https://github.com/smnorris/bcfishpass
Model and monitor aquatic habitat connectivity in BC. Tools to plan and prioritize the assessment and remediation of barriers.
https://github.com/smnorris/bcfishpass
british-columbia connectivity culverts digital-road-atlas dra fish-habitat-models fish-observation fish-passage freshwater-atlas fwa gradient-barriers pscis restoration roads stream-network
Last synced: 24 days ago
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Model and monitor aquatic habitat connectivity in BC. Tools to plan and prioritize the assessment and remediation of barriers.
- Host: GitHub
- URL: https://github.com/smnorris/bcfishpass
- Owner: smnorris
- License: apache-2.0
- Created: 2020-11-07T01:26:03.000Z (over 4 years ago)
- Default Branch: main
- Last Pushed: 2025-04-11T23:41:28.000Z (26 days ago)
- Last Synced: 2025-04-12T00:29:31.877Z (26 days ago)
- Topics: british-columbia, connectivity, culverts, digital-road-atlas, dra, fish-habitat-models, fish-observation, fish-passage, freshwater-atlas, fwa, gradient-barriers, pscis, restoration, roads, stream-network
- Language: PLpgSQL
- Homepage: https://smnorris.github.io/bcfishpass
- Size: 33.5 MB
- Stars: 8
- Watchers: 3
- Forks: 13
- Open Issues: 58
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# 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](https://smnorris.github.io/bcfishpass/) for details.
## General requirements
- bash
- GDAL
- PostgreSQL / PostGIS
- Python
- [bcdata](https://github.com/smnorris/bcdata)
- [fwapg](https://github.com/smnorris/fwapg)
- [bcfishobs](https://github.com/smnorris/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/
#### 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