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
• support mapping in office and field via a comprehensive QGIS layer file

See the Documentation for details.

General requirements

• bash
• GDAL (tested with v3.6)
• a PostgreSQL / PostGIS database (tested with v14/v3.3)
• Python (tested with v3.11.0)
• bcdata
• fwapg
• bcfishobs

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

Install required tools using your preferred method. For local development, conda can be simplest:

conda env create -f environment.yml
conda activate bcfishpass

A Docker image is also provided:

docker pull ghcr.io/smnorris/bcfishpass:main

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

Set up the database schema:

jobs/setup

Load FWA data:

git clone https://github.com/smnorris/fwapg
cd fwapg
mkdir -p .make; touch .make/db  # just reload data
mkdir -p data
make --debug=basicjobs/load_fwa

Load all additional data:

jobs/load_static
jobs/load_monthly
jobs/load_weekly

Run bcfishobs:

git clone git@github.com:smnorris/bcfishobs.git
cd bcfishobs
mkdir -p .make
make -t .make/setup
make -t .make/load_static
make -t .make/fiss_fish_obsrvtn_pnt_sp
make --debug=basic

Finally, navigate back to the root bcfishpass folder and build bcfishpass:

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.