updates

virtual environment

README.md

@@ -2,11 +2,11 @@
 
 Supporting code for Bayesian Transporter research - still under development. 
 
-### Todo:
-- update installation requirements and getting started
 
 ### Usage:
-for MLE use `run_optimizer.py`, for Bayesian use `run_emcee.py` or `run_pocomc.py`
+for MLE use `run_optimizer.py`, for Bayesian use `run_emcee.py` or `run_pocomc.py`\
+
+create an environment with required packages/dependencies using `conda env create -f environment.yml`
 
 ### Limitations / issues
 - parallelization issues with libroadrunner. see: https://github.com/sys-bio/tellurium/issues/563 

environment.yml

@@ -0,0 +1,169 @@
+name: py311_bt
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - appnope=0.1.3=pyhd8ed1ab_0
+  - arviz=0.15.1=pyhd8ed1ab_0
+  - asttokens=2.2.1=pyhd8ed1ab_0
+  - backcall=0.2.0=pyh9f0ad1d_0
+  - backports=1.0=pyhd8ed1ab_3
+  - backports.functools_lru_cache=1.6.4=pyhd8ed1ab_0
+  - brotli=1.0.9=hb7f2c08_8
+  - brotli-bin=1.0.9=hb7f2c08_8
+  - brotlipy=0.7.0=py311h5547dcb_1005
+  - bzip2=1.0.8=h0d85af4_4
+  - c-ares=1.18.1=h0d85af4_0
+  - ca-certificates=2022.12.7=h033912b_0
+  - cached-property=1.5.2=hd8ed1ab_1
+  - cached_property=1.5.2=pyha770c72_1
+  - certifi=2022.12.7=pyhd8ed1ab_0
+  - cffi=1.15.1=py311ha86e640_3
+  - comm=0.1.3=pyhd8ed1ab_0
+  - contourpy=1.0.7=py311hd2070f0_0
+  - cryptography=40.0.1=py311h61927ef_0
+  - cycler=0.11.0=pyhd8ed1ab_0
+  - debugpy=1.6.6=py311h814d153_0
+  - decorator=5.1.1=pyhd8ed1ab_0
+  - executing=1.2.0=pyhd8ed1ab_0
+  - fonttools=4.39.2=py311h5547dcb_0
+  - freetype=2.12.1=h3f81eb7_1
+  - h5netcdf=1.1.0=pyhd8ed1ab_1
+  - h5py=3.8.0=nompi_py311hcf977c2_101
+  - hdf5=1.14.0=nompi_hbf0aa07_103
+  - idna=3.4=pyhd8ed1ab_0
+  - importlib-metadata=6.1.0=pyha770c72_0
+  - importlib_metadata=6.1.0=hd8ed1ab_0
+  - ipykernel=6.22.0=pyh736e0ef_0
+  - ipython=8.11.0=pyhd1c38e8_0
+  - jedi=0.18.2=pyhd8ed1ab_0
+  - jupyter_client=8.1.0=pyhd8ed1ab_0
+  - jupyter_core=5.3.0=py311h6eed73b_0
+  - kiwisolver=1.4.4=py311hd2070f0_1
+  - krb5=1.20.1=h049b76e_0
+  - lcms2=2.15=h2dcdeff_1
+  - lerc=4.0.0=hb486fe8_0
+  - libaec=1.0.6=hf0c8a7f_1
+  - libblas=3.9.0=16_osx64_openblas
+  - libbrotlicommon=1.0.9=hb7f2c08_8
+  - libbrotlidec=1.0.9=hb7f2c08_8
+  - libbrotlienc=1.0.9=hb7f2c08_8
+  - libcblas=3.9.0=16_osx64_openblas
+  - libcurl=7.88.1=h6df9250_1
+  - libcxx=15.0.7=h71dddab_0
+  - libdeflate=1.18=hac1461d_0
+  - libedit=3.1.20191231=h0678c8f_2
+  - libev=4.33=haf1e3a3_1
+  - libffi=3.4.2=h0d85af4_5
+  - libgfortran=5.0.0=11_3_0_h97931a8_31
+  - libgfortran5=12.2.0=he409387_31
+  - libjpeg-turbo=2.1.5.1=hb7f2c08_0
+  - liblapack=3.9.0=16_osx64_openblas
+  - libnghttp2=1.52.0=he2ab024_0
+  - libopenblas=0.3.21=openmp_h429af6e_3
+  - libpng=1.6.39=ha978bb4_0
+  - libsodium=1.0.18=hbcb3906_1
+  - libsqlite=3.40.0=ha978bb4_0
+  - libssh2=1.10.0=h47af595_3
+  - libtiff=4.5.0=hedf67fa_6
+  - libwebp-base=1.3.0=hb7f2c08_0
