caam37830 · yianc-uc · Oct 26, 2020 · Oct 26, 2020 · Oct 26, 2020 · Nov 7, 2020
diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
@@ -0,0 +1,48 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Python package
+
+on: [push]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.8]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install flake8 pytest
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      working-directory: ./test
+      run: |
+        pytest test.py
+        pytest testimproveagent.py
+        pytest testpde.py
+    - name: Run scripts
+      working-directory: ./scripts
+      run: |
+        python scripts.py
+        python time_series_plot.py
+        python covidsir.py
+        python improveagentscript.py
+        python mask.py
+        python map.py
+        python pdesimulation.py
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,137 @@
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
diff --git a/README.md b/README.md
@@ -0,0 +1,18 @@
+# project-group-2
+project-group-2 created by GitHub Classroom
+
+For this project, we create a directory docs which includes a python package sir, a scripts directory, and a test directory for sir package.
+
+The scripts directory includes the scripts for running basic, spatial agent-based, ODE simulation and three variations. The scripts.py is used for running the basic ode and agent-based simulation model. The improveagentscript.py is used for running the spatial agent-based model, and the pdesimulation.py is used for running spatial pde model. The map.py, time_series_plot.py, mask.py,covidsir.py are used for all three variations. Apart from the python files, we also include the required html files for interactive visualization in scripts directory. All these files will be regenerated as we run the github action. Thus, we just put all the files in scripts directory.
+
+The sir package includes ode.py, odemask.py, improveagent.py, agent.py, pde.py. The __init__.py is used for claiming that sir is a package. We import other files in __init__.py so that we can import sir in test directory. The ode.py is used for basic continuous ode generation model and the variation for fitting the Covid-19 data with sir model. The agent.py is used for basic agent-based sir model. The improveagent.py is used for spatial agent-based sir model. The pde.py is used for spatial pde model. The odemask.py is used for for mask variation.
+
+The test package include test.py, testimproveagent.py, and testpde.py. The test.py is used for testing functions in sir.agent; the testimproveagent.py is used for testing functions in sir.improveagent; the testpde.py is used for testing functions in sir.pde.
+
+To run the scripts, you may change to the scripts directory and run scripts. To be specific, "cd scripts/" and "python improveagentscript.py".
+
+To test the files, you may change to the test directory and test files. For instance, "cd test/" and "pytest test.py".
+
+For the midterm checkpoint, we have midtermreport.pdf as well its latex version included in the doc directory.
+For the final checkpoint, we have finalreport.pdf with its latex version included in the doc directory.
+All the visualization html files are included in scripts directory.
