, 0.463679, -0.163666])
55 |     actual = hydrocalcs.percent_error(observed_data, modeled_data)
56 | 
57 |     np.testing.assert_allclose(actual, expected, atol=1e-6)
58 | 
59 | 
60 | def test_percent_difference(observed_data, modeled_data):
61 | 
62 |     expected = np.array([0.35971223, -0.16116035, 0.3058104, 0.464756, -0.1635323])
63 |     actual = hydrocalcs.percent_difference(observed_data, modeled_data)
64 | 
65 |     np.testing.assert_allclose(actual, expected, atol=1e-6)
66 | 
67 | 
68 | def test_r_squared(observed_data, modeled_data):
69 | 
70 |     expected = 0.99768587638100936
71 |     actual = hydrocalcs.r_squared(observed_data, modeled_data)
72 | 
73 |     np.testing.assert_allclose(actual, expected)
74 | 
75 | 
76 | def test_nash_sutcliffe(observed_data, modeled_data):
77 | 
78 |     expected = 0.99682486631016043
79 |     actual = hydrocalcs.nash_sutcliffe(observed_data, modeled_data)
80 | 
81 |     np.testing.assert_allclose(actual, expected)
82 | 


--------------------------------------------------------------------------------
/tests/test_modelconfigfile.py:
--------------------------------------------------------------------------------
 1 | """Tests for modelconfigfile module."""
 2 | 
 3 | import pytest
 4 | from pathlib import Path, PurePath
 5 | 
 6 | from waterpy.exceptions import (ModelConfigFileErrorInvalidSection,
 7 |                                    ModelConfigFileErrorInvalidFilePath,
 8 |                                    ModelConfigFileErrorInvalidOption)
 9 | from waterpy import modelconfigfile
10 | 
11 | 
12 | def test_modelconfig_obj(modelconfig_obj):
13 |     expected_sections = ["Inputs", "Outputs", "Options"]
14 |     expected_input_dir = Path.cwd()
15 |     expected_parameters_file = PurePath(expected_input_dir).joinpath(
16 |                                                     "parameters.csv")
17 |     expected_timeseries_file = PurePath(expected_input_dir).joinpath(
18 |                                                     "timeseries.csv")
19 |     expected_twi_file = PurePath(expected_input_dir).joinpath(
20 |                                                     "twi.csv")
21 |     expected_output_dir = Path.cwd()
22 |     expected_option_pet = "hamon"
23 |     expected_option_snowmelt = True
24 | 
25 |     actual_sections = modelconfig_obj.sections()
26 |     actual_input_dir = modelconfig_obj["Inputs"]["input_dir"]
27 |     actual_parameters_file = modelconfig_obj["Inputs"]["parameters_file"]
28 |     actual_timeseries_file = modelconfig_obj["Inputs"]["timeseries_file"]
29 |     actual_twi_file = modelconfig_obj["Inputs"]["twi_file"]
30 |     actual_output_dir = modelconfig_obj["Outputs"]["output_dir"]
31 |     actual_option_pet = modelconfig_obj["Options"]["option_pet"]
32 |     actual_option_snowmelt = modelconfig_obj["Options"].getboolean("option_snowmelt")
33 | 
34 |     assert actual_sections == expected_sections
35 |     assert actual_input_dir == str(expected_input_dir)
36 |     assert actual_parameters_file == str(expected_parameters_file)
37 |     assert actual_timeseries_file == str(expected_timeseries_file)
38 |     assert actual_twi_file == str(expected_twi_file)
39 |     assert actual_output_dir == str(expected_output_dir)
40 |     assert actual_option_pet == expected_option_pet
41 |     assert actual_option_snowmelt == expected_option_snowmelt
42 | 
43 | 
44 | def test_modelconfig_obj_no_sections(modelconfig_obj_invalid_sections):
45 |     with pytest.raises(ModelConfigFileErrorInvalidSection) as err:
46 |         modelconfigfile.check_config_sections(modelconfig_obj_invalid_sections)
47 | 
48 |     assert "Invalid section" in str(err.value)
49 | 
50 | 
51 | def test_modelconfig_obj_invalid_filepath(modelconfig_obj_invalid_filepath):
52 |     with pytest.raises(ModelConfigFileErrorInvalidFilePath) as err:
53 |         modelconfigfile.check_config_filepaths(modelconfig_obj_invalid_filepath)
54 | 
55 |     assert "Invalid file path" in str(err.value)
56 | 
57 | 
58 | def test_modelconfig_obj_invalid_options(modelconfig_obj_invalid_options):
59 |     with pytest.raises(ModelConfigFileErrorInvalidOption) as err:
60 |         modelconfigfile.check_config_options(modelconfig_obj_invalid_options)
61 | 
62 |     assert "Invalid option" in str(err.value)
63 | 


--------------------------------------------------------------------------------
/tests/test_parametersfile.py:
--------------------------------------------------------------------------------
  1 | """Tests for parametersfile module."""
  2 | 
  3 | from io import StringIO
  4 | import pytest
  5 | 
  6 | from topmodelpy.exceptions import (ParametersFileErrorInvalidHeader,
  7 |                                    ParametersFileErrorInvalidScalingParameter,
  8 |                                    ParametersFileErrorInvalidLatitude,
  9 |                                    ParametersFileErrorInvalidSoilDepthTotal,
 10 |                                    ParametersFileErrorInvalidSoilDepthAB,
 11 |                                    ParametersFileErrorInvalidFieldCapacity,
 12 |                                    ParametersFileErrorInvalidMacropore,
 13 |                                    ParametersFileErrorInvalidImperviousArea,)
 14 | from topmodelpy import parametersfile
 15 | 
 16 | 
 17 | def test_parameters_file_read_in(parameters_file):
 18 |     expected = {
 19 |         "scaling_parameter": {
 20 |             "value": 10,
 21 |             "units": "millimeters",
 22 |             "description": "a description",
 23 |         },
 24 |     }
 25 |     filestream = StringIO(parameters_file)
 26 |     actual = parametersfile.read_in(filestream)
 27 | 
 28 |     assert isinstance(actual["scaling_parameter"]["value"], float)
 29 |     assert actual["scaling_parameter"]["value"] == (
 30 |            expected["scaling_parameter"]["value"])
 31 |     assert actual["scaling_parameter"]["units"] == (
 32 |            expected["scaling_parameter"]["units"])
 33 |     assert actual["scaling_parameter"]["description"] == (
 34 |            expected["scaling_parameter"]["description"])
 35 | 
 36 | 
 37 | def test_parameters_file_invalid_header(parameters_file_invalid_header):
 38 |     filestream = StringIO(parameters_file_invalid_header)
 39 | 
 40 |     with pytest.raises(ParametersFileErrorInvalidHeader) as err:
 41 |         parametersfile.read_in(filestream)
 42 | 
 43 |     assert "Invalid header" in str(err.value)
 44 | 
 45 | 
 46 | def test_parameters_file_invalid_scaling_parameter():
 47 |     invalid_value = 0
 48 |     with pytest.raises(ParametersFileErrorInvalidScalingParameter) as err:
 49 |         parametersfile.check_scaling_parameter(invalid_value)
 50 | 
 51 |     assert "Invalid scaling parameter" in str(err.value)
 52 | 
 53 | 
 54 | def test_parameters_file_invalid_latitude():
 55 |     invalid_value = -1
 56 |     with pytest.raises(ParametersFileErrorInvalidLatitude) as err:
 57 |         parametersfile.check_latitude(invalid_value)
 58 | 
 59 |     assert "Invalid latitude" in str(err.value)
 60 | 
 61 | 
 62 | def test_parameters_file_invalid_soil_depth_total():
 63 |     invalid_value = 0
 64 |     with pytest.raises(ParametersFileErrorInvalidSoilDepthTotal) as err:
 65 |         parametersfile.check_soil_depth_total(invalid_value)
 66 | 
 67 |     assert "Invalid soil depth total" in str(err.value)
 68 | 
 69 | 
 70 | def test_parameters_file_invalid_soil_depth_ab_horizon_lt_zero():
 71 |     invalid_value = 0
 72 |     soil_depth_total = 1
 73 |     with pytest.raises(ParametersFileErrorInvalidSoilDepthAB) as err:
 74 |         parametersfile.check_soil_depth_ab_horizon(invalid_value, soil_depth_total)
 75 | 
 76 |     assert "Invalid soil depth ab horizon" in str(err.value)
 77 | 
 78 | 
 79 | def test_parameters_file_invalid_soil_depth_ab_horizon_gt_soil_depth_total():
 80 |     invalid_value = 10
 81 |     soil_depth_total = 1
 82 |     with pytest.raises(ParametersFileErrorInvalidSoilDepthAB) as err:
 83 |         parametersfile.check_soil_depth_ab_horizon(invalid_value, soil_depth_total)
 84 | 
 85 |     assert "Invalid soil depth ab horizon" in str(err.value)
 86 | 
 87 | 
 88 | def test_parameters_file_invalid_field_capacity_fraction():
 89 |     invalid_value = 2
 90 |     with pytest.raises(ParametersFileErrorInvalidFieldCapacity) as err:
 91 |         parametersfile.check_field_capacity(invalid_value)
 92 | 
 93 |     assert "Invalid field capacity" in str(err.value)
 94 | 
 95 | 
 96 | def test_parameters_file_invalid_macropore_fraction():
 97 |     invalid_value = 2
 98 |     with pytest.raises(ParametersFileErrorInvalidMacropore) as err:
 99 |         parametersfile.check_macropore(invalid_value)
100 | 
101 |     assert "Invalid macropore" in str(err.value)
102 | 
103 | 
104 | def test_parameters_file_invalid_impervious_area_fraction():
105 |     invalid_value = 2
106 |     with pytest.raises(ParametersFileErrorInvalidImperviousArea) as err:
107 |         parametersfile.check_impervious_area(invalid_value)
108 | 
109 |     assert "Invalid impervious area" in str(err.value)
110 | 


--------------------------------------------------------------------------------
/tests/test_timeseriesfile.py:
--------------------------------------------------------------------------------
 1 | """Tests for timeseriesfile module."""
 2 | 
 3 | from datetime import datetime
 4 | from io import StringIO
 5 | import numpy as np
 6 | import pandas as pd
 7 | import pytest
 8 | 
 9 | from topmodelpy.exceptions import (TimeseriesFileErrorInvalidHeader,
10 |                                    TimeseriesFileErrorMissingValues,
11 |                                    TimeseriesFileErrorMissingDates,
12 |                                    TimeseriesFileErrorInvalidTimestep)
13 | from topmodelpy import timeseriesfile
14 | 
15 | 
16 | def test_timeseries_file_read_in(timeseries_file):
17 |     expected = pd.DataFrame({
18 |         "date": np.array([
19 |                     datetime(2017, 1, 1, 0, 0),
20 |                     datetime(2017, 1, 2, 0, 0),
21 |                     datetime(2017, 1, 3, 0, 0),
22 |                     datetime(2017, 1, 4, 0, 0),
23 |                     datetime(2017, 1, 5, 0, 0)]),
24 |         "temperature": np.array([1.0, 1.1, 1.2, 1.3, 1.4]),
25 |         "precipitation": np.array([2.0, 2.1, 2.2, 2.3, 2.4]),
26 |         "pet": np.array([3.0, 3.1, 3.2, 3.3, 3.4]),
27 |         "flow_observed": np.array([4.0, 4.1, 4.2, 4.3, 4.4]),
28 |     })
29 |     filestream = StringIO(timeseries_file)
30 |     actual = timeseriesfile.read_in(filestream)
31 | 
32 |     np.testing.assert_allclose(actual["precipitation"],
33 |                                expected["precipitation"])
34 |     np.testing.assert_allclose(actual["temperature"],
35 |                                expected["temperature"])
36 |     np.testing.assert_allclose(actual["pet"],
37 |                                expected["pet"])
38 |     np.testing.assert_allclose(actual["flow_observed"],
39 |                                expected["flow_observed"])
40 |     assert actual.dtypes.all() == "float64"
41 |     assert isinstance(actual.index, pd.DatetimeIndex)
42 |     assert (actual.index[1] - actual.index[0]).days == 1
43 | 
44 | 
45 | def test_timeseries_file_invalid_header(timeseries_file_invalid_header):
46 |     filestream = StringIO(timeseries_file_invalid_header)
47 | 
48 |     with pytest.raises(TimeseriesFileErrorInvalidHeader) as err:
49 |         timeseriesfile.read_in(filestream)
50 | 
51 |     assert "Invalid header" in str(err.value)
52 | 
53 | 
54 | def test_timeseries_file_missing_dates(timeseries_file_missing_dates):
55 |     filestream = StringIO(timeseries_file_missing_dates)
56 | 
57 |     with pytest.raises(TimeseriesFileErrorMissingDates) as err:
58 |         timeseriesfile.read_in(filestream)
59 | 
60 |     assert "Missing dates" in str(err.value)
61 | 
62 | 
63 | def test_timeseries_file_missing_values(timeseries_file_missing_values):
64 |     filestream = StringIO(timeseries_file_missing_values)
65 | 
66 |     with pytest.raises(TimeseriesFileErrorMissingValues) as err:
67 |         timeseriesfile.read_in(filestream)
68 | 
69 |     assert "Missing values" in str(err.value)
70 | 
71 | 
72 | def test_timeseries_file_invalid_timestep(timeseries_file_invalid_timestep):
73 |     filestream = StringIO(timeseries_file_invalid_timestep)
74 | 
75 |     with pytest.raises(TimeseriesFileErrorInvalidTimestep) as err:
76 |         timeseriesfile.read_in(filestream)
77 | 
78 |     print(err.value)
79 |     assert "Invalid timestep" in str(err.value)
80 | 


