Merge pull request #55 from IMMM-SFA/speedtest

migrate from numexpr to numba

.github/workflows/build_linux.yml → .github/workflows/build.yml

@@ -1,4 +1,4 @@
-name: linux
+name: build
 
 on: [push]
 

README.md

@@ -1,7 +1,6 @@
-[![linux](https://github.com/IMMM-SFA/mosartwmpy/actions/workflows/build_linux.yml/badge.svg)](https://github.com/IMMM-SFA/mosartwmpy/actions/workflows/build_linux.yml)
-[![osx](https://github.com/IMMM-SFA/mosartwmpy/actions/workflows/build_osx.yml/badge.svg)](https://github.com/IMMM-SFA/mosartwmpy/actions/workflows/build_osx.yml)
-[![windows](https://github.com/IMMM-SFA/mosartwmpy/actions/workflows/build_windows.yml/badge.svg)](https://github.com/IMMM-SFA/mosartwmpy/actions/workflows/build_windows.yml)
+[![build](https://github.com/IMMM-SFA/mosartwmpy/actions/workflows/build.yml/badge.svg)](https://github.com/IMMM-SFA/mosartwmpy/actions/workflows/build.yml)
 [![codecov](https://codecov.io/gh/IMMM-SFA/mosartwmpy/branch/main/graph/badge.svg?token=IPOY8984MB)](https://codecov.io/gh/IMMM-SFA/mosartwmpy)
+[![DOI](https://joss.theoj.org/papers/10.21105/joss.03221/status.svg)](https://doi.org/10.21105/joss.03221)
 [![DOI](https://zenodo.org/badge/312114600.svg)](https://zenodo.org/badge/latestdoi/312114600)
 
 ## mosartwmpy

build.sh

@@ -0,0 +1,3 @@
+rm -f dist/*
+python -m build
+python -m twine upload dist/*

config.yaml

@@ -6,29 +6,23 @@ simulation:
     # path to a directory for writing output files; will be created if doesn't exist
     output_path: ./output
     # date to begin the simulation
-    start_date: 1981-05-24
+    start_date: 1981-05-01
     # date to end the simulation
-    end_date: 1981-05-26
+    end_date: 1981-05-30
 
-# For example -- to change the input files, update the paths below:
+grid:
+  path: ./input/domains/mosart.nc
+  land:
+    path: ./input/domains/land.nc
 
-# grid:
-#     # path to the grid domain file; can be absolute or relative to the source code root
-#     path: /pic/projects/im3/iwmm/rof/mosart/MOSART_NLDAS_8th_20160426.nc
-#     land:
-#       # path to the land grid domain file; can be absolute or relative to the source code root
-#       path: /pic/projects/im3/iwmm/share/domains/domain.clm/domain.lnd.nldas2_0224x0464_c110415.nc
-# runoff:
-#     # whether or not to read runoff input from file
-#     read_from_file: true
-#     # path to the runoff file; can be absolute or relative to the source code root
-#     path: /pic/projects/im3/iwmm/lnd/dlnd7/NLDAS/Livneh_NLDAS_1980_2011.nc
-# water_management:
-#     # flag to turn this feature on or off
-#     enabled: true
-#     demand:
-#       # path to the demand file; can be absolute or relative to the source code root
-#       path: /pic/projects/im3/iwmm/input_data/demand/GCAM_waterdemand_nc/rcp8.5/RCP8.5_GCAM_water_demand_{year}_{month}.nc
-#     reservoirs:
-#       # path to the reservoir parameter file; can be absolute or relative to the source code root
-#       path: /pic/projects/im3/iwmm/input_data/runoff/US_reservoir_8th_NLDAS3_updated_20200421.nc
+runoff:
+  read_from_file: true
+  path: ./input/runoff/runoff_1981_05.nc
+
+water_management:
+  enabled: true
+  demand:
+    read_from_file: true
+    path: ./input/demand/demand_1981_05.nc
+  reservoirs:
+    path: ./input/reservoirs/reservoirs.nc

