1.1.1

.github/workflows/black.yml

@@ -0,0 +1,10 @@
+name: Lint
+
+on: [push, pull_request]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: psf/black@stable

.github/workflows/citests.yml

@@ -0,0 +1,31 @@
+name: Test
+
+on: 
+  push:
+  pull_request:
+
+jobs:
+  tests:
+    name: "Python ${{ matrix.python-version }}"
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        python-version: ["3.6", "3.7", "3.8", "3.9", "3.10"]
+
+    steps:
+      - uses: "actions/checkout@v2"
+      - uses: "actions/setup-python@v2"
+        with:
+          python-version: "${{ matrix.python-version }}"
+
+      - name: "Install dependencies"
+        run: |
+          python -m pip install --upgrade pip
+          pip install pipenv
+          pipenv install --dev
+          pipenv install coveralls --skip-lock
+
+      - name: Test with pytest
+        run: |
+          pipenv run pytest --cov=app

.travis.yml

@@ -4,6 +4,8 @@ python:
   - "3.6"
   - "3.7"
   - "3.8"
+  - "3.9"
+  - "3.10"
 env:
   global:
     - PIPENV_VENV_IN_PROJECT=1

Pipfile

@@ -10,7 +10,6 @@ black = "*"
 pylint = "*"
 
 [packages]
-numpy = "*"
 
 [requires]
-python_version = "3.7"
+python_version = "3.9"

PyTCI/models/base.py

@@ -1,5 +1,5 @@
 class Three:
-    """ Base 3 compartment model"""
+    """Base 3 compartment model"""
 
     def setup(self):
 
@@ -45,14 +45,14 @@ def from_clearances(self):
         self.k31 = (self.k13 * self.v1) / self.v3
 
     def give_drug(self, drug_milligrams):
-        """ add bolus of drug to central compartment """
+        """add bolus of drug to central compartment"""
         self.x1 = self.x1 + drug_milligrams / self.v1
 
     def wait_time(self, time_seconds):
-        """ model distribution of drug between compartments over specified time period """
+        """model distribution of drug between compartments over specified time period"""
 
         def one_second(self):
-            """ time steps must be one second for accurate modelling """
+            """time steps must be one second for accurate modelling"""
 
             x1k10 = self.x1 * self.k10
             x1k12 = self.x1 * self.k12
@@ -73,21 +73,21 @@ def one_second(self):
             one_second(self)
 
     def reset_concs(self, old_conc):
-        """ resets concentrations using python dictionary"""
+        """resets concentrations using python dictionary"""
         self.x1 = old_conc["ox1"]
         self.x2 = old_conc["ox2"]
         self.x3 = old_conc["ox3"]
         self.xeo = old_conc["oxeo"]
 
     def zero_comps(self):
-        """ sets all compartment concentrations to 0 """
+        """sets all compartment concentrations to 0"""
         self.x1 = 0
         self.x2 = 0
         self.x3 = 0
         self.xeo = 0
 
     def effect_bolus(self, target: float):
-        """ determines size of bolus needed over 10 seconds to achieve target at ttpe """
+        """determines size of bolus needed over 10 seconds to achieve target at ttpe"""
 
         # store concentrations so we can reset after search
         old_conc = {"ox1": self.x1, "ox2": self.x2, "ox3": self.x3, "oxeo": self.xeo}
@@ -114,23 +114,23 @@ def effect_bolus(self, target: float):
         return round(mgpersec * 10, 2)
 
     def tenseconds(self, mgpersec: float):
-        """ gives set amount of drug every second for 10 seconds """
+        """gives set amount of drug every second for 10 seconds"""
         for _ in range(10):
             self.give_drug(mgpersec)
             self.wait_time(1)
 
         return self.x1
 
     def giveoverseconds(self, mgpersec: float, secs: float):
-        """ gives set amount of drug every second for user defined period"""
+        """gives set amount of drug every second for user defined period"""
         for _ in range(secs):
             self.give_drug(mgpersec)
             self.wait_time(1)
 
         return self.x1
 
     def plasma_infusion(self, target: float, time: int, period: int = 10):
-        """ returns list of infusion rates to maintain desired plasma concentration
+        """returns list of infusion rates to maintain desired plasma concentration
         inputs:
         target: desired plasma concentration in ug/min
         time: infusion duration in seconds
@@ -174,7 +174,7 @@ def plasma_infusion(self, target: float, time: int, period: int = 10):
         return pump_instructions
 
     def effect_target(self, target: float, time: int, period: int = 10):
-        """ returns list of infusion rates to maintain desired plasma concentration
+        """returns list of infusion rates to maintain desired plasma concentration
         inputs:
         target: desired plasma concentration in units/ml
         time: infusion duration in seconds

PyTCI/models/dexmedetomidine.py

@@ -3,23 +3,23 @@
 
 
 class Dexmed(Three):
-    """ base class for demedetomidine"""
+    """base class for demedetomidine"""
 
     pass
 
 
 class Hannivoort(Dexmed):
     def __init__(self, weight: int):
-        """ 3 compartment dexmedetomidine Pk model
+        """3 compartment dexmedetomidine Pk model
 
         Units:
         weight(kg)
 
