A Python package for the mathematical modeling of infectious diseases via compartmental models

epispot

Last update: Dec 28, 2022

Related tags

Data Analysis modeling epidemiology infectious-diseases infectious-disease-models coronavirus covid-19

Overview

epispot v2

A Python package for the mathematical modeling of infectious diseases via compartmental models. Originally designed for epidemiologists, epispot can be adapted for almost any type of modeling scenario.

Features

The epispot package currently only supports compartmental models, though we plan to expand the package to work for stochastic agent-based and spatial models as well. Currently, epispot offers the following:

Quick compilation of compartmental models with the following compartments:
- Susceptible
- Infected
- Recovered
- Removed
- Exposed
- Dead
- Critical
- Hospitalized
Custom-defined compartments for research
Built-in graphing and visualization engine
- Plots model predictions interactively
- Creates comparisons between models

Due to its diverse range of features, epispot can be used for both research and experimental modeling. If you would like to add more modeling support, please see the contributing section.

Installation

The epispot package can be installed from PyPI, Anaconda, or be built from the source. Before reading this guide, it is important to note that there are actually two different versions of the epispot package. The first of which is the master package, which will always have a version tag like v#.#.#. This package is used to release stable versions of epispot. However, during important events, like the COVID-19 pandemic, the nightly package is used to publish new features quickly. However, these versions may be unstable.

PyPI

This is the easiest way to install epispot. Fire up a terminal and type:

pip install epispot

For the nightly version, use

pip install epispot-nightly

Pip will ask you to install numpy and matplotlib as dependencies if you haven't already. Additionally, it may require you to install fire for the CLI. These can be installed beforehand with:

pip install numpy
pip install matplotlib
pip install fire

Anaconda

Please note that the nightly version is not available on the conda package registry. However, it is still possible to install on conda-based systems with

pip install epispot-nightly

which uses pip from Anaconda to install it.

The standard version of epispot is published to conda using the conda-forge channel. To install, please use:

conda config --add channels conda-forge
conda install -c conda-forge epispot

Building from the source

This is the hardest way to install epispot and it is recommended that you use either PyPI or Anaconda to install it instead. However, if you would like to contribute to the repository, this will be particularly useful.

Clone the repository with:

git clone https://github.com/epispot/epispot  # clone epispot/epispot
cd epispot  # open project
pip install -r requirements.txt  # install package requirements
pip install -r bin/requirements.txt  # Install CLI requirements

Then, build the nightly version with

python setup-nightly.py install

For the stable version, first checkout a release branch with something like:

git checkout v2.1.1
python setup.py install

Quick Demo

Installing epispot from pip and then compiling a simple SIR model in less than 40 seconds.

Documentation

The documentation for the epispot package is generated automatically from the Python source code using Pdoc3. You can view the documentation for both the nightly and stable builds of epispot here.

At first, the documentation may seem a bit hard to understand, especially if you're new to epidemiology. That's why epispot has put together an entire manual describing some basic concepts you'll need to know to master epispot. You can view it here. The GitHub source is available here.

Usage/Examples

The GitHub repository has a vast array of samples using epispot. You can start by checking out the explorables/ directory. In it, you'll find many programs designed for helping you get started with epispot and some hands-on examples.

Badges

Statuses

Pipeline	Status
Travis CI
CodeCov
PyPI main
PyPI nightly
Security

Feedback

If you have any feedback, please

Create a discussion on GitHub
Create an issue if you've found a bug
Submit a PR if you want to add a new feature
Contact a CODEOWNER

Contributing

Contributions are always welcome! See CONTRIBUTING.md for instructions on how to get started, including environment setup and instructions to build from the source. Please note also that epispot has many guides dedicated to certain types of contributions. Please see

DOCUMENTATION.md for documentation additions
SECURITY.md for epispot's security policy

Citation

If you plan on using epispot in your project, please abide by the GPLv3 license. This requires that any changes you make to epispot must be open-sourced under the GPLv3 license as well and that you give credit to the author, which you can do by citing the project in your research, linking back to the original repository, or mentioning the author @quantum9innovation.