--------------------------------------------------------------------------------
/tests/test_topmodel.py:
--------------------------------------------------------------------------------
  1 | """Test Topmodel class."""
  2 | 
  3 | import numpy as np
  4 | 
  5 | from topmodelpy.topmodel import Topmodel
  6 | 
  7 | 
  8 | def test_topmodel_init(parameters_wolock,
  9 |                        timeseries_wolock,
 10 |                        twi_wolock,
 11 |                        twi_weighted_mean_wolock):
 12 |     """Test Topmodel class initialization"""
 13 | 
 14 |     # Initialize Topmodel
 15 |     topmodel = Topmodel(
 16 |         scaling_parameter=parameters_wolock["scaling_parameter"],
 17 |         saturated_hydraulic_conductivity=(
 18 |             parameters_wolock["saturated_hydraulic_conductivity"]
 19 |         ),
 20 |         macropore_fraction=parameters_wolock["macropore_fraction"],
 21 |         soil_depth_total=parameters_wolock["soil_depth_total"],
 22 |         soil_depth_ab_horizon=parameters_wolock["soil_depth_ab_horizon"],
 23 |         field_capacity_fraction=parameters_wolock["field_capacity_fraction"],
 24 |         latitude=parameters_wolock["latitude"],
 25 |         basin_area_total=parameters_wolock["basin_area_total"],
 26 |         impervious_area_fraction=parameters_wolock["impervious_area_fraction"],
 27 |         twi_values=twi_wolock["twi"].values,
 28 |         twi_saturated_areas=twi_wolock["proportion"].values,
 29 |         twi_mean=twi_weighted_mean_wolock,
 30 |         precip_available=timeseries_wolock["precip_minus_pet"].values,
 31 |         flow_initial=1,
 32 |         soil_depth_roots=1,
 33 |         timestep_daily_fraction=1
 34 |     )
 35 | 
 36 |     assert(topmodel.scaling_parameter ==
 37 |            parameters_wolock["scaling_parameter"])
 38 |     assert(topmodel.saturated_hydraulic_conductivity ==
 39 |            parameters_wolock["saturated_hydraulic_conductivity"])
 40 |     assert(topmodel.macropore_fraction ==
 41 |            parameters_wolock["macropore_fraction"])
 42 |     assert(topmodel.soil_depth_total ==
 43 |            parameters_wolock["soil_depth_total"])
 44 |     assert(topmodel.soil_depth_ab_horizon ==
 45 |            parameters_wolock["soil_depth_ab_horizon"])
 46 |     assert(topmodel.field_capacity_fraction ==
 47 |            parameters_wolock["field_capacity_fraction"])
 48 |     assert(topmodel.latitude ==
 49 |            parameters_wolock["latitude"])
 50 |     assert(topmodel.basin_area_total ==
 51 |            parameters_wolock["basin_area_total"])
 52 |     assert(topmodel.impervious_area_fraction ==
 53 |            parameters_wolock["impervious_area_fraction"])
 54 |     np.testing.assert_allclose(topmodel.twi_values,
 55 |                                twi_wolock["twi"].values)
 56 |     np.testing.assert_allclose(topmodel.twi_saturated_areas,
 57 |                                twi_wolock["proportion"].values)
 58 |     assert(topmodel.twi_mean ==
 59 |            twi_weighted_mean_wolock)
 60 |     np.testing.assert_allclose(topmodel.precip_available,
 61 |                                timeseries_wolock["precip_minus_pet"].values)
 62 |     assert(topmodel.flow_initial == 1)
 63 |     assert(topmodel.soil_depth_roots == 1)
 64 |     assert(topmodel.timestep_daily_fraction == 1)
 65 | 
 66 | 
 67 | def test_topmodel_run(parameters_wolock,
 68 |                       timeseries_wolock,
 69 |                       twi_wolock,
 70 |                       twi_weighted_mean_wolock):
 71 |     """Test Topmodel run with input data from Dave Wolock's Topmodel version.
 72 |     Note:
 73 |         This version and Wolock's version produce predicted flow values are
 74 |         are close (max difference is 0.047 or 4.7%). However, there are small
 75 |         differences likely due to a slightly different twi mean values and
 76 |         floating point differences from rounding.  This test allows for a
 77 |         small relative tolerance (rtol) of 0.05 for assertions.
 78 | 
 79 |     Reference:
 80 |         Python Relative tolerance (rtol) vs Absolute tolerance (atol)
 81 |         https://www.python.org/dev/peps/pep-0485/#defaults
 82 |     """
 83 | 
 84 |     # Initialize Topmodel
 85 |     topmodel = Topmodel(
 86 |         scaling_parameter=parameters_wolock["scaling_parameter"],
 87 |         saturated_hydraulic_conductivity=(
 88 |             parameters_wolock["saturated_hydraulic_conductivity"]
 89 |         ),
 90 |         macropore_fraction=parameters_wolock["macropore_fraction"],
 91 |         soil_depth_total=parameters_wolock["soil_depth_total"],
 92 |         soil_depth_ab_horizon=parameters_wolock["soil_depth_ab_horizon"],
 93 |         field_capacity_fraction=parameters_wolock["field_capacity_fraction"],
 94 |         latitude=parameters_wolock["latitude"],
 95 |         basin_area_total=parameters_wolock["basin_area_total"],
 96 |         impervious_area_fraction=parameters_wolock["impervious_area_fraction"],
 97 |         twi_values=twi_wolock["twi"].values,
 98 |         twi_saturated_areas=twi_wolock["proportion"].values,
 99 |         twi_mean=twi_weighted_mean_wolock,
100 |         precip_available=timeseries_wolock["precip_minus_pet"].values,
101 |         flow_initial=1,
102 |         timestep_daily_fraction=1,
103 |         soil_depth_roots=1
104 |     )
105 | 
106 |     topmodel.run()
107 | 
108 |     diff = (topmodel.flow_predicted
109 |             - timeseries_wolock["flow_predicted"].values)
110 |     print("Difference between Lant and Wolock: {}".format(diff))
111 |     print("Max difference: {}".format(max(diff)))
112 |     print("The difference occurred at index: {}".format(np.where(diff ==
113 |                                                                  max(diff))))
114 |     np.testing.assert_allclose(topmodel.flow_predicted,
115 |                                timeseries_wolock["flow_predicted"].values,
116 |                                rtol=0.05)
117 | 


--------------------------------------------------------------------------------
/tests/test_twifile.py:
--------------------------------------------------------------------------------
 1 | """Tests for twi module."""
 2 | 
 3 | from datetime import datetime
 4 | from io import StringIO
 5 | import numpy as np
 6 | import pandas as pd
 7 | import pytest
 8 | 
 9 | from topmodelpy.exceptions import (TwiFileErrorInvalidHeader,
10 |                                    TwiFileErrorMissingValues,
11 |                                    TwiFileErrorInvalidProportion)
12 | from topmodelpy import twifile
13 | 
14 | 
15 | def test_twi_file_read_in(twi_file):
16 |     expected = pd.DataFrame({
17 |         "bin": np.array([1, 2, 3, 4, 5]),
18 |         "twi": np.array([0.02, 0.03, 0.04, 0.05, 0.06]),
19 |         "proportion": np.array([0.10, 0.15, 0.25, 0.30, 0.20]),
20 |         "cells": np.array([10, 15, 25, 30, 20]),
21 |     })
22 |     filestream = StringIO(twi_file)
23 |     actual = twifile.read_in(filestream)
24 | 
25 |     np.testing.assert_allclose(actual["bin"],
26 |                                expected["bin"])
27 |     np.testing.assert_allclose(actual["twi"],
28 |                                expected["twi"])
29 |     np.testing.assert_allclose(actual["proportion"],
30 |                                expected["proportion"])
31 |     np.testing.assert_allclose(actual["cells"],
32 |                                expected["cells"])
33 |     assert actual.dtypes.all() == "float64"
34 | 
35 | 
36 | def test_twi_file_invalid_header(twi_file_invalid_header):
37 |     filestream = StringIO(twi_file_invalid_header)
38 | 
39 |     with pytest.raises(TwiFileErrorInvalidHeader) as err:
40 |         twifile.read_in(filestream)
41 | 
42 |     assert "Invalid header" in str(err.value)
43 | 
44 | 
45 | def test_twi_file_missing_values(twi_file_missing_values):
46 |     filestream = StringIO(twi_file_missing_values)
47 | 
48 |     with pytest.raises(TwiFileErrorMissingValues) as err:
49 |         twifile.read_in(filestream)
50 | 
51 |     assert "Missing values" in str(err.value)
52 | 
53 | 
54 | def test_twi_file_invalid_proportion(twi_file_invalid_proportion):
55 |     filestream = StringIO(twi_file_invalid_proportion)
56 | 
57 |     with pytest.raises(TwiFileErrorInvalidProportion) as err:
58 |         twifile.read_in(filestream)
59 | 
60 |     assert "Invalid sum of proportion" in str(err.value)
61 | 


--------------------------------------------------------------------------------
/tests/testdata/twi_wolock.csv:
--------------------------------------------------------------------------------
 1 | bin,twi,proportion,cells 
 2 | 1,11.6817837,0.003704784,0.370478397
 3 | 2,11.21175,0.005604416,0.560441613
 4 | 3,10.7417173,0.008413193,0.841319282
 5 | 4,10.2716837,0.012517415,1.2517415
 6 | 5,9.80165005,0.018429315,1.84293147
 7 | 6,9.33161736,0.026795687,2.67956872
 8 | 7,8.86158371,0.038372401,3.83724011
 9 | 8,8.39155006,0.053925101,5.39251007
10 | 9,7.9215169,0.073987022,7.3987022
11 | 10,7.45148373,0.098363318,9.83633175
12 | 11,6.98145008,0.125227734,12.5227734
13 | 12,6.51141691,0.149650559,14.9650559
14 | 13,6.04138327,0.161592662,16.1592662
15 | 14,5.5713501,0.14437668,14.437668
16 | 15,5.10131645,0.079039745,7.9039745
17 | 16,0,0,0
18 | 17,0,0,0
19 | 18,0,0,0
20 | 19,0,0,0
21 | 20,0,0,0
22 | 


--------------------------------------------------------------------------------
/topmodelpy/__init__.py:
--------------------------------------------------------------------------------
 1 | # -*- coding: utf-8 -*-
 2 | """
 3 |     topmodelpy
 4 |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 5 |     is a command line interface for a rainfall-runoff model that predicts the amount of water flow in rivers.
 6 | 
 7 |     Nutshell
 8 |     --------
 9 |     Here a small example of using topmodelpy
10 | 
11 |     :authors: 2019 by Jeremiah Lant, see AUTHORS
12 |     :license: CC0 1.0, see LICENSE file for details
13 | """
14 | 
15 | __version__ = "0.1.0"
16 | 


--------------------------------------------------------------------------------
/topmodelpy/cli.py:
--------------------------------------------------------------------------------
 1 | """Main `topmodelpy` command line interface"""
 2 | 
 3 | 
 4 | import click
 5 | import sys
 6 | 
 7 | from topmodelpy.main import topmodelpy
 8 | 
 9 | 
10 | class Options:
11 |     def __init__(self):
12 |         self.verbose = False
13 |         self.show = False
14 | 
15 | 
16 | # Create a decorator to pass options to each command
17 | pass_options = click.make_pass_decorator(Options, ensure=True)
18 | 
19 | 
20 | @click.group()
21 | @click.option("-v", "--verbose", is_flag=True,
22 |               help="Print model run details.")
23 | @click.option("-s", "--show", is_flag=True,
24 |               help="Show output plots.")
25 | @click.pass_context
26 | def main(options, verbose, show):
27 |     """Topmodelpy is a command line tool for a rainfall-runoff
28 |     model that predicts the amount of water flow in rivers.
29 |     """
30 |     options.verbose = verbose
31 |     options.show = show
32 | 
33 | 
34 | @main.command()
35 | @click.argument("configfile", type=click.Path(exists=True))
36 | @pass_options
37 | def run(options, configfile):
38 |     """Run Topmodel with a model configuration file.
39 | 
40 |     The model configuration file contains the specifications for a model run.
41 |     This command takes in the path to model configuration file.
42 |     """
43 |     try:
44 |         click.echo("Running model...")
45 |         topmodelpy(configfile, options)
46 |         click.echo("Finished!")
47 |         click.echo("Output saved as specified in the model config file.")
48 |     except Exception as err:
49 |         click.echo(err)
50 |         sys.exit(1)
51 | 
52 |     if options.verbose:
53 |         click.echo("Verbose on")
54 |     if options.show:
55 |         click.echo("Show on")
56 | 
57 | 
58 | @main.command()
59 | @pass_options
60 | def runexample(options):
61 |     try:
62 |         click.echo("Run example")
63 |     except Exception as err:
64 |         click.echo(err)
65 | 
66 |     if options.verbose:
67 |         click.echo("Verbose on")
68 |     if options.show:
69 |         click.echo("Show on")
70 | 


