Installation

Conda install (recommended)

Conda install is recommended as it will include all necessary dependencies (especially GDAL).

Requirements

It is recommened with mamba, that is much faster than conda to solve environment constraints.

If you already have a conda installed, install mamba in base environment:

conda install mamba -n base -c conda-forge

If you do not have conda installed, we recommend installing mambaforge.

Install

mamba env create -n fordead -f https://gitlab.com/fordead/fordead_package/-/raw/master/environment.yml
conda activate fordead

The conda environment can be deleted using the following command :

conda env remove -n fordead

Pypi install

Virtualenv is recommended in order to avoid side effects on other installed packages: see Creation of a virtualenv.

Requirements

Fordead depends on Rasterio for raster manipulations: see requirements for Rasterio.

Git may also be needed git.

Install

pip install -r https://gitlab.com/fordead/fordead_package/-/raw/master/requirements.txt

Using Docker

It is also possible to use this package using a docker. The docker image associated with this package already includes a conda environment with python and required dependencies, allowing to run containers in which to use this package. To use this docker image, if you are on windows, you must first install Docker Desktop.

Then use the following command to pull the docker image from this package's gitlab page.

docker pull registry.gitlab.com/fordead/fordead_package

Now you can create a container from the command line. By default docker containers can't access your directories, for it to be able to read and write data, you must specify a directory with all necessary data, the fordead package, and planned output directories.

docker run -t -i --name MYCONTAINER -v <YOUR_WORKING_DIRECTORY>:/mnt registry.gitlab.com/fordead/fordead_package /bin/bash

The contents of this working directory will be available in the "/mnt" directory inside the container. For example, if you have the directory "E:/fordead/fordead_package", and you use the command docker run -t -i --name fordead -v E:/fordead:/mnt registry.gitlab.com/fordead/fordead_package /bin/bash, its absolute path will then be "/mnt/fordead_package" in the container.

Then activate the virtual environment containing all dependencies, and install the fordead package.

conda activate fordead
cd <your_fordead_package_directory>
pip install .

You can now use all of fordead's command line functions or run python scripts using fordead functions from there.

When you are done, you can stop the container using docker stop fordead. If you wish to work using this container again, it is already created and already has fordead installed, and you can simply use :

docker start MYCONTAINER
docker exec -it MYCONTAINER /bin/bash

You can detach from the container using CTRL-D, and reattach or attach several times to access it with multiple command lines using docker exec -it MYCONTAINER /bin/bash.