viro-seq-utils 1.5.0

Utilities modules for sequences, alignments and phylogeny from Toulouse virology laboratory.

Sequence, alignments and phylogeny utilities

Python package providing utilities for:

• sequences (nucleotides or amino acids)
• alignments
• phylogeny

Creating the pip package and upload

See Generating distribution archive from this page.

On the local computer, not on the cluster, go to the directory containing the *.toml file and run:

python3 -m pip install --upgrade build

python3 -m build

Upload of the new or updated package

upload to the TestPyPi repository

Use Twine to upload the new package or the new version of the package to TestPyPi:

python3 -m twine upload --repository testpypi dist/*

When prompted for the username, enter __token__ and the password of the token for test.pypi.org (see bitwarden token test.pypi.org).

To test if the package is correctly uploaded and functional, create a virtual env and install the package.

# virtual env
python3 -m venv test_env
source test_env/bin/activate

# download package
python -m pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple viro-seq-utils

# launch Python
python

Test the package:

from viro_seq_utils import aln_utils

The upload is OK if no error message is displayed.

Remove the virtual environment:

deactivate

rm -r test_env/

upload to the PyPi repository

Use Twine to upload the new package or the new version of the package to PyPi:

python3 -m twine upload dist/*

When prompted for thr username, enter __token__ and the password of the token: pypi.org (see bitwarden token pypi.org).