Initial commit

.flake8

@@ -0,0 +1,33 @@
+[flake8]
+exclude=
+    ./.git,
+    ./pkmodel.egg-info,
+ignore=
+    # Block comment should start with '# '
+    # Not if it's a commented out line
+    E265,
+
+    # "Do not assign a labmda expression, use a def".
+    # This is a silly rule
+    E731,
+
+    # Ambiguous variable names
+    # It's absolutely fine to have i and I
+    E741,
+
+    # List comprehension redefines variable
+    # Re-using throw-away variables like `i`, `x`, etc. is a Good Idea
+    F812,
+
+    # Undefined name
+    # Good rule, but the check doesn't support dynamically created variables
+    F821,
+
+    # Blank line at end of file
+    # These can increase readability (in many editors)
+    W391,
+
+    # Binary operator on new line
+    # This is now advised in pep8
+    W503,
+

.gitignore

@@ -0,0 +1,132 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# vim
+.vim/
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2020 SABS-R3
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -0,0 +1,2 @@
+# 2020-software-engineering-projects-pk
+starter pk modelling repository

pkmodel/__init__.py

@@ -0,0 +1,13 @@
+"""pkmodel is a Pharmokinetic modelling library.
+
+It contains functionality for creating, solving, and visualising the solution
+of Parmokinetic (PK) models
+
+"""
+# Import version info
+from .version_info import VERSION_INT, VERSION  # noqa
+
+# Import main classes
+from .model import Model    # noqa
+from .protocol import Protocol    # noqa
+from .solution import Solution     # noqa

pkmodel/model.py

@@ -0,0 +1,17 @@
+#
+# Model class
+#
+
+class Model:
+    """A Pharmokinetic (PK) model
+
+    Parameters
+    ----------
+
+    value: numeric, optional
+        an example paramter
+
+    """
+    def __init__(self, value=42):
+        self.value = value
+

pkmodel/protocol.py

@@ -0,0 +1,17 @@
+#
+# Protocol class
+#
+
+class Protocol:
+    """A Pharmokinetic (PK) protocol
+
+    Parameters
+    ----------
+
+    value: numeric, optional
+        an example paramter
+
+    """
+    def __init__(self, value=43):
+        self.value = value
+

pkmodel/solution.py

@@ -0,0 +1,17 @@
+#
+# Solution class
+#
+
+class Solution:
+    """A Pharmokinetic (PK) model solution
+
+    Parameters
+    ----------
+
+    value: numeric, optional
+        an example paramter
+
+    """
+    def __init__(self, value=44):
+        self.value = value
+

pkmodel/tests/__init__.py

@@ -0,0 +1,13 @@
+#
+# Test module for pkmodel.
+#
+# To run all tests, use ``python -m unittest discover``.
+#
+# To run a particular test, use e.g.
+#  ``python -m unittest pkmodel.tests.test_model``.
+#
+# For this project, we chose to place the tests inside the code directory. See
+# https://stackoverflow.com/questions/61151/where-do-the-python-unit-tests-go
+# for an extended discussion.
+#
+

pkmodel/tests/test_model.py

@@ -0,0 +1,15 @@
+import unittest
+import pkmodel as pk
+
+
+class ModelTest(unittest.TestCase):
+    """
+    Tests the :class:`Model` class.
+    """
+    def test_create(self):
+        """
+        Tests Model creation.
+        """
+        model = pk.Model()
+        self.assertEqual(model.value, 42)
+

pkmodel/tests/test_protocol.py

@@ -0,0 +1,15 @@
+import unittest
+import pkmodel as pk
+
+
+class ProtocolTest(unittest.TestCase):
+    """
+    Tests the :class:`Protocol` class.
+    """
+    def test_create(self):
+        """
+        Tests Protocol creation.
+        """
+        model = pk.Protocol()
+        self.assertEqual(model.value, 43)
+

pkmodel/tests/test_solution.py

@@ -0,0 +1,15 @@
+import unittest
+import pkmodel as pk
+
+
+class SolutionTest(unittest.TestCase):
+    """
+    Tests the :class:`Solution` class.
+    """
+    def test_create(self):
+        """
+        Tests Solution creation.
+        """
+        model = pk.Solution()
+        self.assertEqual(model.value, 44)
+

pkmodel/version_info.py

@@ -0,0 +1,14 @@
+#
+# Version information for pkmodel.
+#
+# See: https://packaging.python.org/guides/single-sourcing-package-version/
+#
+# Version as a tuple (major, minor, revision)
+#  - Changes to major are rare
+#  - Changes to minor indicate new features, possible slight backwards
+#    incompatibility
+#  - Changes to revision indicate bugfixes, tiny new features
+VERSION_INT = 1, 0, 0
+
+# String version of the version number
+VERSION = '.'.join([str(x) for x in VERSION_INT])

prototype.py

@@ -0,0 +1,52 @@
+import matplotlib.pylab as plt
+import numpy as np
+import scipy.integrate
+
+def dose(t, X):
+    return X
+
+def rhs(t, y, Q_p1, V_c, V_p1, CL, X):
+    q_c, q_p1 = y
+    transition = Q_p1 * (q_c / V_c - q_p1 / V_p1)
+    dqc_dt = dose(t, X) - q_c / V_c * CL - transition
+    dqp1_dt = transition
+    return [dqc_dt, dqp1_dt]
+
+model1_args = {
+    'name': 'model1',
+    'Q_p1': 1.0,
+    'V_c': 1.0,
+    'V_p1': 1.0,
+    'CL': 1.0,
+    'X': 1.0,
+}
+
+model2_args = {
+    'name': 'model2',
+    'Q_p1': 2.0,
+    'V_c': 1.0,
+    'V_p1': 1.0,
+    'CL': 1.0,
+    'X': 1.0,
+}
+
+t_eval = np.linspace(0, 1, 1000)
+y0 = np.array([0.0, 0.0])
+
+fig = plt.figure()
+for model in [model1_args, model2_args]:
+    args = [
+        model['Q_p1'], model['V_c'], model['V_p1'], model['CL'], model['X']
+    ]
+    sol = scipy.integrate.solve_ivp(
+        fun=lambda t, y: rhs(t, y, *args),
+        t_span=[t_eval[0], t_eval[-1]],
+        y0=y0, t_eval=t_eval
+    )
+    plt.plot(sol.t, sol.y[0, :], label=model['name'] + '- q_c')
+    plt.plot(sol.t, sol.y[1, :], label=model['name'] + '- q_p1')
+
+plt.legend()
+plt.ylabel('drug mass [ng]')
+plt.xlabel('time [h]')
+plt.show()