For research, you can also use epispot's DOI to reference the project:

The recommended citation for epispot is:

quantum9innovation (2021, April 2). epispot/epispot: (Version 2.1.0). Zenodo. http://doi.org/10.5281/zenodo.4624423

Authors

Please see our CODEOWNERS file for authors. Because epispot is an open-source project, different pieces of our code have different authors. However, if citing epispot or using it in another project, you can put @quantum9innovation as the lead author.

Acknowledgements

Idea & Inspiration

The original idea for epispot came from a 3Blue1Brown video on basic infectious disease dynamics and an interactive article in the Washington Post. This in turn inspired the very basic infectious disease dynamics simulated here. However, what finally set the package into motion was a series of articles by Henry Froese, available on Medium here, along with their corresponding interactive notebooks.

Code Development & Maintenance

The epispot project is built on open source code and is itself open-source. The initial core development was fueled by @quantum9innovation and much of the codebase was maintained by @Quantalabs. Additionally, thank you to all of epispot's open-source contributors!

Dependencies

The epispot team also relies on the following open-source projects as dependencies:

NumPy (GitHub), the fundamental package for scientific computing with Python
Matplotlib (GitHub), plotting with Python
Google Fire (Github), a library for automatically generating command line interfaces (CLIs) from absolutely any Python object.

External Code Management Tools

For code maintenance, epispot uses various tools including:

Coverage.py (PyPI) for code coverage report generation
Pdoc3 (GitHub) for automatic documentation generation
GitBook (Website) for documentation hosting
CodeCov (Website) for code coverage report analysis
LGTM (Website) for CodeQL analysis
DeepSource (Website) for static code analysis
GitLocalize (Website) for localization of documentation
Zenodo (Website) for automatic DOI & citations

Comments

[dep]: Update numpy requirement from ~=1.21.5 to ~=1.22.0
Updates the requirements on numpy to permit the latest version.

Release notes

Sourced from numpy's releases.

v1.22.0

NumPy 1.22.0 Release Notes

NumPy 1.22.0 is a big release featuring the work of 153 contributors spread over 609 pull requests. There have been many improvements, highlights are:

Annotations of the main namespace are essentially complete. Upstream is a moving target, so there will likely be further improvements, but the major work is done. This is probably the most user visible enhancement in this release.

A preliminary version of the proposed Array-API is provided. This is a step in creating a standard collection of functions that can be used across application such as CuPy and JAX.

NumPy now has a DLPack backend. DLPack provides a common interchange format for array (tensor) data.

New methods for quantile, percentile, and related functions. The new methods provide a complete set of the methods commonly found in the literature.

A new configurable allocator for use by downstream projects.

These are in addition to the ongoing work to provide SIMD support for commonly used functions, improvements to F2PY, and better documentation.

The Python versions supported in this release are 3.8-3.10, Python 3.7 has been dropped. Note that 32 bit wheels are only provided for Python 3.8 and 3.9 on Windows, all other wheels are 64 bits on account of Ubuntu, Fedora, and other Linux distributions dropping 32 bit support. All 64 bit wheels are also linked with 64 bit integer OpenBLAS, which should fix the occasional problems encountered by folks using truly huge arrays.

Expired deprecations

Deprecated numeric style dtype strings have been removed

Using the strings "Bytes0", "Datetime64", "Str0", "Uint32", and "Uint64" as a dtype will now raise a TypeError.

(gh-19539)

Expired deprecations for loads, ndfromtxt, and mafromtxt in npyio

numpy.loads was deprecated in v1.15, with the recommendation that users use pickle.loads instead. ndfromtxt and mafromtxt were both deprecated in v1.17 - users should use numpy.genfromtxt instead with the appropriate value for the usemask parameter.

(gh-19615)

... (truncated)

Commits

4adc87d Merge pull request #20685 from charris/prepare-for-1.22.0-release

fd66547 REL: Prepare for the NumPy 1.22.0 release.

