bob-carpenter / kmers Goto Github PK

It seems I can't import the package (import kmerexpr gives ModuleNotFoundError) and the individual files (import simulate_reads) can only be imported when installed in editable mode. I tried installing through github, locally, and in editable mode. I'm using python 3.9 and pip 22.2.2.

Not sure how to fix it. Maybe setup.cfg:L18-28 needs to be tweaked to match this structure with a src/ folder between the base of the repository and the kmerexpr package?

Fixing this might mess existing import statements? For example in simple_example.py:L1-L7, imports such as import simulate_reads as sr should probably be import kmerexpr.simulate_reads as sr to work when the file is called from another directory?

Reproducing the errors

Attached are scripts to reproduce the issue (and their outputs): testing.zip.

The scripts assume they are in a folder containing the repo in a subfolder called kmers_repo
(after git clone https://github.com/bob-carpenter/kmers kmers_repo)

/test/ < console here
     /kmers_repo/
     /test_install_github.sh
     /test_install_local.sh
     /test_install_local_editable.sh

The scripts install the library and try to import kmerexpr and simulate_reads.

Note: the scripts need to first uninstall kmerexpr and might mess up existing installations.

• test_install_github.sh = pip install git+https://github.com/bob-carpenter/kmers.
  python -c "import kmerexpr" ❌
  python -c "import simulate_reads" ❌
• test_install_local.sh = pip install ./kmers_repo.
  python -c "import kmerexpr" ❌
  python -c "import simulate_reads" ❌
• test_install_local_editable.sh = pip install -e ./kmers_repo.
  python -c "import kmerexpr" ❌
  python -c "import simulate_reads" ✔️