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update source install instructions in README
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whitews committed Oct 9, 2023
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2 changes: 1 addition & 1 deletion .github/workflows/wheels.yml
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Expand Up @@ -25,11 +25,11 @@ jobs:
run: python -m pip install cibuildwheel==2.15.0

- name: Build wheels
run: python -m cibuildwheel --output-dir wheelhouse
env:
CIBW_SKIP: pp* *-musllinux_* *-manylinux_i686 *-win32 # skip PyPy, musllinux, 32-bit Linux & win32 builds
CIBW_ARCHS_MACOS: x86_64 arm64
CIBW_BUILD: cp37-* cp38-* cp39-* cp310-* cp311-* cp312-*
run: python -m cibuildwheel --output-dir wheelhouse

- name: Store artifacts
uses: actions/upload-artifact@v3
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39 changes: 17 additions & 22 deletions docs/index.rst
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Expand Up @@ -12,31 +12,27 @@ FlowUtils Documentation
.. image:: https://img.shields.io/pypi/pyversions/flowutils.svg
:target: https://pypi.org/project/flowutils/

FlowUtils is a Python package containing various utility functions related
to flow cytometry analysis, primarily focused on compensation,
transformation, and gating tasks commonly used within the flow community.

FlowUtils is part of a suite of Python libraries for analyzing flow
cytometry data. It was developed as an extension to the light-weight
`FlowIO library <https://github.com/whitews/FlowIO>`_. FlowIO reads and
writes Flow Cytometry Standard (FCS) files, and has zero dependencies.
For higher level interaction with flow cytometry data, including
GatingML & FlowJo 10 support, see the related
FlowUtils is a Python package containing utility functions related
to flow cytometry analysis. Primarily focused on the commonly used
tasks of compensation and transformation, FlowUtils aims to be a
stable and reliable source with minimal dependencies.

It is part of a suite of Python cytometry libraries, which also
include FlowIO and FlowKit. The
`FlowIO library <https://github.com/whitews/FlowIO>`_
reads and writes Flow Cytometry Standard (FCS) files, and has zero
dependencies. For higher level interaction with flow cytometry data,
including GatingML & FlowJo 10 support, see the related
`FlowKit project <https://github.com/whitews/FlowKit>`_.

Installation
------------

FlowUtils uses C extensions for significant performance
improvements. For the most common platforms and Python versions, pre-built
binaries are available in PyPI (and installable via pip).

If a pre-built binary of FlowUtils is not available for your environment,
then the C extensions must be compiled using the source package. NumPy
must be installed prior to compiling these extensions. If compiling using gcc,
version 5 or later is required.

Compiling FlowUtils from source can also result in NumPy C API incompatibilities. See the `NumPy docs <https://numpy.org/devdocs/user/depending_on_numpy.html>`_ for more information.
FlowUtils uses C extensions for significant performance improvements.
For the most common platforms and Python versions, pre-built binaries
are available in PyPI (and installable via pip). If a pre-built binary
of FlowUtils is not available for your environment, then the C
extensions must be compiled using the source package.

From PyPI
.........
Expand All @@ -50,10 +46,9 @@ From GitHub source code

.. code-block:: python
pip install numpy>=1.20
git clone https://github.com/whitews/flowutils
cd flowutils
python setup.py install
pip install .
----

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