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 .