Added a CLI

.coveragerc

@@ -1,5 +1,7 @@
 [run]
-source = epispot
+source =
+    epispot
+    bin
 
 [report]
 show_missing = True

.github/workflows/build.yml

@@ -21,14 +21,15 @@ jobs:
         python -m pip install --upgrade pip
         pip install flake8
         pip install -U pytest
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        pip install -r bin/requirements.txt
+        pip install -r requirements.txt
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Test code for errors
+    - name: Test package source code for errors
       run: |
         python tests/CI/test_sir.py
         python tests/CI/test_seir.py
@@ -39,3 +40,7 @@ jobs:
         python tests/CI/test_fit.py
         python tests/CI/test_recurrent.py
         python tests/CI/test_critical.py
+    - name: Test CLI for errors
+      run: |
+        python setup.py develop
+        epispot about

.github/workflows/coverage.yml

@@ -26,6 +26,7 @@ jobs:
     - name: Generate Coverage Report
       continue-on-error: true
       run: |
+        python -m coverage report
         python -m coverage xml
     - name: Upload to codecov
       run: |

CHANGELOG.md

@@ -0,0 +1,12 @@
+# Nightly Changelog
+@v2.1.1.2
+___
+
+- v2.1.1.2
+    - Added *very* basic epispot CLI functionality
+      - See `bin/requirements.txt` for CLI requirements
+    - Fire up a terminal and enter
+    ```shell
+    $ epispot about
+    ```
+    - Added this changelog for nightly package

README.md

@@ -11,41 +11,38 @@
 A tool for creating and testing epidemiological models faster than ever for the mathematical modeling of infectious 
 diseases. An idea from https://github.com/henrifroese/infectious_disease_modelling.
 
-**This is a nightly build of epispot. Releases may contain unstable code and issues are to be expected.\
-Additionally, code within this branch may be deprecated at any time.\
-See the official stable build and all its features [here](https://pypi.org/project/epispot/)**
-
-To ensure that you are using the latest version, run the following command regularly*:\
-`pip install epispot-nightly --upgrade` \
-*updates are published after every commit (~1/day)
+> **This is a nightly build of epispot. Releases may contain unstable code and issues are to be expected.\
+> Additionally, code within this branch may be deprecated at any time.\
+> See the official stable build and all its features [here](https://pypi.org/project/epispot/)**
 
 <br>
 
 ## Installation
 
 Epispot nightly can _only_ be installed on pip at this time.
 Install with:
-```
+```shell
 pip install epispot-nightly
 ```
 As a shorthand, use `import epispot as epi`.
 Both nightly and stable packages cannot be used at the same time in the same file.
+To ensure that you are using the latest version, run the following command regularly*:\
+```shell
+pip install epispot-nightly --upgrade
+```
+
+*updates are published after every commit (~1/day)\
+See [CHANGELOG.md](https://www.github.com/epispot/epispot/tree/nightly/CHANGELOG.md)
+for detailed update information
 
 ## Getting Started
 
-Make sure you are already familiar with epispot. You can view the new functions and changes by using the built in python `help()` command.
+Make sure you are already familiar with [epispot](https://www.pypi.org/project/epispot).
+If not, checkout the [tests/ directory](https://www.github.com/epispot/epispot/tree/nightly/tests)
+for hands-on examples.
+You can view the new functions and changes by using the built-in Python `help()` command.
 Epispot docs are located [here](https://epispot.github.io/epispot).
 
-## Latest Release Notes
-
- - 3/13/21 2.0.1.23 Add documentation, triggering workflow. See commit description for deeper info.
- - 2/26/21 2.0.1.22 Automations
-   - Automated code coverage reports
-   - Working on automating release notes 
- - 2/12/21 2.0.1.17 Actions Test
- - 2/12/21 2.0.1.16: Stability Improvements
-    - Allows for faster bug and issue tracking
-
 ## Stay one step ahead
 ### And preview the latest features
 Documentation can easily be accessed from function, class, and file docstrings.

bin/epispot

@@ -0,0 +1,45 @@
+#!/usr/bin/env python
+
+"""Shell Initialization"""
+import pathlib
+import epispot
+
+__color__ = False
+
+try:
+    import fire
+except:
+    print("Please install Fire to use epispot's CLI")
+    print('>>> pip install fire')
+
+try:
+    __color__ = True
+    import termcolor
+except:
+    print('Color output will be suppressed. To use colors run')
+    print('>>> pip install termcolor')
+
+
+class Shell(object):
+    """The base shell for epispot containing linking commands for Fire"""
+
+    def __init__(self, color=False):
+        """Initialize the epispot shell"""
+
+        self.color = color
+        self.path = pathlib.Path(__file__).parent.absolute()
+        self.version = 'shell-v0.1.0-alpha epispot-{0}'.format(epispot.__version__)
+
+    def about(self):
+        """Basic information about the epispot CLI"""
+
+        print('Epispot was invoked via the epispot CLI')
+        print('Path: {0}'.format(self.path))
+        print('Version: {0}'.format(self.version))
+        print('Color output enabled (True/False): {0}'.format(self.color))
+
+
+if __name__ == '__main__':
+    fire.Fire(Shell(
+        color=__color__
+    ))

bin/requirements.txt

@@ -0,0 +1,3 @@
+epispot
+fire
+termcolor

requirements.txt

@@ -1,3 +1,2 @@
 matplotlib
-numpy
-sphinx
+numpy

setup.py

@@ -12,6 +12,7 @@
     long_description_content_type="text/markdown",
     url="https://www.github.com/epispot/epispot/tree/nightly",
     packages=setuptools.find_packages(),
+    scripts=['bin/epispot'],
     classifiers=[
         "Programming Language :: Python :: 3.7",
         "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",