125304b wip

c283859 Merge pull request #20682 from charris/backport-20416

5399c03 Merge pull request #20681 from charris/backport-20954

f9c45f8 Merge pull request #20680 from charris/backport-20663

794b36f Update armccompiler.py

d93b14e Update test_public_api.py

7662c07 Update init.py

311ab52 Update armccompiler.py

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unsupported :no_entry: low-priority :arrow_down_small: dependabot
opened by dependabot[bot] 8
Initialization Testing
Adds initialization testing to package

From PR #48, after PR #49

New Feature

Adds sanity and dependency checks to the epispot/__init__.py file and adds classifiers and other metadata to both setup.py and setup-nightly.py.

Known Issues

No known issues.

Code Breakdown

epispot/__init__.py

Sanity checks

Dependency checks

Increased package documentation

Ported from README.md

release.py

Updated to be compatible with new initialization file

setup.py, setup-nightly.py

Adds classifiers

Adds more URLs

doc :scroll: feat :rocket: low-priority :arrow_down_small: src
opened by quantum9Innovation 8
Add Dependabot
Is your feature request related to a problem? Please describe. This feature is unrelated to any current issues in epispot. However, using Dependabot will not only make epispot's code more secure, but it allow epispot to support the latest versions of each of our dependencies. Previously, this was not a problem—however, as new versions of epispot add more and more external dependencies, it is critical that we monitor security vulnerabilities and release notes constantly.

Describe the solution you'd like Solving this problem will require the following steps:

[x] #80

[x] #81

[x] #87

[x] #82

Describe alternatives you've considered No alternative solutions have been considered. Dependabot is usually the norm for dependency management, especially since it integrates nicely with GitHub.
feat :rocket: help wanted :helicopter: good first issue :+1: nightly :crescent_moon: low-priority :arrow_down_small: dependabot
opened by quantum9Innovation 7
[op:spaghetti] Standardize parameters
Parameters for all compartments other than the Susceptible compartment should include a rate and probability, organized into an easily-understandable matrix which is then parsed by the Model class. The reason for this is to eliminate the double-parameter chaos created in epispot v2.

The double-parameter issue

Currently, epispot v2 requires parameters to be specified twice. First to the compartment from which people are leaving and second to the compartment which people are entering. This is because each compartment does not have access to the other compartments' derivatives. However, there is a simple fix for this; every compartment needs to be able to change the derivative of every other compartment. This means that all the derivatives need to be stored at the Model level and distributed to all the compartments. Each compartment should not make a direct assignment to the derivative but rather add or subtract some value from the derivative. Using this system, every compartment can change the derivative of every other compartment, avoiding the complication of having to enter parameters in twice.

An example solution

The model first learns what compartments are going to be compiled. For this example, we'll use the following compartment codes: A, B, C. Here's a diagram of how they all connect:

┌───────────────────┐ │ ▼ ┌───┐ ┌───┐ ┌───┐ │ A │ ──▶ │ C │ ──▶ │ B │ └───┘ └───┘ └───┘

Now we examine how we can represent this as a parameter matrix. We will refer as the compartments from which an arrow extends as the from compartments. On the other hand, compartments which receive an arrow will be referred to as to compartments.

In code

Each from compartment gets its own subarray. Each element of this subarray corresponds to its respective to compartment. This in turn contains a tuple with the structure ({probability}, {rate}). For our diagram, the matrix looks like this in Python:

matrix = [ [(1/2, 1/3), (1/5, 1/2)], # A: [B, C] [(1/2, 1/6)], # C: [B] ]

Sidenote

Notice how the matrix simply does not include elements or subarrays that aren't necessary; B has no subarray of its own and C lacks a tuple describing rates and probabilities for A. We can do this because of how we describe connections between compartments:

Describing connections

This won't change much from epispot v2. Here's how connections are described, using our example with A, B, and C. The following graph:

┌───────────────────┐ │ ▼ ┌───┐ ┌───┐ ┌───┐ │ A │ ──▶ │ C │ ──▶ │ B │ └───┘ └───┘ └───┘

becomes the following matrix in Python:

connections = [ ['B', 'C'], # A [], # B ['B'] # C ]

Sidenote

Notice how, even despite having any connections, B must be included in this matrix. This matrix differs from the rate and probability matrix because here epispot does not yet know what the connections are. After epispot receives this matrix, the Model class can then parse following parameter matrices by assuming that non-connections are skipped.

