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.
- bash
- GDAL (tested with v3.6)
- a PostgreSQL / PostGIS database (tested with v14/v3.3)
- Python (tested with v3.11.0)
- bcdata
- fwapg
- bcfishobs
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:https://postgres@localhost:5432/bcfishpass
Load FWA:
git clone https://github.com/smnorris/fwapg
cd fwapg
make --debug=basic
Load/run bcfishobs:
git clone [email protected]:smnorris/bcfishobs.git
cd bcfishobs
make --debug=basic
Create db schema:
jobs/db_setup
Load source data:
jobs/load_static
jobs/load_monthly
jobs/load_weekly
jobs/load_modelled_stream_crossings
Run the model:
jobs/model_stream_crossings # (optionally - this is only needs to be run on the primary provincial bcfishpass database)
jobs/model_prep
jobs/model_run
Backup strategies will vary but it can be useful to dump the entire database to file.
This appends the date and commit tag date to the file name:
pg_dump -Fc $DATABASE_URL > bcfishpass.$(git describe --tags --abbrev=0).$(date +%F).dump