updates

fixed environment config and updated readme
ZuckermanLab · Sep 17, 2023 · a9923b3 · a9923b3
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diff --git a/README.md b/README.md
@@ -4,9 +4,12 @@ Supporting code for Bayesian Transporter research - still under development.
 
 
 ### Usage:
-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` \
+
+to run the provided example, update the filepaths in the `...config.yaml` file, and update the `...config.yaml` file path in `run_optimizer.py`, `run_emcee.py` and `run_pocomc.py`as needed.
+
+for MLE with Scipy Optimization use `python YOUR_PATH_HERE/run_optimizer.py`, for Bayesian use `python YOUR_PATH_HERE/run_emcee.py` or `python YOUR_PATH_HERE/run_pocomc.py` to use the EMCEE or PocoMC packages respectively\
 
-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 

diff --git a/environment.yml b/environment.yml
@@ -128,7 +128,6 @@ dependencies:
   - 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