Installing chaste_codegen

This page describes installation of chaste_codegen. For usage information see Code Generation from CellML.

chaste_codegen is a Python 3 tool with a number of requirements:

• python3
• python3-venv
• python3-pip

When using the Chaste Ubuntu package, the prerequisites, should be installed for you automatically.

Installing chaste_codegen with an internet connection#

If required, a manual copy of chaste_codegen can be installed as follows:

python3 -m venv </path/to/new/venv>
python3 -m </path/to/new/venv>/bin/python -m pip install --upgrade pip setuptools wheel
python3 -m </path/to/new/venv>/bin/python -m pip install chaste_codegen

where </path/to/new/venv> is the path to the directory the virtual Python 3 environment with chaste_codegen is placed in. This directory must not exist prior to creating the environment, but you can name it anything you like.

Installing chaste_codegen without an internet connection#

On systems that are isolated from the internet, chaste_codegen cannot be installed directly from PyPI. The following steps would enable a manual installation and allow building Chaste.

Create a build directory and change into it e.g.

mkdir chaste_build
cd chaste_build

Create and activate a virtual environment as follows:

python3 -m venv codegen_python3_venv
source codegen_python3_venv/bin/activate

You should now see something like:

(codegen_python3_venv) me@machine:~/chaste_develop$

To see what packages are currently installed, run

python3 -m pip list

pip, setuptools and wheel are likely to already be installed and you may not need to reinstall them.

Manually download appropriate versions of the following packages from PyPI and transfer them to the isolated system.

- pip > 20.2
- wheel > 0.35
- setuptools > 50.3
- pip > 20.2
- decorator >=4.4.2, <5
- importlib-metadata >=1.7, <2
- isodate >=0.6.0, <1
- lxml >=4.5.2, <5
- MarkupSafe >=1.1.1, <2
- mpmath >=1.1.0, <2
- networkx >=2.4, <3
- packaging >=20.4, <21
- Pint >=0.9, <1
- pyparsing >=2.4.7, <3
- rdflib >=5.0.0, <6
- six >=1.15.0, <2
- sympy >=1.6.1, <2
- zipp >=1.2.0, <2
- cellmlmanip >=0.2.0, <0.3
- Jinja2 >=2.11.2, <3
- chaste_codegen>=0.5.0, <0.6.0

Install the packages manually in the order above, with the virtual environment activated:

• Uncompress the archive if needed.
• Change into the directory containing setup.py
• If there are any installation instructions contained in the documentation, follow them. Otherwise, use python3 setup.py install