

README - GENERAL INFORMATION

Title of Project: CompoundingPharma – Dynamic production sequencing to minimize patient delays for compounded medications 

Grant Agreement: Horizon Europe MSCA Postdoctoral Fellowship No. 101150714 
Repository Version: Final Project Update 2026-02-19

Project acronym: CompoundingPharma 

Principal Investigator: Kraig Delana <ORCID: 0000-0002-0485-9950>
Institution: IE Business School 
Email: kraig.delana@ie.edu



OVERVIEW & INTEROPERABILITY

This README illustrates how to run the code and generate the outputs associated with the fluid model simulation as presented in section 5.2 (and appendix E) of the associated paper. 

The simulation code has been implemented in Python (.py files) using open-source libraries.  The files can be opened and run in any IDE compatible with python, e.g., Spyder or Visual Studio Code (or run directly) and is sectioned into cells with pseudocode documentation provided inline describing code function. Instructions to reproduce the results are included below, and the outputs of the code are included for convenience in the associated output folder. 



RUN SIMULATION -- Manuscript_Stochastic_Simulation_v0006.py

1. To generate data for the output folder, open and run the code file in the IDE of your choosing (or run directly). 
         
2. The code file will populate the output files (specified below) into the output file directory:

stochastic/
│
└── output/
    │    
    ├── avg_hybridsdre_v_old.png
    ├── avg_sdre_v_old.png
    ├── hybridxindex.png
    ├── max_hybridsdre_v_old.png
    ├── max_sdre_v_old.png
    ├── oldest.png
    ├── sdre.png
    ├── sdre_hybrid.png
    ├── stochastic_sojourn_times.png
    
    ├── Summary_hybrid_sdre_policy.csv
    ├── Summary_hybrid_xindex_policy.csv
    ├── Summary_Oldest_policy.csv
    ├── Summary_sdre_policy.csv
    └── Summary_xindex_policy.csv


EXPECTED RUNTIME: Approx. 40 Minutes 

COMPUTATIONAL ENVIRONMENT:

The code was executed on the following system:

	Operating system: Microsoft Windows 11 Enterprise (Version 10.0.26200)
	System architecture: x64-based PC
	CPU: Intel(R) Core(TM) Ultra 9 285H (16 cores, 16 logical processors)
	RAM: 68 GB
	Python version: 3.13.5
	Environment: Anaconda (conda)

A complete specification of the Anaconda environment is provided below: 