docs/_static/style.css

@@ -0,0 +1,48 @@
+/* Override some aspects of the pydata-sphinx-theme */
+
+:root {
+  /* Use softer blue from bootstrap's default info color */
+  --pst-color-info: 23, 162, 184;
+}
+
+/* Main index page overview cards */
+
+.intro-card {
+  background: #fff;
+  border-radius: 0;
+  padding: 30px 10px 20px 10px;
+  margin: 10px 0px;
+}
+
+.intro-card p.card-text {
+  margin: 0px;
+}
+
+.intro-card .card-img-top {
+  margin: 0px;
+  height: 52px;
+}
+
+.intro-card .card-header {
+  border: none;
+  background-color:white;
+  color: #150458 !important;
+  font-size: var(--pst-font-size-h5);
+  font-weight: bold;
+  padding: 0.5rem 0rem 0.5rem 0rem;
+}
+
+.intro-card .card-footer {
+  border: none;
+  background-color:white;
+}
+
+.intro-card .card-footer p.card-text{
+  max-width: 220px;
+  margin-left: auto;
+  margin-right: auto;
+}
+
+.card-body {
+    padding: 0.5rem;
+}

docs/conf.py

@@ -32,10 +32,11 @@
 # ones.
 extensions = [
     'nbsphinx',
-    'recommonmark',                                                             
-    'sphinx.ext.napoleon',                                                      
-    'sphinx.ext.autodoc',                                                       
-    'sphinx_rtd_theme' 
+    'recommonmark',
+    'sphinx.ext.napoleon',
+    'sphinx.ext.autodoc',
+    'sphinx_panels',
+    'sphinx_rtd_theme'
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -57,4 +58,10 @@
 # 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 = ['_static']
+html_static_path = ['_static']
+html_css_files = ['style.css']
+
+panels_delimiters = (r"^\>{3,}$", r"^\^{3,}$", r"^\+{3,}$")
+
+import mosartwmpy
+version = str(mosartwmpy.__version__)

docs/index.rst

@@ -1,30 +1,89 @@
-mosartwmpy
-==========
+:notoc:
 
-Introduction
-------------
-.. toctree::
-   :maxdepth: 1
+.. mosartwmpy documentation master file, created by
 
-   README.md
+.. module:: mosartwmpy
 
-Tutorial
---------
-.. toctree::
-   :maxdepth: 1
+************************
+mosartwmpy documentation
+************************
 
-   tutorial.ipynb
+**Date**: |today| **Version**: |version|
 
-Tips and Tricks
----------------
-.. toctree::
-   :maxdepth: 1
+**Useful links**:
+`Source Repository <https://github.com/immm-sfa/mosartwmpy>`__ |
+`Issues & Ideas <https://github.com/immm-sfa/mosartwmpy/issues>`__
+
+`mosartwmpy` is a Python translation of MOSART-WM, a water routing and reservoir management model written in Fortran.
+
+
+.. panels::
+    :card: + intro-card text-center
+    :column: col-lg-6 col-md-6 col-sm-6 col-xs-12 d-flex
+
+    >>>
+    :img-top: _static/cognitive.svg
+
+    Getting started
+    ^^^
+
+    Get to know the *mosartwmpy* model.
+
+    +++
+    .. link-button:: README
+            :type: ref
+            :text: Getting started
+            :classes: btn-block btn-secondary stretched-link
+
+    >>>
+    :img-top: _static/education.svg
+
+    Tutorial
+    ^^^
+
+    Follow along with this Jupyter notebook to learn the ropes of *mosartwmpy*.
+
+    +++
+    .. link-button:: tutorial
+            :type: ref
+            :text: Tutorial
+            :classes: btn-block btn-secondary stretched-link
+
+    >>>
+    :img-top: _static/soccer.svg
+
+    Tips & tricks
+    ^^^
+
+    Learn about ways to manage Python virtual environments.
+
+    +++
+    .. link-button:: virtualenv
+            :type: ref
+            :text: Virtual environments
+            :classes: btn-block btn-secondary stretched-link
+
+    >>>
+    :img-top: _static/api.svg
+
+    API reference
+    ^^^
+
+    A detailed description of the *mosartwmpy* API.
+
+    +++
+    .. link-button:: mosartwmpy
+            :type: ref
+            :text: API
+            :classes: btn-block btn-secondary stretched-link
 