         Reference:
-        Hannivoort, L, et al 
+        Hannivoort, L, et al
         Development of an Optimized Pharmacokinetic Model of Dexmedetomidine Using Target-controlled Infusion in Healthy Volunteers
-        Anesthesiology 8 2015, Vol.123, 357-367. 
-        doi:10.1097/ALN.0000000000000740 
+        Anesthesiology 8 2015, Vol.123, 357-367.
+        doi:10.1097/ALN.0000000000000740
         """
 
         self.v1 = 1.78 * (weight / 70)
@@ -48,7 +48,7 @@ def __init__(self, height: int):
         Dyck, JB, et al
         Computer-controlled infusion of intravenous dexmedetomidine hydrochloride in adult human volunteers
         Anesthesiology. 1993 May;78(5):821-8.
-        PMID:8098191 DOI:10.1097/00000542-199305000-00003 
+        PMID:8098191 DOI:10.1097/00000542-199305000-00003
         """
 
         self.v1 = 7.99

PyTCI/models/propofol.py

@@ -5,13 +5,13 @@
 
 
 class Propofol(Three):
-    """ Base Class for Propofol 3 compartment model """
+    """Base Class for Propofol 3 compartment model"""
 
     pass
 
 
 class Schnider(Propofol):
-    """ Implementation of the schnider model """
+    """Implementation of the schnider model"""
 
     # UNITS:
     # age: years
@@ -44,7 +44,7 @@ def __init__(self, age, weight, height, sex):
 
 
 class Marsh(Propofol):
-    """ Marsh 3 compartment Propofol Pk Model
+    """Marsh 3 compartment Propofol Pk Model
 
     Units required:
     weight (kg)
@@ -113,7 +113,7 @@ class Paedfusor(Propofol):
 
     Reference:
     Absalom, A, Kenny, G
-    BJA: British Journal of Anaesthesia, Volume 95, Issue 1, 1 July 2005, Pages 110, 
+    BJA: British Journal of Anaesthesia, Volume 95, Issue 1, 1 July 2005, Pages 110,
     https://doi.org/10.1093/bja/aei567
     """
 
@@ -150,7 +150,7 @@ class Eleveld(Propofol):
     Special methods for this model
     .venous()
     Switches from arterial(default) to venous targerting
-    
+
 
     .with_opiates()
     models co-administration with opiates
@@ -193,16 +193,16 @@ def __init__(self, age: int, weight: float, height: int, sex: str):
         theta18 = 0.68
 
         def ageing(i, age):
-            """ ageing function"""
+            """ageing function"""
             return exp(i * (age - 35))
 
         def sigmoid(x, e50, y):
-            """ sigmoid function from eleveld paper """
+            """sigmoid function from eleveld paper"""
             sig = (x ** y) / ((x ** y) + (e50 ** y))
             return sig
 
         def central(i):
-            """ central function """
+            """central function"""
             return sigmoid(i, theta12, 1)
 
         # clearance maturation
@@ -225,13 +225,9 @@ def central(i):
         v3ref = theta03
 
         if sex == "m":
-            self.Q1 = (
-                theta04 * (weight / 70) ** 0.75 * (clmat / clmatref)
-            )
+            self.Q1 = theta04 * (weight / 70) ** 0.75 * (clmat / clmatref)
         else:
-            self.Q1 = (
-                theta15 * (weight / 70) ** 0.75 * (clmat / clmatref)
-            )
+            self.Q1 = theta15 * (weight / 70) ** 0.75 * (clmat / clmatref)
 
         self.Q2 = (
             theta05 * (self.v2 / v2ref) ** 0.75 * (1 + theta16 * (1 - q3mat / q3matref))
@@ -244,19 +240,17 @@ def central(i):
         self.setup()
 
     def with_opiates(self):
-        """ switches the opiate parameters
-            using this method indicates opiates are being administered concurrently 
-            
+        """switches the opiate parameters
+        using this method indicates opiates are being administered concurrently
+
         """
         opiatesv3 = exp(self.theta13 * self.age)
         opiatescl = exp(self.theta11 * self.age)
 
         self.v3 *= opiatesv3
         self.Q1 *= opiatescl
-
-        self.from_clearances()
-
 
+        self.from_clearances()
 
     # def venous():
     #     """ switches the following parameters to target venous concentrations

PyTCI/models/remifentanil.py

@@ -4,7 +4,7 @@
 
 
 class Remifentanil(Three):
-    """ Base Class for remifentanil models """
+    """Base Class for remifentanil models"""
 
     pass
 
@@ -48,11 +48,11 @@ class Eleveld(Remifentanil):
 
     def __init__(self, age, weight, height, sex):
         def ageing(i, age):
-            """ ageing function"""
+            """ageing function"""
             return exp(i * (age - 35))
 
         def sigmoid(x, e50, y):
-            """ sigmoid function from eleveld paper """
+            """sigmoid function from eleveld paper"""
             sig = (x ** y) / ((x ** y) + (e50 ** y))
             return sig
 
@@ -84,7 +84,7 @@ def sigmoid(x, e50, y):
         if sex == "m":
             Fsex = 1
         elif sex == "f":
-            Fsex = 1 + Θ5 * sigmoid(age, 12, 6) * (1- sigmoid(age, 45, 6))
+            Fsex = 1 + Θ5 * sigmoid(age, 12, 6) * (1 - sigmoid(age, 45, 6))
 
         self.v1 = v1ref * Fsize * ageing(Θ2, age)
         self.v2 = v2ref * Fsize * ageing(Θ3, age) * Fsex