Merge pull request #41 from marshall-lab/develop

merge for v0.1.0

.github/workflows/unit-tests.yml

@@ -25,10 +25,18 @@ jobs:
       run: |
         pip install flake8
         # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        flake8 src --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
+        flake8 src --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Check code formatting with black
+      run: |
+        pip install black
+        black . --check
+    - name: Static Type Checking with mypy
+      run: |
+        pip install mypy
+        mypy titan
     - name: Test with pytest
       run: |
         pip install pytest
-        pytest
+        python -m pytest

.gitignore

@@ -1,7 +1,21 @@
 *.pyc
-*.txt
 *.png
 .idea/
 venv/
 venv/*
+
+__pycache__/
+__pycache__/*
+.python-version
+poetry.lock
+pyproject.toml
+.pytest_cache/
+.pytest_cache/*
+.mypy_cache
+
 .vscode/
+
+ipynb/.ipynb_checkpoints/
+
+results/*.txt
+results/*/*.txt

LICENSE

@@ -1,29 +1,21 @@
-BSD 3-Clause License
+MIT License
 
-Copyright (c) 2017, Maximilian King
-All rights reserved.
+Copyright (c) 2019 Marshall Lab
 
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
 
-* Redistributions of source code must retain the above copyright notice, this
-  list of conditions and the following disclaimer.
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
 
-* Redistributions in binary form must reproduce the above copyright notice,
-  this list of conditions and the following disclaimer in the documentation
-  and/or other materials provided with the distribution.
-
-* Neither the name of the copyright holder nor the names of its
-  contributors may be used to endorse or promote products derived from
-  this software without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -6,7 +6,7 @@ Agent populations are defined as graphs (nodes connected by edges). Nodes in the
 
 ## Getting Started
 
-To get started, install the requirements listed in the `requirements.txt` using a local python install or virtual env. Once installed, the model can be run using the `MP_simulation.py` program and configured using the `params.py` file.
+To get started, install the requirements listed in the `requirements.txt` using a local python install or virtual env. Once installed, the model can be run using the `run_titan.py` program and configured using the `params.py` file.
 
 ### Prerequisites
 
@@ -18,36 +18,37 @@ pip install -r requirements.txt
 
 ### Installing
 
-Currently, TITAN does not require any further installation as the source code exists within this repo in `/src`
+Currently, TITAN does not require any further installation as the source code exists within this repo in `/titan`
 
 ## Running the Model
 
-To run the model, execute the `MP_simluation.py` program within the `/src/` directory. It will natively read in the `params.py` configuration file as the input parameters for the model. These can be configured as desired for the target model setting and configuration. Other examples of calibrated settings exist within the `/settings/` directory. 
+To run the model, execute the `run_titan.py` program within the `/titan/` directory. It will natively read in the `params.py` configuration file as the input parameters for the model. These can be configured as desired for the target model setting and configuration. Other examples of calibrated settings exist within the `/settings/` directory.
 
-Results of the model are generated and aggregated into the `/src/results/` directory. If the model is re-run, the existing results will be overwriten. A helper script has been written to prepare simulations for use with OSCAR, and is labelled `subTitan.sh` in the root directory.
+Results of the model are generated and aggregated into the `/results/` directory. If the model is re-run, the existing results will be overwriten. A helper script has been written to prepare simulations for use with OSCAR, and is labelled `subTitan.sh` in the root directory.
 
 
 ### Running the tests
 
+`python -m pytest`
+
 TODO: Test coverage and examples.
 
 
 ## Built With
 * [Python3.x](https://www.python.org/downloads/release/python-374/) - Programming language
 * [Networkx](https://networkx.github.io/) - Network structure backend
-* [Numpy](http://www.numpy.org/) - Numberical libraries
+* [Numpy](http://www.numpy.org/) - Numerical libraries
 
 
 ## Authors
 
-* **Lars Seeman** - *Initial work* 
-* **Max King** - *Continued development* 
-* **Sarah Bessey** - *Continued development* 
-* **Mary McGrath** - *Continued development* 
+* **Lars Seeman** - *Initial work*
+* **Max King** - *Continued development*
+* **Sarah Bessey** - *Continued development*
+* **Mary McGrath** - *Continued development*
 
 ## License
 
 This project is licensed under the MIT License - see the [LICENSE.md](LICENSE.md) file for details
 
 ## Acknowledgments
-