Copy changes from documentation

- epispot/
    - Update __init__.py with new docs and funcs
    - Update fitters.py with new docs
- Update README-nightly.md with new changes

README-nightly.md

@@ -6,8 +6,8 @@
 
 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.
 
-> This is a nightly version of epispot and may contain possibly unstable code.\
-> **Please see usage instructions prior to adding this project as a dependency**\
+> This is a nightly version of epispot and may contain possibly unstable code.  
+> **Please see usage instructions prior to adding this project as a dependency**  
 > If you prefer to use the stable version of epispot, please see
 > the [project on PyPI](https://pypi.org/project/epispot)
 
@@ -78,9 +78,10 @@ This is the hardest way to install `epispot-nightly` but it can be particularly
 Clone the repository with:
 
 ```shell
-git clone https://github.com/epispot/epispot  # clone epispot/epispot
-cd epispot  # open project
-pip install -r requirements-nightly.txt  # install package requirements
+git clone https://github.com/epispot/epispot
+cd epispot/requirements
+pip install -r pre-requirements.txt  # helps avoid version conflicts
+pip install -r requirements-nightly.txt
 ```
 
 If you're planning on helping out in the development process, it will be  helpful to install a few extra requirements with:
@@ -111,16 +112,18 @@ Please also note that security updates are not provided on previous nightly vers
 
 ## Getting Started
 
-Make sure you are already familiar with [epispot](https://www.pypi.org/project/epispot). If not, you can find epispot's auto-generated documentation [here](https://epispot.github.io/epispot/). Additionally, we highly recommend reading the [epispot manual](https://epispot.gitbook.io) to get a better understanding of the documentation and how to use epispot.
+Make sure you are already familiar with [epispot](https://www.pypi.org/project/epispot). If not, continue reading the auto-generated documentation published to this site. Additionally, we highly recommend reading the [epispot manual](https://epispot.gitbook.io) to get a better understanding of the documentation and how to use epispot.
 
-## Statuses
+## Current Statuses
+
+Please note that these statuses reflect the most recent CI checks and are not related to this specific version. The following statuses show the progress of the current development.
 
 | Pipeline | Status |
 | --- | --- |
-| Travis CI | [![Build Status](https://www.travis-ci.com/epispot/epispot.svg?branch=master)](https://www.travis-ci.com/epispot/epispot) |
+| Build (3.7-3.9) | [![Build](https://github.com/epispot/epispot/actions/workflows/build.yml/badge.svg)](https://github.com/epispot/epispot/actions/workflows/build.yml) |
 | CodeCov | [![codecov](https://codecov.io/gh/epispot/epispot/branch/master/graph/badge.svg?token=WGIM127RFY)](https://codecov.io/gh/epispot/epispot) |
-| PyPI main | ![latest-release](https://shields.mitmproxy.org/pypi/v/epispot.svg?color=success) |
-| PyPI nightly | ![latest-release](https://shields.mitmproxy.org/pypi/v/epispot-nightly.svg?color=success) |
+| PyPI main (latest) | ![latest-release](https://shields.mitmproxy.org/pypi/v/epispot.svg?color=success) |
+| PyPI nightly (latest) | ![latest-release](https://shields.mitmproxy.org/pypi/v/epispot-nightly.svg?color=success) |
 | Security | ![GitHub issue custom search in repo](https://img.shields.io/github/issues-search/epispot/epispot?color=success&label=known%20vulnerabilities&query=VULNERABILITY%20is:open%20is:issue) |
 
 ## Contributing

epispot/__init__.py

@@ -2,7 +2,7 @@
 .. include:: ../README.md
 <!-- 
 Documentation available at: 
-https://epispot.github.io/epispot/en/v3.0.0-alpha-1 
+https://epispot.github.io/epispot/en/v3.0.0-alpha-2 
 -->
 """
 
