Update readme

README.md

@@ -27,20 +27,52 @@ limitations under the License. -->
 compartmental
 </h1>
 <h2 align="center">
-.
-</h2><br></br>
-<h3 align="center">
-.
-</h3><br></br>
-
-
+Utility tools for Approximate Bayesian computation on compartmental models 
+</h2>
 
+<br>
 <div align="center">
 
 <a href="https://quanticpony.github.io/compartmental/">
 <img src=https://img.shields.io/github/deployments/QuanticPony/compartmental/github-pages?label=documentation>
 </a>
-<br></br>
+<br></br></br>
+<h3 align="center">
+
+</h3>
+
+
+
+
 
 </div>
-<br></br>
+
+# 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**.

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

docs/README.md

@@ -0,0 +1,78 @@
+<!-- Copyright 2023 Unai Lería Fortea & Pablo Vizcaíno García
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License. -->
+
+[![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/)
+
+<br></br>
+<h1 align="center">
+compartmental
+</h1>
+<h2 align="center">
+Utility tools for Approximate Bayesian computation on compartmental models 
+</h2>
+
+<br>
+<div align="center">
+
+<a href="https://quanticpony.github.io/compartmental/">
+<img src=https://img.shields.io/github/deployments/QuanticPony/compartmental/github-pages?label=documentation>
+</a>
+<br></br></br>
+<h3 align="center">
+
+</h3>
+
+
+
+
+
+</div>
+
+# 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**.

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()
+  })

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 
+
 
 $$
-\begin{equation*}
-    P_{infection}^{j} = 1- \left(1-\lambda\frac{I}{N}\right)^{\left<k_j\right>}; \quad \textrm{with} \quad j=active, lockdown.
-\end{equation*}
+\begin{align} 
+    \tag{4.3} P_{infection} &= p(t)\cdot P_{infection}^{active} + (1-p(t))(1-sh(1-\phi))\cdot P_{infection}^{lockdown}, \\
+    P_{infection}^{j} &= 1- \left(1-\lambda\frac{I}{N}\right)^{\left<k_j\right>}; \quad \textrm{with} \quad j=active, lockdown.\\
+    sh &= (1-\frac{I}{N})^{\sigma-1}
+\end{align}
 $$
 
+
 The configuration could be:
 
 ```json

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/

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