+  - libxcb=1.13=h0d85af4_1004
+  - libzlib=1.2.13=hfd90126_4
+  - llvm-openmp=16.0.0=h61d9ccf_0
+  - matplotlib=3.7.1=py311h6eed73b_0
+  - matplotlib-base=3.7.1=py311h2bf763f_0
+  - matplotlib-inline=0.1.6=pyhd8ed1ab_0
+  - munkres=1.1.4=pyh9f0ad1d_0
+  - ncurses=6.3=h96cf925_1
+  - nest-asyncio=1.5.6=pyhd8ed1ab_0
+  - numpy=1.24.2=py311ha9d2c9f_0
+  - openjpeg=2.5.0=h13ac156_2
+  - openssl=3.1.0=hfd90126_0
+  - packaging=23.0=pyhd8ed1ab_0
+  - parso=0.8.3=pyhd8ed1ab_0
+  - pexpect=4.8.0=pyh1a96a4e_2
+  - pickleshare=0.7.5=py_1003
+  - pillow=9.4.0=py311hf47c0a6_2
+  - pip=23.0.1=pyhd8ed1ab_0
+  - platformdirs=3.2.0=pyhd8ed1ab_0
+  - pooch=1.7.0=pyha770c72_3
+  - prompt-toolkit=3.0.38=pyha770c72_0
+  - prompt_toolkit=3.0.38=hd8ed1ab_0
+  - psutil=5.9.4=py311h5547dcb_0
+  - pthread-stubs=0.4=hc929b4f_1001
+  - ptyprocess=0.7.0=pyhd3deb0d_0
+  - pure_eval=0.2.2=pyhd8ed1ab_0
+  - pycparser=2.21=pyhd8ed1ab_0
+  - pygments=2.14.0=pyhd8ed1ab_0
+  - pyopenssl=23.1.0=pyhd8ed1ab_0
+  - pyparsing=3.0.9=pyhd8ed1ab_0
+  - pysocks=1.7.1=pyha2e5f31_6
+  - python=3.11.0=he7542f4_1_cpython
+  - python-dateutil=2.8.2=pyhd8ed1ab_0
+  - python_abi=3.11=3_cp311
+  - pytz=2023.2=pyhd8ed1ab_0
+  - pyyaml=6.0=py311h5547dcb_5
+  - pyzmq=25.0.2=py311habfacb3_0
+  - readline=8.2=h9e318b2_1
+  - requests=2.28.2=pyhd8ed1ab_0
+  - setuptools=67.6.0=pyhd8ed1ab_0
+  - six=1.16.0=pyh6c4a22f_0
+  - stack_data=0.6.2=pyhd8ed1ab_0
+  - tk=8.6.12=h5dbffcc_0
+  - tornado=6.2=py311h5547dcb_1
+  - traitlets=5.9.0=pyhd8ed1ab_0
+  - typing-extensions=4.5.0=hd8ed1ab_0
+  - typing_extensions=4.5.0=pyha770c72_0
+  - tzdata=2023b=h71feb2d_0
+  - urllib3=1.26.15=pyhd8ed1ab_0
+  - wcwidth=0.2.6=pyhd8ed1ab_0
+  - wheel=0.40.0=pyhd8ed1ab_0
+  - xarray=2023.3.0=pyhd8ed1ab_0
+  - xarray-einstats=0.5.1=pyhd8ed1ab_0
+  - xorg-libxau=1.0.9=h35c211d_0
+  - xorg-libxdmcp=1.1.3=h35c211d_0
+  - xz=5.2.6=h775f41a_0
+  - yaml=0.2.5=h0d85af4_2
+  - zeromq=4.3.4=he49afe7_1
+  - zipp=3.15.0=pyhd8ed1ab_0
+  - zstd=1.5.2=hbc0c0cd_6
+  - pip:
+    - amici==0.16.1
+    - antimony==2.13.2
+    - appdirs==1.4.4
+    - attrs==22.2.0
+    - charset-normalizer==3.1.0
+    - corner==2.2.1
+    - dill==0.3.6
+    - emcee==3.1.4
+    - filelock==3.11.0
+    - iniconfig==2.0.0
+    - jinja2==3.1.2
+    - joblib==1.2.0
+    - libroadrunner==2.3.2
+    - markupsafe==2.1.2
+    - mpmath==1.3.0
+    - networkx==3.1
+    - pandas==1.5.3
+    - pdoc==14.0.0
+    - pkgconfig==1.5.5
+    - plotly==5.13.1
+    - pluggy==1.0.0
+    - pocomc==0.2.4
+    - pytest==7.2.2
+    - python-libcombine==0.2.19
+    - python-libnuml==1.1.6
+    - python-libsbml==5.19.7
+    - python-libsedml==2.0.32
+    - scikit-learn==1.2.2
+    - scipy==1.10.1
+    - seaborn==0.12.2
+    - sympy==1.11.1
+    - tellurium==2.2.7
+    - tenacity==8.2.2
+    - threadpoolctl==3.1.0
+    - toposort==1.10
+    - torch==2.0.0
+    - tqdm==4.65.0
+    - wurlitzer==3.0.3
+prefix: /opt/miniconda3/envs/py311_bt