diff --git a/doc/checkpoint/Figure1_discrete_bsmall_T10.png b/doc/checkpoint/Figure1_discrete_bsmall_T10.png
diff --git a/doc/checkpoint/Figure1_discrete_bsmall_T20.png b/doc/checkpoint/Figure1_discrete_bsmall_T20.png
diff --git a/doc/checkpoint/Figure1_discrete_bsmall_T30.png b/doc/checkpoint/Figure1_discrete_bsmall_T30.png
diff --git a/doc/checkpoint/Figure1_discrete_bsmall_infectT10.png b/doc/checkpoint/Figure1_discrete_bsmall_infectT10.png
diff --git a/doc/checkpoint/Figure1_discrete_bsmall_infectT20.png b/doc/checkpoint/Figure1_discrete_bsmall_infectT20.png
diff --git a/doc/checkpoint/Figure1_discrete_bsmall_infectT30.png b/doc/checkpoint/Figure1_discrete_bsmall_infectT30.png
diff --git a/doc/checkpoint/Figure1_discrete_diagT10infect.png b/doc/checkpoint/Figure1_discrete_diagT10infect.png
diff --git a/doc/checkpoint/Figure1_discrete_diagT10total.png b/doc/checkpoint/Figure1_discrete_diagT10total.png
diff --git a/doc/checkpoint/Figure1_discrete_diagT20infect.png b/doc/checkpoint/Figure1_discrete_diagT20infect.png
diff --git a/doc/checkpoint/Figure1_discrete_diagT20total.png b/doc/checkpoint/Figure1_discrete_diagT20total.png
diff --git a/doc/checkpoint/Figure1_discrete_diagT30infect.png b/doc/checkpoint/Figure1_discrete_diagT30infect.png
diff --git a/doc/checkpoint/Figure1_discrete_diagT30total.png b/doc/checkpoint/Figure1_discrete_diagT30total.png
diff --git a/doc/checkpoint/Figure1_discrete_sir_b2_k1.png b/doc/checkpoint/Figure1_discrete_sir_b2_k1.png
diff --git a/doc/checkpoint/Figure1_discrete_sir_b2_k2.png b/doc/checkpoint/Figure1_discrete_sir_b2_k2.png
diff --git a/doc/checkpoint/Figure1_discrete_sir_b2_k3.png b/doc/checkpoint/Figure1_discrete_sir_b2_k3.png
diff --git a/doc/checkpoint/Figure1_discrete_sir_b5_k1.png b/doc/checkpoint/Figure1_discrete_sir_b5_k1.png
diff --git a/doc/checkpoint/Figure1_discrete_sir_b5_k2.png b/doc/checkpoint/Figure1_discrete_sir_b5_k2.png
diff --git a/doc/checkpoint/Figure1_discrete_sir_b5_k3.png b/doc/checkpoint/Figure1_discrete_sir_b5_k3.png
diff --git a/doc/checkpoint/Figure2_ode_b2k1.png b/doc/checkpoint/Figure2_ode_b2k1.png
diff --git a/doc/checkpoint/Figure2_ode_b2k2.png b/doc/checkpoint/Figure2_ode_b2k2.png
diff --git a/doc/checkpoint/Figure2_ode_b2k3.png b/doc/checkpoint/Figure2_ode_b2k3.png
diff --git a/doc/checkpoint/Figure2_ode_b5k1.png b/doc/checkpoint/Figure2_ode_b5k1.png
diff --git a/doc/checkpoint/Figure2_ode_b5k2.png b/doc/checkpoint/Figure2_ode_b5k2.png
diff --git a/doc/checkpoint/Figure2_ode_b5k3.png b/doc/checkpoint/Figure2_ode_b5k3.png
diff --git a/doc/checkpoint/Figure2_ode_infT10_bsmall.png b/doc/checkpoint/Figure2_ode_infT10_bsmall.png
diff --git a/doc/checkpoint/Figure2_ode_infT20_bsmall.png b/doc/checkpoint/Figure2_ode_infT20_bsmall.png
diff --git a/doc/checkpoint/Figure2_ode_infT30_bsmall.png b/doc/checkpoint/Figure2_ode_infT30_bsmall.png
diff --git a/doc/checkpoint/Figure2_ode_infectT10.png b/doc/checkpoint/Figure2_ode_infectT10.png
diff --git a/doc/checkpoint/Figure2_ode_infectT20.png b/doc/checkpoint/Figure2_ode_infectT20.png
diff --git a/doc/checkpoint/Figure2_ode_infectT30.png b/doc/checkpoint/Figure2_ode_infectT30.png
diff --git a/doc/checkpoint/Figure2_ode_totalT10.png b/doc/checkpoint/Figure2_ode_totalT10.png
diff --git a/doc/checkpoint/Figure2_ode_totalT10_bsmall.png b/doc/checkpoint/Figure2_ode_totalT10_bsmall.png