Development

For now, development of this feature will not interfere with the package itself. Rather, the development will be done in a separate module and tested with dummy compartments (as we did above), before it is transitioned into the actual Model class.

[x] #74

[x] #75

[x] #76

feat :rocket: help wanted :helicopter: high-priority :arrow_up_small:
opened by quantum9Innovation 7
[dep/dev]: Update pytest requirement from ~=7.1.2 to ~=7.1.3
Updates the requirements on pytest to permit the latest version.

Release notes

Sourced from pytest's releases.

7.1.3

pytest 7.1.3 (2022-08-31)

Bug Fixes

#10060: When running with --pdb, TestCase.tearDown is no longer called for tests when the class has been skipped via unittest.skip or pytest.mark.skip.

#10190: Invalid XML characters in setup or teardown error messages are now properly escaped for JUnit XML reports.

#10230: Ignore .py files created by pyproject.toml-based editable builds introduced in pip 21.3.

#3396: Doctests now respect the --import-mode flag.

#9514: Type-annotate FixtureRequest.param as Any as a stop gap measure until 8073{.interpreted-text role="issue"} is fixed.

#9791: Fixed a path handling code in rewrite.py that seems to work fine, but was incorrect and fails in some systems.

#9917: Fixed string representation for pytest.approx{.interpreted-text role="func"} when used to compare tuples.

Improved Documentation

#9937: Explicit note that tmpdir{.interpreted-text role="fixture"} fixture is discouraged in favour of tmp_path{.interpreted-text role="fixture"}.

Trivial/Internal Changes

#10114: Replace atomicwrites dependency on windows with [os.replace]{.title-ref}.

Commits

4645bcd Remove incorrect output in how-to/fixtures.rst

fadfb4f Prepare release version 7.1.3

ab96ea8 Merge pull request #10258 from pytest-dev/backport-10252-to-7.1.x

fc0e024 [7.1.x] Fix regendoc

8f5088f Merge pull request #10249 from pytest-dev/backport-10231-to-7.1.x

aae93d6 Ignore type-errors related to attr.asdict

71b79fc [7.1.x] Ignore editable installation modules

89f7518 Merge pull request #10222 from pytest-dev/backport-10171-to-7.1.x

88fc45b [7.1.x] Update fixtures.rst w/ finalizer order

d0b53d6 Merge pull request #10221 from pytest-dev/backport-10217-to-7.1.x

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dependabot
opened by dependabot[bot] 6
[Stub] Issue status test

This issue is a stub: do not comment. It is intended to test the new claim.yml and mod.yml workflows that aim to provide automatic issue labeling based on issue comments. See commit 5eb8ce14b666ffa909a0f797e544ce97457a4dc2 for more information.

opened by quantum9Innovation 6
Use `pytest`
Set up pytest as main testing framework

After PR #46, solves issue #47

New Feature

Transforms old tests to use pytest as the main testing framework. pytest allows for

more testing accuracy

easily accessible testing suite

fast testing due to local cache

assert-based testing and bounds It also adds GitHub CODEOWNERS

Known Issues

Fixes #47 "Getting started with pytest"

Code Breakdown

.github/CODEOWNERS

Adds CODEOWNERS

.github/workflows/

build.yml, coverage.yml

Changed testing to use $ python -m pytest command

Optimizes workflows (@Quantalabs check optimizations)

bin/epispot

Replace broad except with except ImportError

bin/requirements.txt

Removes epispot due to pip install -r bin/requirements.txt command in workflows which installs epispot from PyPI instead of from the source

epispot/init.py

Add shortened README and guide to top of file (for help() commands)

Add dependency and sanity checks (@Quantalabs please see)

Remove __ from metadata variable names to make them globally accessible

Add documentation on metadata

epispot/

Add # pragma: no cover on soon-to-be deprecated functions

explorables/

Remove all tests, former testing suites, examples, and tutorials and move them to this directory to keep tests/ directory clean

tests/

Replace testing suite with new one that uses pytest

release.py

Update to be compatible with new __init__.py

setup.py, setup-nightly.py

Add more metadata and classifier information

Additional Notes

There's a lot going on in this PR and it may need to be broken up into multiple PRs. For now, it will be created as a draft PR just because of the sheer scale of the PR. Additionally, before moving into merge stage, all merge conflicts should be resolved and all basic checks (build and code coverage) should pass. After we enter the merge stage, reviewers should analyze code for compatibility issues and other code quality-related alerts will be dealt with if necessary.

