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v3a3

Pre-release
Pre-release

Important Notes

Python

Python 3.10 is now officially supported (in epispot and all its core dependencies)! 🎆
As of now, Python 3.10 will become the standard environment for testing epispot's future releases (though we will continue to test on 3.7-3.9).

Dependencies

All updates shown below:

  • matplotlib@3.5.0
  • numpy@1.21.4
  • plotly@5.4.0
  • pytest@6.2.5
  • coverage@6.1
  • codecov@2.1.12
  • pdoc3@0.10.0
  • SciencePlots@1.0.9

Security

This release adopts a new and stronger security policy than before, emphasizing compatibility with Google's OSS Vulnerability Guide. We encourage you to take a look at the new changes here.

Changes

Note: See the project changelog for more detailed information.

No new features were introduced in this update, only environment changes.

Version-specific Information

This release is the third in a series of alpha releases of epispot v3.0, succeeding v3.0.0-alpha-2 'standard params'.
Code coverage is at 95.56%, details available on CodeCov
Version documentation available in English at https://epispot.github.io/epispot/en/v3.0.0-alpha-3/

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)

What's Changed

New Contributors

  • @deepsource-autofix made their first contribution in #97

Full Changelog: v3.0.0-alpha-2...v3.0.0-alpha-3

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standard-params

Pre-release
Pre-release

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)

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massive-plots

Pre-release
Pre-release

v3.0.0-alpha-1 (massive-plots)

Installation Instructions

This is a nightly release, meaning that it is only available through the epispot-nightly project on PyPI. However, if you have Anaconda, you can still install it into your environment, just using pip. Installation instructions for both systems are shown below:

pip install epispot-nightly==3.0.0a1

Important Notes

Deprecations

All functions from the epi.plots module have now been deprecated. Please use epi.plots.native as a replacement for these functions. Alternatively, you can continue using the latest v2 build of the nightly version, v2.1.1.15. This will be supported until the official stable release of epispot v3.

Dependencies

The new plots subpackage in epispot requires SciencePlots and plotly, two new dependencies added to the requirements-nightly.txt file. These new dependencies are used for improving graph quality in epispot and generating quick plots without extensive computation.

Changes

Note: See the project changelog for more detailed information.

This release adds new plotting features to epispot, available through the epi.plots subpackage. This subpackage in turn contains two new modules, web and native. The web module includes utilities for graphing with plotly and the native module utilities for creating scientific plots of models with matplotlib. More details about these new features can be found in the documentation for this release.

Version-specific Information

This version is the first of many alpha versions of epispot v3.0 (unreleased as of yet).
Code coverage is at 90.16%, details available on CodeCov
Version documentation available in English at https://epispot.github.io/epispot/en/v3.0.0-alpha-1/
At the time of release, there exist no issues related to this version.

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)

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Minor patch: fixes incorrect nightly merge from master
If using v2.1.0: update via pip install epispot --upgrade

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Introducing pre-compiled models!
Instead of writing long and useless blocks of code to set up simple models, you can now create them via the pre module.
For example, create an SIR model with just:

SIR = epi.pre.SIR(R_0=2.5, N=1e5, p_recovery=0.5, recovery_rate=1/7)

Install via pip with pip install epispot==2.1.0

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New updates for the Discord Bot covid19-tracker:

  • A new experimental fitting algorithm was added
    • Call as epi.fitters.tree_search()
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Wear your 😷. Slow the spread. Welcome the Endemic (v2.0.0)

Latest: Stable Build
On PyPi: latest-release
Introduces new graph annotation commands (see the plots module). Install on pip as pip install epispot==2.0.0

Packaging Docs Features
ready ✔️ docstrings ✔️ compartments ✔️
pip ✔️ docs ✔️ spatial models
conda tutorials 🟡 interactive plots 🟡
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Added the epispot.fitters module.

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🎆 for version Herd Immunity (v1.0.0)

Note: this is the first fully-supported production-ready release.
Now the first release on PyPi latest-release
Comes with Susceptible, Infected, Recovered, Exposed, Critical, Hospitalized, and Dead compartments. Install on pip as pip install epispot==1.0.0

Packaging Docs Features
ready ✔️ docstrings ✔️ compartments ✔️
pip ✔️ docs spatial models
conda tutorials 🟡 interactive plots