Implement test data generator

[Aratz]

Description

This PR implements a test data generator. The generator is split into three parts:

1. Generate the topology of the graph representing a cell. For now it uses a simple downsampling technique to match the desired average degree. If necessary, this can be improved later with techniques matching a more realistic degree distribution.
2. Populate the graph with markers, splitting the markers from the panel file into three abundance levels. Hashing markers are also added at this stage.
3. Generate reads by randomly sampling rows from an edgelist and save them to fastq files.

This PR then reworks the denoise tests (currently the slowest of the testbase) to use synthetic data. Overall this cuts the total run time by around 3 minutes.

Fixes: PNA-2602

Type of change

Please delete options that are not relevant.

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• This change requires a documentation update

How Has This Been Tested?

Each function and helper function of the test generator has its own tests. This has also been tested end to end by generating fastq files and putting them through the nf-core pipeline.

PR checklist:

• This comment contains a description of changes (with reason).
• I have performed a self-review of my own code
• I have made corresponding changes to the documentation
• My changes generate no new warnings
• I have added tests that prove my fix is effective or that my feature works
• I have checked my code and documentation and corrected any misspellings
• I have documented any significant changes to the code in CHANGELOG.md

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Pull request overview

Copilot reviewed 16 out of 17 changed files in this pull request and generated 2 comments.

[Aratz]

Test failures seem to be due to the dependency updates. Will fix these tests to make them more robust to such numerical artifacts

[ptajvar]

Great addition! I am just wondering whether it should live under common or pna given that other than topology.py, the rest is mostly exclusive for pna. Looks good to go to me otherwise.

[Aratz]

Ah, I see, I think maybe for now it can stay where it is, if we develop a new product or something we can see if it's worth to move it elsewhere 👍 Thank you!