Create .gitignore

.gitignore

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+# Custom files
+*.obj
+*.pdf
+*.png
+*.zip
+modules.rst
+
+# Other files
+.idea
+.vscode
+.DS_Store
+
+# History files
+.Rhistory
+.Rapp.history
+
+# Session Data files
+.RData
+
+# Example code in package build process
+*-Ex.R
+
+# Output files from R CMD build
+/*.tar.gz
+
+# Output files from R CMD check
+/*.Rcheck/
+
+# RStudio files
+.Rproj.user/
+
+# Datasets
+*.DTA
+*.dta
+
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+
+# knitr and R markdown default cache directories
+/*_cache/
+/cache/
+
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+
+# Shiny token, see https://shiny.rstudio.com/articles/shinyapps.html
+rsconnect/
+
+
+
+## Python ignores
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+.idea/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# 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/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+docs/fpsim*
+docs/api/_autosummary/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# dotenv
+.env
+
+# virtualenv
+.venv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+output/
+
+# EMOD specific
+status.txt
+config.json
+demographics.json
+campaign.json
+*.dtk
+.DS_Store
+.DS_Store
+dropbox/.DS_Store
+.DS_Store

README.md

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-# HMB_contraception
-Analysis of impact of hormonal contraception on HMB, which in turn impacts schooling and anemia
+# Heavy Menstrual Bleeding Add-On
+This repository contains code to add in heavy menstrual bleeding (HMB) dynamics to FPsim. 
+
+This includes:
+- Adding a heavy menstrual bleeding state for agents and parameterizing with data
+- Adding an iron-deficient anemia state for agents, and providing an odds ratio to link HMB to anemia
+- Allowing HMB to probabilistically disrupt schooling for girls
+
+For questions about this analysis, please contact info@fpsim.org

tests.py

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+'''' 
+Testing
+''''