--------------------------------------------------------------------------------
/topmodelpy/exceptions.py:
--------------------------------------------------------------------------------
  1 | """Exceptions for topmodel.py
  2 | """
  3 | 
  4 | 
  5 | class TopmodelpyException(Exception):
  6 |     """
  7 |     Base exception class.  All custom exceptions subclass this class.
  8 |     """
  9 |     def __str__(self):
 10 |         return self.message
 11 | 
 12 | 
 13 | class ModelConfigFileErrorInvalidSection(TopmodelpyException):
 14 |     """
 15 |     Raised when a model config file does not contain required sections.
 16 |     """
 17 |     def __init__(self, invalid_sections, valid_sections):
 18 |         self.message = (
 19 |             "Error with model config file.\n"
 20 |             "Invalid section(s):\n"
 21 |             "  {}\n"
 22 |             "Valid sections are:\n"
 23 |             "  {}\n".format(invalid_sections, valid_sections)
 24 |         )
 25 | 
 26 | 
 27 | class ModelConfigFileErrorInvalidFilePath(TopmodelpyException):
 28 |     """
 29 |     Raised when a model config file does not contain vaild file paths.
 30 |     """
 31 |     def __init__(self, filepath):
 32 |         self.message = (
 33 |             "Error with model config file.\n"
 34 |             "Invalid file path:\n"
 35 |             "  {}".format(filepath)
 36 |         )
 37 | 
 38 | 
 39 | class ModelConfigFileErrorInvalidOption(TopmodelpyException):
 40 |     """
 41 |     Raised when a model config file does not contain valid options.
 42 |     """
 43 |     def __init__(self, invalid_options, valid_options):
 44 |         self.message = (
 45 |             "Error with model config file.\n"
 46 |             "Invalid option(s):\n"
 47 |             "  option_pet = {pet}\n"
 48 |             "  option_snowmelt = {snowmelt}\n"
 49 |             "".format(**invalid_options)
 50 |         )
 51 |         self.message = self.message + (
 52 |             "Valid options (contained in each respective list):\n"
 53 |             "  option_pet = {pet}\n"
 54 |             "  option_snowmelt = {snowmelt}\n"
 55 |             "".format(**valid_options)
 56 |         )
 57 | 
 58 | 
 59 | class ParametersFileErrorInvalidHeader(TopmodelpyException):
 60 |     """
 61 |     Raised when a file is not a properly formatted parameters csv file.
 62 |     """
 63 |     def __init__(self, invalid_header, valid_header):
 64 |         self.message = (
 65 |             "Error with parameters file.\n"
 66 |             "Invalid header:\n"
 67 |             "  {}\n"
 68 |             "Valid header:\n"
 69 |             "  {}\n"
 70 |             "".format(invalid_header, valid_header)
 71 |         )
 72 | 
 73 | 
 74 | class ParametersFileErrorInvalidScalingParameter(TopmodelpyException):
 75 |     """
 76 |     Raised when a file is not a properly formatted parameters csv file.
 77 |     """
 78 |     def __init__(self, invalid_value):
 79 |         self.message = (
 80 |             "Error with parameters file.\n"
 81 |             "Invalid scaling parameter:\n"
 82 |             "  {}\n"
 83 |             "Valid scaling parameter:\n"
 84 |             "  scaling_parameter > 0\n"
 85 |             "".format(invalid_value)
 86 |         )
 87 | 
 88 | 
 89 | class ParametersFileErrorInvalidLatitude(TopmodelpyException):
 90 |     """
 91 |     Raised when a file is not a properly formatted parameters csv file.
 92 |     """
 93 |     def __init__(self, invalid_value):
 94 |         self.message = (
 95 |             "Error with parameters file.\n"
 96 |             "Invalid latitude:\n"
 97 |             "  {}\n"
 98 |             "Valid latitude:\n"
 99 |             "  0 <= latitude <= 90\n"
100 |             "".format(invalid_value)
101 |         )
102 | 
103 | 
104 | class ParametersFileErrorInvalidSoilDepthTotal(TopmodelpyException):
105 |     """
106 |     Raised when a file is not a properly formatted parameters csv file.
107 |     """
108 |     def __init__(self, invalid_value):
109 |         self.message = (
110 |             "Error with parameters file.\n"
111 |             "Invalid soil depth total:\n"
112 |             "  {}\n"
113 |             "Valid soil depth total:\n"
114 |             "  soil_depth_total > 0\n"
115 |             "".format(invalid_value)
116 |         )
117 | 
118 | 
119 | class ParametersFileErrorInvalidSoilDepthAB(TopmodelpyException):
120 |     """
121 |     Raised when a file is not a properly formatted parameters csv file.
122 |     """
123 |     def __init__(self, invalid_value, soil_depth_total):
124 |         self.message = (
125 |             "Error with parameters file.\n"
126 |             "Invalid soil depth ab horizon:\n"
127 |             "  {}\n"
128 |             "Valid soil depth ab horizon:\n"
129 |             "  soil_depth_ab_horizon > 0\n"
130 |             "  soil_depth_ab_horizon < {} (soil_depth_total)\n"
131 |             "".format(invalid_value, soil_depth_total)
132 |         )
133 | 
134 | 
135 | class ParametersFileErrorInvalidFieldCapacity(TopmodelpyException):
136 |     """
137 |     Raised when a file is not a properly formatted parameters csv file.
138 |     """
139 |     def __init__(self, invalid_value):
140 |         self.message = (
141 |             "Error with parameters file.\n"
142 |             "Invalid field capacity:\n"
143 |             "  {}\n"
144 |             "Valid field capacity:\n"
145 |             "  0 <= field_capacity_fraction <=1\n"
146 |             "".format(invalid_value)
147 |         )
148 | 
149 | 
150 | class ParametersFileErrorInvalidMacropore(TopmodelpyException):
151 |     """
152 |     Raised when a file is not a properly formatted parameters csv file.
153 |     """
154 |     def __init__(self, invalid_value):
155 |         self.message = (
156 |             "Error with parameters file.\n"
157 |             "Invalid macropore:\n"
158 |             "  {}\n"
159 |             "Valid macropore:\n"
160 |             "  0 <= macropore_fraction <=1\n"
161 |             "".format(invalid_value)
162 |         )
163 | 
164 | 
165 | class ParametersFileErrorInvalidImperviousArea(TopmodelpyException):
166 |     """
167 |     Raised when a file is not a properly formatted parameters csv file.
168 |     """
169 |     def __init__(self, invalid_value):
170 |         self.message = (
171 |             "Error with parameters file.\n"
172 |             "Invalid impervious area:\n"
173 |             "  {}\n"
174 |             "Valid impervious area:\n"
175 |             "  0 <= imprevious_area_fraction <=1\n"
176 |             "".format(invalid_value)
177 |         )
178 | 
179 | 
180 | class TimeseriesFileErrorInvalidHeader(TopmodelpyException):
181 |     """
182 |     Raised when a file is not a properly formatted timeseries csv file.
183 |     """
184 |     def __init__(self, invalid_header, valid_header):
185 |         self.message = (
186 |             "Error with timeseries file.\n"
187 |             "Invalid header:\n"
188 |             "  {}\n"
189 |             "Valid header:\n"
190 |             "  {}\n"
191 |             "".format(invalid_header, valid_header)
192 |         )
193 | 
194 | 
195 | class TimeseriesFileErrorMissingValues(TopmodelpyException):
196 |     """
197 |     Raised when a file is not a properly formatted timeseries csv file.
198 |     """
199 |     def __init__(self, missing_values):
200 |         self.message = (
201 |             "Error with timeseries file.\n"
202 |             "Missing values:\n"
203 |             "  {}\n"
204 |             "".format(missing_values)
205 |         )
206 | 
207 | 
208 | class TimeseriesFileErrorMissingDates(TopmodelpyException):
209 |     """
210 |     Raised when a file is not a properly formatted timeseries csv file.
211 |     """
212 |     def __init__(self, timestamps_near_missing):
213 |         self.message = (
214 |             "Error with timeseries file.\n"
215 |             "Missing dates near:\n"
216 |             "  {}\n"
217 |             "".format(timestamps_near_missing)
218 |         )
219 | 
220 | 
221 | class TimeseriesFileErrorInvalidTimestep(TopmodelpyException):
222 |     """
223 |     Raised when a file is not a properly formatted timeseries csv file.
224 |     """
225 |     def __init__(self, invalid_timestep):
226 |         self.message = (
227 |             "Error with timeseries file.\n"
228 |             "Invalid timestep:\n"
229 |             "  {}\n"
230 |             "Valid timestep:\n"
231 |             "  timestep <= 1 (sub-daily or daily)\n"
232 |             "".format(invalid_timestep)
233 |         )
234 | 
235 | 
236 | class TwiFileErrorInvalidHeader(TopmodelpyException):
237 |     """
238 |     Raised when a file is not a properly formatted twi csv file.
239 |     """
240 |     def __init__(self, invalid_header, valid_header):
241 |         self.message = (
242 |             "Error with twi file.\n"
243 |             "Invalid header:\n"
244 |             "  {}\n"
245 |             "Valid header:\n"
246 |             "  {}\n"
247 |             "".format(invalid_header, valid_header)
248 |         )
249 | 
250 | 
251 | class TwiFileErrorMissingValues(TopmodelpyException):
252 |     """
253 |     Raised when a file is not a properly formatted twi csv file.
254 |     """
255 |     def __init__(self, missing_values):
256 |         self.message = (
257 |             "Error with twi file.\n"
258 |             "Missing values:\n"
259 |             "  {}\n"
260 |             "".format(missing_values)
261 |         )
262 | 
263 | 
264 | class TwiFileErrorInvalidProportion(TopmodelpyException):
265 |     """
266 |     Raised when a file is not a properly formatted twi csv file.
267 |     """
268 |     def __init__(self, invalid_proportion):
269 |         self.message = (
270 |             "Error with twi file.\n"
271 |             "Invalid sum of proportion column:\n"
272 |             "  {}\n"
273 |             "Valid sum of proportion column:\n"
274 |             "  1.0\n"
275 |             "".format(invalid_proportion)
276 |         )
277 | 


