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Installation

Create a clean virtual environment

Ideally, before installation, create a clean python3.10+ virtual environment to deploy the package. The recommended python version is 3.12. Python 2 is not supported. For example one can use conda or virtualenvwrapper.

With virtualenvwrapper:

mkvirtualenv nanocompore -p python3.12

With conda:

conda create -n nanocompore python=3.12

pip3 install nanocompore

conda install -c bioconda nanocompore

Option 2: Clone the repository and install locally in develop mode with uv

With this option, the package will be locally installed in editable or develop mode. This allows the package to be both installed and editable in project form. This is the recommended option if you wish to modify the code and/or participate to the development of the package (see contribution guidelines).

Make sure you have uv installed (instructions).

# Clone repo localy
git clone https://github.com/tleonardi/nanocompore.git

# Enter in repo directory
cd nanocompore

# Install the dependencies with uv
uv sync

Testing the installation (Optional)

If nanocompore is installed in develop mode (Option 2) it is recommended to run the unit tests and integration tests to verify the installation. The test framework pytest needs to be installed manually to run the test in the virtual environment where NanoCompore is also installed.

Then run pytest in the directory where nanocompore was downloaded. 

uv run pytest tests

If all the tests are successful you should get a similar output:

====================== test session starts ==========================
platform linux -- Python 3.12.8, pytest-8.3.5, pluggy-1.5.0
rootdir: /home/mzdravkov/nanocompore
configfile: pyproject.toml
plugins: cov-6.1.1, xdist-3.6.1, jaxtyping-0.2.38
collected 51 items

tests/test_common.py .                                         [  1%]
tests/test_comparisons.py ...........                          [ 23%]
tests/test_config.py ..................                        [ 58%]
tests/test_eventalign_collapse.py ...                          [ 64%]
tests/test_main.py .                                           [ 66%]
tests/test_postprocessing.py .......                           [ 80%]
tests/test_preprocessing.py .                                  [ 82%]
tests/test_run.py .......                                      [ 96%]
tests/test_uncalled4.py ..                                     [100%]

===================== 51 passed, 7 warnings in 18.98s =================