-
Notifications
You must be signed in to change notification settings - Fork 1
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Update readme to include option to manually download wheels.
- Loading branch information
Showing
1 changed file
with
26 additions
and
14 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
|
@@ -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 | ||
^^^^^^^^^^^^^^^ | ||
|
@@ -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 | ||
|
@@ -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: [email protected] 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 |