[BUG] Synthetic example dataset doesn't work
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- Python
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Description
Describe the bug
When installing this package via pip in a venv and using the example dataset, method load_example_data in pydeseq2\utils.py fails because it cannot read the file "test_counts.csv" because there isn't one. I Had to copy it manually from the repo.
There is no dataset folder in C:...\venv\lib\site-packages\datasets\synthetic\test_counts.csv
To Reproduce
pip install pydesq2
run this example: https://pydeseq2.readthedocs.io/en/latest/auto_examples/plot_minimal_pydeseq2_pipeline.html
Expected behavior
File should be present and the code should open and parse the file.
Desktop (please complete the following information):
- win10x64
- python 3.9
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with load_example_data in pydeseq2/utils.py and trace how test_counts.csv is included when the package is installed with pip. Verify the installed package contains datasets/synthetic/test_counts.csv and rerun the minimal PyDESeq2 pipeline example to confirm the file is opened and parsed successfully.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100