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