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
• bcfishobs

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

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

Install all other required tools/dependencies using your preferred package manager or via Docker. A conda environment and a Dockerfile are provided:

Conda

conda env create -f environment.yml
conda activate bcfishpass
jobs/<script>

Docker

docker compose build
docker compose up -d
docker compose run --rm runner jobs/<script>

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 this command:

docker-compose up -d

Connect to the db from your host OS via the port specified in docker-compose.yml:

psql -p 8001 -U postgres bcfishpass

Stop the containers (without deleting):

docker compose stop

Delete the containers:

docker compose down

To build/load/dump a small database for development/testing:

docker compose build
docker compose up -d
cd test
docker compose run --rm runner build_db.sh

Note that build_db.sh dumps all required inputs to a postgresql dump file - once it has been run once, a testing database can be quickly restored from the dump rather than loading from scratch:

cd ..
docker compose down           # shut down the vm
rm -rf postgres-data          # remove the testing db data folder
docker compose up -d          # restart docker, create_db is automatically run
pg_restore -d $DATABASE_URL test/bcfishpass_test.dump  # call restore from local OS

Run the models on the testing watershed groups:

docker compose run --rm runner test.sh