Fix environment (#180)

* Create a new `arguments.py` file to hold standardized arguments across COMO

* Use the newly-created `arguments.py` standard

* Add arguments from `create_context_speciifc_model.py`

* Refactor code to incorporate standardized arguments across COMO

* Include `disease_analysis.py` arguments

* Refactor code to incorporate standardized arguments across COMO

* Add arguments from `knock_out_simulation.py`

* Refactor code to incorporate standardized arguments across COMO

* Added `merge_xomics.py` arguments

* Use standardized `arguments.py`

* Added proteomics arguments

* Use standardized `arguments.py`

* Added `rnaseq_gen.py` arguments

* Use standardized `arguments.py` file

* Added `rnaseq_preproces.py` arguments

* Use new `arguments.py` standard

* Fixed imports based on unit test results

* Fix fast bioservices usage

* Use multi_bioservices for this branch for now becuase we have not merged the related pull request yet

* Fix usage of multi/fast bioservices

* Fix multi_bioservices usage

* Install multi_bioservices for this brach

Author: Josh Loecker

environment.yaml

@@ -60,7 +60,7 @@ dependencies:
   # - conda-forge::xlrd~=2.0.1
   - gurobi::gurobi
   - pip:
-      - git+https://github.com/JoshLoecker/fast_bioservices
+      - multi_bioservices
       # - escher==1.7.3
       - git+https://github.com/JoshLoecker/escher.git@python38#subdirectory=py
       - framed==0.5.*