PyMedPhys

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Published June 13, 2020 | Version v0.30.0
Software Open

pymedphys/pymedphys: v0.30.0

Authors/Creators

  • 1. Riverina Cancer Care Centre
  • 2. Institute of Medical Physics (USyd)
  • 3. @actions

Description

Breaking changes
  • Removed the proof of concept pymedphys bundle CLI as well all of its associated code.
  • Removed a range of unused files from the pymedphys.data_path API.
  • The previous install options pip install pymedphys[pytest] and pip install pymedphys[pylint] have been removed and replaced with pip install pymedphys[tests].
New Features
  • Added a new toolbox for retrieving PTW Quickcheck measurement data and write it to a csv file. pymedphys labs quickcheck to-csv your.quickcheck.ip path/to/output.csv
  • Added pymedphys dev tests to the CLI.
    • Moved all of tests into the pymedphys repo itself. Now the automated testing suite is able to be run from a pypi install.
    • This CLI has options such as --run-only-pydicom, --run-only-slow, and --run-only-pylinac so that upstream tools can run tests on this downstream project.
    • These extra options are directly passed through to pytest. To achieve this, made the pymedphys CLI be able to optionally handle arbitrary commands.
  • Made the Zenodo download tool retry up to four times should the download fail.
  • Added DICOM helpers functionality and updated the Mosaiq helpers as a part of the UTHSCSA TPS/OIS comparison project. Not yet exposed as part of the API. See _mosaiq/helpers.py#L353-L482
  • Added more debugging strings to the iCOM CLI. See these outputs by running pymedphys --debug icom listen external.nss.ip.address your/output/directory
    • These were added to support remotely debugging the iCOM listen software. To see the conversation around debugging that tool see the PyMedPhys forum discussion
  • Format of MU in logging display now rounded to one decimal.
Dependency changes
  • Now depending on pylibjpeg-libjpeg in order to decode lossless-jpeg files.
  • m2r is no longer used to build the docs.
  • No longer using tox for tests.
Bug fixes
  • Fixed an issue where the iCOM listener could not handle Machine IDs that were not entirely an integer.
  • Fixed a case where on some Windows environments pymedphys dev docs would not run.
  • Fixed a case where on some Windows environments pymedphys gui would not run.
  • Fixed issue where the pymedphys logfile orchestration CLI would not be able to create an index.json, or a range of the needed directories on its first run.
Documentation updates
  • Fixed an issue where the displayed CSV files for configuring pymedphys logfile orchestration would actually cause an error due to excess spaces used for display purposes.
Development changes
  • Removed any file that was larger than 300 kB from the git history bring down clone times to a manageable state.
    • The pre-commit tool now does not allow commits greater than 300 kB.
    • All testing files that were larger than 300 kB have been moved to Zenodo.
  • All tests have been moved from /tests into /pymedphys/tests, running these tests can now be undergone by calling pymedphys dev tests
    • No longer using tox.

Files

pymedphys/pymedphys-v0.30.0.zip

Files (2.6 MB)

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md5:0421bc2a38c9e7b73daa885dab9ffa87
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Additional details

Related works

Is supplement to
https://github.com/pymedphys/pymedphys/tree/v0.30.0 (URL)