--------------------------------------------------------------------------------
/topmodelpy/hydrocalcs.py:
--------------------------------------------------------------------------------
  1 | """
  2 | Module of hydrologic calculations.
  3 | 
  4 | References:
  5 | 
  6 | Engineering and Design - Runoff from Snowmelt
  7 | U.S. Army Corps of Engineers
  8 | Engineering Manual 1110-2-1406
  9 | https://www.wcc.nrcs.usda.gov/ftpref/wntsc/H&H/snow/COEemSnowmeltRunoff.pdf
 10 | """
 11 | 
 12 | import numpy as np
 13 | from scipy import stats
 14 | 
 15 | 
 16 | def pet(dates, temperatures, latitude, method="hamon"):
 17 |     """Calculate potential evapotranspiration for various methods.
 18 | 
 19 |     :param dates: An array of python datetimes
 20 |     :type dates: numpy.ndarray
 21 |     :param temperatures: An array of temperatures , in degrees Celsius
 22 |     :type temperatures: numpy.ndarray
 23 |     :param latitude: A latitude, in decimal degrees
 24 |     :type latitude: float
 25 |     :return pet: array of pet values, in millimeters per day
 26 |     :rtype pet: numpy.ndarray
 27 |     """
 28 |     if method.lower() == "hamon":
 29 |         return pet_hamon(dates, temperatures, latitude)
 30 | 
 31 | 
 32 | def pet_hamon(dates, temperatures, latitude):
 33 |     """Calculate the amount of potential evapotranspiration in millimeters
 34 |     per day using the Hamon equation.
 35 | 
 36 |     :param dates: An array of python datetimes
 37 |     :type dates: numpy.ndarray
 38 |     :param temps: An array of temps, in degrees Celsius
 39 |     :type temps: numpy.ndarray
 40 |     :param latitude: A latitude, in decimal degrees
 41 |     :type latitude: float
 42 |     :return pet: array of pet values, in millimeters per day
 43 |     :rtype pet: numpy.ndarray
 44 | 
 45 |     .. notes::
 46 |        Equation:
 47 | 
 48 |        (1) PET = 0.1651 * Ld * RHOSAT * KPEC
 49 | 
 50 |        where
 51 | 
 52 |            PET          daily potential evapotranspiration (mm/day)
 53 |            Ld           daytime length (daylight hours), time from sunrise
 54 |                         to sunset in multiples of 12 hours (hours)
 55 |            RHOSAT       saturated vapor density at the daily mean air
 56 |                         temperature (T), g/m**3
 57 |            KPEC         calibration coefficient, dimensionless
 58 |                         set to 1.2 for southeastern United States
 59 | 
 60 |        Sub-equations:
 61 | 
 62 |        (2) RHOSAT = 216.7 * ESAT / (T + 273.3)
 63 | 
 64 |        (3) ESAT = 6.108 * EXP(17.26939 * T / (T + 237.3))
 65 | 
 66 |        where
 67 | 
 68 |            T       daily mean air temperature, (celsius)
 69 |            ESAT    saturated vapor pressure at the given T, (mb)
 70 | 
 71 |        (4) Ld = (w / 15) * 2
 72 | 
 73 |        where
 74 | 
 75 |            w       the sunset hour angle (degrees); Earth moves 15° per hour
 76 | 
 77 |        (5) w = arccos(-1 * tan(declination) * tan(latitude))
 78 | 
 79 |        where
 80 | 
 81 |            latitude           angle distance of a place north  or south of the
 82 |                               earth's equator (radians)
 83 | 
 84 |            declination        angle between the Sun's rays and the equatorial
 85 |                               plane (radians); the declination of the Earth is
 86 |                               the angular distance at solar noon between the
 87 |                               Sun and the Equator, north-positive
 88 | 
 89 |        (6) declination = 23.45° * sin((360 * (284 + N) / 365))
 90 | 
 91 |        where
 92 | 
 93 |            N                  number of days after January 1 (the Julian Day)
 94 | 
 95 |        References:
 96 |            - Lu et al. (2005). A comparison of six potential evapotranspiration
 97 |              methods for reginal use in the southeastern United States.
 98 | 
 99 |            - Brock, Thomas. (1981). Calculating solar radiation for ecological
100 |              studies. Ecological Modeling.
101 | 
102 |            - https://en.wikipedia.org/wiki/Position_of_the_Sun
103 |     """
104 |     if len(dates) != len(temperatures):
105 |         raise IndexError(
106 |             "Length of dates: {}\n",
107 |             "Length of temperatures: {}\n",
108 |             "Lengths of dates and temperatures must be equal"
109 |             "".format(len(dates), len(temperatures))
110 |         )
111 | 
112 |     DEG2RAD = np.pi/180
113 |     RAD2DEG = 180/np.pi
114 |     CALIBCOEFF = 1.2
115 | 
116 |     pet = []
117 |     for date, temperature in zip(dates, temperatures):
118 | 
119 |         # Declination
120 |         # Note: using python datetimes whih have .timetuple() method
121 |         day_num = date.timetuple().tm_yday
122 |         angle = 360 * ((284 + day_num) / 365) * DEG2RAD
123 |         declination = (23.45 * DEG2RAD) * np.sin(angle)
124 | 
125 |         # calculate sunset hour angle in degrees (w)
126 |         sunset_hour_angle = (
127 |             np.arccos(-1 * np.tan(declination) * np.tan(latitude * DEG2RAD))
128 |             * RAD2DEG
129 |         )
130 | 
131 |         # calculate daytime length in 12 hour unit (Ld)
132 |         daytime_length = abs((sunset_hour_angle / 15) * 2) / 12
133 | 
134 |         # calculate saturated vapor pressure (ESAT)
135 |         saturated_vapor_pressure = (
136 |             6.108 * np.exp((17.26939 * temperature) / (temperature + 237.3))
137 |         )
138 | 
139 |         # calculate saturated vapor density (RHOSAT)
140 |         saturated_vapor_density = (
141 |             (216.7 * saturated_vapor_pressure) / (temperature + 273.3)
142 |         )
143 | 
144 |         # calculate potential evapotranspiration
145 |         potential_evapotranspiration = (
146 |             0.1651 * daytime_length * saturated_vapor_density * CALIBCOEFF
147 |         )
148 | 
149 |         # add to list
150 |         pet.append(potential_evapotranspiration)
151 | 
152 |     # convert list to numpy array
153 |     pet = np.array(pet)
154 | 
155 |     return pet
156 | 
157 | 
158 | def snowmelt(precipitation,
159 |              temperatures,
160 |              temperature_cutoff,
161 |              snowmelt_rate_coeff_with_rain,
162 |              snowmelt_rate_coeff,
163 |              timestep_daily_fraction):
164 |     """Snow melt routine.
165 | 
166 |     :param precipitation: Precipitation rates, in millimeters per day
167 |     :type precipitation: numpy.ndarray
168 |     :param temperatures: Temperatures, in degrees Fahrenheit
169 |     :type temperatures: numpy.ndarray
170 |     :param temperature_cutoff: Temperature when melt begins,
171 |                                in degrees Fahrenheit
172 |     :type temperature_cutoff: float
173 |     :param snowmelt_rate_coeff_with_rain: Snowmelt coefficient when raining,
174 |                                           1/degrees Fahrenheit
175 |     :type snowmelt_rate_coeff_with_rain: float
176 |     :param snowmelt_rate_coeff: Snowmelt rate coefficient (often variable),
177 |                                 in inches per degree Fahrenheit
178 |     :type snowmelt_rate_coeff: float
179 |     :param timestep_daily_fraction: Model timestep as a fraction of a day
180 |     :type timestep_daily_fraction: float
181 |     :return: Tuple of arrays of adjusted precipitation, snowmelt,
182 |              and snowpack values, each array is in millimeters per day
183 |     :rtype: Tuple
184 | 
185 |     """
186 |     precip_inches = precipitation / 25.4  # mm to inches
187 | 
188 |     snowprecip = []
189 |     snowmelts = []
190 |     snowpacks = []
191 | 
192 |     snowmelt = 0
193 |     snowpack = 0
194 |     for temp, precip_inch in zip(temperatures, precip_inches):
195 | 
196 |         # If temp is high enough then there is snowmelt,
197 |         # calculate amount of snowmelt, else no snowmelt,
198 |         # snowpack accumulates by full precip amount
199 |         if temp >= temperature_cutoff:
200 |             # If it is raining, calculate snowmelt with rain,
201 |             # else calculate snowmelt without rain
202 |             if precip_inch > 0:
203 |                 snowmelt = snowmelt_rain_on_snow_heavily_forested(
204 |                     precip_inch,
205 |                     temp,
206 |                     temperature_cutoff,
207 |                     snowmelt_rate_coeff_with_rain
208 |                 )
209 | 
210 |                 # adjust daily snowmelt to same timestep as precip and temp
211 |                 snowmelt = snowmelt * timestep_daily_fraction
212 | 
213 |             else:
214 |                 snowmelt = snowmelt_temperature_index(
215 |                     temp,
216 |                     temperature_cutoff,
217 |                     snowmelt_rate_coeff
218 |                 )
219 | 
220 |                 # adjust daily snowmelt to same timestep as precip and temp
221 |                 snowmelt = snowmelt * timestep_daily_fraction
222 | 
223 |             # If there is more snowmelt than snowpack available to melt, then
224 |             # add the amount of snowpack available to the snowmelt
225 |             if snowmelt >= snowpack:
226 |                 snowmelt = snowpack
227 | 
228 |             # Remove the amount of snowmelt from the snowpack,
229 |             # and add the amount of snowmelt to the current precip amount
230 |             snowpack = snowpack - snowmelt
231 |             precip_inch = precip_inch + snowmelt
232 | 
233 |         # If temp is too cold for melting, then add the precip (snow) amount
234 |         # to the snow pack and assume no water infiltrates on cold days by
235 |         # setting precip to zero
236 |         else:
237 |             snowpack = snowpack + precip_inch
238 |             precip_inch = 0
239 | 
240 |         snowprecip.append(precip_inch)
241 |         snowmelts.append(snowmelt)
242 |         snowpacks.append(snowpack)
243 | 
244 |     snowprecip = np.array(snowprecip) * 25.4  # inches to mm
245 |     snowmelts = np.array(snowmelts) * 25.4  # inches to mm
246 |     snowpacks = np.array(snowpacks) * 25.4  # inches to mm
247 | 
248 |     return snowprecip, snowmelts, snowpacks
249 | 
250 | 
251 | def snowmelt_rain_on_snow_heavily_forested(precipitation,
252 |                                            temperatures,
253 |                                            temperature_cutoff=32.0,
254 |                                            rain_melt_coeff=0.007):
255 |     """Calculate the amount of snowmelt rain-on-snow situations in
256 |     heavily forested areas using a generalized equation for rain-on-snow
257 |     situations in heavily forested areas (the mean canopy cover is greater
258 |     than 80%). This snowmelt calculation is from the family of energy budget
259 |     solutions.
260 | 
261 |     :param precipitation: Precipitation rates, in inches/day
262 |     :type precipitation: numpy.ndarray
263 |     :param temperatures: Temperatures, in degrees Fahrenheit
264 |     :type temperatures: numpy.ndarray
265 |     :param temperature_cutoff: Temperature when melt begins,
266 |                                in degrees Fahrenheit
267 |     :type temperature_cutoff: float
268 |     :param rain_melt_coeff: Snowmelt coefficient when raining,
269 |                              1/degrees Fahrenheit
270 |     :type rain_melt_coeff: float
271 |     :return snowmelt: Snowmelt values, in inches per day
272 |     :rtype snowmelt: numpy.ndarray
273 | 
274 |     .. note::
275 | 
276 |     Equation:
277 | 
278 |     M = (0.074 + 0.007 * P_r) * (T_a - 32) + 0.05
279 | 
280 |     where
281 | 
282 |     M           snowmelt, inches/day
283 |     P_r         rate of precipitation, inches/day
284 |     T_a         temperature of saturated air, at 3 meters (10 ft) level,
285 |                 degrees Fahrenheit
286 | 
287 |     Reference:
288 | 
289 |     Engineering and Design - Runoff from Snowmelt
290 |     U.S. Army Corps of Engineers
291 |     Engineering Manual 1110-2-1406
292 |     Chapter 5-3. Generalized Equations, Rain-on-Snow Situations, Equation 5-20
293 |     https://www.wcc.nrcs.usda.gov/ftpref/wntsc/H&H/snow/COEemSnowmeltRunoff.pdf
294 |     """
295 |     return (
296 |         (0.074 + rain_melt_coeff * precipitation)
297 |         * (temperatures - temperature_cutoff) + 0.05
298 |     )
299 | 
300 | 
301 | def snowmelt_rain_on_snow_open_to_partly_forested(precipitation,
302 |                                                   temperatures,
303 |                                                   winds,
304 |                                                   temperature_cutoff=32.0,
305 |                                                   rain_melt_coeff=0.007,
306 |                                                   basin_wind_coeff=0.5):
307 |     """Calculate the amount of snowmelt rain-on-snow situations in
308 |     partially forested areas using a generalized equation for
309 |     rain-on-snow situations in partially forested areas (the mean canopy
310 |     cover is greater than 10%-80%). Snowmelt calculation is from the family
311 |     of energy budget solutions.
312 | 
313 |     :param precipitation: Precipitation rates, in inches/day
314 |     :type precipitation: numpy.ndarray
315 |     :param temperatures: Temperatures of saturated air,
316 |                          in degrees Fahrenheit
317 |     :type temperatures: numpy.ndarray
318 |     :param winds: Winds, in miles per hour
319 |     :type winds: numpy.ndarray
320 |     :param temperature_cutoff: Temperature when melt begins,
321 |                                in degrees Fahrenheit
322 |     :type temperature_cutoff: float
323 |     :param rain_melt_coeff: Snowmelt coefficient when raining,
324 |                              1/degrees Fahrenheit
325 |     :type rain_melt_coeff: float
326 |     :param basin_wind_coeff: Basin wind exposure coefficient, fraction
327 |     :type basin_wind_coeff: float
328 |     :return snowmelt: Snowmelt values, in inches per day
329 |     :rtype snowmelt: numpy.ndarray
330 | 
331 |     .. note::
332 | 
333 |     Equation:
334 | 
335 |     M = (0.029 + 0.0084 * k * v + 0.007 * P_r) * (T_a - 32) + 0.09
336 | 
337 |     where
338 | 
339 |     M           snowmelt, inches/day
340 |     k           basin wind exposure coefficient, unitless
341 |     v           wind velocity, miles/hour
342 |     P_r         rate of precipitation, inches/day
343 |     T_a         temperature of saturated air, at 3 meters (10 ft) level,
344 |                 degrees Fahrenheit
345 | 
346 |     Reference:
347 | 
348 |     Engineering and Design - Runoff from Snowmelt
349 |     U.S. Army Corps of Engineers
350 |     Engineering Manual 1110-2-1406
351 |     Chapter 5-3. Generalized Equations, Rain-on-Snow Situations, Equation 5-19
352 |     https://www.wcc.nrcs.usda.gov/ftpref/wntsc/H&H/snow/COEemSnowmeltRunoff.pdf
353 |     """
354 |     return (
355 |         (0.029
356 |          + (0.0084 * basin_wind_coeff * winds)
357 |          + (rain_melt_coeff * precipitation))
358 |         * (temperatures - temperature_cutoff) + 0.09
359 |     )
360 | 
361 | 
362 | def snowmelt_temperature_index(temperatures,
363 |                                temperature_cutoff=32.0,
364 |                                melt_rate_coeff=0.06):
365 |     """Calculate the amount of snowmelt using a temperature index method,
366 |     also called degree-day method. This method has its limitations as noted
367 |     in the reference.
368 | 
369 |     :param temperatures: Temperatures, in degrees Fahrenheit
370 |     :type temperatures: numpy.ndarray
371 |     :param temperature_cutoff: Temperature when melt begins,
372 |                                in degrees Fahrenheit
373 |     :type temperature_cutoff: float
374 |     :param melt_rate_coeff: Snowmelt rate coefficient (often variable),
375 |                             in inches per degree Fahrenheit
376 |     :type melt_rate_coeff: float
377 |     :return snowmelt: Snowmelt values, in inches per day
378 |     :rtype snowmelt: numpy.ndarray
379 | 
380 |     .. note::
381 | 
382 |     Equation:
383 | 
384 |     M = C_m * (T_a - T_b)
385 | 
386 |     where
387 | 
388 |     M           snowmelt, inches per period
389 |     C_m         melt-rate coefficient, inches/(degree Fahrenheit/period)
390 |     T_a         air temperature, degrees Fahrenheit
391 |     T_b         base temperature, degrees Fahrenheit
392 | 
393 |     Reference:
394 | 
395 |     Engineering and Design - Runoff from Snowmelt
396 |     U.S. Army Corps of Engineers
397 |     Engineering Manual 1110-2-1406
398 |     Chapter 6-1. Generalized Equations, Rain-on-Snow Situations, Equation 6-1
399 |     https://www.wcc.nrcs.usda.gov/ftpref/wntsc/H&H/snow/COEemSnowmeltRunoff.pdf
400 |     """
401 |     return melt_rate_coeff * (temperatures - temperature_cutoff)
402 | 
403 | 
404 | def weighted_mean(values, weights):
405 |     """Calculate the weighted mean.
406 | 
407 |     :param values: Array of values
408 |     :type values: numpy.ndarray
409 |     :param weights: Array of weights
410 |     :type weights: numpy.ndarray
411 |     :rtype: float
412 |     """
413 |     weighted_mean = (values * weights).sum() / weights.sum()
414 | 
415 |     return weighted_mean
416 | 
417 | 
418 | def absolute_error(observed, modeled):
419 |     """Calculate the absolute error between two arrays.
420 | 
421 |     :param observed: Array of observed data
422 |     :type observed: numpy.ndarray
423 |     :param modeled: Array of modeled data
424 |     :type modeled: numpy.ndarray
425 |     :rtype: numpy.ndarray
426 |     """
427 |     error = observed - modeled
428 | 
429 |     return error
430 | 
431 | 
432 | def mean_squared_error(observed, modeled):
433 |     """Calculate the mean square error between two arrays.
434 | 
435 |     :param observed: Array of observed data
436 |     :type observed: numpy.ndarray
437 |     :param modeled: Array of modeled data
438 |     :type modeled: numpy.ndarray
439 |     :rtype: float
440 |     """
441 |     error = absolute_error(observed, modeled)
442 |     mse = np.mean(error**2)
443 | 
444 |     return mse
445 | 
446 | 
447 | def relative_error(observed, modeled):
448 |     """Calculate the relative change between two arrays.
449 | 
450 |     :param observed: Array of observed data
451 |     :type observed: numpy.ndarray
452 |     :param modeled: Array of modeled data
453 |     :type modeled: numpy.ndarray
454 |     :rtype: numpy.ndarray
455 |     """
456 |     error = absolute_error(observed, modeled) / observed
457 | 
458 |     return error
459 | 
460 | 
461 | def percent_error(observed, modeled):
462 |     """Calculate the percent error between two arrays.
463 | 
464 |     :param observed: Array of observed data
465 |     :type observed: numpy.ndarray
466 |     :param modeled: Array of modeled data
467 |     :type modeled: numpy.ndarray
468 |     :rtype: numpy.ndarray
469 |     """
470 |     error = relative_error(observed, modeled) * 100
471 | 
472 |     return error
473 | 
474 | 
475 | def percent_difference(observed, modeled):
476 |     """Calculate the percent difference between two arrays.
477 | 
478 |     :param observed: Array of observed data
479 |     :type observed: numpy.ndarray
480 |     :param modeled: Array of modeled data
481 |     :type modeled: numpy.ndarray
482 |     :rtype: numpy.ndarray
483 |     """
484 |     mean = np.mean((observed, modeled), axis=0)
485 |     percent_diff = ((modeled - observed) / mean) * 100
486 | 
487 |     return percent_diff
488 | 
489 | 
490 | def r_squared(observed, modeled):
491 |     """Calculate the Coefficient of Determination. Used to indicate how well
492 |     data points fit a line or curve. Use numpy.coeff for computation.
493 | 
494 |     :param observed: Array of observed data
495 |     :type observed: numpy.ndarray
496 |     :param modeled: Array of modeled data
497 |     :type modeled: numpy.ndarray
498 |     :rtype: float
499 |     """
500 |     r = np.corrcoef(observed, modeled)[0, 1]
501 |     coefficient = r**2
502 | 
503 |     return coefficient
504 | 
505 | 
506 | def nash_sutcliffe(observed, modeled):
507 |     """Calculate the Nash-Sutcliffe (model efficiency coefficient).
508 |     Used to assess the predictive power of hydrological models.
509 | 
510 |     E = 1 - sum((observed - modeled) ** 2)) / (sum((observed - mean_observed)**2 )))
511 | 
512 |     :param observed: Array of observed data
513 |     :type observed: numpy.ndarray
514 |     :param modeled: Array of modeled data
515 |     :type modeled: numpy.ndarray
516 |     :rtype: float
517 |     """
518 |     mean_observed = np.mean(observed)
519 |     numerator = np.sum((observed - modeled) ** 2)
520 |     denominator = np.sum((observed - mean_observed)**2)
521 |     coefficient = 1 - (numerator/denominator)
522 | 
523 |     return coefficient
524 | 
525 | 
526 | def flow_duration(values):
527 |     """Calculate the exceedance probabilities for a set of values for use in
528 |     plotting a flow duration curve.
529 | 
530 |     :param observed: Array of flow values
531 |     :type observed: numpy.ndarray
532 |     :param modeled: Array of modeled data
533 |     :return tuple: Tuple of probabilities, sorted values
534 |     :rtype: tuple
535 |     """
536 |     # Sort the values
537 |     values_sorted = np.sort(values)
538 | 
539 |     # Rank data from smallest to largest
540 |     ranks = stats.rankdata(values_sorted, method="average")
541 | 
542 |     # Reverse the order
543 |     ranks = ranks[::-1]
544 | 
545 |     # Compute the exceedance probabilities
546 |     probabilities = (
547 |         [(ranks[i] / (len(values) + 1)) * 100 for i in range(len(values))]
548 |     )
549 | 
550 |     return probabilities, values_sorted
551 | 


