bob-carpenter / kmers Goto Github PK
View Code? Open in Web Editor NEWk-mer based genomics
License: BSD 3-Clause "New" or "Revised" License
k-mer based genomics
License: BSD 3-Clause "New" or "Revised" License
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?
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"
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