Closes #47
doc :scroll: duplicate feat :rocket: high-priority :arrow_up_small: src tests repo
opened by quantum9Innovation 6
Added a CLI
Basic CLI Structure Implemented

New Feature

This PR adds a basic built-in CLI to epispot nightly that comes preinstalled with setup.py. The keyword to initiate it is epispot followed by a command. Currently the only available command is about. The shell uses Fire and termcolor as dependencies although it can run without termcolor by suppressing color (see the __color__ flag). To test the shell, run:

$ epispot about >>> Epispot was invoked via the epispot CLI >>> Path: /home/user/anaconda3/lib/python3.8/site-packages/epispot_nightly-2.1.1.1-py3.8.egg/EGG-INFO/scripts >>> Version: shell-v0.1.0-alpha epispot-v2.1.1.1 >>> Color output enabled (True/False): True

Known Issues

Coverage does not work on CLI scripts.

Planning on adding an enhancement to run models from the CLI; will require the addition of automatic parameter substitutions that will be implemented in another branch.

Code Breakdown

.coveragerc

Added bin/ as a directory however still not implemented in codecov reports (issue)

.github/workflows

Added to support build tests for CLI

coverage.yml

Added more verbosity for issue solving related to code coverage reporting

CHANGELOG.md

Added a CHANGELOG to track progress on the nightly package

README.md

Removed Release Notes on README.md to create CHANGELOG.md

bin/requirements.txt

Added separate CLI requirements (Fire, termcolor (optional))

requirements.txt

Removed unnecessary requirements (sphinx)

setup.py

Added scripts indicator to add epispot to the command line

Additional Notes

Similar to branch #cli Ideally merge when:

Code and implementation has been thoroughly reviewed

New workflows have been approved by @Quantalabs 's review Ignoring:

LGTM, CodeFactor, and other code quality checks (except built-in GitHub CodeQL)

Currently transitioning to Deepsource

duplicate feat :rocket: high-priority :arrow_up_small:
opened by quantum9Innovation 6
[dep]: Update scienceplots requirement from ~=1.0.9 to ~=2.0.0
Updates the requirements on scienceplots to permit the latest version.

Release notes

Sourced from scienceplots's releases.

SciencePlots (v2.0.0)

Fix import on case sensitive OSs

Finally bump to this major version, following breaking change

Remember, now import scienceplots is needed on top of your scripts!

Changelog

Sourced from scienceplots's changelog.

v2.0.0 (21-Nov-2022)

Fix import on case sensitive OSs

Finally bump to this version, following breaking change of distribution

v1.1.0 (07-Nov-2022)

Major change in distribution system

Now needs import directive import scienceplots

Fix not using raw string in plot-example.py

Update README

v1.0.9 (16-Sep-2021)

notebook:

make Latex fonts sans-serif

Fix bug with Latex packages:

e.g., \usepackage{amsmath, amssymb, sfmath} --> \usepackage{amsmath} \usepackage{amssymb} \usepackage{sfmath}

Add pyproject.toml file (see PEP 517/518)

Minor updates to README, including adding more papers to publication list

v1.0.8 (02-Jun-2021)

nature:

Added style for Nature articles

Uses sans-serif fonts

latex-sans:

Added style for using LaTeX with sans-serif fonts

std-colors:

Added style to recover the standard color cycle of the SciencePlots package

For example, if you use plt.style.use(["science", "ieeee"]). The figure will use the "ieee"color cycle. To revert to the standard color cycle, you can useplt.style.use(["science", "ieee", "std-colors"])``.

science:

Added amssymb to LaTeX preamble

grid:

Set axes.axisbelow to True

Minor updates to README

v1.0.7 (28-Feb-2021)

