New assembly class

[manulera]

For a while, I have been meaning to move the new class for assembly that I am using in OpenCloning into pydna, and finally I have found the time to do so in the below PR:

#369

This new assembly class is more abstract, and can represent virtually any join between sequences, and that's what I use in OpenCloning for:

• Gibson Assembly
• Ligation
• Restriction + Ligation / Golden Gate
• Gibson
• Homologous recombination
• PCR
• Overlap extension PCR
• Cre/Lox recombination
• etc.

The good thing is that then you don't have to implement a new to join the sequences for each type of manipulation, instead you just need to write a function like the previous algorithm in the Assembly class to find common parts. This is going to simplify a lot the code, and the ability to extend it.

In addition, the new class fixes a bunch of bugs with annotation and duplicated/missing products from the current assembly implementation, listed as issues here: https://github.com/pydna-group/pydna/issues?q=is%3Aissue%20state%3Aopen%20label%3Afixed-with-new-assembly-model

The best way to get familiar with this implementation, is to have a look at this notebook that goes through a few examples.

This is an important update, so your feedback would be really appreciated.

Just a reminder, if you want to run the code from a particular branch:

# Create an activate a virtual env
python -m venv .venv
source .venv/bin/activate

# Get the repository
git clone https://github.com/pydna-group/pydna
cd pydna
git checkout new-assembly-model

# Install the package
pip install -e .

Then you can run the notebook (depending on what you use you may have to install extra deps to open a jupyter notebook in this python environment).