name: base
channels:
  - defaults
  - conda-forge
dependencies:
  - _anaconda_depends=2025.06=py313_mkl_2
  - aiobotocore=2.19.0=py313haa95532_0
  - aiohappyeyeballs=2.4.4=py313haa95532_0
  - aiohttp=3.11.10=py313h827c3e9_0
  - aioitertools=0.7.1=pyhd3eb1b0_0
  - aiosignal=1.2.0=pyhd3eb1b0_0
  - alabaster=0.7.16=py313haa95532_0
  - altair=5.5.0=py313haa95532_0
  - anaconda-anon-usage=0.7.1=py313hfc23b7f_100
  - anaconda-auth=0.8.6=py313haa95532_0
  - anaconda-catalogs=0.2.0=py313haa95532_2
  - anaconda-cli-base=0.5.2=py313haa95532_0
  - anaconda-client=1.13.0=py313haa95532_1
  - anaconda-navigator=2.6.6=py313haa95532_2
  - anaconda-project=0.11.1=py313haa95532_1
  - anaconda_powershell_prompt=1.1.0=haa95532_1
  - anaconda_prompt=1.1.0=haa95532_1
  - annotated-types=0.6.0=py313haa95532_0
  - anyio=4.7.0=py313haa95532_0
  - appdirs=1.4.4=pyhd3eb1b0_0
  - archspec=0.2.3=pyhd3eb1b0_0
  - argon2-cffi=21.3.0=pyhd3eb1b0_0
  - argon2-cffi-bindings=21.2.0=py313h827c3e9_1
  - arrow=1.3.0=py313haa95532_0
  - arrow-cpp=19.0.0=h33d5241_2
  - astroid=3.3.8=py313haa95532_0
  - astropy=7.0.0=py313h827c3e9_0
  - astropy-iers-data=0.2025.1.13.0.34.51=py313haa95532_0
  - asttokens=3.0.0=py313haa95532_0
  - async-lru=2.0.4=py313haa95532_0
  - asyncssh=2.17.0=py313haa95532_0
  - atomicwrites=1.4.0=py_0
  - attrs=24.3.0=py313haa95532_0
  - automat=24.8.1=py313haa95532_0
  - autopep8=2.0.4=pyhd3eb1b0_0
  - aws-c-auth=0.6.19=h2bbff1b_0
  - aws-c-cal=0.5.20=h2bbff1b_0
  - aws-c-common=0.8.5=h2bbff1b_0
  - aws-c-compression=0.2.16=h2bbff1b_0
  - aws-c-event-stream=0.2.15=hd77b12b_0
  - aws-c-http=0.6.25=h2bbff1b_0
  - aws-c-io=0.13.10=h2bbff1b_0
  - aws-c-mqtt=0.7.13=h2bbff1b_0
  - aws-c-s3=0.1.51=h2bbff1b_0
  - aws-c-sdkutils=0.1.6=h2bbff1b_0
  - aws-checksums=0.1.13=h2bbff1b_0
  - aws-crt-cpp=0.18.16=hd77b12b_0
  - aws-sdk-cpp=1.11.212=h6a15179_0
  - babel=2.16.0=py313haa95532_0
  - bcrypt=4.3.0=py313h636fa0f_0
  - beautifulsoup4=4.12.3=py313haa95532_0
  - binaryornot=0.4.4=pyhd3eb1b0_1
  - black=24.10.0=py313haa95532_0
  - blas=1.0=mkl
  - bleach=6.2.0=py313haa95532_0
  - blinker=1.9.0=py313haa95532_0
  - blosc=1.21.3=h6c2663c_0
  - bokeh=3.6.2=py313haa95532_0
  - boltons=24.1.0=py313haa95532_0
  - boost-cpp=1.82.0=h59b6b97_2
  - botocore=1.36.3=py313haa95532_0
  - bottleneck=1.4.2=py313h2cb717b_0
  - brotli-python=1.0.9=py313h5da7b33_9
  - bzip2=1.0.8=h2bbff1b_6
  - c-ares=1.19.1=h2bbff1b_0
  - c-blosc2=2.17.1=h0eb4811_0
  - ca-certificates=2025.11.12=h4c7d964_0
  - cachetools=5.5.1=py313haa95532_0
  - certifi=2025.11.12=pyhd8ed1ab_0
  - cffi=1.17.1=py313h827c3e9_1
  - chardet=4.0.0=py313haa95532_1003
  - charset-normalizer=3.3.2=pyhd3eb1b0_0
  - click=8.1.8=py313haa95532_0
  - cloudpickle=3.0.0=py313haa95532_0
  - colorama=0.4.6=py313haa95532_0
  - colorcet=3.1.0=py313haa95532_0
  - comm=0.2.1=py313haa95532_0
  - conda=25.7.0=py313hfa70ccb_0
  - conda-anaconda-telemetry=0.1.2=py313haa95532_1
  - conda-anaconda-tos=0.2.0=py313haa95532_0
