Installation¶

NEXCISION is a dependency-free Python command-line tool and requires Python 3.10 or later.

PyPI¶

Install the current stable release from PyPI:

python -m pip install nexcision

To install the current release explicitly by version:

python -m pip install nexcision==0.1.1

Confirm the installed version with:

nexcise --version

Bioconda¶

The recommended installation method for Conda-based bioinformatics environments is Bioconda:

conda install -c conda-forge -c bioconda nexcision

Confirm the installed version with:

nexcise --version

Install the stable tagged release from GitHub¶

The current stable software release is NEXCISION v0.1.1.

Install that exact release directly from GitHub:

python -m pip install \
  git+https://github.com/RhysWhite/nexcision.git@v0.1.1

Or clone the repository and install the tagged release locally:

git clone https://github.com/RhysWhite/nexcision.git
cd nexcision
git checkout v0.1.1
python -m pip install .

Then confirm the installation:

nexcise --version

Expected output:

NEXCISION 0.1.1

Install the current development branch¶

The main branch may contain documentation, packaging, or development changes made after the most recent tagged software release.

To install the current main branch:

python -m pip install \
  git+https://github.com/RhysWhite/nexcision.git

For reproducible analyses, prefer a tagged release or a versioned package rather than an unpinned development branch.

Command-line entry point¶

Installation provides the nexcise command:

nexcise --help

The command accepts two required positional inputs:

nexcise NEXUS REGIONS

where:

• NEXUS is the input NEXUS matrix;
• REGIONS is a whitespace-delimited file defining genomic intervals to remove.

Output paths, coordinate parsing, dimension handling, and explicit safety opt-ins are controlled with command-line options described in the remaining documentation.

Supported Python versions¶

The package metadata require Python 3.10 or later.

The repository test workflow runs the test suite on Python 3.10–3.14 across Ubuntu, macOS, and Windows. A separate packaging job builds and installs a wheel, reruns the tests against that installed wheel, and reproduces the bundled example.

Archival release¶

NEXCISION v0.1.1 is archived in Zenodo:

DOI: 10.5281/zenodo.21936049