Quick Installation¶
To quickly get started with running pyrcel, complete the following steps:
Set up a new Python environment; we recommend using mambaforge:
$ mamba create -n pyrcel_quick_start python=3.11
Activate the new Python environment and install the model and its dependencies. If you install the published version from PyPi (recommended), then you also need to install Assimulo using the Mamba package manager - but no other manual dependency installation is necessary:
$ mamba activate pyrcel_quick_start
$ pip install pyrcel
$ mamba install -c conda-forge assimulo
Run a test simulation using the CLI tool and a sample YAML file from pyrcel/examples/*.yml (you may want to clone the repository or download them locally):
$ run_parcel simple.yml
Detailed Installation Notes¶
From PyPI¶
If you already have all the dependencies satisfied, then you can install the
latest release from PyPI by using
pip
:
$ pip install pyrcel
From source code¶
To grab and build the latest bleeding-edge version of the model, you should use
pip
and point it to the source code repository on github:
$ pip install git+git://github.com/darothen/pyrcel.git
This should automatically build the necessary Cython modules and export the code package to your normal package installation directory. If you wish to simply build the code and run it in place, clone the repository, navigate to it in a terminal, and invoke the build command by hand:
$ python setup.py build_ext --inplace
This should produce the compiled file parcel_aux.so in the model package.
You can also install the code from the cloned source directory by invoking
pip install
from within it; this is useful if you’re updating or
modifying the model, since you can install an “editable” package which
points directly to the git-monitored code:
$ cd path/to/pyrcel/
$ pip install -e .
Dependencies¶
This code was originally written for Python 2.7, and then futurized to Python 3.3+ with hooks for backwards compatibility. It should work on modern Python versions, and we recommend using Python 3.11+ for the greatest compatibility with required dependencies.
The easiest way to manage dependencies is to use a tool like Mambaforge <https://conda-forge.org/miniforge/>
to set up an environment. Suitable environment files can be found in the pyrcel/ci
directory.
Necessary dependencies¶
All of these (except for Assimulo; see the note below) can be installed via pip:
Note
As of version 1.2.0, the model integration components are being re-written and only the CVODE interface is exposed. As such, Assimulo is temporarily a core and required dependency; in the future the other solvers will be re-enabled. You should first try to install Assimulo via conda
$ mamba install -c conda-forge assimulo
since this will automatically take care of obtaining necessary compiled dependencies like sundials. However, for best results you may want to manually install Assimulo, since the conda-forge recipe may default to a sundials/OpenBLAS combination which could degare the performance of the model.
Numerical solver dependencies¶
Recommended additional packages¶
Note
These are not required for the model to run, but are useful for post-processing and visualization of the model output. They should be installed automatically if you install the model from PyPI or the source code repository.
Testing¶
A nose test-suite is under construction. To check that your model is configured and running correctly, you copy and run the notebook corresponding to the basic run example, or run the command-line interface version of the model with the pre-packed simple run case:
$ cd path/to/pyrcel/
$ ./run_parcel examples/simple.yml
Bugs / Suggestions¶
The code has an issue tracker on github and I strongly encourage you to note any problems with the model there, such as typos or weird behavior and results. Furthermore, I’m looking for ways to expand and extend the model, so if there is something you might wish to see added, please note it there or send me an e-mail. The code was written in such a way that it should be trivial to add physics in a modular fashion.