  - conda-build=25.5.0=py313hcfce1f1_0
  - conda-content-trust=0.2.0=py313haa95532_1
  - conda-index=0.6.1=py313haa95532_0
  - conda-libmamba-solver=25.4.0=pyhd3eb1b0_0
  - conda-pack=0.7.1=py313haa95532_0
  - conda-package-handling=2.4.0=py313haa95532_0
  - conda-package-streaming=0.11.0=py313haa95532_0
  - conda-repo-cli=1.0.165=py313haa95532_0
  - conda-token=0.6.0=pyhd3eb1b0_0
  - constantly=23.10.4=py313haa95532_0
  - contourpy=1.3.1=py313h214f63a_0
  - cookiecutter=1.7.3=pyhd3eb1b0_0
  - cpp-expected=1.1.0=h214f63a_0
  - cryptography=44.0.1=py313hbd6ee87_0
  - cssselect=1.2.0=py313haa95532_0
  - curl=8.12.1=h51539b2_0
  - cycler=0.11.0=pyhd3eb1b0_0
  - cytoolz=1.0.1=py313h827c3e9_0
  - dask=2025.2.0=py313haa95532_0
  - dask-core=2025.2.0=py313haa95532_0
  - dask-expr=2.0.0=py313haa95532_0
  - datashader=0.18.0=py313haa95532_0
  - debugpy=1.8.11=py313h5da7b33_0
  - decorator=5.1.1=pyhd3eb1b0_0
  - defusedxml=0.7.1=pyhd3eb1b0_0
  - deprecated=1.2.13=py313haa95532_0
  - diff-match-patch=20200713=pyhd3eb1b0_0
  - dill=0.3.8=py313haa95532_0
  - distributed=2025.2.0=py313haa95532_0
  - distro=1.9.0=py313haa95532_0
  - docstring-to-markdown=0.11=py313haa95532_0
  - docutils=0.21.2=py313haa95532_0
  - et_xmlfile=1.1.0=py313haa95532_1
  - evalidate=2.0.3=py313haa95532_0
  - executing=0.8.3=pyhd3eb1b0_0
  - expat=2.7.1=h8ddb27b_0
  - filelock=3.17.0=py313haa95532_0
  - flake8=7.1.1=py313haa95532_0
  - flask=3.1.0=py313haa95532_0
  - fmt=9.1.0=h6d14046_1
  - fonttools=4.55.3=py313h827c3e9_0
  - freeglut=3.4.0=h8a1e904_1
  - freetype=2.13.3=h0620614_0
  - frozendict=2.4.2=py313haa95532_0
  - frozenlist=1.5.0=py313h827c3e9_0
  - fsspec=2025.3.2=py313h4442805_0
  - gflags=2.2.2=hd77b12b_1
  - gitdb=4.0.7=pyhd3eb1b0_0
  - gitpython=3.1.43=py313haa95532_0
  - glog=0.5.0=hd77b12b_1
  - gmp=6.3.0=h537511b_0
  - gmpy2=2.2.1=py313h827c3e9_0
  - greenlet=3.1.1=py313h5da7b33_0
  - h11=0.16.0=py313haa95532_0
  - h5py=3.12.1=py313h535c9fb_1
  - hdf5=1.14.5=ha36df97_2
  - heapdict=1.0.1=pyhd3eb1b0_0
  - holoviews=1.20.2=py313haa95532_0
  - httpcore=1.0.9=py313haa95532_0
  - httpx=0.28.1=py313haa95532_0
  - hvplot=0.11.3=py313haa95532_0
  - hyperlink=21.0.0=pyhd3eb1b0_0
  - icc_rt=2022.1.0=h6049295_2
  - icu=73.1=h6c2663c_0
  - idna=3.7=py313haa95532_0
  - imageio=2.37.0=py313haa95532_0
  - imagesize=1.4.1=py313haa95532_0
  - imbalanced-learn=0.13.0=py313haa95532_0
  - importlib-metadata=8.5.0=py313haa95532_0
  - incremental=24.7.2=pyhd3eb1b0_0
  - inflection=0.5.1=py313haa95532_1
  - iniconfig=1.1.1=pyhd3eb1b0_0
  - intake=2.0.7=py313haa95532_0
  - intel-openmp=2023.1.0=h59b6b97_46320
  - intervaltree=3.1.0=pyhd3eb1b0_0
  - ipykernel=6.29.5=py313haa95532_1
  - ipython=8.30.0=py313haa95532_0
  - ipywidgets=8.1.5=py313haa95532_0
  - isort=6.0.1=py313haa95532_0
  - itemadapter=0.3.0=pyhd3eb1b0_0
  - itemloaders=1.3.2=py313haa95532_0
  - itsdangerous=2.2.0=py313haa95532_0
  - jaraco.classes=3.2.1=pyhd3eb1b0_0
