model.solve()

The model class works properly but is too slow for useful inference times. This is likely because of unnecessary logs in the background of Myokit.

Currently solving the test one compartment model takes 0.745 sec.

more details:

>>> p = pstats.Stats('tests/model/profile_solve')
>>> p.sort_stats('cumulative').print_stats(50)
Wed Dec 18 12:19:03 2019    tests/model/profile_solve

         335637 function calls (324001 primitive calls) in 0.745 seconds

   Ordered by: cumulative time
   List reduced from 3297 to 50 due to restriction <50>

   ncalls  tottime  percall  cumtime  percall filename:lineno(function)
    676/1    0.005    0.000    0.746    0.746 {built-in method builtins.exec}
        1    0.000    0.000    0.746    0.746 tests/model/profile_solve.py:15(<module>)
        1    0.000    0.000    0.498    0.498 /Users/david/Workspace/sabs-r3/PKPD/PKPD/model/model.py:73(solve)
        1    0.000    0.000    0.487    0.487 /Users/david/Workspace/sabs-r3/PKPD/env/lib/python3.7/site-packages/myokit/_sim/cvodesim.py:82(__init__)
        1    0.000    0.000    0.486    0.486 /Users/david/Workspace/sabs-r3/PKPD/env/lib/python3.7/site-packages/myokit/_sim/__init__.py:88(_compile)
   507/21    0.000    0.000    0.410    0.020 <frozen importlib._bootstrap>:211(_call_with_frames_removed)
        1    0.000    0.000    0.339    0.339 /Users/david/Workspace/sabs-r3/PKPD/env/lib/python3.7/site-packages/setuptools/__init__.py:142(setup)
        1    0.000    0.000    0.327    0.327 /usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/core.py:57(setup)
        1    0.000    0.000    0.323    0.323 /usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/dist.py:960(run_commands)
     10/2    0.000    0.000    0.323    0.162 /usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/dist.py:970(run_command)
      8/5    0.000    0.000    0.322    0.064 /usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/cmd.py:308(run_command)
        1    0.000    0.000    0.287    0.287 /usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/command/build.py:128(run)
        1    0.000    0.000    0.285    0.285 /Users/david/Workspace/sabs-r3/PKPD/env/lib/python3.7/site-packages/setuptools/command/build_ext.py:75(run)
        1    0.000    0.000    0.285    0.285 /usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/command/build_ext.py:278(run)
        1    0.000    0.000    0.284    0.284 /usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/command/build_ext.py:443(build_extensions)
        1    0.000    0.000    0.284    0.284 /usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/command/build_ext.py:471(_build_extensions_serial)
        1    0.000    0.000    0.284    0.284 /Users/david/Workspace/sabs-r3/PKPD/env/lib/python3.7/site-packages/setuptools/command/build_ext.py:193(build_extension)
        1    0.000    0.000    0.284    0.284 /usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/command/build_ext.py:486(build_extension)
   411/16    0.002    0.000    0.283    0.018 <frozen importlib._bootstrap>:978(_find_and_load)
   411/16    0.001    0.000    0.283    0.018 <frozen importlib._bootstrap>:948(_find_and_load_unlocked)
        2    0.000    0.000    0.282    0.141 /usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/ccompiler.py:909(spawn)
        2    0.000    0.000    0.282    0.141 /usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/spawn.py:16(spawn)
        2    0.000    0.000    0.282    0.141 /usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/spawn.py:88(_spawn_posix)
   387/20    0.001    0.000    0.280    0.014 <frozen importlib._bootstrap>:663(_load_unlocked)
        3    0.280    0.093    0.280    0.093 {built-in method posix.waitpid}
   325/19    0.001    0.000    0.279    0.015 <frozen importlib._bootstrap_external>:722(exec_module)
        1    0.000    0.000    0.243    0.243 /usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/ccompiler.py:511(compile)
        1    0.000    0.000    0.242    0.242 /usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/unixccompiler.py:111(_compile)
   425/84    0.000    0.000    0.188    0.002 {built-in method builtins.__import__}
  371/368    0.001    0.000    0.158    0.000 <frozen importlib._bootstrap>:576(module_from_spec)
    41/39    0.000    0.000    0.151    0.004 <frozen importlib._bootstrap_external>:1040(create_module)
    41/39    0.150    0.004    0.151    0.004 {built-in method _imp.create_dynamic}

New execution time: 0.327 including initialization. Just solving the ODE after initialization is now much faster.

Progress:

• Implementation complete.
• Fully tested.

Data display and check boxes for user to clarify data structure

Data file is displayed in home tab, once selected and a first structural analysis is performed (are patient IDs/ dose schedule present. These properties are highlighted in the data display.

The presence of bespoken properties are identified by heuristic methods, are hence prone to errors. Thus check boxes are provided to enable the user to correct the heuristic tests.

Progress:

• [x ] Implementation complete.
• [ x] manually tested.

May I inquire about how one might use this software to calculate the simulated PD data and its associated parameters?

