/saugatucket-fish-passage

Scripts for data processing and analysis of Saugatucket River fish passage data.

Primary LanguageJupyter Notebook

saugatucket-fish-passage

Processing and analysis of fish passage data along the Saugatucket River, RI.

Project Organization

├── LICENSE
├── Makefile           <- Makefile with commands like `make data` or `make train`
├── README.md          <- The top-level README for developers using this project.
├── data
│   ├── external       <- Data from third party sources.
│   ├── interim        <- Intermediate data that has been transformed.
│   ├── processed      <- The final, canonical data sets for modeling.
│   └── raw            <- The original, immutable data dump.
│
├── models             <- Trained and serialized models, model predictions, or model summaries
│
├── notebooks          <- Jupyter notebooks. Naming convention is a number (for ordering),
│                         the creator's initials, and a short `-` delimited description, e.g.
│                         `1.0-jqp-initial-data-exploration`.
│
├── references         <- Data dictionaries, manuals, and all other explanatory materials.
│
├── reports            <- Generated analysis as HTML, PDF, LaTeX, etc.
│   └── figures        <- Generated graphics and figures to be used in reporting
│
├── environment.yml    <- The requirements file for reproducing the analysis environment with
│                         Anaconda`
│
├── setup.py           <- makes project pip installable (pip install -e .) so src can be imported
├── src                <- Source code for use in this project.
│   ├── __init__.py    <- Makes src a Python module
│   │
│   └── data           <- Scripts to download or generate data
│       └── make_dataset.py

Project based on the cookiecutter data science project template. #cookiecutterdatascience

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Cloning the GitHub Repository

To clone this GitHub repository to your local machine on Windows, follow these steps:

  1. Open Command Prompt, PowerShell, or GitBash.
  2. Navigate to the directory where you want to clone the repository using the cd command. For example:
cd path\to\desired\directory
  1. Use the following command to clone the repository:
git clone https://github.com/gtdang/saugatucket-fish-passage.git
  1. Once the cloning process is complete, navigate into the cloned repository directory:
cd repository-name

Creating a Python Environment

This repository contains an environment.yml file to create an environment with Anaconda:

  1. Install Anaconda or miniconda if you have not already.

  2. Use the following command create and activate the conda environment:

conda env create -f environment.yml
conda activate sfp
  1. Next install the data processing functions from the source code with the following command:
pip install -e .

This will allow us to import functions in our notebooks. The functions are contained in the src directory/module in this project.

Launching jupyter lab

Net we launch the JuptyerLab IDE to run the notebooks in this project.

jupyter lab