  - jaraco.context=6.0.0=py313haa95532_0
  - jaraco.functools=4.1.0=py313haa95532_0
  - jedi=0.19.2=py313haa95532_0
  - jellyfish=1.1.3=py313h8ecf97c_0
  - jinja2=3.1.6=py313haa95532_0
  - jinja2-time=0.2.0=pyhd3eb1b0_3
  - jmespath=1.0.1=py313haa95532_0
  - joblib=1.4.2=py313haa95532_0
  - jpeg=9e=h827c3e9_3
  - json5=0.9.25=py313haa95532_0
  - jsonpatch=1.33=py313haa95532_1
  - jsonpointer=2.1=pyhd3eb1b0_0
  - jsonschema=4.23.0=py313haa95532_0
  - jsonschema-specifications=2023.7.1=py313haa95532_0
  - jupyter=1.1.1=py313haa95532_0
  - jupyter-lsp=2.2.5=py313haa95532_0
  - jupyter_client=8.6.3=py313haa95532_0
  - jupyter_console=6.6.3=py313haa95532_1
  - jupyter_core=5.7.2=py313haa95532_0
  - jupyter_events=0.12.0=py313haa95532_0
  - jupyter_server=2.15.0=py313haa95532_0
  - jupyter_server_terminals=0.5.3=py313haa95532_0
  - jupyterlab=4.3.4=py313haa95532_0
  - jupyterlab-variableinspector=3.2.4=py313haa95532_0
  - jupyterlab_pygments=0.3.0=py313haa95532_0
  - jupyterlab_server=2.27.3=py313haa95532_0
  - jupyterlab_widgets=3.0.13=py313haa95532_0
  - keyring=25.6.0=py313haa95532_0
  - kiwisolver=1.4.8=py313h5da7b33_0
  - krb5=1.20.1=h5b6d351_0
  - lazy_loader=0.4=py313haa95532_0
  - lcms2=2.16=h62be587_1
  - lerc=4.0.0=h5da7b33_0
  - libabseil=20250127.0=cxx17_h52369b4_0
  - libarchive=3.7.7=h9243413_0
  - libboost=1.82.0=h3399ecb_2
  - libbrotlicommon=1.0.9=h827c3e9_9
  - libbrotlidec=1.0.9=h827c3e9_9
  - libbrotlienc=1.0.9=h827c3e9_9
  - libclang=14.0.6=default_hb5a9fac_2
  - libclang13=14.0.6=default_h8e68704_2
  - libcurl=8.12.1=h9da9810_0
  - libdeflate=1.22=h5bf469e_0
  - libevent=2.1.12=h56d1f94_1
  - libffi=3.4.4=hd77b12b_1
  - libgrpc=1.71.0=hf4237ab_0
  - libiconv=1.16=h2bbff1b_3
  - liblief=0.16.4=h585ebfc_0
  - libmamba=2.0.5=hcd6fe79_1
  - libmambapy=2.0.5=py313h214f63a_1
  - libmpdec=4.0.0=h827c3e9_0
  - libpng=1.6.39=h8cc25b3_0
  - libpq=17.4=h70ee33d_0
  - libprotobuf=5.29.3=hac4c8cb_0
  - libre2-11=2024.07.02=h5da7b33_0
  - libsodium=1.0.18=h62dcd97_0
  - libsolv=0.7.30=hf2fb9eb_1
  - libspatialindex=1.9.3=h6c2663c_0
  - libssh2=1.11.1=h2addb87_0
  - libthrift=0.15.0=h4364b78_2
  - libtiff=4.7.0=h404307b_0
  - libwebp-base=1.3.2=h3d04722_1
  - libxml2=2.13.8=h866ff63_0
  - libxslt=1.1.41=h0739af5_0
  - linkify-it-py=2.0.0=py313haa95532_0
  - llvmlite=0.44.0=py313h8b1c7eb_1
  - locket=1.0.0=py313haa95532_0
  - lxml=5.3.0=py313h395c83e_1
  - lz4=4.3.2=py313h827c3e9_1
  - lz4-c=1.9.4=h2bbff1b_1
  - lzo=2.10=he774522_2
  - m2-msys2-runtime=2.5.0.17080.65c939c=3
  - m2-patch=2.7.5=2
  - markdown=3.8=py313haa95532_0
  - markdown-it-py=2.2.0=py313haa95532_1
  - markupsafe=3.0.2=py313h827c3e9_0
  - matplotlib=3.10.0=py313haa95532_1
  - matplotlib-base=3.10.0=py313h7aa5d4e_1
  - matplotlib-inline=0.1.6=py313haa95532_0
  - mbedtls=3.5.1=h5da7b33_1
  - mccabe=0.7.0=pyhd3eb1b0_0
  - mdit-py-plugins=0.3.0=py313haa95532_0
  - mdurl=0.1.0=py313haa95532_0
  - menuinst=2.2.0=py313h5da7b33_1
  - mistune=3.1.2=py313haa95532_0
