Fix dgfs #449

teddygroves · 2023-10-16T09:32:28Z

This change partially implements #442, making it possible to fix the values of formation energy parameters in the parameter input file.

The interface is as follows for independent dgf input:

dgf = [
  {location = -1, metabolite = "M1", scale = 0.05, fixed_value = -1},
]

or like this for multivariate input:

[dgf]
ids = ["M1", "M2", "M3"]
mean_vector = [1, 2, 3]
covariance_matrix = [[1,2,3], [1, 2, 3], [1, 2, 3]]
[dgf.fixed_values]
M1 = -1

I think this change is just about ready~~, the only thing to do is update the documentation~~.

Checklist:

Updated any relevant documentation
Add an adr doc if appropriate
Include links to any relevant issues in the description
Unit tests passing
Integration tests passing

carrascomj

I am getting and error where no [dgf.fixed_values] block is specified in the priors.

Traceback (most recent call last):
  File "/home/georg/.virtualenvs/maud-branch/bin/maud", line 8, in <module>
    sys.exit(cli())
  File "/home/georg/.virtualenvs/maud-branch/lib/python3.10/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
  File "/home/georg/.virtualenvs/maud-branch/lib/python3.10/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
  File "/home/georg/.virtualenvs/maud-branch/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/georg/.virtualenvs/maud-branch/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/georg/.virtualenvs/maud-branch/lib/python3.10/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
  File "/home/georg/.virtualenvs/maud-branch/lib/python3.10/site-packages/maud/cli.py", line 166, in simulate_command
    click.echo(do_simulate(data_path, output_dir, n))
  File "/home/georg/.virtualenvs/maud-branch/lib/python3.10/site-packages/maud/cli.py", line 193, in do_simulate
    stanfit = simulate(mi, samples_path, n)
  File "/home/georg/.virtualenvs/maud-branch/lib/python3.10/site-packages/maud/running_stan.py", line 152, in simulate
    set_up_output_dir(output_dir, mi)
  File "/home/georg/.virtualenvs/maud-branch/lib/python3.10/site-packages/maud/running_stan.py", line 191, in set_up_output_dir
    cmdstanpy.utils.write_stan_json(input_path_train, mi.stan_input_train)
  File "/home/georg/.virtualenvs/maud-branch/lib/python3.10/site-packages/pydantic/main.py", line 756, in __getattr__
    return super().__getattribute__(item)  # Raises AttributeError if appropriate
  File "/home/georg/.virtualenvs/maud-branch/lib/python3.10/site-packages/maud/data_model/maud_input.py", line 41, in stan_input_train
    train, _ = get_stan_inputs(
  File "/home/georg/.virtualenvs/maud-branch/lib/python3.10/site-packages/maud/getting_stan_inputs.py", line 45, in get_stan_inputs
    fixed_param_input = get_fixed_param_input(parameters, kinetic_model)
  File "/home/georg/.virtualenvs/maud-branch/lib/python3.10/site-packages/maud/getting_stan_inputs.py", line 79, in get_fixed_param_input
    "ix_dgf_free": list(range(1, len(dgf.location) + 1)),
  File "/home/georg/.virtualenvs/maud-branch/lib/python3.10/site-packages/pydantic/main.py", line 759, in __getattr__
    raise AttributeError(f'{type(self).__name__!r} object has no attribute {item!r}')
AttributeError: 'Dgf' object has no attribute 'location'
```

teddygroves · 2023-10-16T14:55:10Z

I am getting and error where no [dgf.fixed_values] block is specified in the priors.

Traceback (most recent call last):
  File "/home/georg/.virtualenvs/maud-branch/bin/maud", line 8, in <module>
    sys.exit(cli())
  File "/home/georg/.virtualenvs/maud-branch/lib/python3.10/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
  File "/home/georg/.virtualenvs/maud-branch/lib/python3.10/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
  File "/home/georg/.virtualenvs/maud-branch/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/georg/.virtualenvs/maud-branch/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/georg/.virtualenvs/maud-branch/lib/python3.10/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
  File "/home/georg/.virtualenvs/maud-branch/lib/python3.10/site-packages/maud/cli.py", line 166, in simulate_command
