pyfvs 0.3.5

Python wrappers and utilities for using the Forest Vegetation Simulator

PyFVS

Python wrappers and utilities for using the Forest Vegetation Simulator

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Project Status

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PyFVS wraps a fork of the official FVS code with minimal, non-core, modifications.

PyFVS currently supports Windows and Linux using the GCC family of compilers.

Documentation

Check out the AI generated documentation wiki.

Features

• FVS Class

  • FVS Step API
    • Growth cycle interation
    • Within-cycle blocking callbacks for fine-grained inspection and sub-model interaction
  • Initialize inventory trees from arrays and dataframes
  • Runtime interaction with FVS internal arrays and variables
    • Facilitates out-of-core event logic
    • Sub-cycle analysis of model components and data

• Keyword Generator:

  • Object oriented FVS keyword file generation
  • Automates keyword file formatting and runtime handling

• Command line interface

Variants

Not all FVS variants are currently implement. More will be added as time allows.

• PN - Pacific Northwest Coast
• WC - Westside Cascades
• SO - South Central Oregon and Northeast California
• OP - ORGANON Pacific Northwest
• OC - ORGANON Southwest
• EC - East Cascades
• CA - Inland California and Southern Cascades
• NC - Klamath Mountains (Northern California)
• BM - Blue Mountains
• IE - Inland Empire (Northern Idaho)
• CI - Central Idaho
• AK - Alaska
• WS - Western Sierra Nevada

Parity with Official Binaries

PyFVS is designed to be consistent with the official FVS binaries. Before a release all variants are run through a series of unit test to ensure functionality and equivalence with official FVS binaries.

• Variant specific unit tests from official FVS releases
• Additional unit tests for specific functionality

Usage

NOTE: The PyFVS API is beta. Names and arguments may change as features evolve. Deprecation warnings will be raised when possible. However, there is guarantee of backward compatibility.

Command Line

>pyfvs --help
>pyfvs run PN -k path/to/keywords.key

Run a simulation using an existing keyword file and treelist

from pyfvs import fvs
f = fvs.FVS('PN')
kwds = 'path/to/keywords.key'
f.init_projection(kwds)

# Iterate through the simulation cycles
for cycle in f:
    print(f.year)
    # Do something interesting

# Closeout the simulation
f.end_projection()

Genarate keywords for a bareground simulation

from pyfvs import fvs,keywords
f = fvs.FVS('PN')
# Setup the KeywordSet for the simulation
kw = f.keywords
# Grow for 20 periods
kw += keywords.NUMCYCLE(20)
# Add default STDINFO keyword
kw += keywords.STDINFO()
# This is a bareground simulation, so no treelist
kw += keywords.NOTREES()
# Initialize the ESTAB keywordset
est = keywords.ESTAB()
# Add 350 planted DF seedlings to the ESTAB
est += keywords.PLANT(1,'DF',350)
# Add the ESTAB keywordset to the simulation
kw += est
# Execute the simulation
f.run()
# Print the summary table
print(f.summary)

Development

Clone the 'dev' branch, including all submodules

git clone --branch dev --recurse-submodules https://github.com/forest-modeling/PyFVS.git

For local development a Pixi environment is included in pyproject.toml.

# Install Pixi on Linux
curl -fsSL https://pixi.sh/install.sh | sh

# Install Pixi on Windows
powershell -ExecutionPolicy Bypass -c "irm -useb https://pixi.sh/install.ps1 | iex"

Initialize the environment in the root of the project

pixi init --pyproject

pixi shell

Local Development Build

The Pixi environment includes GCC and GFortran compilers from Conda-Forge. Use the included Pixi task to install PyFVS in the current environment in development mode. Pass an optional comma separated list of lower case variant abbreviations to restrict the build to target variants. Additionally, an optional build mode can be passed, debug or release.

pixi run dev "pn,wc" debug

Development mode in Pixi is consistent with Pip. Additionally, PyFVS is built with Meson and Meson-Python. Changes to source files, Python or Fortran, will trigger a recompile on the next import. Alternatively, you can trigger a build by calling the dev task again.

Run Tests

pixi run test

Build Wheels

Wheel files for the current system will be placed in the dist folder along with an sdist source archive.

pixi run build "pn,wc"