A standard Python installation is required, as well as any additional Python modules that are listed in the README file under the “Dependencies” section. PyRDM is designed to run on the Linux operating system.
It is recommended that users use the terminal to install and run PyRDM.
Downloading and installing¶
PyRDM can either be installed from source or through a Conda package, both of which are described below.
PyRDM’s source code is hosted on GitHub and can be found here: https://github.com/pyrdm/pyrdm. The first step is to download the source code using:
git clone https://github.com/pyrdm/pyrdm.git pyrdm
The core dependencies that PyRDM needs to function can then be installed by navigating to the base directory of PyRDM (i.e. the directory that the Makefile is in) using
sudo pip install -r requirements.txt
Use the following command to install the PyRDM library:
sudo make install
sudo is likely to be necessary here if the default install
directory is located outside of
/home. This will yield a system-wide
install of PyRDM, which is recommended.
Note 2: In order for Python to find the PyRDM module, you will need
to add the PyRDM base directory to your
variable, unless you have used
sudo as mentioned in Note 1 above.
This can be achieved using:
You may wish to add this statement to your
/etc/bash.bashrc files so the
PYTHONPATH is set correctly each time you log in.
Users of Conda can install PyRDM and its dependencies using
conda install -c ctjacobs -c pypi -c auto -c ioos -c conda-forge pyrdm
You should copy the contents of the file
pyrdm.ini.example to a new
pyrdm.ini and save it in the
/home/your_username/.config directory. If this directory does not
exist, please create it first using
The contents of the new file
pyrdm.ini should then be modified as
per the guidance in the following subsections.
Zenodo uses a personal access token to handle authentication.
PyRDMas the name of the token. Ensure that
deposit:writeare selected, as per figure:zenodo_token.
Create. The access token should be pasted into the
[zenodo]section of the
Zenodo requires at least one author’s name and affiliation to be present when creating a deposition. For a software deposition, PyRDM will try to obtain this information from the
AUTHORSfile. However, for a dataset deposition, this information needs to be provided under the
[general]section of the
PyRDM provides limited support for publishing with DSpace-based services which use the SWORD protocol (version 2).
- Locate the URL of the SWORD Service Document, and add it under the
[dspace]section of the
pyrdm.iniconfiguration file. Note: this URL may need to be obtained from the system administrator.
- Add the title of the DSpace Collection that you want to publish in. Note: the publication’s privacy settings are determined by the DSpace Collection, not by the
privateparameter in PyRDM.
- Add your user name and password used to access the DSpace server. Note: this is currently stored in plain text, so make sure that the PyRDM configuration file is not readable by other users.
PyRDM comes with a suite of unit tests which verify the correctness of its functionality. It is recommended that you run these unit tests before using PyRDM by executing:
on the command line. Many of these tests require access to a Figshare and a Zenodo
account, so please ensure that the
pyrdm.ini setup file contains
valid authentication tokens.