--------------------------------------------------------------------------------
/topmodelpy/main.py:
--------------------------------------------------------------------------------
  1 | """Main module that runs topmodelpy.
  2 | 
  3 | This module contains functionality that:
  4 |     - Read model configurationo file
  5 |     - Read all input files
  6 |     - Preprocess input data
  7 |         - Calculate the timestep daily fraction
  8 |         - Calculate pet if not in timeseries
  9 |         - Calculates adjusted precipitation from snowmelt
 10 |         - Calculate the twi weighted mean
 11 |     - Run Topmodel
 12 |     - Post process results
 13 |         - Write output *.csv file of results
 14 |         - Plot output
 15 | """
 16 | import pandas as pd
 17 | from pathlib import PurePath
 18 | from topmodelpy import (hydrocalcs,
 19 |                         modelconfigfile,
 20 |                         parametersfile,
 21 |                         timeseriesfile,
 22 |                         twifile,
 23 |                         plots,
 24 |                         report)
 25 | from topmodelpy.topmodel import Topmodel
 26 | 
 27 | 
 28 | def topmodelpy(configfile, options):
 29 |     """Read inputs, preprocesse data, run Topmodel, and postprocess
 30 |     results, write *.csv outputfiles and make plots.
 31 | 
 32 |     :param configfile: The file path to the model config file that
 33 |     contains model specifications
 34 |     :type param: string
 35 |     :param options: The options sent from the cli
 36 |     :type options: Click.obj
 37 |     """
 38 |     config_data = modelconfigfile.read(configfile)
 39 |     parameters, timeseries, twi = read_input_files(config_data)
 40 | 
 41 |     preprocessed_data = preprocess(config_data, parameters, timeseries, twi)
 42 |     topmodel_data = run_topmodel(parameters, twi, preprocessed_data)
 43 |     postprocess(config_data, timeseries, preprocessed_data, topmodel_data)
 44 | 
 45 | 
 46 | def read_input_files(configdata):
 47 |     """Read input files from model configuration file.
 48 | 
 49 |     Returns a tuple of:
 50 |         dictionary from parameters file
 51 |         pandas.DataFrame from timeseries file
 52 |         pandas.DataFrame from twi file
 53 | 
 54 |     :param config: A ConfigParser object that behaves much like a dictionary.
 55 |     :type config: ConfigParser
 56 |     :return: Tuple of parameters dict, timeseries dataframe, twi dataframe
 57 |     :rtype: tuple
 58 |     """
 59 |     parameters = parametersfile.read(configdata["Inputs"]["parameters_file"])
 60 |     timeseries = timeseriesfile.read(configdata["Inputs"]["timeseries_file"])
 61 |     twi = twifile.read(configdata["Inputs"]["twi_file"])
 62 | 
 63 |     return parameters, timeseries, twi
 64 | 
 65 | 
 66 | def preprocess(config_data, parameters, timeseries, twi):
 67 |     """Preprocess data for topmodel run.
 68 | 
 69 |     Calculate timestep daily fraction, usually 1 for daily timesteps
 70 |         - 1 day = 86400 seconds
 71 |     Calculate pet if pet is not in timeseries dataframe
 72 |     Calculate snowmelt and adjusted precipitation from snowmelt routine
 73 |         - Snowmelt routine requires temperatures in Fahrenheit.
 74 |         - The temperature cutoff from the parameters dict is in Fahrenheit.
 75 |         - snowprecip is the adjusted precipitation from snowmelt.
 76 |         - The snowmelt and snowpack variables are not used at this time.
 77 |     Calculate the difference between the adjusted precip and pet for Topmodel.
 78 |     Calculate the weighted twi mean for Topmodel.
 79 | 
 80 |     :param parameters: The parameters for the model.
 81 |     :type parameters: Dict
 82 |     :param timeseries: A dataframe of all the timeseries data.
 83 |     :type timeseries: Pandas.DataFrame
 84 |     :param twi: A dataframe of all the twi data.
 85 |     :type twi: Pandas.DataFrame
 86 |     :return preprocessed_data: A dict of the calculated variables from
 87 |                                preprocessing.
 88 |     :rtype: dict
 89 |     """
 90 |     # Calculate the daily timestep as a fraction
 91 |     timestep_daily_fraction = (
 92 |         (timeseries.index[1] - timeseries.index[0]).total_seconds() / 86400.0
 93 |     )
 94 | 
 95 |     # Get pet as a numpy array from the input timeseries if it exists,
 96 |     # otherwise calculate it.
 97 |     if "pet" in timeseries.columns:
 98 |         pet = timeseries["pet"].to_numpy() * timestep_daily_fraction
 99 |     else:
100 |         pet = hydrocalcs.pet(
101 |             dates=timeseries.index.to_pydatetime(),
102 |             temperatures=timeseries["temperature"].to_numpy(),
103 |             latitude=parameters["latitude"]["value"],
104 |             method="hamon"
105 |         )
106 |         pet = pet * timestep_daily_fraction
107 | 
108 |     # If snowmelt option is turned on, then compute snowmelt and the difference
109 |     # between the adjusted precip with pet.
110 |     # Otherwise, just compute the difference between the original precip with
111 |     # pet.
112 |     snowprecip, snowmelt, snowpack = None, None, None
113 |     if config_data["Options"].getboolean("option_snowmelt"):
114 |         # Calculate the adjusted precipitation based on snowmelt
115 |         # Note: snowmelt function needs temperatures in Fahrenheit
116 |         snowprecip, snowmelt, snowpack = hydrocalcs.snowmelt(
117 |             timeseries["precipitation"].to_numpy(),
118 |             timeseries["temperature"].to_numpy() * (9/5) + 32,
119 |             parameters["snowmelt_temperature_cutoff"]["value"],
120 |             parameters["snowmelt_rate_coeff_with_rain"]["value"],
121 |             parameters["snowmelt_rate_coeff"]["value"],
122 |             timestep_daily_fraction
123 |         )
124 | 
125 |         # Calculate the difference between the adjusted precip (snowprecip)
126 |         # and pet.
127 |         precip_minus_pet = snowprecip - pet
128 |     else:
129 |         # Calculate the difference between the original precip and pet
130 |         precip_minus_pet = timeseries["precipitation"].to_numpy() - pet
131 | 
132 |     # Calculate the twi weighted mean
133 |     twi_weighted_mean = hydrocalcs.weighted_mean(values=twi["twi"],
134 |                                                  weights=twi["proportion"])
135 | 
136 |     # Return a dict of calculated data
137 |     preprocessed_data = {
138 |         "timestep_daily_fraction": timestep_daily_fraction,
139 |         "pet": pet,
140 |         "precip_minus_pet": precip_minus_pet,
141 |         "snowprecip": snowprecip,
142 |         "snowmelt": snowmelt,
143 |         "snowpack": snowpack,
144 |         "twi_weighted_mean": twi_weighted_mean,
145 |     }
146 | 
147 |     return preprocessed_data
148 | 
149 | 
150 | def run_topmodel(parameters, twi, preprocessed_data):
151 |     """Run Topmodel.
152 | 
153 |     :param parameters: The parameters for the model.
154 |     :type parameters: Dict
155 |     :param twi: A dataframe of all the twi data.
156 |     :type twi: Pandas.DataFrame
157 |     :param preprocessed_data: A dict of the calculated variables from
158 |                               preprocessing.
159 |     :type: dict
160 |     :return topmodel_data: A dict of relevant data results from Topmodel
161 |     :rtype: dict
162 |     """
163 |     # Initialize Topmodel
164 |     topmodel = Topmodel(
165 |         scaling_parameter=parameters["scaling_parameter"]["value"],
166 |         saturated_hydraulic_conductivity=(
167 |             parameters["saturated_hydraulic_conductivity"]["value"]
168 |         ),
169 |         macropore_fraction=parameters["macropore_fraction"]["value"],
170 |         soil_depth_total=parameters["soil_depth_total"]["value"],
171 |         soil_depth_ab_horizon=parameters["soil_depth_ab_horizon"]["value"],
172 |         field_capacity_fraction=parameters["field_capacity_fraction"]["value"],
173 |         latitude=parameters["latitude"]["value"],
174 |         basin_area_total=parameters["basin_area_total"]["value"],
175 |         impervious_area_fraction=parameters["impervious_area_fraction"]["value"],
176 |         flow_initial=parameters["flow_initial"]["value"],
177 |         twi_values=twi["twi"].to_numpy(),
178 |         twi_saturated_areas=twi["proportion"].to_numpy(),
179 |         twi_mean=preprocessed_data["twi_weighted_mean"],
180 |         precip_available=preprocessed_data["precip_minus_pet"],
181 |         timestep_daily_fraction=preprocessed_data["timestep_daily_fraction"]
182 |     )
183 | 
184 |     # Run Topmodel
185 |     topmodel.run()
186 | 
187 |     # Return a dict of relevant calculated values
188 |     topmodel_data = {
189 |         "flow_predicted": topmodel.flow_predicted,
190 |         "saturation_deficit_avgs": topmodel.saturation_deficit_avgs,
191 |         "saturation_deficit_locals": topmodel.saturation_deficit_locals,
192 |         "unsaturated_zone_storages": topmodel.unsaturated_zone_storages,
193 |         "root_zone_storages": topmodel.root_zone_storages,
194 |     }
195 | 
196 |     return topmodel_data
197 | 
198 | 
199 | def postprocess(config_data, timeseries, preprocessed_data, topmodel_data):
200 |     """Postprocess data for output.
201 | 
202 |     Output csv files
203 |     Plot timseries
204 |     """
205 |     # Get output timeseries data
206 |     output_df = get_output_dataframe(timeseries,
207 |                                      preprocessed_data,
208 |                                      topmodel_data)
209 | 
210 |     # Get output comparison stats
211 |     output_comparison_data = get_comparison_data(output_df)
212 | 
213 |     # Write output data
214 |     write_output_csv(df=output_df,
215 |                      filename=PurePath(
216 |                          config_data["Outputs"]["output_dir"],
217 |                          config_data["Outputs"]["output_filename"]))
218 | 
219 |     # Write output data matrices
220 |     if config_data["Options"].getboolean("option_write_output_matrices"):
221 |         write_output_matrices_csv(config_data, timeseries, topmodel_data)
222 | 
223 |     # Plot output data
224 |     plot_output_data(df=output_df,
225 |                      comparison_data=output_comparison_data,
226 |                      path=config_data["Outputs"]["output_dir"])
227 | 
228 |     # Write report of output data
229 |     write_output_report(df=output_df,
230 |                         comparison_data=output_comparison_data,
231 |                         filename=PurePath(
232 |                             config_data["Outputs"]["output_dir"],
233 |                             config_data["Outputs"]["output_report"]))
234 | 
235 | 
236 | def get_output_dataframe(timeseries, preprocessed_data, topmodel_data):
237 |     """Get the output data of interest.
238 | 
239 |     Returns a Pandas Dataframe of all output data of interest.
240 |     """
241 |     output_data = {}
242 |     if preprocessed_data["snowprecip"] is not None:
243 |         output_data["snowprecip"] = preprocessed_data["snowprecip"]
244 | 
245 |     if "pet" not in timeseries.columns:
246 |         output_data["pet"] = preprocessed_data["pet"]
247 | 
248 |     output_data["precip_minus_pet"] = preprocessed_data["precip_minus_pet"]
249 | 
250 |     output_data["flow_predicted"] = topmodel_data["flow_predicted"]
251 |     output_data["saturation_deficit_avgs"] = topmodel_data["saturation_deficit_avgs"]
252 | 
253 |     output_df = timeseries.assign(**output_data)
254 | 
255 |     return output_df
256 | 
257 | 
258 | def get_comparison_data(output_df):
259 |     """Get comparison statistics.
260 | 
261 |     Return a dictionary of descriptive statistics and if output data contains
262 |     an observed flow, then compute the Nash-Sutcliffe statistic.
263 |     """
264 |     output_comparison_data = {}
265 |     if "flow_observed" in output_df.columns:
266 |         output_comparison_data["nash_sutcliffe"] = (
267 |             hydrocalcs.nash_sutcliffe(
268 |                 observed=output_df["flow_observed"].to_numpy(),
269 |                 modeled=output_df["flow_predicted"].to_numpy())
270 |         )
271 |         output_comparison_data["absolute_error"] = (
272 |             hydrocalcs.absolute_error(
273 |                 observed=output_df["flow_observed"].to_numpy(),
274 |                 modeled=output_df["flow_predicted"].to_numpy())
275 |         )
276 |         output_comparison_data["mean_squared_error"] = (
277 |             hydrocalcs.mean_squared_error(
278 |                 observed=output_df["flow_observed"].to_numpy(),
279 |                 modeled=output_df["flow_predicted"].to_numpy())
280 |         )
281 | 
282 |     return output_comparison_data
283 | 
284 | 
285 | def write_output_csv(df, filename):
286 |     """Write output timeseries to csv file.
287 | 
288 |     Creating a pandas Dataframe to ease of saving a csv.
289 |     """
290 |     df.rename = {
291 |         "temperature": "temperature (celsius)",
292 |         "precipitation": "precipitation (mm/day)",
293 |         "pet": "pet (mm/day)",
294 |         "precip_minus_pet": "precip_minus_pet (mm/day)",
295 |         "flow_observed": "flow_observed (mm/day)",
296 |         "flow_predicted": "flow_predicted (mm/day)",
297 |         "saturation_deficit_avgs": "saturation_deficit_avgs (mm/day)",
298 |         "snowprecip": "snowprecip (mm/day)",
299 |     }
300 |     df.to_csv(filename,
301 |               float_format="%.2f")
302 | 
303 | 
304 | def write_output_matrices_csv(config_data, timeseries, topmodel_data):
305 |     """Write output matrices.
306 | 
307 |     Matrices are of size: len(timeseries) x len(twi_bins)
308 | 
309 |     The following are the matrices saved.
310 |          saturation_deficit_locals
311 |          unsaturated_zone_storages
312 |          root_zone_storages
313 |     """
314 |     num_cols = topmodel_data["saturation_deficit_locals"].shape[1]
315 |     header = ["bin_{}".format(i) for i in range(1, num_cols+1)]
316 | 
317 |     saturation_deficit_locals_df = (
318 |         pd.DataFrame(topmodel_data["saturation_deficit_locals"],
319 |                      index=timeseries.index)
320 |     )
321 | 
322 |     unsaturated_zone_storages_df = (
323 |         pd.DataFrame(topmodel_data["unsaturated_zone_storages"],
324 |                      index=timeseries.index)
325 |     )
326 | 
327 |     root_zone_storages_df = (
328 |         pd.DataFrame(topmodel_data["root_zone_storages"],
329 |                      index=timeseries.index)
330 |     )
331 | 
332 |     saturation_deficit_locals_df.to_csv(
333 |         PurePath(
334 |             config_data["Outputs"]["output_dir"],
335 |             config_data["Outputs"]["output_filename_saturation_deficit_locals"]
336 |         ),
337 |         float_format="%.2f",
338 |         header=header,
339 |     )
340 | 
341 |     unsaturated_zone_storages_df.to_csv(
342 |         PurePath(
343 |             config_data["Outputs"]["output_dir"],
344 |             config_data["Outputs"]["output_filename_unsaturated_zone_storages"]
345 |         ),
346 |         float_format="%.2f",
347 |         header=header,
348 |     )
349 | 
350 |     root_zone_storages_df.to_csv(
351 |         PurePath(
352 |             config_data["Outputs"]["output_dir"],
353 |             config_data["Outputs"]["output_filename_root_zone_storages"]
354 |         ),
355 |         float_format="%.2f",
356 |         header=header,
357 |     )
358 | 
359 | 
360 | def plot_output_data(df, comparison_data, path):
361 |     """Plot output timeseries."""
362 |     for key, series in df.iteritems():
363 |         filename = PurePath(path, "{}.png".format(key.split(" ")[0]))
364 |         plots.plot_timeseries(
365 |             dates=df.index.to_pydatetime(),
366 |             values=series.values,
367 |             mean=series.mean(),
368 |             median=series.median(),
369 |             mode=series.mode()[0],
370 |             max=series.max(),
371 |             min=series.min(),
372 |             label="{} (mm/day)".format(key),
373 |             filename=filename)
374 | 
375 |     plots.plot_flow_duration_curve(
376 |         values=df["flow_predicted"].to_numpy(),
377 |         label="flow_predicted (mm/day)",
378 |         filename=PurePath(path, "flow_duration_curve.png"))
379 | 
380 |     if "flow_observed" in df.columns:
381 |         plots.plot_timeseries_comparison(
382 |             dates=df.index.to_pydatetime(),
383 |             observed=df["flow_observed"].to_numpy(),
384 |             modeled=df["flow_predicted"].to_numpy(),
385 |             absolute_error=comparison_data["absolute_error"],
386 |             nash_sutcliffe=comparison_data["nash_sutcliffe"],
387 |             mean_squared_error=comparison_data["mean_squared_error"],
388 |             label="flow (mm/day)",
389 |             filename=PurePath(path, "flow_observed_vs_flow_predicted.png"))
390 | 
391 |         plots.plot_flow_duration_curve_comparison(
392 |             observed=df["flow_observed"].to_numpy(),
393 |             modeled=df["flow_predicted"].to_numpy(),
394 |             label="flow (mm/day)",
395 |             filename=PurePath(path, "flow_duration_curved_observed_vs_predicted.png"))
396 | 
397 | 
398 | def write_output_report(df, comparison_data, filename):
399 |     """Write an html web page with interactive plots."""
400 |     plots_html_data = {}
401 |     for key, value in df.iteritems():
402 |         plots_html_data[key] = plots.plot_timeseries_html(
403 |             dates=df.index.to_pydatetime(),
404 |             values=value,
405 |             label="{} (mm/day)".format(key))
406 | 
407 |     flow_duration_curve_data = {
408 |         "flow_duration_curve_html": plots.plot_flow_duration_curve_html(
409 |             values=df["flow_predicted"].to_numpy(),
410 |             label="flow_predicted (mm/day)")
411 |     }
412 | 
413 |     if comparison_data:
414 |         comparison_plot_html = plots.plot_timeseries_comparison_html(
415 |             dates=df.index.to_pydatetime(),
416 |             observed=df["flow_observed"].to_numpy(),
417 |             modeled=df["flow_predicted"].to_numpy(),
418 |             absolute_error=comparison_data["absolute_error"],
419 |             label="flow (mm/day)")
420 |         comparison_data.update({"comparison_plot_html": comparison_plot_html})
421 | 
422 |         flow_duration_curve_comparison_hmtl = (
423 |             plots.plot_flow_duration_curve_comparison_html(
424 |                 observed=df["flow_observed"].to_numpy(),
425 |                 modeled=df["flow_predicted"].to_numpy(),
426 |                 label="flow (mm/day)")
427 |         )
428 |         flow_duration_curve_data.update(
429 |             {"flow_duration_curve_comparison_html": flow_duration_curve_comparison_hmtl}
430 |         )
431 | 
432 |     report.save(df=df,
433 |                 plots=plots_html_data,
434 |                 comparison_data=comparison_data,
435 |                 flow_duration_curve_data=flow_duration_curve_data,
436 |                 filename=filename)
437 | 


