FAQs#

What if I don’t want to create a Python virtual environment?#

You can skip the virtual environment if you prefer. In that case, follow every step in Installation & updates except the ones that create or activate the environment.

Note that installing ExoSim into your system Python may require administrator privileges.

ExoSim is installed but not working: what can I do?#

In our experience, most errors raised after a failed run fall into three groups:

  1. Python raises ImportError: No module named #### because it cannot import a module ExoSim depends on.

    You can usually fix this by installing the missing dependency:

    pip install ####

    If the installation reports errors, you may need administrator privileges. On a Unix system:

    sudo pip install ####

  2. Python raises ImportError: No module named exosim.

    This means ExoSim is not installed in the environment you are using. Run the installation procedure again, or see the solution in What if I don’t want to create a Python virtual environment?.

What versioning system is used?#

We use a versioning scheme compliant with the PEP440 standard. Given a version number X.Y.Z:

  • X is the major identifier. A change here means a large part of the code has been refactored, and the release is not compatible with previous versions.

  • Y is the minor identifier. It changes when we add features or change how part of the code works. Users will notice these changes and should check the documentation if errors occur.

  • Z is the patch identifier. We fixed a bug or optimised something, and users will probably not notice the difference.

You may also see versions of the form X.YbZ, where b stands for beta. Other suffixes are c (release candidate) and r (release, usually omitted), which mark stable, distributable versions.

How can I check which ExoSim version I’m using?#

There are several ways.

The quickest is to open this documentation and look under the logo in the left-hand panel, or to open the changelog, which lists every release. This tells you the version the documentation describes, not necessarily the one you have installed.

To check the installed version, run this from the ExoSim virtual environment:

pip show exosim

The output includes a Version line. From a Python session you can instead run:

import exosim
exosim.__version__

The version is also recorded in the output files of every ExoSim module, in the ExoSim version metadata, and in the exosim.log file.

Make sure the installed version matches the one in the documentation. If it does not, upgrade your installation.

If you installed ExoSim with pip (see install from PyPI):

pip install exosim --upgrade

If you installed from the GitHub source (see install from Git), go to your ExoSim directory, pull the latest changes, and update the environment:

cd /your_path/ExoSim2.0
git pull
uv sync --extra dev

Then check the version again.

Tip

If you use Anaconda Python, its IDE can list every package installed in each virtual environment together with its version.

How can I load HDF5 data into my code?#

Once your dataset is stored in an .h5 file, you can read it with the h5py package. Assuming the file is called data_file.h5:

import h5py

with h5py.File('data_file.h5', 'r+') as input_file:
    ...

The file can now be navigated like a Python dictionary. The h5py documentation covers reading and writing data (https://docs.h5py.org/en/stable/high/dataset.html#reading-writing-data); here is a short example:

import h5py

with h5py.File('data_file.h5', 'r+') as input_file:
    data = input_file['first_level']['second_level']['dataset_name'][()]

This navigates the file to the dataset dataset_name under first_level/second_level and loads its full content into the data variable.

Load signals and tables#

You can also load stored data back into its original Python class. For example, you can cast a stored table into an QTable with astropy.io.misc.hdf5.read_table_hdf5:

import h5py
from astropy.io.misc.hdf5 import read_table_hdf5

with h5py.File('data_file.h5', 'r+') as input_file:
    table_data = input_file['first_level']['table_group']
    table = read_table_hdf5(table_data)

Here table_data is the group loaded from the HDF5 file; it holds both the table and its metadata, stored as .__table_column_meta__.

For the Signal class, use exosim.output.hdf5.utils.load_signal:

import h5py
from exosim.output.hdf5.utils import load_signal

with h5py.File('data_file.h5', 'r+') as input_file:
    signal_group = input_file['first_level']['stored_signal_name']
    signal = load_signal(signal_group)