Link to accompanying paper

click here to go to the arxiv document

Installation

Please execute the following commands in your terminal to install the labproject package and its dependencies. We recommend using a conda environment to avoid conflicts with other packages.

# clone the repository
git clone https://github.com/mackelab/labproject.git

# (optional but recommended) create conda environment
conda create -n labproject python=3.9
conda activate labproject

# install labproject package with dependencies
python3 -m pip install --upgrade pip
cd labproject
pip install -e ".[dev,docs]"

# install pre-commit hooks for black auto-formatting
pre-commit install

pip install -e . installs the labproject package in editable mode, i.e. changes to the code are immediately reflected in the package.

The environment now contains, numpy, scipy, matplotlib, torch, and jupyter.

Development

Develop code in your desired way, e.g. in local notebooks (you don't commit them, they will be automatically ignored). The public notebooks i.e. for the website can be found in docs/notebooks/, if you want to share the whole notebook then move it in this directory.

Metrics

If you implemented a well-documented and reliable function that computes a metric, then move it to in labproject/metrics simply by add a new file my_metric.py.

Plotting

If you implemented a nice plotting function, then move it to in labproject/plotting.py. Especially if it is applicable to multiple tasks.

Running experiments

After committing and pushing your changes, GitHub will execute every run_{name}.py and update the figures in Overleaf.

You can also run it yourself with python labproject/run_{name}.py. Any results, will however not be pushed into the repository.

Documentation

We use mkdocs to create the public version of our tutorials (notebooks) and the API documentation. mkdocs are written in Markdown and are found in docs/.

After installing the necessary dependencies with pip install -e ".[docs]", you can view your local version with mkdocs serve in labproject/ and then open http://127.0.0.1:8000/. Every push to the main branch will also publish the current version on: http://www.mackelab.org/labproject/

To add your notebooks as pages in the docs, add the following to mkdocs.yml:

pages:
  - Notebooks: 
    - Example Notebook: notebooks/example.ipynb
    - FID notebook: notebooks/fid.ipynb
    - UR_NOTEBOOK_NAME: notebook/UR_NOTEBOOK_FILE

To add your functions to the API documentation, add the following to docs/api.md:

### Your module
::: labproject.your_module
    options:
      heading_level: 4

To build it locally use mkdocs build (or mkdocs serve to view it locally). After pushing to the main branch, the documentation will be automatically updated.

For adding new pages, create a new markdown file in docs/ and add it to mkdocs.yml:

pages:
  - 'your_new_page.md'

Every docstring in the code will be automatically added to the API documentation. We will use "Google Style" docstrings, see here for an example.

Notebooks

The jupyter notebooks are found in docs/notebooks/.

For your convenience, at the beginning of the jupyter notebook, run

%load_ext autoreload
%autoreload 2

for automatic reloading of modules, in case you make any running changes to the labproject code.