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 +1,19 @@
-# 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 provide a database of differential equation models and associated observed time series data that represent interesting and challenging problems for inference. The database provides methods for running these models and accessing the associated observed data files using Python.
 
-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.
+While the [`pints.toy`](https://pints.readthedocs.io/en/latest/toy/index.html) 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
+| Model | Reference | Features |
+| ----- | --------- | -------- |
+| [Rainfall-runoff river discharge data, French Broad River at Asheville, NC.](streamflow/) | [[1]](https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2009WR008933) | Importance of numerical accuracy, complex noise process, potential model misspecification |
+
+## Examples
+
+The [examples](examples/) directory contains example notebooks for each of the models.
+
+## References
+
+[1] Schoups, G., & Vrugt, J. A. (2010). A formal likelihood function for parameter and predictive inference of hydrologic models with correlated, heteroscedastic, and non‐Gaussian errors. _Water Resources Research_, 46(10).

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