Hydrology model

.github/workflows/unit-python-ver-test.yml

@@ -32,13 +32,30 @@ jobs:
           python-version: ${{ matrix.python-version }}
           architecture: x64
 
+      - name: Install SUNDIALS
+        run: |
+          sudo apt-get -qq update;
+          sudo apt-get install -y libopenblas-dev liblapack-dev
+          wget https://github.com/LLNL/sundials/releases/download/v5.1.0/sundials-5.1.0.tar.gz
+          tar xzf sundials-5.1.0.tar.gz
+          mkdir build-sundials-5.1.0
+          cd build-sundials-5.1.0/
+          cmake -DLAPACK_ENABLE=ON -DSUNDIALS_INDEX_SIZE=64 -DCMAKE_INSTALL_PREFIX=$GITHUB_WORKSPACE ../sundials-5.1.0/
+          make install
+          export SUNDIALS_INST=$GITHUB_WORKSPACE
+          export LD_LIBRARY_PATH=$GITHUB_WORKSPACE/lib:$LD_LIBRARY_PATH
+
       - name: Install models
         run: |
+          export SUNDIALS_INST=$GITHUB_WORKSPACE
+          export LD_LIBRARY_PATH=$GITHUB_WORKSPACE/lib:$LD_LIBRARY_PATH
           python --version
           python -m pip install --upgrade pip setuptools wheel
           python -m pip install -e ./streamflow/
-          python -m pip install -e ./streamflow/[dev]
+          python -m pip install -e ./streamflow/[dev,cvode]
 
       - name: run unit tests
         run: |
+          export SUNDIALS_INST=$GITHUB_WORKSPACE
+          export LD_LIBRARY_PATH=$GITHUB_WORKSPACE/lib:$LD_LIBRARY_PATH
           python run-tests.py --unit

README.md

@@ -1,9 +1,9 @@
-# pints-models
+# bayesian-differential-equations-db
 
-The purpose of pints-models is to present Python implementations of scientific time series models from various disciplines.
+The purpose of bayesian-differential-equations-db is to present Python implementations of scientific time series models from various disciplines.
 
 While the `pints.toy` module already includes a number of simple models and distributions, this repository is intended for more complex models associated with real experimental data.
 
 ## Models and data
 
-Hydrology
+[Rainfall runoff model and river discharge data for the French Broad River at Asheville, North Carolina.](streamflow/)

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = differential-equations-inference-db
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/make.bat

@@ -0,0 +1,36 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+set SPHINXPROJ=differential-equations-inference-db
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+
+:end
+popd

docs/source/conf.py

@@ -0,0 +1,147 @@
+# -*- coding: utf-8 -*-
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+import sphinx
+
+# -- General configuration ------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.doctest',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.napoleon',
+    'sphinx.ext.viewcode',
+]
+
+# Autodoc defaults
+if int(sphinx.__version__.split('.')[1]) < 8:
+    autodoc_default_flags = [
+        'members',
+        'inherited-members',
+        # 'show-inheritance',
+    ]
+else:
+    autodoc_default_options = {
+        'members': None,
+        'inherited-members': None,
+    }
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = u'model'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This patterns also effect to html_static_path and html_extra_path
+exclude_patterns = []
+
+# Suppress warnings about unused footnotes (i.e. citations of papers)
+suppress_warnings = [
+    'ref.footnote',
+]
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = False
+
+
+# -- Options for HTML output ----------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'alabaster'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#
+html_theme_options = {
+
+    # See: https://alabaster.readthedocs.io/en/latest/customization.html
+
+    # Fixed sidebar is unusable: Doesn't have its own scrollbar!
+    # 'fixed_sidebar': True,
+
+    'page_width': '1280px',
+    'sidebar_width': '320px',
+}
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = []
+
+
+# -- Options for HTMLHelp output ------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'modelsdoc'
+
+
+# -- Options for LaTeX output ---------------------------------------------
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    #
+    # 'papersize': 'letterpaper',
+
+    # The font size ('10pt', '11pt' or '12pt').
+    #
+    # 'pointsize': '10pt',
+
+    # Additional stuff for the LaTeX preamble.
+    #
+    # 'preamble': '',
+
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
+}

docs/source/index.rst

@@ -0,0 +1,9 @@
+Welcome to the differential-equations-inference-db documentation
+================================================================
+
+Contents
+========
+
+.. toctree::
+
+    pystreamflow

docs/source/pystreamflow.rst

@@ -0,0 +1,22 @@
+************
+pystreamflow
+************
+
+The pystreamflow model can be used to study river discharge data.
+
+This package provides a PINTS Forward Model for simulation and inference, and a
+function for loading precipitation, evaporation, and discharge data in Pandas
+format.
+
+.. currentmodule:: pystreamflow
+
+Forward model
+*************
+
+.. autoclass:: pystreamflow.RiverModel
+  :members: __init__, simulate, set_model_data
+
+Data
+****
+
+.. autofunction:: pystreamflow.load_data

run-tests.py

@@ -12,7 +12,7 @@ def run_unit_tests():
     """
     Runs unit tests (without subprocesses).
     """
-    model_dirs = ['streamflow/pystreamflow']
+    model_dirs = [os.path.join('streamflow', 'pystreamflow')]
 
     for dir in model_dirs:
         tests = os.path.join(dir, 'tests')

streamflow/README.md

@@ -1 +1,37 @@
+# pystreamflow
+
 pystreamflow enables efficient simulation and inference for rainfall runoff differential equation models of the sort that arise in hydrological modelling of river basins.
+
+## Installation
+
+1. Navigate to `differential-equations-inference-db/streamflow/` (this directory)
+1. For a simple install, run `pip install .`
+1. To install with support for the CVODE solver via scikits.odes, run `pip install .[cvode]`
+
+### Installing with CVODE
+
+The CVODE solver enables faster model evaluations and inference, but it requires you to install the SUNDIALS C library and the scikits.odes Python package. The following is a typical install process for the 5.1.0 version of SUNDIALS:
+
+```
+sudo apt-get install libopenblas-dev liblapack-dev
+wget https://github.com/LLNL/sundials/releases/download/v5.1.0/sundials-5.1.0.tar.gz
+tar xzf sundials-5.1.0.tar.gz
+mkdir build-sundials-5.1.0
+cd build-sundials-5.1.0/
+cmake -DLAPACK_ENABLE=ON -DSUNDIALS_INDEX_SIZE=64 ../sundials-5.1.0/
+make install
+```
+
+scikits.odes is pip installable, and an attempt will be made to install it when `pip install .[cvode]` is executed. However, system-specific troubleshooting is often required; see the scikit.odes [installation documentation](https://scikits-odes.readthedocs.io/en/latest/installation.html) for details.
+
+If you have conda, an alternative is to use conda forge:
+
+```
+conda install -c conda-forge scikits.odes
+```
+
+## Usage
+
+Once installed, the streamflow model can be accessed using the `pystreamflow.RiverModel` class and the data can be accessed using the `pystreamflow.load_data` function. The raw data files are available [here](pystreamflow/data/), and the model code is [here](pystreamflow/model.py).
+
+The [notebook](examples/data_and_inference.ipynb) in the examples directory contains code for loading the data and running inference with MCMC.