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Update readme to include option to manually download wheels. #57

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40 changes: 26 additions & 14 deletions README.rst
Original file line number Diff line number Diff line change
Expand Up @@ -27,23 +27,33 @@ Installation

The Python module is distributed as a `wheel`_ binary package which defines the package dependencies.

The package `rap_sitkcore` is an optional dependency. It can be specified when installing with the optional dependency
package notation `tbpcxr[sitkcore]`. The `rap_sitkcore` package is hosted on the NIAID artifactory. It provides
additional robust reading for problematic `TBPortals`_ DICOM file which should be addressed in the published
dataset.
The package `rap_sitkcore`_ is an optional dependency used for reading DICOM files. It provides
additional robust reading for difficult `TBPortals`_ DICOM files which may be addressed in some published
datasets.

Internal NIAID Artifactory
^^^^^^^^^^^^^^^^^^^^^^^^^^
- Option 1: Manually Download Wheels from Github Releases

Internally the `tbpcxr` package is hosted on the NIAID Python Package Index (PyPI) hosted on artifactory and is
installable with `pip`. This enables internal dependencies to be automatically download from the artifactory. The
internal repository can be automatically used by setting an environment variable::
The wheels can be downloaded from the `Github Releases`_ page and the optional dependency package `rap_sitkcore` can
be downloaded separately from the `Github rap_sitkcore Releases`_ page. Then the two wheels should be installed together::

PIP_EXTRA_INDEX_URL=https://{USERNAME}:{PASSWORD}@artifactory.niaid.nih.gov/artifactory/api/pypi/bcbb-pypi/simple
python -m pip tbpcxr-0.5.1-py3-none-any.whl rap_sitkcore-0.5.5-py3-none-any.whl

Then the `tbpcxr` package can be installed::

python -m pip install tbpcxr[sitkcore]

- Option 2: Use Internal NIAID Artifactory

It can be specified when installing with the optional dependency package notation `tbpcxr[sitkcore]`. The
`rap_sitkcore` package is hosted on the NIAID artifactory.

Internally the `tbpcxr` package is hosted on the NIAID Python Package Index (PyPI) hosted on artifactory and is
installable with `pip`. This enables internal dependencies to be automatically download from the artifactory. The
internal repository can be automatically used by setting an environment variable::

PIP_EXTRA_INDEX_URL

Then the `tbpcxr` package can be installed::

python -m pip install tbpcxr[sitkcore]

Github Releases
^^^^^^^^^^^^^^^
Expand All @@ -56,7 +66,7 @@ The wheel lists the package dependencies which are required for successful insta
packages. If the internal "artifactory" repository is not configured then these additional dependencies will need to be
manually downloaded and installed before install `tbpcxr`. The downloaded wheels can be installed::

python -m pip install tbpcxr-0.1-py3-none-any.whl
python -m pip install tbpcxr-0.5.1-py3-none-any.whl


Contact
Expand All @@ -67,9 +77,11 @@ Please use the `GitHub Issues`_ for support and code issues related to the tbp-c
Additionally, we can be emailed at: bioinformatics@niaid.nih.gov Please include "tbp-cxr-outlier" in the subject line.

.. _TBPortals: https://tbportals.niaid.nih.gov/
.. _rap_sitkcore: https://github.com/niaid/rap_sitkCore
.. _SimpleITK toolkit: https://simpleitk.org
.. _pip: https://pip.pypa.io/en/stable/quickstart/
.. _Github Actions: https://github.com/niaid/tbp-cxr-outlier/actions?query=branch%3Amaster
.. _GitHub Issues: https://github.com/niaid/tbp-cxr-outlier
.. _wheel: https://www.python.org/dev/peps/pep-0427/
.. _Github Releases: https://github.com/niaid/tbp-cxr-outlier/releases
.. _Github Releases: https://github.com/niaid/tbp-cxr-outlier/releases/latest
.. _Github rap_sitkcore Releases: https://github.com/niaid/rap_sitkCore/releases/latest