Test MultiOutputModel

In the same spirit as the one-compartment model add a three compartment model for testing.

Progress:

• Implementation complete.
• Fully tested.

Catch errors

Use try/except blocks to catch errors that we know are possible. Requested Jan 15th.

Progress:

• Implementation complete.
• Fully tested.

Model Class

Adding functionality to model class

Progress:
Most functions copied over

• Implementation complete.
• Fully tested.

Model units

Add a function to mmt read-in to grab param units and check that they are consistent. Requested Jan 15th.

Progress:

• Read in units
• Check units
• Give preferred units

Inference options

Allow bounded or non-bounded problems. Requested Jan 15th.

Progress:

• Implementation complete.
• Fully tested.

MultiOutputModel Class

Extension of pints.ForwardModel for MultiOutputProblem. Changes to to SingleOutputModel are almost trivial and are mainly in the simulate method.

Progress:

• Implementation complete.
• Fully tested.

"Method or Function Name"

"Short description of the method/function."

Progress:

• [ x] Implementation complete.
• [x ] Fully tested.

find_optimal_parameter

Within the SingleOutputProblem class the find_optimal_parameter method finds a set of parameters that optimises a chosen objective function.

Progress:

• Implementation complete.
• Fully tested.

I've just tried to install and run the PKPD gui, pip install looked like it worked fine.

There wasn't any information on how to run the gui? I tried:

python PKPD/gui/mainWindow.py

and got the following error:

WARNING:myokit._config:Unable to auto-detect Sundials version.
WARNING:myokit._config:Sundials version not set in myokit.ini and version auto-detection failed.
Traceback (most recent call last):
  File "PKPD/gui/mainWindow.py", line 8, in <module>
    from PKPD.inference import inference as inf
  File "/home/mrobins/git/PKPD/PKPD/inference/inference.py", line 4, in <module>
    import pints
ModuleNotFoundError: No module named 'pints'

looks like pints isn't installed by setup.py. even though pints doesn't have a pip install route, you can add a url dependency to setup.py, see here: https://stackoverflow.com/questions/32688688/how-to-write-setup-py-to-include-a-git-repo-as-a-dependency

_set_window_size

Method of the MainWindow class to set its window size.

Progress:

• Implementation complete.
• Fully tested.

_set_tab_structure

Sets up how the tab structure will work and look.

Progress:

• Implementation complete.
• Fully tested.

Performance improvement

Within Myokit and Pints some methods perform, for our means, irrelevant checks and data type conversions, because we only allow interaction via GUI and thus have full control over data types.

We might be able to improve performance by copying the relevant functionality and leave out checks.

Progress:

• Implementation complete.
• Fully tested.

"_set_geometry"

"Function to add a layout to the main window."

Progress:

• Implementation complete.
• Fully tested.

Model Repository

"Create Model Repository in an easily generalizable manner. Update the Code to read-in those model files."

Progress:

• Create 1-comparment model (bolus + subcut)
• Update SingleOutput routine
• Create 2-compartment model (bolus + subcut)
• Update MultiOutput routine
• Create 3-compartment model (bolus + subcut)
• Create handler to choose the dimensionality of output and which compartments should be fitted and which be plotted. (Could by default choose centralCompartment for 1 dim data.)

Minimal home tab

• File dialog for the model & protocol .mmt file
• File dialog for the data file
• Button to forward to simulation tab.

Progress:

• Implementation complete.
• manually tested.

Hi guys!

Few quick comments after looking at your travis config

1. There's a lot of PINTS constants that you don't need (these lines can all go, I think)
2. You have a very big requirements.txt file with "pinned" (version-specific) dependencies, not sure you need this!
3. PINTS isn't pip installable yet, so you'll need to do something more complicated, e.g. adding this to your travis before_install bit: - pip install -e git://github.com/pints-team/pints.git#egg=pints
4. There's no setup.py file, so pip install . won't do anything

setup.py

"Create a setup.py that install PINTS and other dependencies."

Progress:

• Implementation complete.
• Fully tested.

Display mmt file

Make a small library of simple mmt files for the user to base theirs on, and preferably display the file in the gui. Requested Jan 15th.

Progress:

• Library of mmts
• Display mmt
• Editable mmt

Minimal simulation tab

Create minimal simulation tab:

• plot data
• read parameter in model and allow for input of initial values
• find optimal parameters upon pressing an inference button
• display found parameters with stats somewhere
• plot model solution into data figure

Progress:

• Implementation complete.
• Fully tested.

#21 Myokit is not playing nicely with Travis.

Plot options

Boundaries, logarithmic y-axis option. Requested Jan 15th.

Progress:

• Implementation complete.
• Fully tested.

"Method or Function Name"

"Short description of the method/function."

Progress:

• Implementation complete.
• Fully tested.

MultiOutputProblem class

In spirit the same as the SingleOutputProblem but now solving the ODEs with the MultiOutputModel and suited to infer parameters from higher dimensional models.

Progress:

• Implementation complete.
• Fully tested.