@@ -48,70 +48,73 @@ def _dependency_check():
 from . import plots
 
 
-def _sanity_check():
-    """Pre-defined sanity check to check for installation errors"""
-
-    if not version or not source:  # pragma: no cover
-        message = \
-        '''
-        Version information and/or source for your epispot installation could not be found.
-        This likely means
-         (1) this version of epispot is deprecated or dated
-         (2) your installation of epispot is unstable
-        Try reinstalling epispot
-         (1) From PyPI:
-             $ pip install epispot
-         (2) From Anaconda:
-             $ conda config --add channels conda-forge
-             $ conda install -c conda-forge epispot
-         (3) From the GitHub Source:
-             $ git clone https://github.com/epispot/epispot
-             $ cd epispot
-             $ python install setup-nightly.py
-        If this fails or has failed before, then revert to epispot's last stable version.
-        Again, you can do this via
-         (1) PyPI:
-             (a) Go to https://pypi.org/project/epispot
-             (b) Scroll to the last MAJOR release in the form `a.0.0`
-             (c) Install via `$ pip install epispot==a.0.0` -- replace `a` with version #
-         (2) GitHub Source:
-             (a) Go to https://github.com/epispot/epispot
-             (b) Click the 'branches' tab
-             (c) Select the last branch with name `vA.0.0` for some version number A
-             (d) Install as `.zip`
-             (e) Unzip
-             (f) Run `$ python install setup.py`
-        '''
-        raise DeprecationWarning(message)
+# helper funcs
+def _check_versions():
+    """Checks for version conflicts"""
+    pass
+
+def _check_install():
+    """Checks for installation errors"""
+    pass
+
+def _check_updates():
+    """Checks for updates"""
+    pass
+
+def sanity_check():
+    """
+    Sanity check to check for basic installation errors, 
+    version conflicts, upgrades, etc.
+
+    **Run this if you experience any problems with epispot and before 
+    submitting any issues**
+    
+    """
+    # check for installation errors
+    if not source or not version:
+        _check_install()
+
+    # check for version conflicts
+    import sys
+    if (sys.version_info[0] < 3) or \
+       (sys.version_info[0] == 3 and sys.version_info[1] < 7):
+        raise RuntimeError('Epispot requires Python 3.7 or later') # pragma: no cover
+    else:
+        _check_versions()
+
+    # check for updates
+    _check_updates()
 
 
 # version info
-version = '3.0.0-alpha-1'
+version = '3.0.0-alpha-2'
 """
-Epispot's version info (updated every nightly release)
-Get with:
+Epispot's version info (updated every release)\n
+Check version information with:
 
 ```
     >>> print(epispot.version)
 ```
+
+Version information is also available through the `__version__` 
+property, included for legacy support.
 """
+__version__ = version  # alias for version
 
 stable = False
 """
 Build stability:
 
-- True → main package (stable)
-- False → nightly package (possibly unstable)
+- True ⇒ main package (stable)
+- False ⇒ nightly package (possibly unstable)
 """
 
 # metadata
 source = 'https://www.github.com/epispot/epispot'
-"""URL to GitHub source"""
-docs = 'https://epispot.github.io/epispot'
-"""Project documentation (not version-specific)"""
+"""URL to VCS source"""
+raw = f'https://raw.githubusercontent.com/epispot/epispot/v{version}/'
+"""URL to raw VCS source (must append file path)"""
+docs = f'https://epispot.github.io/epispot/en/v{version}/'
+"""Project documentation (version-specific)"""
 issues = 'https://www.github.com/epispot/epispot/issues'
-"""Submit new issues or bugs here"""
-
-
-_sanity_check()  # complete installation
-del _sanity_check
+"""Bug tracker"""

epispot/fitters.py

@@ -15,6 +15,10 @@ def grad_des(get_model_pred, real_data,
              N, samples, delta=0.0001,
              verbose=False):  # pragma: no cover
     """
+    .. warning::
+       This function is currently deprecated.
+       Fixes will be added in future alpha releases.
+
     The gradient descent fitter. This is not stochastic.
     For long timespans, this may take a long time to converge.
 
@@ -98,6 +102,10 @@ def tree_search(get_model_pred, real_data,
                 epochs, N, samples,
                 verbose=False):  # pragma: no cover
     """
+    .. warning::
+       This function is currently deprecated.
+       Fixes will be added in future alpha releases.
+
     Note: This is an experimental fitter
     """