pymedphys/pymedphys: v0.30.0

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].

• 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
  • See labs/quickcheck/qcheck.py
• 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.

• 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.

• Fixed an issue where the iCOM listener could not handle Machine IDs that were not entirely an integer.
  • See _icom/mappings.py#L6 for changes.
  • See the PyMedPhys forum discussion for details.
• 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.
  • See the PyMedPhys forum discussion for more details.

• 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.
  • See the PyMedPhys forum discussion for more details.

• 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.