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CryPTSys / PharmaPy

A numerical platform for the digital design of pharmaceutical processes
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Cleaned code from dev meeting (10/4/2023) #91

Closed djlaky closed 1 year ago

djlaky commented 1 year ago
  1. Changed Kinetics to correctly require 'partic_species' to function when stoich_matrix is supplied (lost old functionalities).

https://github.com/dlakes94/PharmaPy/blob/136d5384227417426e7f0bf4f64d24dbdd5861aa/PharmaPy/Kinetics.py#L242-L243

  1. Changed cyipopt to be an optional import. Included try/except on import and throw an error when cyipopt is not found when 'IPOPT' is specified as the method for parameter estimation. Tested and works well.

https://github.com/dlakes94/PharmaPy/blob/136d5384227417426e7f0bf4f64d24dbdd5861aa/PharmaPy/ParamEstim.py#L25-L29

https://github.com/dlakes94/PharmaPy/blob/136d5384227417426e7f0bf4f64d24dbdd5861aa/PharmaPy/ParamEstim.py#L622-L623

  1. Added negatives that were lost in translating code to remove deprecated method dependency. (Lines 694, 1054, 1562, and 1675 in Reactors.py --> https://github.com/dlakes94/PharmaPy/blob/136d5384227417426e7f0bf4f64d24dbdd5861aa/PharmaPy/Reactors.py)

  2. Updated requirements.txt to get rid of optional dependency (cyipopt). See "1." above.

  3. Updated setup.py to be more readable and succinct the file given by another user. (https://github.com/yoooruz/PharmaPy/blob/master/setup.py)