install issue

[Thexiyang]

thanks for this nice tool. when i install using this: pip install ., the issue pops out:

Building wheels for collected packages: genome_spot
  Building wheel for genome_spot (setup.py) ... error
  error: subprocess-exited-with-error

  × python setup.py bdist_wheel did not run successfully.
  │ exit code: 1
  ╰─> [34 lines of output]
      running bdist_wheel
      running build
      running build_py
      creating build
      creating build/lib
      creating build/lib/genome_spot
      copying genome_spot/genome_spot.py -> build/lib/genome_spot
      copying genome_spot/helpers.py -> build/lib/genome_spot
      copying genome_spot/_version.py -> build/lib/genome_spot
      copying genome_spot/join_outputs.py -> build/lib/genome_spot
      copying genome_spot/__init__.py -> build/lib/genome_spot
      creating build/lib/genome_spot/bioinformatics
      copying genome_spot/bioinformatics/signal_peptide.py -> build/lib/genome_spot/bioinformatics
      copying genome_spot/bioinformatics/protein.py -> build/lib/genome_spot/bioinformatics
      copying genome_spot/bioinformatics/__init__.py -> build/lib/genome_spot/bioinformatics
      copying genome_spot/bioinformatics/dna.py -> build/lib/genome_spot/bioinformatics
      copying genome_spot/bioinformatics/genome.py -> build/lib/genome_spot/bioinformatics
      creating build/lib/genome_spot/model_training
      copying genome_spot/model_training/download_trait_data.py -> build/lib/genome_spot/model_training
      copying genome_spot/model_training/make_holdout_sets.py -> build/lib/genome_spot/model_training
      copying genome_spot/model_training/run_model_selection.py -> build/lib/genome_spot/model_training
      copying genome_spot/model_training/train_models.py -> build/lib/genome_spot/model_training
      copying genome_spot/model_training/__init__.py -> build/lib/genome_spot/model_training
      copying genome_spot/model_training/make_training_dataset.py -> build/lib/genome_spot/model_training
      creating build/lib/genome_spot/taxonomy
      copying genome_spot/taxonomy/balance.py -> build/lib/genome_spot/taxonomy
      copying genome_spot/taxonomy/taxonomy.py -> build/lib/genome_spot/taxonomy
      copying genome_spot/taxonomy/__init__.py -> build/lib/genome_spot/taxonomy
      copying genome_spot/taxonomy/partition.py -> build/lib/genome_spot/taxonomy
      creating build/lib/genome_spot/bioinformatics/hmm
      copying genome_spot/bioinformatics/hmm/hmm_signal_peptide.joblib -> build/lib/genome_spot/bioinformatics/hmm
      running build_scripts
      creating build/scripts-3.8
      error: [Errno 21] Is a directory: 'genome_spot/'
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for genome_spot
  Running setup.py clean for genome_spot
Failed to build genome_spot
ERROR: Could not build wheels for genome_spot, which is required to install pyproject.toml-based projects

[till-bornemann]

Hey, just wanted to mention that i have the same issue running pip install . (and terminating with the same error) as Thexiyang. I'm working on an Ubuntu server, have loaded a conda env made specifically for genomespot and (obviously run the pip install .command in the folder downloaded via your git clone command). I was able to run the pip install -r requirements.txt command without errors (i tried that after the pip install .failed to see if that might fix the first error).

Additionally, i'd suggest adding the specific python version your software needs (3.8.16 is what an incompatibility error gave me so i changed my python3 version in the conda env to it) in the README dependency list.

Best, Till

[tylerbarnum]

Thanks for raising these issues. Hopefully resolved by PR #5 so try and again let us know.

The issue causing error: [Errno 21] Is a directory: 'genome_spot/' was that I pointed to a directory instead of a script in setup.py. The python version requirement has been relaxed as well. Works for 3.10 and 3.11 in our hands.

[till-bornemann]

Hi Tyler, just wanted to let you know that it indeed fixed it for me. Thanks!

Till