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

Development 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.

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 quickstart

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

docker compose build
docker compose up -d

Create the database schema and load FWA and other required data (this takes some time):

docker compose run --rm runner test/build_db.sh

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=8000 like this:

psql postgresql://postgres@localhost:8000/bcfishpass_test
psql -p 8000 -U postgres bcfishpass_test                     # shorter

Note that the specific localhost port mapped to the postgres port (5432) in the docker container can be modified in within the docker-compose.yml file.

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

docker compose run --rm runner test/test.sh

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

docker compose run -it --rm runner bash