For Developers

Developer Installation

To install the python interface and allow for changes to the code to be immediately updated in your package, clone the main git repository and navigate to the crisscross_kit directory. Next, run:

pip install -e .

You may also choose to install the package dependencies using other package managers, such as conda. The requirements are listed in requirements.txt.

• To install with pip run the following: pip install -r requirements.txt
• For conda run the following: conda install -c conda-forge --file requirements.txt
• For PyVista, install the dependencies from requirements_pyvista.txt.
• For Blender, simply run pip install bpy

Useful locations

The crisscross_kit/crisscross/scripts directory contains various scripts the team has used for testing or creating different megastructure designs, which can be used as a basis for any new design.

The crisscross_kit/crisscross/dna_source_plates directory contains various source plates used by the crisscross team. These layouts can be adopted or adjusted as necessary.

File Formats

Design File (.xlsx)

Designs are stored as Excel files with these worksheets:

Worksheet	Contents
slat_layer_x	Slat positions on layer x
handle_interface_x	Assembly handles between layer x and layer x + 1
cargo_layer_x_y_z	Cargo tags placed on layer x, where y/z are lower/upper and h2/h5
seed__layer_x_y_z	Placement of seed handles. Syntax identical to that of cargo.
metadata	Layer colours, slat counts, etc.
slat_types	Slat type for each slat placed in the design.
slat_handle_links	Any links enforced between different handles in the design.

Source Plate File (.xlsx)

DNA source plates follow this format:

Column	Description
well	Plate position (A1, A2, ...)
name	Handle identifier (see naming convention)
sequence	DNA sequence
description	Optional descriptor
concentration	Staple concentration (in uM)

Naming convention: CATEGORY-VALUE-hSIDE-position_SLATPOS

Examples: - ASSEMBLY_HANDLE-1-h2-position_1 - CARGO-marker-h5-position_16 - FLAT-none-h2-position_1

Building for PyPI

For developers looking to build the package for PyPI, you can use the following commands from the crisscross_kit directory of the repository:

First, make sure the build tools are installed:

pip install build twine setuptools-scm

Next, build the package:

python -m build

The build command will create a dist folder containing the .whl and .tar.gz files for the package. These can be uploaded to PyPI using:

twine upload dist/*

You will need to have a PyPI account and set up your credentials in ~/.pypirc for the upload to work (you will also need to be set as a collaborator on the crisscross_kit project too).

Local Docs Generation

The documentation available here is built using mkdocs. You can build a local version of the docs using the following commands from the docs directory:

mkdocs build

mkdocs serve

You can then view the docs from http://127.0.0.1:8000/ for quick debugging.

GitHub Actions

Building and releasing all packages to PyPi is automated using a GitHub actions workflow (.github/workflows/deploy_crisscross_kit_to_pypi.yml). Briefly, this workflow builds the package for all operating systems (including the C code for eqcorr2d) and uploads the resulting wheels to PyPi. The same workflow can be emulated locally if necessary.

The workflow is triggered automatically when a new tag with format 'python-x.y.z' is pushed to the repository on the main branch.

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