    click.echo(do_simulate(data_path, output_dir, n))
  File "/home/georg/.virtualenvs/maud-branch/lib/python3.10/site-packages/maud/cli.py", line 193, in do_simulate
    stanfit = simulate(mi, samples_path, n)
  File "/home/georg/.virtualenvs/maud-branch/lib/python3.10/site-packages/maud/running_stan.py", line 152, in simulate
    set_up_output_dir(output_dir, mi)
  File "/home/georg/.virtualenvs/maud-branch/lib/python3.10/site-packages/maud/running_stan.py", line 191, in set_up_output_dir
    cmdstanpy.utils.write_stan_json(input_path_train, mi.stan_input_train)
  File "/home/georg/.virtualenvs/maud-branch/lib/python3.10/site-packages/pydantic/main.py", line 756, in __getattr__
    return super().__getattribute__(item)  # Raises AttributeError if appropriate
  File "/home/georg/.virtualenvs/maud-branch/lib/python3.10/site-packages/maud/data_model/maud_input.py", line 41, in stan_input_train
    train, _ = get_stan_inputs(
  File "/home/georg/.virtualenvs/maud-branch/lib/python3.10/site-packages/maud/getting_stan_inputs.py", line 45, in get_stan_inputs
    fixed_param_input = get_fixed_param_input(parameters, kinetic_model)
  File "/home/georg/.virtualenvs/maud-branch/lib/python3.10/site-packages/maud/getting_stan_inputs.py", line 79, in get_fixed_param_input
    "ix_dgf_free": list(range(1, len(dgf.location) + 1)),
  File "/home/georg/.virtualenvs/maud-branch/lib/python3.10/site-packages/pydantic/main.py", line 759, in __getattr__
    raise AttributeError(f'{type(self).__name__!r} object has no attribute {item!r}')
AttributeError: 'Dgf' object has no attribute 'location'

Thanks - I think this is fixed by ba18f98

carrascomj

It needs a rebase, otherwise LGTM!

carrascomj · 2023-10-18T15:42:58Z

maud/data_model/maud_parameter.py

+    @computed_field
+    def fixed_ids(self) -> Optional[List[List[str]]]:
+        """Set the fixed_ids field."""
+        if self.name != "dgf":


Probably, this would better modeled with an extra class that inherits from MaudParameter that requires implementing these two methods. I think we can leave that for the next time we want to fix a different kind of parameter.

Yeah there's definitely lots of room for improvement on how this is implemented, especially the inits and stan code generation. I think it'll be nice to think about this between now and when we want to generalise to other (all?) parameters.

teddygroves added 8 commits October 12, 2023 23:00

allow fixing dgfs

e38706d

Fix bug

8adfbfb

Merge branch 'main' into fix_dgf

c5b0258

Update docs

c967f19

Fix tests

aa95bcc

Update methionine input with fixed values

c7e9a92

Update tox cmdstan version and example ode input data

feed2d7

Update example ode inits

cfed202

teddygroves changed the title ~~[WIP] Fix dgfs~~ Fix dgfs Oct 16, 2023

teddygroves requested review from carrascomj and NicholasCowie October 16, 2023 12:54

teddygroves added 2 commits October 16, 2023 15:28

Fix setting inits

c96c2d7

Update cmdstan version in running_stan.py

88afed9

carrascomj requested changes Oct 16, 2023

View reviewed changes

teddygroves added 2 commits October 16, 2023 16:51

Fix fixed value indexing

de1f2f0

fix stan input bug for unfixed params

ba18f98

teddygroves added 5 commits October 17, 2023 08:54

Fix setup.py cmdstan version

0a6de64

save metric

faa751a

Fix free dgf inits

7a5f041

Update methionine fixed dgfs

afce615

save metric files

b26905b

carrascomj approved these changes Oct 18, 2023

View reviewed changes

teddygroves added 3 commits October 19, 2023 09:33

Update solver settings in linear and methionine models

8f8ce45

Merge branch 'main' into fix_dgf

0146fa1

Fix expected solver params

631a17f

teddygroves merged commit 52390de into main Oct 19, 2023
6 checks passed

teddygroves mentioned this pull request Oct 19, 2023

Don't use priors for fixed dgfs #451

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Fix dgfs #449

Fix dgfs #449

teddygroves commented Oct 16, 2023 •

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teddygroves Oct 19, 2023

Fix dgfs #449

Fix dgfs #449

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