diff --git a/doc/checkpoint/Figure2_ode_totalT20.png b/doc/checkpoint/Figure2_ode_totalT20.png
diff --git a/doc/checkpoint/Figure2_ode_totalT20_bsmall.png b/doc/checkpoint/Figure2_ode_totalT20_bsmall.png
diff --git a/doc/checkpoint/Figure2_ode_totalT30.png b/doc/checkpoint/Figure2_ode_totalT30.png
diff --git a/doc/checkpoint/Figure2_ode_totalT30_bsmall.png b/doc/checkpoint/Figure2_ode_totalT30_bsmall.png
diff --git a/doc/checkpoint/Reference3.bib b/doc/checkpoint/Reference3.bib
@@ -0,0 +1,21 @@
+@author{Steff2020mask,
+title = {{To mask or not to mask: Modeling the potential for face mask
+use by the general public to curtail the COVID-19 pandemic}},
+author = {Eikenberry, S. and Mancuso,M. and Iboi,E. and Phan,T. and Eikenberry,K. and Kuang,Y. and Kostelich,E. and Gumel,A.},
+journal = {Infectious Disease Modelling},
+pages = {293--308},
+year = {2020},
+}
+
+@online{SARSsource,
+title = {{SARS 2003 Outbreak Dataset}},
+author = {kp,D.},
+year = 2020,
+url = {https://www.kaggle.com/imdevskp/sars-outbreak-2003-complete-dataset}
+}
+
+@online{Johnhopkins,
+title = {{CSSEGISandData}},
+year = 2020,
+url = {https://github.com/CSSEGISandData?tab=overview&from=2020-07-01&to=2020-07-31}
+}
diff --git a/doc/checkpoint/midtermreport.aux b/doc/checkpoint/midtermreport.aux
@@ -0,0 +1,72 @@
+\relax 
+\providecommand\hyper@newdestlabel[2]{}
+\abx@aux@refcontext{nty/global//global/global}
+\providecommand\HyperFirstAtBeginDocument{\AtBeginDocument}
+\HyperFirstAtBeginDocument{\ifx\hyper@anchor\@undefined
+\global\let\oldcontentsline\contentsline
+\gdef\contentsline#1#2#3#4{\oldcontentsline{#1}{#2}{#3}}
+\global\let\oldnewlabel\newlabel
+\gdef\newlabel#1#2{\newlabelxx{#1}#2}
+\gdef\newlabelxx#1#2#3#4#5#6{\oldnewlabel{#1}{{#2}{#3}}}
+\AtEndDocument{\ifx\hyper@anchor\@undefined
+\let\contentsline\oldcontentsline
+\let\newlabel\oldnewlabel
+\fi}
+\fi}
+\global\let\hyper@last\relax 
+\gdef\HyperFirstAtBeginDocument#1{#1}
+\providecommand\HyField@AuxAddToFields[1]{}
+\providecommand\HyField@AuxAddToCoFields[2]{}
+\@writefile{toc}{\boolfalse {citerequest}\boolfalse {citetracker}\boolfalse {pagetracker}\boolfalse {backtracker}\relax }
+\@writefile{lof}{\boolfalse {citerequest}\boolfalse {citetracker}\boolfalse {pagetracker}\boolfalse {backtracker}\relax }
+\@writefile{lot}{\boolfalse {citerequest}\boolfalse {citetracker}\boolfalse {pagetracker}\boolfalse {backtracker}\relax }
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+\newlabel{fig:figure3}{{9}{5}{Phase diagrams for percentage of population infected and removed (i+r), continuous}{figure.9}{}}
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+\newlabel{fig:figure3}{{10}{5}{Phase diagrams for percentage of population infected and removed (i+r), continuous}{figure.10}{}}
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+\abx@aux@cite{SARSsource}
+\abx@aux@segm{0}{0}{SARSsource}
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+\abx@aux@segm{0}{0}{SARSsource}
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+\abx@aux@segm{0}{0}{Johnhopkins}
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+\@writefile{toc}{\defcounter {refsection}{0}\relax }\@writefile{toc}{\contentsline {section}{\numberline {5}Bibliography}{8}{section.5}\protected@file@percent }
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