Installation

FOGGIE-Trident must be installed installed from source, but all other dependencies can be installed using their stable, released versions. Occasionally, bugs in yt or yt_astro_analysis may get fixed and there is a delay before new stable versions are released. It is then necessary to install those packages from source. See Installing Development Versions of yt and yt_astro_analysis for information on that.

Install Conda

Conda is a package manager providing a clean, stand-alone installation of python that is self-contained in its installation directory. yt & trident require a modern installation of python to work. conda provides that installation.

You can see if conda is already installed by running:

$ conda -h

If conda is installed, move to the next step. Otherwise install Mini-conda.

Use the appropriate conda install script for your architecture. We recommend getting the latest version of conda for Python3 for your architecture here: https://repo.continuum.io/miniconda/

For modern macs:

$ curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
$ bash Miniconda3-latest-MacOSX-x86_64.sh

For modern linux machines:

$ wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
$ bash Miniconda3-latest-Linux-x86_64.sh

At the end of the installation step, allow conda to add its installation directory to the $PATH.

Clone FOGGIE-Trident Repository and Install

Clone the FOGGIE-Trident repository and install from it by doing the following:

$ git clone git@github.com:foggie-sims/trident trident
$ cd trident
$ pip install -e .

This will install all hard dependencies as well. You will need to keep this directory.

Install Additional Dependencies

You may also want to install mpi4py to allow trident to run in parallel. This is not required, but can be done with either conda or pip.

$ conda install mpi4py

$ pip install mpi4py

Updating Your FOGGIE-Trident Installation

To pull in the latest changes, return to your trident directory and use git to update your repository.

$ cd trident
$ git pull origin main

Get Ionization Table and Verify Installation

In order to calculate the ionization fractions for various ions from density, temperature, metallicity fields, you will need an ionization table datafile and a configuration file. Because this datafile can be large, it is not packaged with the main source code. The first time you try to do anything that requires it, Trident will attempt to automatically set this all up for you with a series of interactive prompts. This step requires an internet connection the first time you run it.

In addition, Trident provides a simple test function to verify that your install is functioning correctly. This function not only tries to set up your configuration and download your ion table file, but it will create a simple one-zone dataset, generate a ray through it, and create a spectrum from that ray. This should execute very quickly, and if it succeeds it demonstrates that your installation has been totally successful:

$ python
>>> import trident
>>> trident.verify()
...Series of Interactive Prompts...

If you cannot directly access the internet on this computer, or you lack write access to your $HOME directory, or this step fails for any reason, please follow our documentation on Manually Installing your Ionization Table.

Science!

Congratulations, you’re now ready to use Trident! Please refer to the documentation for how to use it with your data or with one of our sample datasets. A good place to start is the annotated example, and the example scripts found in the source code.

Installing Development Versions of yt and yt_astro_analysis

Installing yt or yt_astro_analysis from source is similar to installing trident. Clone the repo and use pip to install.

yt

$ git clone https://github.com/yt-project/yt yt
$ cd yt
$ pip install -e .

yt_astro_analysis

$ git clone https://github.com/yt-project/yt_astro_analysis yt_astro_analysis
$ cd yt_astro_analysis
$ pip install -e .

Updating yt and yt_astro_analysis Installations

To update either yt or yt_astro_analysis do:

$ cd <repo-directory>
$ git pull origin main
$ pip install -e .

Note, the final step of pip install -e . is necessary whenever cython files have been modified, as these require rebuilding.

Manually Installing your Ionization Table

If for some reason you are unable to install the config file and ionization table data automatically, you must set it up manually. When Trident runs, it looks for a configuration file called config.tri in the $HOME/.trident directory or alternatively in the current working directory (for users lacking write access to their $HOME directories). This configuration file is simple in that it tells Trident a few things about your install including the location and filename of your desired ionization table. Manually create a text file called config.tri with contents following the form:

[Trident]
ion_table_dir = ~/.trident
ion_table_file = hm2012_hr.h5

To manually obtain an ion table datafile, download and gunzip one from: http://trident-project.org/data/ion_table . While the config.tri file needs to exist in your $HOME/.trident directory or in the working directory when you import trident, the ion_table datafile can exist anywhere on the file system. Just assure that the config file points to the proper location and filename of the ion table datafile.

Now, to confirm everything is working properly, verify your installation following Get Ionization Table and Verify Installation. If this fails or you have additional problems, please contact our mailing list.

Uninstallation or Switching Code Versions

If you installed via pip, do:

$ pip uninstall trident

To fully remove the code from your system, remember to remove any ion table datafiles you may have downloaded in your $HOME/.trident directory, and follow the instructions for how to uninstall yt.