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
• PostgreSQL / PostGIS
• Python
• bcdata
• fwapg

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

If running the scripts on your host OS, install required tools/dependencies using your preferred package manager. See the Dockerfile for the list of tools required. Note that all scripts presume the path to an existing PostGIS enabled database is defined by the environment variable $DATABASE_URL:

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

Docker

Clone the repository as above, build and start the containers:

docker compose up -d

Load FWA and other required data:

docker compose run --rm runner jobs/setup

Docker is configured to write the database to postgres-data - even if containers are deleted, the database will be retained here. If you have shut down Docker or the container, start it up again with the same up command:

docker-compose up -d

Connect to the db from clients on your host OS (eg psql/QGIS/PgAdmin/etc) via localhost and port=8001 (modify port as required via .env file):

psql postgresql://postgres@localhost:8001/bcfishpass
psql -p 8001 -U postgres bcfishpass                     # shorter

To run default habitat models on the watershed groups specified in parameters/example_testing:

docker compose run --rm runner jobs/test

Drop in to the docker container to interactively run scripts as needed:

docker compose run -it --rm runner bash