Feature fixed par plist for AmiciObjective #59
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…xity and are super fast
… current AmiciObjective instance
Codecov Report
@@ Coverage Diff @@
## master #59 +/- ##
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+ Coverage 85.12% 86.5% +1.38%
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Files 23 23
Lines 1062 1097 +35
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+ Hits 904 949 +45
+ Misses 158 148 -10
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| @@ -86,6 +84,108 @@ def res(x, sensi_orders): | |||
| # extract parameter names from model | |||
| self.x_names = list(self.amici_model.getParameterNames()) | |||
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| def get_bound_fun(self): | |||
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Looks good to me. I think that beforehand amici always had to compute sensis for all parameters, and using model.setParameterList() now, only those that are not fixed are computed?
Can you shortly document why get_bound_fun and rebind_fun are necessary? Just so we don't run into similar problems in the future.
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Correct. Will add documentation
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@FFroehlich : In the doc you say for get_bound_fun(self) that
Generate a fun function that calls _call_amici with MODE_FUN. Defining
a non-class function that references self as a local variable will bind
the function to a copy of the current self object and will
accordingly not take future changes to self into account.
I currently need to work on related stuff here. I do not completely understand what the problem is. Could you shortly explain please? If I do the following:
class A:
def __init__(self):
self.x = 1
def nested_fun(y):
print(self.x, y)
self.fun = nested_fun
a = A()
a.fun(2) # gives [1 2]
a.x = 42
a.fun(2) # gives [42 2]I get the output I would expect, i.e. the references inside self are updated correctly.
Allow creating Problem from pre-existing data frames* Allow creating Problem from pre-existing data frames * Flake... * Model name and sbml_file should not be mandatory * Refactor Problem. Remove file names, pickle DataFrames and Model directly. See discussion #61 * Fix whitespace-checking issues, extend check (Closes #59) * Make petablint more error-tolerant and prettify * Speedup handle_missing_overrides for larger problems (229s->64s) * Speedup handle_missing_overrides; match names a bit looser * Doc. Fail. * Use ctor in Problem.from_files
…for_observable (fixes #59) (#60) Revert "More informative error messages in case of wrongly set observable and noise parameters (Closes PEtab-dev/PEtab#118) (PEtab-dev/PEtab#155)" This reverts commit 8fab85e.
Modifies AmiciObjective to make use of Model.setParameterList() to reduce computational cost if a large number of parameters is fixed.