Installation

We support three ways to install cazy_webscraper.

Requirements

  • A POSIX-compliant operating system, e.g. Linux or MacOS.

  • Python 3.8 or later

  • An internet connection (to access CAZy and download data)

Installing with Bioconda

Tip

The most recent stable release of cazy_webscraper should always be avaiable from the bioconda channel.

To install cazy_webscraper using bioconda and all required packages, you can use the following command:

conda install -c bioconda cazy_webscraper

Note

If conda is not installed on your system, please see the conda website for instructions.

Installing with pip/PyPI

Tip

The most recent stable release of cazy_webscraper should always be avaiable from PyPI.

To install cazy_webscraper and all required packages using pip, you can use the following command:

python -m pip install cazy-webscraper

Installing from source

cazy_webscraper can be installed from the source code available at the GitHub repository.

Warning

The cazy_webscraper repository provides the development version of cazy_webscraper. This is the version that is most recently updated, but it may not be the latest stable version. In particular, the development version may contain features that are not yet in a stable version, and it may contain bugs.

Tip

To obtain the most recent stable source code from the cazy_webscraper repository, download a release from the releases page and extract the archive.

Attention

If you are using conda, you can use the Makefile in the cazy_webscraper repository to install cazy_webscraper from source, with the command make setup_env.

Obtaining cazy_webscraper source

The development version of cazy_webscraper is available at the GitHub repository and can be downloaded in the following ways.

To clone the cazy_webscraper repository using git, you can use the following command:

git clone https://github.com/HobnobMancer/cazy_webscraper

This will download the most recent development version of cazy_webscraper into a new directory called cazy_webscraper.

Alternatively, the development version can be downloaded as an archive file from the link below.. button:

* `source code .zip file <https://github.com/HobnobMancer/cazy_webscraper/archive/refs/heads/master.zip>`_

This file can be extracted and will create the directory cazy_webscraper.

Required packages

cazy_webscraper requires several packages to be installed, in order to run. You can install these packages using the requirements files in the cazy_webscraper directory. The commands needed depend on your working environment.

Using pip/PyPI

All third-party packages can be installed using pip/PyPI:

pip install -r requirements.txt
pip install -r requirements-dev.txt  # only needed if you are developing the code
pip install -r requirements-pip.txt  # only needed if you are developing the code

Using conda

The conda package manager can be used to install all required packages for running cazy_webscraper, but the sphinx package is not available in conda and must be installed using pip:

conda install --file requirements.txt
conda install --file requirements-dev.txt  # only needed if you are developing the code
pip install -r requirements-pip.txt        # only needed if you are developing the code

Installing cazy_webscraper

The cazy_webscraper package can be installed from source using the following command, issued from the root directory of the cazy_webscraper repository:

python setup.py install

If you are intending to edit or develop the code, you can use the develop option instead of install:

pip install -e .