diff --git a/README.md b/README.md index 0e32342..fb435cd 100644 --- a/README.md +++ b/README.md @@ -27,20 +27,52 @@ limitations under the License. --> compartmental

-. -



-

-. -



- - +Utility tools for Approximate Bayesian computation on compartmental models + +
-

+


+

+ +

+ + + +
-

+ +# Instalation +**compartmental** releases are available as wheel packages on [PyPI](https://pypi.org/project/compartmental/). You can install the last version using `pip`: +``` +pip install compartmental +``` + + +# Documentation +Documentations is automatically generated from code on main push and hosted in github-pages [here](https://quanticpony.github.io/compartmental/). + +# Help +Just open an issue with the `question` tag ([or clic here](https://github.com/QuanticPony/compartmental/issues/new?assignees=QuanticPony&labels=question&template=question.md&title=)), I would love to help! + +# Contributing +You can contribute with: + +* Examples +* Documentation +* [Bug report/fix](https://github.com/QuanticPony/compartmental/issues/new?assignees=QuanticPony&labels=bug&template=bug_report.md&title=) +* [Features](https://github.com/QuanticPony/compartmental/issues/new?assignees=QuanticPony&labels=new-feature&template=feature_request.md&title=) +* Code + +Even only feedback is greatly apreciated. + +Just create an issue and let me know you want to help! + + +# Licensing +**compartmental** is released under the **Apache License Version 2.0**. \ No newline at end of file diff --git a/compartmental/__init__.py b/compartmental/__init__.py index d1cb790..55c5164 100644 --- a/compartmental/__init__.py +++ b/compartmental/__init__.py @@ -12,7 +12,7 @@ # See the License for the specific language governing permissions and # limitations under the License. -__version__ = "0.0.3" +__version__ = "0.1.0" _CUPY_MODE_: bool from . import generic_model diff --git a/docs/README.md b/docs/README.md new file mode 100644 index 0000000..fb435cd --- /dev/null +++ b/docs/README.md @@ -0,0 +1,78 @@ + + +[![PyPI Downloads](https://img.shields.io/pypi/dm/compartmental.svg?label=downloads)](https://pypi.org/project/compartmental/) +[![PyPI Version](https://img.shields.io/pypi/v/compartmental?)](https://pypi.org/project/compartmental/) + +![Commit activity](https://img.shields.io/github/commit-activity/m/QuanticPony/compartmental) +[![License](https://img.shields.io/pypi/l/compartmental)](LICENSE) +[![Build](https://img.shields.io/github/actions/workflow/status/QuanticPony/compartmental/ci-master.yml)](https://github.com/QuanticPony/compartmental/actions) + +[![Python Version](https://img.shields.io/pypi/pyversions/compartmental)](https://pypi.org/project/compartmental/) +[![Wheel](https://img.shields.io/pypi/wheel/compartmental)](https://pypi.org/project/compartmental/) + +