Add support for CJK fonts:

see README for details

Add example of CJK fonts:

see Fig 14a, Fig 14b, Fig 14c, Fig 14d

science style:

use default serif font

ieee style:

use Times font

... (truncated)

Commits

65da69c Bump to v2.0.0

4fd34ca Change package to lowercase. Fixes #74 (#75)

08fa606 Fix #74

6545c72 Bump to v1.1.0

f49a826 readme: add import scienceplots to instructions + add new publication

a508b4c Merge pull request #69 from echedey-ls/master

7641a70 Add import to examples

d152224 Rename package import directive as SciencePlots

a2ecf0e Name to uppercase and fall back to prev release

ec39f71 Package name to lowercase

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dependabot
opened by dependabot[bot] 5
[dep]: Update matplotlib requirement from ~=3.4.2 to ~=3.4.3
Updates the requirements on matplotlib to permit the latest version.

Release notes

Sourced from matplotlib's releases.

REL: v3.4.3

This is the third bugfix release of the 3.4.x series.

This release contains several critical bug-fixes:

Clarify deprecation of Axes.figbox

Disable MultiCursor widget on Axes subplots which it is not tracking

Don't simplify path in LineCollection.get_segments

Fix DPI in subfigures, affecting tick spacing, and scatter marker size

Fix broken EPS output when using Type 42 STIX fonts

Fix change in tick behaviour when calling Axes.clear

Fix class docstrings for Norms created from Scales

Fix compatibility with NumPy 1.21.0

Fix crash on broken TrueType fonts

Fix incorrect hits from Path.intersects_path

Fix leak if affine_transform is passed invalid vertices

Fix legends of stackplot with edgecolors='face'

Fix plot directive when building in parallel

Fix supxlabel and supylabel behaviour in constrained layout

Fix tests with latest Inkscape and Ghostscript

Improve DateFormatter styling for month names when usetex=True

Re-disable autoscaling after interactive zoom

Work around bug in Pillow 8.3.0

Commits

919145f REL: v3.4.3

b6f40b2 Merge branch 'v3.4.2-doc' into v3.4.x

b8068c3 DOC: Update GitHub stats for 3.4.3.

c946d3c Merge pull request #20830 from meeseeksmachine/auto-backport-of-pr-20826-on-v...

4b5ea5a Backport PR #20826: Fix clear of Axes that are shared.

da6b1fe Merge pull request #20823 from meeseeksmachine/auto-backport-of-pr-20817-on-v...

7cf7368 Backport PR #20817: Make test_change_epoch more robust.

7d5754e Merge pull request #20820 from meeseeksmachine/auto-backport-of-pr-20771-on-v...

83b0190 no draw_no_output

00acdbb Update lib/matplotlib/tests/test_figure.py

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unsupported :no_entry: low-priority :arrow_down_small: dependabot
opened by dependabot[bot] 5
[dep/dev]: Update pdoc3 requirement from ~=0.9.2 to ~=0.10.0
Updates the requirements on pdoc3 to permit the latest version.

Changelog

Sourced from pdoc3's changelog.

0.10.0 (2021-08-03)

Python 3.6+ required.

New support for variable doc-comments (directly above variable definition or on the same line; starting with '#:').

Improved formatting of typing annotations.

Respect PYTHONWARNINGS environment variable.

Various other small bugs and fixes.

0.9.2 (2020-11-25)

Stop touching objects blacklisted with __pdoc__.

Use last __init__ to document class signature (e.g. in case of @typing.overload).

Better formatting of nptyping and typing.NewType annotations.

Fix minor lunr search bugs from the previous version.

0.9.1 (2020-09-28)

Fix circular imports and generally handling of typing annotations when they are unresolvable (regression since 0.9.0).

0.9.0 (2020-08-27)

New offline search function using Lunr.js (see lunr_config config tunable).

Correctly enumerate members of Enum and typed-only namespaces.

Inspect __init__ to obtain true/overridden class instantiation parameters.

Bump Highlight.js and use its 'python-repl' annotation for doctests.

0.8.5 (2020-08-27)

Fix installation issue on non-UTF-8 platforms.

Fix working with 'develop' installations in virtual environments.

0.8.4 (2020-06-30)

Fix inline code interpretation inside fenced code blocks.

