standard-params

v3.0.0-alpha-2 (standard-params)

Installation Instructions

This is the second in the series of epispot v3 alpha releases, following the massive plots release. As with the last one, it must be installed using pip. Install with:

pip install epispot-nightly==3.0.0a2

Important Notes

Python

All versions of Python 3.6 are no longer supported. This follows a change in our CI/CD provider and multiple updates to manifest files. If you are using Python 3.6, please upgrade to 3.7, the oldest supported release right now.

Deprecations

As this is a pre-release to the epispot v3 release, there are many, many new changes. Unfortunately, this also leads to a huge number of deprecations. However, we believe that the new changes in epispot v3.0.0-alpha-2 will be very easy to adapt to and simplify the user experience greatly. The main deprecation is that of the Model object, which now has a different structure and must be formed according to the new ideas proposed in #73. Additionally, the epispot.fitters module (while still available) is now deprecated; new alternatives will be shipped in a future release. We hope you will read more about these changes and send us any feedback you have.

Dependencies

No new dependencies have been added to the package source code; however, we have now officially updated the list of packages sent out on the PyPI package registry to reflect our internal requirements files. This release we have bumped NumPy to 1.21.1 from 1.21.0.

Changes

Note: See the project changelog for more detailed information.

This release completely redesigns the central Model object in epispot. In brief, we now support custom compartments and combinations through a new Compartment object and we now pass parameters into the Model object instead of to the Compartment object. The name 'standard-params' comes from the fact that now the parameters (that are really just probabilities and rates) have been organized into an easily-understandable matrix. More discussion about this feature can be found here.

Version-specific Information

This release is the second in a series of alpha releases of epispot v3.0, succeeding v3.0.0-alpha-1 'massive plots'.
Code coverage is at 95.50%, details available on CodeCov
Version documentation available in English at https://epispot.github.io/epispot/en/v3.0.0-alpha-2/

At the time of release, there is 1 issue related to this version:

• #77 "Accept shortened parameter matrices"

Statuses

There exists 1 LGTM code quality alert for this release. The latest LGTM code quality scan is available here.
There exist no known security vulnerabilities at this time. (This release will not receive security updates)