--------------------------------------------------------------------------------
/topmodelpy/modelconfigfile.py:
--------------------------------------------------------------------------------
 1 | """Module for reading a model configuration file.
 2 | 
 3 | The configuration file is in the standard INI file format. The file contains
 4 | three sections:
 5 | 1. Inputs - section for model input files
 6 | 2. Outputs - section for model output files
 7 | 3. Options - section for model options
 8 | """
 9 | 
10 | from configparser import ConfigParser, ExtendedInterpolation
11 | from pathlib import Path
12 | 
13 | from .exceptions import (ModelConfigFileErrorInvalidSection,
14 |                          ModelConfigFileErrorInvalidFilePath,
15 |                          ModelConfigFileErrorInvalidOption)
16 | 
17 | 
18 | def read(filepath):
19 |     """Read model config file.
20 | 
21 |     Read and process the model configuration file that is in the standard INI
22 |     data format.
23 | 
24 |     :param filepath: A valid file path
25 |     :type filepath: string
26 |     :return: A ConfigParser object that behaves much like a dictionary.
27 |     :rtype: ConfigParser
28 |     """
29 |     filepath = Path(filepath)
30 |     try:
31 |         config = ConfigParser(interpolation=ExtendedInterpolation())
32 |         config.read(filepath)
33 |         check_config(config)
34 |     except ModelConfigFileErrorInvalidSection as err:
35 |         print(err)
36 |     except ModelConfigFileErrorInvalidFilePath as err:
37 |         print(err)
38 |     except ModelConfigFileErrorInvalidOption as err:
39 |         print(err)
40 |     except Exception as err:
41 |         print(err)
42 | 
43 |     return config
44 | 
45 | 
46 | def check_config(config):
47 |     """ Check that the config file has data and that all file paths are valid.
48 | 
49 |     :param config: A ConfigParser object that behaves much like a dictionary.
50 |     :type config: ConfigParser
51 |     """
52 |     check_config_sections(config)
53 |     check_config_filepaths(config)
54 |     check_config_options(config)
55 | 
56 | 
57 | def check_config_sections(config):
58 |     """Check that the config file has sections."""
59 |     valid_sections = ["Inputs", "Outputs", "Options"]
60 |     sections = config.sections()
61 |     if not sections == valid_sections:
62 |         raise ModelConfigFileErrorInvalidSection(sections, valid_sections)
63 | 
64 | 
65 | def check_config_filepaths(config):
66 |     """Check that all the filepaths are valid."""
67 |     for section in config.sections():
68 |         for key in config[section]:
69 |             value = config[section][key]
70 |             if value and (key.endswith("dir") or key.endswith("file")):
71 |                 filepath = Path(value)
72 |                 if not filepath.exists() and not filepath.is_file():
73 |                     raise ModelConfigFileErrorInvalidFilePath(value)
74 | 
75 | 
76 | def check_config_options(config):
77 |     """Check that all the options are valid."""
78 |     valid_options = {
79 |         "pet": ["hamon"],
80 |         "snowmelt": ["yes", "no"],
81 |     }
82 | 
83 |     options = {
84 |         "pet": config["Options"]["option_pet"].lower().strip(),
85 |         "snowmelt": (
86 |             config["Options"]["option_snowmelt"].lower().strip()
87 |         ),
88 |     }
89 | 
90 |     for key in valid_options.keys() and options.keys():
91 |         if options[key] not in valid_options[key]:
92 |             raise ModelConfigFileErrorInvalidOption(options, valid_options)
93 | 


--------------------------------------------------------------------------------
/topmodelpy/parametersfile.py:
--------------------------------------------------------------------------------
  1 | """Module that contains functions to read a parameters file in csv format."""
  2 | 
  3 | import csv
  4 | 
  5 | from .exceptions import (ParametersFileErrorInvalidHeader,
  6 |                          ParametersFileErrorInvalidScalingParameter,
  7 |                          ParametersFileErrorInvalidLatitude,
  8 |                          ParametersFileErrorInvalidSoilDepthTotal,
  9 |                          ParametersFileErrorInvalidSoilDepthAB,
 10 |                          ParametersFileErrorInvalidFieldCapacity,
 11 |                          ParametersFileErrorInvalidMacropore,
 12 |                          ParametersFileErrorInvalidImperviousArea,)
 13 | 
 14 | 
 15 | def read(filepath):
 16 |     """Read data file
 17 |     Open file and create a file object to process with
 18 |     read_file_in(filestream).
 19 | 
 20 |     :param filepath: File path of data file.
 21 |     :type param: string
 22 |     :return data: A dict that contains all the data from the file.
 23 |     :rtype: dict
 24 |     """
 25 |     try:
 26 |         with open(filepath) as f:
 27 |             data = read_in(f)
 28 |         check_data(data)
 29 |         return data
 30 |     except (ParametersFileErrorInvalidHeader,
 31 |             ParametersFileErrorInvalidScalingParameter,
 32 |             ParametersFileErrorInvalidLatitude,
 33 |             ParametersFileErrorInvalidSoilDepthTotal,
 34 |             ParametersFileErrorInvalidSoilDepthAB,
 35 |             ParametersFileErrorInvalidFieldCapacity,
 36 |             ParametersFileErrorInvalidMacropore,
 37 |             ParametersFileErrorInvalidImperviousArea,) as err:
 38 |         print(err)
 39 | 
 40 | 
 41 | def read_in(filestream):
 42 |     """Read and process a filestream.
 43 |     Read and process a filestream of a comma-delimited parameter file.
 44 |     This function takes a filestream of text as input which allows for
 45 |     cleaner unit testing.
 46 | 
 47 |     :param filestream: A filestream of text.
 48 |     :type filestream: _io.TextIOWrapper
 49 |     :return data: A dict that contains all the data from the file.
 50 |     :rtype: dict
 51 |     """
 52 |     fnames = ["name", "value", "units", "description"]
 53 |     reader = csv.DictReader(filestream, fieldnames=fnames)
 54 |     header = next(reader)
 55 |     header_list = [val.lower().strip() for val in header.values()]
 56 |     check_header(header_list, fnames)
 57 | 
 58 |     data = {}
 59 |     for row in reader:
 60 |         name = row["name"].lower().strip()
 61 |         data[name] = {
 62 |             "value": float(row["value"].strip()),
 63 |             "units": row["units"].lower().strip(),
 64 |             "description": row["description"].strip(),
 65 |         }
 66 |     return data
 67 | 
 68 | 
 69 | def check_header(header, valid_header):
 70 |     """Check that column names in header line match what is expected.
 71 | 
 72 |     :param header: Header found in file.
 73 |     :type header: list
 74 |     :param valid_header: Valid header that is expected.
 75 |     :type valid_header: list
 76 |     """
 77 |     if not header == valid_header:
 78 |         raise ParametersFileErrorInvalidHeader(header, valid_header)
 79 | 
 80 | 
 81 | def check_data(data):
 82 |     """Check that all data values from the file are valid.
 83 | 
 84 |     :param data: A dict that contains all the data from the file.
 85 |     :type data: dict
 86 |     """
 87 |     check_scaling_parameter(data["scaling_parameter"]["value"])
 88 |     check_latitude(data["latitude"]["value"])
 89 |     check_soil_depth_total(data["soil_depth_total"]["value"])
 90 |     check_soil_depth_ab_horizon(data["soil_depth_ab_horizon"]["value"],
 91 |                                 data["soil_depth_total"]["value"])
 92 |     check_field_capacity(data["field_capacity_fraction"]["value"])
 93 |     check_macropore(data["macropore_fraction"]["value"])
 94 |     check_impervious_area(data["impervious_area_fraction"]["value"])
 95 | 
 96 | 
 97 | def check_scaling_parameter(value):
 98 |     """Check that the scaling parameter value is valid.
 99 |     Valid scaling parameter value is:
100 |         scaling_parameter > 0
101 | 
102 |     :param value: scaling parameter value.
103 |     :type value: float
104 |     """
105 |     if not value > 0:
106 |         raise ParametersFileErrorInvalidScalingParameter(value)
107 | 
108 | 
109 | def check_latitude(value):
110 |     """Check that the latitude value is valid.
111 |     Valid latitude value are:
112 |       90 >= latitude >= 0
113 | 
114 |     :param value: latitude value.
115 |     :type value: float
116 |     """
117 |     if not value >= 0 or not value <= 90:
118 |         raise ParametersFileErrorInvalidLatitude(value)
119 | 
120 | 
121 | def check_soil_depth_total(value):
122 |     """Check that the soil_depth_total value is valid.
123 |     Valid soil depth value are:
124 |       soil_depth_total > 0
125 | 
126 |     :param value: soil depth total value.
127 |     :type value: float
128 |     """
129 |     if not value > 0:
130 |         raise ParametersFileErrorInvalidSoilDepthTotal(value)
131 | 
132 | 
133 | def check_soil_depth_ab_horizon(value, soil_depth_total):
134 |     """Check that the soil_depth_ab_horizon value is valid.
135 |     Valid soil depth of AB horizon value are:
136 |       soil_depth_ab_horizon > 0
137 |       soil_depth_ab_horizon < soil_depth_total
138 | 
139 |     :param value: soil depth ab horizon value.
140 |     :type value: float
141 |     """
142 |     if not value > 0 or not value < soil_depth_total:
143 |         raise ParametersFileErrorInvalidSoilDepthAB(value, soil_depth_total)
144 | 
145 | 
146 | def check_field_capacity(value):
147 |     """Check that the field capacity fraction value is valid.
148 |     Valid field capacity fraction value are:
149 |       0 <= field_capacity <= 1
150 | 
151 |     :param value: field capacity value.
152 |     :type value: float
153 |     """
154 |     if not value > 0 or not value < 1:
155 |         raise ParametersFileErrorInvalidFieldCapacity(value)
156 | 
157 | 
158 | def check_macropore(value):
159 |     """Check that the macropore value is valid.
160 |     Valid macropore fraction value are:
161 |       0 <= macropore <= 1
162 | 
163 |     :param value: macropore value.
164 |     :type value: float
165 |     """
166 |     if not value > 0 or not value < 1:
167 |         raise ParametersFileErrorInvalidMacropore(value)
168 | 
169 | 
170 | def check_impervious_area(value):
171 |     """Check that the impervious_area value is valid.
172 |     Valid impervious_area fraction value are:
173 |       0 <= impervious_area_fraction <= 1
174 | 
175 |     :param value: impervious area value.
176 |     :type value: float
177 |     """
178 |     if not value > 0 or not value < 1:
179 |         raise ParametersFileErrorInvalidImperviousArea(value)
180 | 