0.8.3 (2020-06-27)

Fix extracting TOC with interleaved doctests in fenced code blocks, regression since 0.8.2.

0.8.2 (2020-06-26)

Enhancements:

New CLI switch --skip-errors for skipping invalid/broken modules with a warning instead of raising an error.

CSS tweak to highlight :target-ed section.

Paths to generated files (with --output-dir) are now printed to stdout.

... (truncated)

Commits

f358893 MNT: Update CHANGELOG for 0.10.0

0073fae REF: More f-strings

1961159 REF: Avoid using _BLACKLISTED_DUMMY 🤡

1bb95b4 BUG: Fix crash on annotating something as typing.Callable

f49faf0 MNT: CI: Install types-Markdown package to avoid mypy warning

251d61a BUG: Don't build Lunr search index when not --html

1c7f454 REF: Remove unused param pdoc.test.run(_check=)

da98dd7 BUG: Fully respect PYTHONWARNINGS, when set

c2c1320 REF: Also replace typing.Union[None, T] -> Optional[T]

bacbd53 TST: Skip failing test for now

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unsupported :no_entry: low-priority :arrow_down_small: dependabot
opened by dependabot[bot] 5
[Feat] Add support for Python 3.11

With the release of Python 3.11, it is imperative that epispot adds support for the new version along with the many updates that it brings. Among other things, the speed improvements offered by this release will have major impacts on the forecasting power of epispot's models by allowing users to generate predictions faster.
feat :rocket: unsupported :no_entry: high-priority :arrow_up_small:

opened by quantum9Innovation 0

Releases(v3.0.0-rc-1)

v3.0.0-rc-1(Aug 21, 2022)

The first release candidate of the v3 release! There are a lot of new changes in this release, so it's best to read the changes directly from the changelog itself.
Source code(tar.gz)
Source code(zip)
v3.0.0-alpha-3(Nov 25, 2021)
Important Notes

Python

Python 3.10 is now officially supported (in epispot and all its core dependencies)! :fireworks: 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:

[email protected]

[email protected]

[email protected]

[email protected]

[email protected]

[email protected]

[email protected]

[email protected]

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

Remove implicit object from the base class by @deepsource-autofix in https://github.com/epispot/epispot/pull/97

SECURITY.md Revision 1 by @quantum9Innovation in https://github.com/epispot/epispot/pull/98

[dep/dev]: Update codecov requirement from ~=2.1.11 to ~=2.1.12 by @dependabot in https://github.com/epispot/epispot/pull/100

[dep/dev]: Update pdoc3 requirement from ~=0.9.2 to ~=0.10.0 by @dependabot in https://github.com/epispot/epispot/pull/101

[dep]: Update plotly requirement from ~=5.1.0 to ~=5.2.1 by @dependabot in https://github.com/epispot/epispot/pull/104

[dep]: Update matplotlib requirement from ~=3.4.2 to ~=3.4.3 by @dependabot in https://github.com/epispot/epispot/pull/103

[dep]: Update numpy requirement from ~=1.21.1 to ~=1.21.2 by @dependabot in https://github.com/epispot/epispot/pull/102

[dep]: Update plotly requirement from ~=5.2.1 to ~=5.2.2 by @dependabot in https://github.com/epispot/epispot/pull/106

[dep]: Update plotly requirement from ~=5.2.2 to ~=5.3.0 by @dependabot in https://github.com/epispot/epispot/pull/107

[dep]: Update plotly requirement from ~=5.3.0 to ~=5.3.1 by @dependabot in https://github.com/epispot/epispot/pull/109

[dep/dev]: Update pytest requirement from ~=6.2.4 to ~=6.2.5 by @dependabot in https://github.com/epispot/epispot/pull/108

[dep]: Update scienceplots requirement from ~=1.0.8 to ~=1.0.9 by @dependabot in https://github.com/epispot/epispot/pull/110

[dep/dev]: Update coverage requirement from ~=5.5 to ~=6.1 by @dependabot in https://github.com/epispot/epispot/pull/116

Python 3.10 by @quantum9Innovation in https://github.com/epispot/epispot/pull/113