-   virtualenv
 
-Application Programming Interface
----------------------------------
 .. toctree::
-   :maxdepth: 1
+    :maxdepth: 1
+    :hidden:
+    :titlesonly:
 
-   mosartwmpy
+    README.md
+    tutorial.ipynb
+    virtualenv
+    mosartwmpy

docs/virtualenv.rst

@@ -1,10 +1,11 @@
 Python Virtual Environments
 ===========================
 
-Maintaining different versions of Python can be a chore, especially when ``mosartwmpy`` is forcing you to use Python 3.9+ 😈. There are many tools for managing Python environments, and many more will probably be developed after I write this, but at this moment in time my two recommendations are:
+Maintaining different versions of Python can be a chore. Thankfully, there are many tools for managing Python environments; here are a few recommendations:
 
-* `PyCharm <https://www.jetbrains.com/pycharm/>`_ IDE -- this is great for developing code in Python, and can automatically create virtual environments for a codebase by detecting versions and dependencies from the ``setup.py`` or ``setup.cfg``.
-* `pyenv <https://github.com/pyenv/pyenv>`_ CLI -- this is a shell based tool for installing and switching between different versions of Python and dependencies. I will give a brief tutorial of using ``pyenv`` below, but recognize that the instructions may change over time so the ``pyenv`` documentation is the best place to look.
+* `PyCharm <https://www.jetbrains.com/pycharm/>`_ IDE -- great for developing code in Python, and can automatically create virtual environments for a codebase by detecting versions and dependencies from the ``setup.py`` or ``setup.cfg``.
+* `Conda <https://docs.conda.io>`_ package manager -- a Python package manager focused on scientific computing that can also manage virtual environments.
+* `pyenv <https://github.com/pyenv/pyenv>`_ CLI -- a shell based tool for installing and switching between different versions of Python and dependencies. I will give a brief tutorial of using ``pyenv`` below, but recognize that the instructions may change over time so the ``pyenv`` documentation is the best place to look.
 
 To create a Python 3.9 virtual environment, try the following steps:
 

mosartwmpy/__init__.py

@@ -1 +1,2 @@
 from .model import Model
+from ._version import __version__

mosartwmpy/_version.py

@@ -0,0 +1 @@
+__version__ = "0.1.0"

mosartwmpy/config/parameters.py

@@ -35,21 +35,21 @@ def __init__(self):
         # minimum main channel slope (replaces 0s from grid file)
         self.channel_slope_minimum = 0.0001
         # kinematic wave condition # TODO what is it?
-        self.kinematic_wave_condition = 1.0e6
+        self.kinematic_wave_parameter = 1.0e6
 
         # reservoir parameters # TODO better describe
         self.reservoir_minimum_flow_condition = 0.05
         self.reservoir_flood_control_condition = 1.0
         self.reservoir_small_magnitude_difference = 0.01
         self.reservoir_regulation_release_parameter = 0.85
-        self.reservoir_runoff_capacity_condition = 0.1
+        self.reservoir_runoff_capacity_parameter = 0.1
         self.reservoir_flow_volume_ratio = 0.9
 
         # number of supply iterations
         self.reservoir_supply_iterations = 3
 
         # minimum depth to perform irrigation extraction [m]
-        self.irrigation_extraction_condition = 0.1
+        self.irrigation_extraction_parameter = 0.1
         # maximum fraction of flow that can be extracted from main channel
         self.irrigation_extraction_maximum_fraction = 0.5