bcfishpass

bcfishpass is a collection of scripts to create and maintain an aquatic connectivity / fish passage database for British Columbia to:

• track known barriers to fish passage (eg dams, waterfalls)
• work with assessed BC Provincial Stream Crossing Information System (PSCIS) crossings
• model potential barriers to fish passage (stream gradient, road/rail stream crossings)
• model passability/accessibility of streams based on species swimming ability
• model streams with potential for spawning and rearing activity (for select species)
• report on habitat/connectivity based indicators to support prioritization of assessment and remediation

Also provided are tools for mapping features in the database:

• basic web viewer
• comprehensive QGIS layer file

See the Documentation for details.

General requirements

• bash
• GDAL (tested with v3.6.2)
• a PostgreSQL / PostGIS database (tested with v14/v3.3.2)
• Python (tested with v3.11.0)
• bcdata (v0.7.6)
• fwapg (v0.4.0)
• bcfishobs (v0.1.1)

Setup

bcfishpass is a collection of shell/sql/Python scripts. To download and use the latest:

git clone https://github.com/smnorris/bcfishpass.git
cd bcfishpass

Presuming PostgreSQL/PostGIS are already installed, the easiest way to install dependencies is likely via conda. An environment.yml file is provided to install the required tools:

conda env create -f environment.yml
conda activate bcfishpass

Note that cdo is required for processing NetCDF discharge files, but this tool is not currently included in the conda environment. If processing discharge based habitat models, install cdo separately:

• conda install cdo (if your system supports this, this may not work on ARM based Macs)
• brew install cdo
• install from from source

If the database you are working with does not already exist, create it:

createdb bcfishpass

All scripts presume that the DATABASE_URL environment variable points to your database. For example:

export DATABASE_URL=postgresql://postgres@localhost:5432/bcfishpass

Once the database is created, load requirements fwapg and bcfishobs as per instructions in the respective projects.

With fwapg and bcfishobs loaded to your database, set up the bcfishpass schema/tables/functions:

cd db; ./setup.sh

Usage

To build all models:

make

Note that it is possible (and often preferred) to build components of the modelling separately. Refer to the various README files in the subfolders within the model folder for more info.