[dep]: Update numpy requirement from ~=1.21.2 to ~=1.21.4 by @dependabot in https://github.com/epispot/epispot/pull/117

[dep]: Update plotly requirement from ~=5.3.1 to ~=5.4.0 by @dependabot in https://github.com/epispot/epispot/pull/118

[dep]: Update matplotlib requirement from ~=3.4.3 to ~=3.5.0 by @dependabot in https://github.com/epispot/epispot/pull/119

Bump version to v3.0.0-alpha-3 by @Quantalabs in https://github.com/epispot/epispot/pull/120

Fix failing docs from #113 by @Quantalabs in https://github.com/epispot/epispot/pull/121

Deploy v3.0.0-alpha-3 by @quantum9Innovation in https://github.com/epispot/epispot/pull/122

New Contributors

@deepsource-autofix made their first contribution in https://github.com/epispot/epispot/pull/97

Full Changelog: https://github.com/epispot/epispot/compare/v3.0.0-alpha-2...v3.0.0-alpha-3
Source code(tar.gz)
Source code(zip)
v3.0.0-alpha-2(Jul 25, 2021)
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)
Source code(tar.gz)
Source code(zip)
v3.0.0-alpha-1(Jun 22, 2021)
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)
Source code(tar.gz)
Source code(zip)
v2.1.1(Apr 5, 2021)

Minor patch: fixes incorrect nightly merge from master If using v2.1.0: update via pip install epispot --upgrade
Source code(tar.gz)
Source code(zip)
v2.1.0(Apr 3, 2021)
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
Source code(tar.gz)
Source code(zip)
v2.0.1(Dec 29, 2020)
New updates for the Discord Bot covid19-tracker:

A new experimental fitting algorithm was added

Call as epi.fitters.tree_search()

Source code(tar.gz)
Source code(zip)
v2.0.0(Oct 25, 2020)

Version 2 Debut

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 :heavy_check_mark: | spatial models ❌ conda ❌ | tutorials 🟡 | interactive plots 🟡
Source code(tar.gz)
Source code(zip)
v1.1.0(Aug 30, 2020)

Added the epispot.fitters module.
Source code(tar.gz)
Source code(zip)
v1.0.0(Aug 22, 2020)

Herd Immunity (v1.0.0)

Note: this is the first fully-supported production-ready release. Now the first release on PyPI

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 ❌
Source code(tar.gz)
Source code(zip)
v0.1.3-beta(Aug 11, 2020)

Added the Dead compartment
Source code(tar.gz)
Source code(zip)
v0.1.2-beta(Aug 9, 2020)

Added the Exposed compartment.
Source code(tar.gz)
Source code(zip)
v0.1.1-beta(Aug 8, 2020)

Install on pip as pip install epispot==0.0.2

Packaging| Docs | Features --- | --- | --- pip ✔️ | docstrings ✔️ | compartments 🟡 conda ❌ | docs ❌ | spatial models ❌ | | tutorials 🟡 | interactive plots ❌
Source code(tar.gz)
Source code(zip)
v0.1-beta(Aug 3, 2020)

Note: this version is still in beta mode. Support for proper documentation, cross-platform packages, tutorials, and more compartments are still to come.

The first version with full package support, as can be found on PyPi at https://pypi.org/project/epispot/0.0.1/. Comes with Susceptible, Infected, and Recovered compartments. Install on pip as pip install epispot==0.0.1

Packaging| Docs | Features --- | --- | --- pip ✔️ | docstrings ✔️ | compartments 🟡 conda ❌ | docs ❌ | spatial models ❌ | | tutorials ❌ | interactive plots ❌
Source code(tar.gz)
Source code(zip)
v0.1-alpha(Jul 19, 2020)
Notes:

⚠️ unsupported These are the first few code bits for the epi-spot package. The first release of epi-spot (v0.1-alpha - 'patient-zero'). Deployed to GitHub Pages, code fully released. Currently no Python package or Wiki.

Support For:

SIR/SEIR/SEIRCD Models

Visualizers on matplotlib.pyplot

Model fitting via gradient descent*

*unstable
Source code(tar.gz)
Source code(zip)