--------------------------------------------------------------------------------
/topmodelpy/plots.py:
--------------------------------------------------------------------------------
  1 | """Module of functions for generating plots.
  2 | 
  3 | """
  4 | 
  5 | import matplotlib.pyplot as plt
  6 | import matplotlib.dates as mdates
  7 | import mpld3
  8 | from pandas.plotting import register_matplotlib_converters
  9 | 
 10 | from topmodelpy import hydrocalcs
 11 | 
 12 | 
 13 | # Register for pandas
 14 | register_matplotlib_converters()
 15 | 
 16 | COLORS = {
 17 |     "temperature": "orange",
 18 |     "precipitation": "navy",
 19 |     "pet": "green",
 20 |     "precip_minus_pet": "darkgreen",
 21 |     "flow_observed": "darkblue",
 22 |     "flow_predicted": "blue",
 23 |     "saturation_deficit_avgs": "gray",
 24 | }
 25 | 
 26 | 
 27 | class MousePositionDatePlugin(mpld3.plugins.PluginBase):
 28 |     """Plugin for displaying mouse position with a datetime x axis."""
 29 | 
 30 |     JAVASCRIPT = """
 31 |     mpld3.register_plugin("mousepositiondate", MousePositionDatePlugin);
 32 |     MousePositionDatePlugin.prototype = Object.create(mpld3.Plugin.prototype);
 33 |     MousePositionDatePlugin.prototype.constructor = MousePositionDatePlugin;
 34 |     MousePositionDatePlugin.prototype.requiredProps = [];
 35 |     MousePositionDatePlugin.prototype.defaultProps = {
 36 |     fontsize: 12,
 37 |     xfmt: "%Y-%m-%d %H:%M:%S",
 38 |     yfmt: ".2f"
 39 |     };
 40 |     function MousePositionDatePlugin(fig, props) {
 41 |     mpld3.Plugin.call(this, fig, props);
 42 |     }
 43 |     MousePositionDatePlugin.prototype.draw = function() {
 44 |     var fig = this.fig;
 45 |     var xfmt = d3.time.format(this.props.xfmt);
 46 |     var yfmt = d3.format(this.props.yfmt);
 47 |     var coords = fig.canvas.append("text").attr("class", "mpld3-coordinates").style("text-anchor", "end").style("font-size", this.props.fontsize).attr("x", this.fig.width - 5).attr("y", this.fig.height - 5);
 48 |     for (var i = 0; i < this.fig.axes.length; i++) {
 49 |       var update_coords = function() {
 50 |         var ax = fig.axes[i];
 51 |         return function() {
 52 |           var pos = d3.mouse(this);
 53 |           x = ax.xdom.invert(pos[0]);
 54 |           y = ax.ydom.invert(pos[1]);
 55 |           coords.text("(" + xfmt(x) + ", " + yfmt(y) + ")");
 56 |         };
 57 |       }();
 58 |       fig.axes[i].baseaxes.on("mousemove", update_coords).on("mouseout", function() {
 59 |         coords.text("");
 60 |       });
 61 |     }
 62 |     };
 63 |     """
 64 | 
 65 |     def __init__(self, fontsize=14, xfmt="%Y-%m-%d %H:%M:%S", yfmt=".2f"):
 66 |         self.dict_ = {
 67 |             "type": "mousepositiondate",
 68 |             "fontsize": fontsize,
 69 |             "xfmt": xfmt,
 70 |             "yfmt": yfmt
 71 |         }
 72 | 
 73 | 
 74 | def plot_timeseries_html(dates, values, label):
 75 |     """Return an html string of the figure"""
 76 | 
 77 |     fig, ax = plt.subplots(subplot_kw=dict(facecolor="#EEEEEE"))
 78 |     fig.set_size_inches(10, 6)
 79 | 
 80 |     colorstr = "k"
 81 |     for key, value in COLORS.items():
 82 |         if key in label:
 83 |             colorstr = value
 84 | 
 85 |     label = label.replace("_", " ").capitalize()
 86 | 
 87 |     ax.grid(color="white", linestyle="solid")
 88 |     ax.set_title("{}".format(label), fontsize=20)
 89 | 
 90 |     ax.plot(dates, values, color=colorstr, linewidth=2)
 91 | 
 92 |     # Connect plugin
 93 |     mpld3.plugins.connect(fig, MousePositionDatePlugin())
 94 | 
 95 |     return mpld3.fig_to_html(fig)
 96 | 
 97 | 
 98 | def plot_timeseries_comparison_html(dates, observed, modeled, absolute_error, label):
 99 |     """Return an html string of the figure"""
100 | 
101 |     fig, axes = plt.subplots(2, 1, sharex=True, subplot_kw=dict(facecolor="#EEEEEE"))
102 |     fig.set_size_inches(10, 8)
103 | 
104 |     # Connect plugin
105 |     mpld3.plugins.connect(fig, MousePositionDatePlugin())
106 | 
107 |     # Plot comparison on first row
108 |     axes[0].grid(True)
109 |     axes[0].set_title("Observed flow vs. Modeled flow")
110 |     axes[0].set_xlabel("Date")
111 |     axes[0].set_ylabel(label)
112 | 
113 |     # Explicitly using matplotlibs new default color palette (blue and orange)
114 |     axes[0].plot(dates, observed, linewidth=2, color="#1f77b4",
115 |                  label="Observed")
116 |     axes[0].plot(dates, modeled, linewidth=2, color="#ff7f0e",
117 |                  label="Modeled")
118 | 
119 |     # Legend
120 |     handles, labels = axes[0].get_legend_handles_labels()
121 |     legend = axes[0].legend(handles, labels, fancybox=True)
122 |     legend.get_frame().set_alpha(0.5)
123 | 
124 |     axes[1].grid(True)
125 |     axes[1].set_title("Absolute Error: Observed - Modeled")
126 |     axes[1].set_xlabel("Date")
127 |     axes[1].set_ylabel("Error (mm/day)")
128 | 
129 |     axes[1].plot(dates, absolute_error, linewidth=2, color="black")
130 | 
131 |     # Rotate and align the tick labels so they look better
132 |     fig.autofmt_xdate()
133 |     axes[1].fmt_xdata = mdates.DateFormatter("%Y-%m-%d")
134 | 
135 |     return mpld3.fig_to_html(fig)
136 | 
137 | 
138 | def plot_flow_duration_curve_html(values, label):
139 |     """Return an html string of the figure"""
140 | 
141 |     fig, ax = plt.subplots(subplot_kw=dict(facecolor="#EEEEEE"))
142 |     fig.set_size_inches(10, 6)
143 | 
144 |     label = label.replace("_", " ").capitalize()
145 | 
146 |     ax.grid(color="white", linestyle="solid")
147 |     ax.set_title("Flow Duration Curve: Observed vs. Modeled", fontsize=20)
148 |     ax.set_xlabel("Exceedance Probability (%)")
149 |     ax.set_ylabel(label)
150 |     ax.set_yscale("log")
151 | 
152 |     probabilities, values_sorted = hydrocalcs.flow_duration(values)
153 | 
154 |     ax.plot(probabilities, values_sorted, linewidth=2)
155 | 
156 |     # Connect plugin
157 |     mpld3.plugins.connect(fig, MousePositionDatePlugin())
158 | 
159 |     return mpld3.fig_to_html(fig)
160 | 
161 | 
162 | def plot_flow_duration_curve_comparison_html(observed, modeled, label):
163 |     """Plot flow duration curve."""
164 | 
165 |     fig, ax = plt.subplots(subplot_kw=dict(facecolor="#EEEEEE"))
166 |     fig.set_size_inches(10, 6)
167 | 
168 |     label = label.replace("_", " ").capitalize()
169 | 
170 |     ax.grid(color="white", linestyle="solid")
171 |     ax.set_title("Flow Duration Curve: Observed vs. Modeled", fontsize=20)
172 |     ax.set_xlabel("Exceedance Probability (%)")
173 |     ax.set_ylabel(label)
174 |     ax.set_yscale("log")
175 | 
176 |     observed_prob, observed_sorted = hydrocalcs.flow_duration(observed)
177 |     modeled_prob, modeled_sorted = hydrocalcs.flow_duration(modeled)
178 | 
179 |     # Explicitly using matplotlibs new default color palette (blue and orange)
180 |     ax.plot(observed_prob, observed_sorted, linewidth=2, color="#1f77b4",
181 |             label="Observed")
182 |     ax.plot(modeled_prob, modeled_sorted, linewidth=2, color="#ff7f0e",
183 |             label="Modeled")
184 | 
185 |     # Legend
186 |     handles, labels = ax.get_legend_handles_labels()
187 |     legend = ax.legend(handles, labels, fancybox=True)
188 |     legend.get_frame().set_alpha(0.5)
189 | 
190 |     # Connect plugin
191 |     mpld3.plugins.connect(fig, MousePositionDatePlugin())
192 | 
193 |     return mpld3.fig_to_html(fig)
194 | 
195 | 
196 | def plot_timeseries(dates,
197 |                     values,
198 |                     mean,
199 |                     median,
200 |                     mode,
201 |                     max,
202 |                     min,
203 |                     label,
204 |                     filename):
205 |     """Plot timeseries."""
206 |     fig, ax = plt.subplots()
207 |     fig.set_size_inches(12, 10)
208 | 
209 |     colorstr = "k"
210 |     for key, value in COLORS.items():
211 |         if key in label:
212 |             colorstr = value
213 | 
214 |     label = label.replace("_", " ").capitalize()
215 | 
216 |     ax.grid()
217 |     ax.set_title(label)
218 |     ax.set_xlabel("Date")
219 |     ax.set_ylabel(label)
220 | 
221 |     ax.plot(dates, values, linewidth=2, color=colorstr)
222 | 
223 |     # Rotate and align the tick labels so they look better
224 |     fig.autofmt_xdate()
225 |     ax.fmt_xdata = mdates.DateFormatter("%Y-%m-%d")
226 | 
227 |     # Add text of descriptive stats to figure
228 |     text = (
229 |         "Mean = {0:.2f}\n"
230 |         "Median = {1:.2f}\n"
231 |         "Mode = {2:.2f}\n"
232 |         "Max = {3:.2f}\n"
233 |         "Min = {4:.2f}"
234 |         "".format(mean, median, mode, max, min)
235 |     )
236 | 
237 |     patch_properties = {
238 |         "boxstyle": "round",
239 |         "facecolor": "white",
240 |         "alpha": 0.5
241 |     }
242 | 
243 |     ax.text(0.05,
244 |             0.95,
245 |             text,
246 |             transform=ax.transAxes,
247 |             fontsize=14,
248 |             verticalalignment="top",
249 |             horizontalalignment="left",
250 |             bbox=patch_properties)
251 | 
252 |     plt.savefig(filename, format="png")
253 |     plt.close()
254 | 
255 | 
256 | def plot_timeseries_comparison(dates,
257 |                                observed,
258 |                                modeled,
259 |                                absolute_error,
260 |                                nash_sutcliffe,
261 |                                mean_squared_error,
262 |                                label,
263 |                                filename):
264 |     """Plot difference between timeseries."""
265 | 
266 |     fig, axes = plt.subplots(2, 1, sharex=True)
267 |     fig.set_size_inches(12, 10)
268 | 
269 |     label = label.replace("_", " ").capitalize()
270 | 
271 |     # Plot comparison on first row
272 |     axes[0].grid(True)
273 |     axes[0].set_title("Observed flow vs. Modeled flow")
274 |     axes[0].set_xlabel("Date")
275 |     axes[0].set_ylabel(label)
276 | 
277 |     # Explicitly using matplotlibs new default color palette (blue and orange)
278 |     axes[0].plot(dates, observed, linewidth=2, color="#1f77b4",
279 |                  label="Observed")
280 |     axes[0].plot(dates, modeled, linewidth=2, color="#ff7f0e",
281 |                  label="Modeled")
282 | 
283 |     # Legend
284 |     handles, labels = axes[0].get_legend_handles_labels()
285 |     legend = axes[0].legend(handles, labels, fancybox=True)
286 |     legend.get_frame().set_alpha(0.5)
287 | 
288 |     # Add text of stats to figure
289 |     text_nash_sutcliffe = (
290 |         "Nash-Sutcliffe = {:.2f}"
291 |         "".format(nash_sutcliffe)
292 |     )
293 | 
294 |     patch_properties = {
295 |         "boxstyle": "round",
296 |         "facecolor": "white",
297 |         "alpha": 0.5
298 |     }
299 | 
300 |     axes[0].text(0.05,
301 |                  0.95,
302 |                  text_nash_sutcliffe,
303 |                  transform=axes[0].transAxes,
304 |                  fontsize=14,
305 |                  verticalalignment="top",
306 |                  horizontalalignment="left",
307 |                  bbox=patch_properties)
308 | 
309 |     # Plot absolute error on second row
310 |     axes[1].grid(True)
311 |     axes[1].set_title("Absolute Error: Observed - Modeled")
312 |     axes[1].set_xlabel("Date")
313 |     axes[1].set_ylabel("Error (mm/day)")
314 | 
315 |     axes[1].plot(dates, absolute_error, linewidth=2, color="black")
316 | 
317 |     # Rotate and align the tick labels so they look better
318 |     fig.autofmt_xdate()
319 |     axes[1].fmt_xdata = mdates.DateFormatter("%Y-%m-%d")
320 | 
321 |     # Add text of stats to figure
322 |     text_mse = (
323 |         "Mean Squared Error = {:.2f}"
324 |         "".format(mean_squared_error)
325 |     )
326 | 
327 |     axes[1].text(0.05,
328 |                  0.95,
329 |                  text_mse,
330 |                  transform=axes[1].transAxes,
331 |                  fontsize=14,
332 |                  verticalalignment="top",
333 |                  horizontalalignment="left",
334 |                  bbox=patch_properties)
335 | 
336 |     plt.savefig(filename, format="png")
337 |     plt.close()
338 | 
339 | 
340 | def plot_flow_duration_curve(values, label, filename):
341 |     """Plot flow duration curve."""
342 |     fig, ax = plt.subplots()
343 |     fig.set_size_inches(12, 10)
344 | 
345 |     label = label.replace("_", " ").capitalize()
346 | 
347 |     ax.grid()
348 |     ax.set_title("Flow Duration Curve")
349 |     ax.set_xlabel("Exceedance Probability (%)")
350 |     ax.set_ylabel(label)
351 |     ax.set_yscale("log")
352 | 
353 |     probabilities, values_sorted = hydrocalcs.flow_duration(values)
354 | 
355 |     ax.plot(probabilities, values_sorted, linewidth=2)
356 | 
357 |     plt.savefig(filename, format="png")
358 |     plt.close()
359 | 
360 | 
361 | def plot_flow_duration_curve_comparison(observed, modeled, label, filename):
362 |     """Plot flow duration curve."""
363 |     fig, ax = plt.subplots()
364 |     fig.set_size_inches(12, 10)
365 | 
366 |     label = label.replace("_", " ").capitalize()
367 | 
368 |     ax.grid()
369 |     ax.set_title("Flow Duration Curve: Observed vs. Modeled")
370 |     ax.set_xlabel("Exceedance Probability (%)")
371 |     ax.set_ylabel(label)
372 |     ax.set_yscale("log")
373 | 
374 |     observed_prob, observed_sorted = hydrocalcs.flow_duration(observed)
375 |     modeled_prob, modeled_sorted = hydrocalcs.flow_duration(modeled)
376 | 
377 |     # Explicitly using matplotlibs new default color palette (blue and orange)
378 |     ax.plot(observed_prob, observed_sorted, linewidth=2, color="#1f77b4",
379 |             label="Observed")
380 |     ax.plot(modeled_prob, modeled_sorted, linewidth=2, color="#ff7f0e",
381 |             label="Modeled")
382 | 
383 |     # Legend
384 |     handles, labels = ax.get_legend_handles_labels()
385 |     legend = ax.legend(handles, labels, fancybox=True)
386 |     legend.get_frame().set_alpha(0.5)
387 | 
388 |     plt.savefig(filename, format="png")
389 |     plt.close()
390 | 