  - mkl=2023.1.0=h6b88ed4_46358
  - mkl-service=2.4.0=py313h827c3e9_2
  - mkl_fft=1.3.11=py313h827c3e9_0
  - mkl_random=1.2.8=py313hce38976_0
  - more-itertools=10.3.0=py313haa95532_0
  - mpc=1.3.1=h827c3e9_0
  - mpfr=4.2.1=h56c3642_0
  - mpmath=1.3.0=py313haa95532_0
  - msgpack-python=1.0.3=py313h214f63a_0
  - msys2-conda-epoch=20160418=1
  - multidict=6.1.0=py313h827c3e9_0
  - multipledispatch=0.6.0=py313haa95532_0
  - mypy=1.14.1=py313h827c3e9_0
  - mypy_extensions=1.0.0=py313haa95532_0
  - narwhals=1.31.0=py313haa95532_1
  - navigator-updater=0.5.1=py313haa95532_0
  - nbclient=0.10.2=py313haa95532_0
  - nbconvert=7.16.6=py313haa95532_0
  - nbconvert-core=7.16.6=py313haa95532_0
  - nbconvert-pandoc=7.16.6=py313haa95532_0
  - nbformat=5.10.4=py313haa95532_0
  - nest-asyncio=1.6.0=py313haa95532_0
  - networkx=3.4.2=py313haa95532_0
  - nlohmann_json=3.11.2=h6c2663c_0
  - nltk=3.9.1=py313hea850e4_0
  - notebook=7.3.2=py313haa95532_1
  - notebook-shim=0.2.4=py313haa95532_0
  - numba=0.61.0=py313h5da7b33_1
  - numexpr=2.10.1=py313h4cd664f_0
  - numpy=2.1.3=py313he6dc315_0
  - numpy-base=2.1.3=py313h6011491_0
  - numpydoc=1.7.0=py313haa95532_0
  - openjpeg=2.5.2=h9b5d1b5_1
  - openpyxl=3.1.5=py313h827c3e9_1
  - openssl=3.1.0=hcfcfb64_3
  - orc=2.1.1=hd1c1d5c_0
  - overrides=7.4.0=py313haa95532_0
  - packaging=24.2=py313haa95532_0
  - pandas=2.2.3=py313h5da7b33_0
  - pandoc=2.12=haa95532_3
  - pandocfilters=1.5.0=pyhd3eb1b0_0
  - panel=1.7.0=py313haa95532_0
  - param=2.2.0=py313haa95532_0
  - parsel=1.8.1=py313haa95532_0
  - parso=0.8.4=py313haa95532_0
  - partd=1.4.2=py313haa95532_0
  - pathspec=0.10.3=py313haa95532_0
  - patsy=1.0.1=py313haa95532_0
  - pcre2=10.42=h0ff8eda_1
  - pexpect=4.8.0=pyhd3eb1b0_3
  - pickleshare=0.7.5=pyhd3eb1b0_1003
  - pillow=11.1.0=py313hea0d53e_1
  - pip=25.1=pyhc872135_2
  - pkce=1.0.3=py313haa95532_0
  - pkginfo=1.12.0=py313haa95532_0
  - platformdirs=4.3.7=py313haa95532_0
  - plotly=5.24.1=py313h4442805_1
  - pluggy=1.5.0=py313haa95532_0
  - ply=3.11=py313haa95532_1
  - poyo=0.5.0=pyhd3eb1b0_0
  - prometheus_client=0.21.1=py313haa95532_0
  - prompt-toolkit=3.0.43=py313haa95532_0
  - prompt_toolkit=3.0.43=hd3eb1b0_0
  - propcache=0.3.1=py313h827c3e9_0
  - protego=0.4.0=py313haa95532_0
  - protobuf=5.29.3=py313h5da7b33_0
  - psutil=5.9.0=py313h827c3e9_1
  - ptyprocess=0.7.0=pyhd3eb1b0_2
  - pure_eval=0.2.2=pyhd3eb1b0_0
  - py-cpuinfo=9.0.0=py313haa95532_0
  - py-lief=0.16.4=py313h585ebfc_0
  - pyarrow=19.0.0=py313h5da7b33_1
  - pyasn1=0.4.8=pyhd3eb1b0_0
  - pyasn1-modules=0.2.8=py_0
  - pybind11-abi=5=hd3eb1b0_0
  - pycodestyle=2.12.1=py313haa95532_0
  - pycosat=0.6.6=py313h827c3e9_2
  - pycparser=2.21=pyhd3eb1b0_0
  - pyct=0.5.0=py313haa95532_0
  - pycurl=7.45.6=py313h51539b2_0
  - pydantic=2.10.3=py313haa95532_0
  - pydantic-core=2.27.1=py313h636fa0f_0
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prefix: C:\Users\kraig.delana\AppData\Local\anaconda3