+

+compartmental +

+

+Utility tools for Approximate Bayesian computation on compartmental models +

+ +
+
+ + + + +


+

+ +

+ + + + + +
+ +# Instalation +**compartmental** releases are available as wheel packages on [PyPI](https://pypi.org/project/compartmental/). You can install the last version using `pip`: +``` +pip install compartmental +``` + + +# Documentation +Documentations is automatically generated from code on main push and hosted in github-pages [here](https://quanticpony.github.io/compartmental/). + +# Help +Just open an issue with the `question` tag ([or clic here](https://github.com/QuanticPony/compartmental/issues/new?assignees=QuanticPony&labels=question&template=question.md&title=)), I would love to help! + +# Contributing +You can contribute with: + +* Examples +* Documentation +* [Bug report/fix](https://github.com/QuanticPony/compartmental/issues/new?assignees=QuanticPony&labels=bug&template=bug_report.md&title=) +* [Features](https://github.com/QuanticPony/compartmental/issues/new?assignees=QuanticPony&labels=new-feature&template=feature_request.md&title=) +* Code + +Even only feedback is greatly apreciated. + +Just create an issue and let me know you want to help! + + +# Licensing +**compartmental** is released under the **Apache License Version 2.0**. \ No newline at end of file diff --git a/docs/index.md b/docs/index.md deleted file mode 100644 index e69de29..0000000 diff --git a/docs/javascripts/mathjax.js b/docs/javascripts/mathjax.js new file mode 100644 index 0000000..0f4b6e6 --- /dev/null +++ b/docs/javascripts/mathjax.js @@ -0,0 +1,16 @@ +window.MathJax = { + tex: { + inlineMath: [["\\(", "\\)"]], + displayMath: [["\\[", "\\]"]], + processEscapes: true, + processEnvironments: true + }, + options: { + ignoreHtmlClass: ".*|", + processHtmlClass: "arithmatex" + } + }; + + document$.subscribe(() => { + MathJax.typesetPromise() + }) \ No newline at end of file diff --git a/examples/MY_MODEL.md b/examples/MY_MODEL.md index 44cf3cb..fbc8915 100644 --- a/examples/MY_MODEL.md +++ b/examples/MY_MODEL.md @@ -17,6 +17,8 @@ This examples follows the model exposed in my [Physics Undergraduate Thesis Proj The main equations of the model are the following: + + $$ \begin{align} \tag{4.5} S_h[t+1] &= S_T[t] \cdot (1-p(t))sh (1-\phi)\\ @@ -29,19 +31,18 @@ $$ \end{align} $$ -Where: -$$ -\begin{equation} \tag{4.3} - P_{infection} = p(t)\cdot P_{infection}^{active} + (1-p(t))(1-sh(1-\phi))\cdot P_{infection}^{lockdown}, -\end{equation} -$$ +Where + $$ -\begin{equation*} - P_{infection}^{j} = 1- \left(1-\lambda\frac{I}{N}\right)^{\left}; \quad \textrm{with} \quad j=active, lockdown. -\end{equation*} +\begin{align} + \tag{4.3} P_{infection} &= p(t)\cdot P_{infection}^{active} + (1-p(t))(1-sh(1-\phi))\cdot P_{infection}^{lockdown}, \\ + P_{infection}^{j} &= 1- \left(1-\lambda\frac{I}{N}\right)^{\left}; \quad \textrm{with} \quad j=active, lockdown.\\ + sh &= (1-\frac{I}{N})^{\sigma-1} +\end{align} $$ + The configuration could be: ```json diff --git a/mkdocs.yml b/mkdocs.yml index 24d1447..05e9de2 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -23,7 +23,7 @@ watch: [README.md, compartmental, examples] nav: - Home: - - Overview: index.md + - Overview: README.md - License: LICENSE.md - Code Reference: reference/ - Examples: examples/ diff --git a/pyproject.toml b/pyproject.toml index 3b056f4..03d10ca 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta" [project] name = "compartmental" -version = "0.0.3" +version = "0.1.0" requires-python = ">=3.8" description = "Compartmental models with ABC inference optimized for GPU use" @@ -20,9 +20,17 @@ maintainers = [ readme = "README.md" license = { text="Apache License 2.0"} -keywords = [] +keywords = ["compartmental models", "fit", "analysis", "ABC", "computation"] -classifiers = [] +classifiers = [ + "Intended Audience :: Education", + "Intended Audience :: Science/Research", + "Programming Language :: Python :: 3", + "License :: OSI Approved :: Apache Software License", + "Operating System :: OS Independent", + "Topic :: Education", + "Topic :: Scientific/Engineering", + "Topic :: Scientific/Engineering :: Visualization"] dependencies = ['numpy'] @@ -31,7 +39,7 @@ dependencies = ['numpy'] "Documentation" = "https://QuanticPony/.github.io/compartmental/" [tool.bumpver] -current_version = "0.0.3" +current_version = "0.1.0" version_pattern = "MAJOR.MINOR.PATCH" commit_message = "Update version: {old_version} -> {new_version}" commit = true