--------------------------------------------------------------------------------
/topmodelpy/report.py:
--------------------------------------------------------------------------------
 1 | """Module that contains functions to render an html file.
 2 | 
 3 | """
 4 | 
 5 | from jinja2 import PackageLoader, Environment
 6 | 
 7 | 
 8 | def render_report(df, plots, comparison_data, flow_duration_curve_data, filename):
 9 |     """Render an html page of the model output data.
10 | 
11 |     :param data: Data to fill template with
12 |     :param type: dictionary
13 |     :param template_filename: The filename of the template to fill
14 |     :type template_filename: string
15 |     """
16 |     loader = PackageLoader("topmodelpy", "templates")
17 |     env = Environment(loader=loader)
18 |     template = env.get_template("report_template.html")
19 | 
20 |     return template.render(df=df,
21 |                            plots=plots,
22 |                            comparison_data=comparison_data,
23 |                            flow_duration_curve_data=flow_duration_curve_data)
24 | 
25 | 
26 | def save(df, plots, comparison_data, flow_duration_curve_data, filename):
27 |     """Save summary as a restructured text file.
28 | 
29 |     :param data: Data to fill template with
30 |     :param type: dictionary
31 |     :param filename: The full path with filename of the output file to write
32 |     :type filename: string
33 |     """
34 |     with open(filename, "w") as f:
35 |         f.write(
36 |             render_report(df, plots, comparison_data, flow_duration_curve_data, filename)
37 |         )
38 | 


--------------------------------------------------------------------------------
/topmodelpy/templates/report_template.html:
--------------------------------------------------------------------------------
  1 | <!doctype html>
  2 | <html lang="en">
  3 |   <head>
  4 |     <!-- Required meta tags -->
  5 |     <meta charset="utf-8">
  6 |     <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
  7 | 
  8 |     <!-- Bootstrap CSS -->
  9 |     <link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/css/bootstrap.min.css" integrity="sha384-ggOyR0iXCbMQv3Xipma34MD+dH/1fQ784/j6cY/iJTQUOhcWr7x9JvoRxT2MZw1T" crossorigin="anonymous">
 10 | 
 11 |     <title>topmodelpy output</title>
 12 |   </head>
 13 |   <body>
 14 |     <div class="container">
 15 |       <div class="row">
 16 |         <div class="col-md-12">
 17 |           <h3>Outputs</h3>
 18 |           <ol>
 19 |             {% for column in df.columns %}
 20 |             <li><a href="#{{key}}">{{ column }}</a></li>
 21 |             {% endfor %}
 22 |           </ol>
 23 |         <div>
 24 |       <div>
 25 |       <div class="row">
 26 |         <div class="col-md-12">
 27 |           {% if comparison_data %}
 28 |           <h3>Comparison Plot</h3>
 29 |           <div>{{ comparison_data["comparison_plot_html"] }}</div>
 30 |           <h5>Descriptive Statistics</h5>
 31 |           <table class="table table-hover">
 32 |             <thead>
 33 |               <tr>
 34 |                 <th scope="col">Statistic</th>
 35 |                 <th scope="col">Value</th>
 36 |               </tr>
 37 |             </thead>
 38 |             <tbody>
 39 |               <tr>
 40 |                 <th scope="row">Nash-Sutcliffe</th>
 41 |                 <td>{{ "{0:0.2f}".format(comparison_data["nash_sutcliffe"]) }}</td>
 42 |               </tr>
 43 |               <tr>
 44 |                 <th scope="row">Mean Squared Error</th>
 45 |                 <td>{{ "{0:0.2f}".format(comparison_data["mean_squared_error"]) }}</td>
 46 |               </tr>
 47 |             </tbody>
 48 |           </table>
 49 |           <h3>Flow Duration Curve Comparison</h3>
 50 |           <div>{{ flow_duration_curve_data["flow_duration_curve_comparison_html"] }}</div>
 51 |           {% endif %}
 52 |         <div>
 53 |       <div>
 54 |       <div class="row">
 55 |         <div class="col-md-12">
 56 |           <h3>Interactive Plots</h3>
 57 |           {% for key, value in plots.items() %}
 58 |           <div>{{ value }}</div>
 59 |           <h5>Descriptive Statistics</h5>
 60 |           <table class="table table-hover">
 61 |             <thead>
 62 |               <tr>
 63 |                 <th scope="col">Statistic</th>
 64 |                 <th scope="col">Value</th>
 65 |               </tr>
 66 |             </thead>
 67 |             <tbody>
 68 |               <tr>
 69 |                 <th scope="row">Mean</th>
 70 |                 <td>{{ "{0:0.2f}".format(df[key].mean()) }}</td>
 71 |               </tr>
 72 |               <tr>
 73 |                 <th scope="row">Median</th>
 74 |                 <td>{{ "{0:0.2f}".format(df[key].median()) }}</td>
 75 |               </tr>
 76 |               <tr>
 77 |                 <th scope="row">Mode</th>
 78 |                 <td>{{ "{0:0.2f}".format(df[key].mode().values[0]) }}</td>
 79 |               </tr>
 80 |               <tr>
 81 |                 <th scope="row">Max</th>
 82 |                 <td>{{ "{0:0.2f}".format(df[key].max()) }}</td>
 83 |               </tr>
 84 |               <tr>
 85 |                 <th scope="row">Min</th>
 86 |                 <td>{{ "{0:0.2f}".format(df[key].min()) }}</td>
 87 |               </tr>
 88 |             </tbody>
 89 |           </table>
 90 |           {% endfor %}
 91 |         <div>
 92 |       <div>
 93 |       <div class="row">
 94 |         <div class="col-md-12">
 95 |           <h3>Flow Duration Curve</h3>
 96 |           <div>{{ flow_duration_curve_data["flow_duration_curve_html"] }}</div>
 97 |         <div>
 98 |       <div>
 99 |     <div>
100 | 
101 |     <!-- Optional JavaScript -->
102 |     <!-- jQuery first, then Popper.js, then Bootstrap JS -->
103 |     <script src="https://code.jquery.com/jquery-3.3.1.slim.min.js" integrity="sha384-q8i/X+965DzO0rT7abK41JStQIAqVgRVzpbzo5smXKp4YfRvH+8abtTE1Pi6jizo" crossorigin="anonymous"></script>
104 |     <script src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.14.7/umd/popper.min.js" integrity="sha384-UO2eT0CpHqdSJQ6hJty5KVphtPhzWj9WO1clHTMGa3JDZwrnQq4sF86dIHNDz0W1" crossorigin="anonymous"></script>
105 |     <script src="https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/js/bootstrap.min.js" integrity="sha384-JjSmVgyd0p3pXB1rRibZUAYoIIy6OrQ6VrjIEaFf/nJGzIxFDsf4x0xIM+B07jRM" crossorigin="anonymous"></script>
106 |   </body>
107 | </html>
108 | 


--------------------------------------------------------------------------------
/topmodelpy/timeseriesfile.py:
--------------------------------------------------------------------------------
 1 | """Module that contains functions to read a timeseries file in csv format."""
 2 | 
 3 | import numpy as np
 4 | import pandas as pd
 5 | 
 6 | from .exceptions import (TimeseriesFileErrorInvalidHeader,
 7 |                          TimeseriesFileErrorMissingDates,
 8 |                          TimeseriesFileErrorMissingValues,
 9 |                          TimeseriesFileErrorInvalidTimestep)
10 | 
11 | 
12 | def read(filepath):
13 |     """Read data file
14 |     Open file and create a file object to process with
15 |     read_file_in(filestream).
16 | 
17 |     :param filepath: File path to data file.
18 |     :type param: string
19 |     :return data: A dataframe of all the timeseries data.
20 |     :rtype: Pandas.DataFrame
21 |     """
22 |     try:
23 |         with open(filepath, "r") as f:
24 |             data = read_in(f)
25 |         return data
26 |     except TimeseriesFileErrorInvalidHeader as err:
27 |         print(err)
28 |     except TimeseriesFileErrorMissingDates as err:
29 |         print(err)
30 |     except TimeseriesFileErrorMissingValues as err:
31 |         print(err)
32 |     except Exception as err:
33 |         print(err)
34 | 
35 | 
36 | def read_in(filestream):
37 |     """Read and process a filestream.
38 |     Read and process a filestream of a comma-delimited parameter file.
39 |     This function takes a filestream of text as input which allows for
40 |     cleaner unit testing.
41 | 
42 |     :param filestream: A filestream of text.
43 |     :type filestream: _io.TextIOWrapper
44 |     :return data: A dict that contains all the data from the file.
45 |     :rtype: dict
46 |     """
47 |     column_short_names = {
48 |         "temperature (celsius)": "temperature",
49 |         "precipitation (mm/day)": "precipitation",
50 |         "pet (mm/day)": "pet",
51 |         "flow_observed (mm/day)": "flow_observed",
52 |     }
53 | 
54 |     data = pd.read_csv(filestream, index_col=0, parse_dates=True, dtype=float)
55 |     data.columns = data.columns.str.strip()
56 |     check_header(data.columns.values.tolist(), list(column_short_names))
57 |     check_missing_dates(data)
58 |     check_missing_values(data)
59 |     check_timestep(data)
60 |     data.rename(columns=column_short_names, inplace=True)
61 | 
62 |     return data
63 | 
64 | 
65 | def check_header(header, valid_header):
66 |     """Check that column names in header line match what is expected.
67 | 
68 |     :param header: Header found in file.
69 |     :type header: list
70 |     :param valid_header: Valid header that is expected.
71 |     :type valid_header: list
72 |     """
73 |     for item in header:
74 |         if item not in valid_header:
75 |             raise TimeseriesFileErrorInvalidHeader(header, valid_header)
76 | 
77 | 
78 | def check_missing_dates(data):
79 |     """Check for any missing dates."""
80 |     if data.index.isna().any():
81 |         missing_indices = np.where(data.index.isna())[0]
82 |         timestamps_near_missing = data.index[missing_indices - 1]
83 |         raise TimeseriesFileErrorMissingDates(timestamps_near_missing.values)
84 | 
85 | 
86 | def check_missing_values(data):
87 |     """Check for any missing data values."""
88 |     if data.isna().values.any():
89 |         missing_values = data[data.isna().any(axis=1)]
90 |         raise TimeseriesFileErrorMissingValues(missing_values)
91 | 
92 | 
93 | def check_timestep(data):
94 |     """Check that the timestep is 1 day or less."""
95 |     timestep = (data.index[1] - data.index[0]).days
96 |     if not timestep <= 1:
97 |         raise TimeseriesFileErrorInvalidTimestep(timestep)
98 | 


--------------------------------------------------------------------------------
/topmodelpy/twifile.py:
--------------------------------------------------------------------------------
 1 | """Module that contains functions to read a twi file in csv format."""
 2 | 
 3 | import numpy as np
 4 | import pandas as pd
 5 | 
 6 | from .exceptions import (TwiFileErrorInvalidHeader,
 7 |                          TwiFileErrorMissingValues,
 8 |                          TwiFileErrorInvalidProportion)
 9 | 
10 | 
11 | def read(filepath):
12 |     """Read data file
13 |     Open file and create a file object to process with
14 |     read_file_in(filestream).
15 | 
16 |     :param filepath: File path to data file.
17 |     :type param: string
18 |     :return data: A dict that contains all the data from the file.
19 |     :rtype: dict
20 |     """
21 |     try:
22 |         with open(filepath, "r") as f:
23 |             data = read_in(f)
24 |         return data
25 |     except TwiFileErrorInvalidHeader as err:
26 |         print(err)
27 |     except TwiFileErrorMissingValues as err:
28 |         print(err)
29 |     except TwiFileErrorInvalidProportion as err:
30 |         print(err)
31 |     except Exception as err:
32 |         print(err)
33 | 
34 | 
35 | def read_in(filestream):
36 |     """Read and process a filestream.
37 |     Read and process a filestream of a comma-delimited parameter file.
38 |     This function takes a filestream of text as input which allows for
39 |     cleaner unit testing.
40 | 
41 |     :param filestream: A filestream of text.
42 |     :type filestream: _io.TextIOWrapper
43 |     :return data: A dict that contains all the data from the file.
44 |     :rtype: dict
45 |     """
46 |     column_names = {
47 |         "bin": "bin",
48 |         "twi": "twi",
49 |         "proportion": "proportion",
50 |         "cells": "cells",
51 |     }
52 | 
53 |     data = pd.read_csv(filestream, dtype=float)
54 |     data.columns = data.columns.str.strip()
55 |     check_header(data.columns.values.tolist(), list(column_names))
56 |     check_missing_values(data)
57 |     check_proportion(data)
58 |     data.rename(columns=column_names, inplace=True)
59 | 
60 |     return data
61 | 
62 | 
63 | def check_header(header, valid_header):
64 |     """Check that column names in header line match what is expected.
65 | 
66 |     :param header: Header found in file.
67 |     :type header: list
68 |     :param valid_header: Valid header that is expected.
69 |     :type valid_header: list
70 |     """
71 |     for item in header:
72 |         if item not in valid_header:
73 |             raise TwiFileErrorInvalidHeader(header, valid_header)
74 | 
75 | 
76 | def check_missing_values(data):
77 |     """Check if any data is missing.
78 | 
79 |     :param data: Pandas DataFrame containing data.
80 |     :type data: pandas.DataFrame
81 |     """
82 |     if data.isnull().values.any():
83 |         missing_values = data[data.isna().any(axis=1)]
84 |         raise TwiFileErrorMissingValues(missing_values)
85 | 
86 | 
87 | def check_proportion(data):
88 |     """Check that the sum of proportion column is close to 1.0.
89 |     rtol=1e-02 means that computed sum should be within 1% of 1.0
90 | 
91 |     :param data: Pandas DataFrame containing data.
92 |     :type data: pandas.DataFrame
93 |     """
94 |     if not np.isclose(data["proportion"].sum(), 1.0, rtol=1e-02):
95 |         raise TwiFileErrorInvalidProportion(data["proportion"].sum())
96 | 


--------------------------------------------------------------------------------
/topmodelpy/utils.py:
--------------------------------------------------------------------------------
 1 | """Utility functions
 2 | 
 3 | """
 4 | 
 5 | import numpy as np
 6 | 
 7 | 
 8 | def nans(shape, dtype=float):
 9 |     """Return an array filled with nan values.
10 | 
11 |     :param shape: A tuple for the shape of the array
12 |     :type shape: tuple
13 |     :returns: numpy.ndarray
14 |     """
15 |     array = np.empty(shape, dtype)
16 |     array[:] = np.nan
17 | 
18 |     return array
19 | 


--------------------------------------------------------------------------------