pcx 0.6.2.post1

PCX is a Python JAX-based library designed to develop highly configurable predictive coding networks.

PCX -- Predictive Coding Networks Made Simple

Introduction

PCX is a Python JAX-based library designed to develop highly configurable predictive coding networks. Please refer to the tutorial notebooks in the examples folder to get started. PCX can be installed by following one of the listed three methods.

Default: Installation via PIP [Method #1].

First, create an environment with Python >= 3.10 and install JAX in the correct version for your accelerator device. For cuda >= 12.0, the command is

pip install -U "jax[cuda12]"

For CPU only:

pip install -U "jax[cpu]"

Then you hav two options:

• Install a stable version
• Clone this repository and install the package by linking to the this folder. The installation of this libary only links to this folder and thus dynamically updates with all your changes.

Install stable version

On the right side of the repository, click on "releases" and download the wheel file. You can install it using

pip install path/to/wheel_file.whl

Alternatively you can use the PyPi version by [work in progress...]

Install dynamically from github

Clone this repository locally and then:

pip install -e /path/to/this/repo/ --config-settings editable_mode=strict

Ensuring Reproducibility: Installation via poetry [Method #2]

TL;DR This is an alternative installation method that creates a fully configured environment to ensure your results are reproducible (no pip install, see previous section for that; no docker install, see the next section for docker install):

1. Install conda.
2. Install poetry.
3. poetry config virtualenvs.create false.
4. Create a conda environment with python>=3.10: conda create -n pcax python=3.10.
5. Activate the environment: conda activate pcax.
6. cd into the root pcax folder.
7. poetry install --no-root.

In this way, we use poetry to make sure the environment is 100% reproducible. If you are not familiar with poetry, now is a good time to skim through the docs.

Development Notes:

1. If you need to add a Python package to the environment, use poetry add package. Avoid pip install!
2. If you want to update a version of an existing package, run poetry update package. It will update the package to the latest available version that fits the constraints.
3. DO NOT update the package versions in the pyproject.toml file manually. Surprisingly, pyproject.toml DOES NOT specify the versions that will be installed, poetry.lock does. So, first check the package version in poetry.lock.
4. DO NOT update the package versions in the poetry.lock file manually. Use poetry update package instead. poetry.lock HAS to be generated and signed automatically.
5. If pyproject.toml and poetry.lock have diverged for some reason (for example, you've merged another branch and resolved conflicts in poetry.lock), use poetry lock --no-update to fix the poetry.lock file.
6. DO NOT commit changes to pyproject.toml without running poetry lock --no-update to synchronize the poetry.lock file. If you commit pyproject.toml that is not in sync with poetry.lock this will break the automatic environment configuration for everyone.

Fully Automatic: Environment in Docker with Dev Containers [Method #3]

Run your development environment in a docker container. This is the most straightforward option to work with pcx, as the development environment is pre-configured for you.

The Dockerfile is located in pcx/docker, with the run.sh script that builds and runs it. You can play with the Dockerfile directly if you know what you are doing or if you don't use VSCode. If you want a fully automated environment setup, then forget about the pcx/docker directory and read on.

Warning: This image should run on CUDA 12.2 or later, but not earlier. Make sure that your nvidia-smi reports CUDA >=12.2. If not, update the base nvidia/cuda image and the fix at the bottom in the docker/Dockerfile to use the same version of CUDA as your host does.

Requirements:

1. A CUDA >=12.2 enabled machine with an NVIDIA GPU. You can do without a GPU, probably, just omit the steps related to the GPU passthrough and configuration.
2. Install docker.
3. Install nvidia-container-toolkit to enable docker to use the GPU.
4. Make sure to re-start the docker daemon after the previous step. For example, on Ubuntu this will be sudo systemctl restart docker.
5. Install Visual Studio Code.
6. Install the Dev Containers extension in VSCode.
7. Optionally, read how to develop inside container with VS Code.

Once everything is done, open this project in VS Code and execute the Dev Containers: Reopen in Container command (Ctrl/Cmd+Shift+P). This will build the docker image and open the project inside that docker image. Building the docker image for the first time may take around 15-30 minutes, depending on your internet speed.

You can always exit the container by running the Dev Containers: Reopen folder locally command. You can rebuild the container by running the Dev Containers: Rebuild Container command.

You can check that you're running inside a container by running hostname. If it outputs meaningless 12 characters, then you are inside a container. If it outputs the name of your machine, you are not in a container.

When running a Jupyter Notebook it will prompt you to select an environment. Select Python Environments -> Python 3.10 (any of them, as they are the same).

Important notes:

1. You are not supposed to modify the docker/Dockerfile unless you perfectly know what you are doing and why.
2. You are not supposed to run the docker container directly. The Dev Containers extension will do this for you. If you think you need to docker run -it then something is really wrong.
3. Use poetry to add a python package to the environment: poetry add --group dev [package]. The --group dev part should be omitted if this package is needed for the core pcx code. Try not to install packages with pip.
4. Please update your docker to >>20.10.9. This image is known not to work with docker <= 20.10.9. It failes with the following message: E: Problem executing scripts APT::Update::Post-Invoke 'rm -f /var/cache/apt/archives/*.deb /var/cache/apt/archives/partial/*.deb /var/cache/apt/*.bin || true'.
5. Sometimes Pylance fails to start because it depends on the Python extension that starts later. In this case, just reload the window by running the Developer: Reload window command.

PyTorch with GPU support: By default, the image will install a CPU-only PyTorch. If you need GPU support with PyTorch, do the following:

1. Open the project in a container using DevContainers as described above.
2. Replace ALL occurrences of source = "torch-cpu" with source = "torch-gpu" in the pyproject.toml file.
3. Run poetry lock --no-update to re-generate the poetry.lock file. Note that you should do it while running inside the container.
4. Run poetry install. Make sure you run it inside the container. It will take up to 20 minutes.

Docs

Go to /docs/README.md to learn how to get them.

## Contributing

If you want to contribute to the project, please read CONTRIBUTING.md