Specific assemblies

[manulera]

This is a major pull request that introduces the following features:

• Specific assemblies:
  • A set of functions (starting with gibson_assembly) that simplify the usage of the Assembly class for the end user.
  • Now, the user does not need to know that they have to pass an algorithm function to the assembly class, or that they need to call assemble_linear or assemble_circular on the returned object. Instead, they get a list of the products of the assembly.
  • Better documentation should be included in the future for filtering-out of results: Better documentation of products returned by assembly #433.
  • There are plenty of examples of how to use these functions in the docstrings, and also in the hackathon notebook at https://github.com/pydna-group/pydna/blob/master/docs/notebooks/hackathon_copenhagen_2025.ipynb
• SnapGene parser:
  • I have added a SnapGene parser to the parsers file, that also gets whether the sequence is circular or linear. Eventually we should transition to a more permissive parser for gb files Better file parser #428
• Hackathon notebook:
  • Will be at this address when merged, for now it's in the branch at docs/notebooks/hackathon_copenhagen_2025.ipynb. Has plenty of examples of these new features.
• New methods supported thanks to algorithm functions:
  • Golden Gate (asrestriction_ligation_assembly).
  • Cre-LoxP
  • Gateway Cloning

[codecov]

Codecov Report

❌ Patch coverage is 92.27468% with 18 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
src/pydna/assembly2.py	88.63%	5 Missing and 5 partials ⚠️
src/pydna/gateway.py	87.93%	6 Missing and 1 partial ⚠️
src/pydna/sequence_regex.py	94.11%	0 Missing and 1 partial ⚠️

@@            Coverage Diff             @@
##           master     #429      +/-   ##
==========================================
+ Coverage   93.13%   93.31%   +0.18%     
==========================================
  Files          37       39       +2     
  Lines        4208     4428     +220     
  Branches      590      636      +46     
==========================================
+ Hits         3919     4132     +213     
+ Misses        242      240       -2     
- Partials       47       56       +9     

Files with missing lines	Coverage Δ
src/pydna/cre_lox.py	100.00% <100.00%> (ø)
src/pydna/parsers.py	86.66% <100.00%> (+0.78%)	⬆️
src/pydna/sequence_regex.py	94.11% <94.11%> (ø)
src/pydna/gateway.py	87.93% <87.93%> (-3.74%)	⬇️
src/pydna/assembly2.py	96.12% <88.63%> (+0.55%)	⬆️

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