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… also fills the defaults now
fbergmann
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Jan 22, 2025
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if i start with a new model i cannot enter a new condition:
Traceback (most recent call last):
File "~/pyPESTO_GUI/src/petab_gui/models/pandas_table_model.py", line 139, in setData
self.insertRows(index.row(), 1)
File "~/pyPESTO_GUI/src/petab_gui/models/pandas_table_model.py", line 104, in insertRows
self._data_frame.loc[end_position + i] = /
~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^
File "~/.conda/envs/env-penguin/Lib/site-packages/pandas/core/indexing.py", line 911, in __setitem__
iloc._setitem_with_indexer(indexer, value, self.name)
File "~/.conda/envs/env-penguin/Lib/site-packages/pandas/core/indexing.py", line 1932, in _setitem_with_indexer
self._setitem_with_indexer_missing(indexer, value)
File "~/.conda/envs/env-penguin/Lib/site-packages/pandas/core/indexing.py", line 2290, in _setitem_with_indexer_missing
raise ValueError("cannot set a frame with no defined columns")
ValueError: cannot set a frame with no defined columns
fbergmann
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Jan 22, 2025
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-
default obs, pearmaetr, observable id's: 'new measurement', 'new observable', 'new parameter' are invalid.
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adding a new observableFormula does not yet fill out the id (leaving it an invalid numeric)
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adding a measurement, adds the new observableid to the observable table ... but a simulation condition is not added to the condition table.
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adding a parameter that exists in the model to the parameter table gives the linter error:
PEtab linter failed at row 1, column 0: Expected numeric values fornominalValuein parameter table for all non-estimated parameters.even thoughestimateis 1. it would be fine if the nominalValue could be taken from the model
# Conflicts: # src/petab_gui/models/pandas_table_model.py
PaulJonasJost
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Jan 22, 2025
…plus conditionId index). Fixes bug mentioned in #55
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Adressed in #57 |
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ok, that fix worked, but only if i manually change C.py on my machine. The merge earlier didnt do it. Next time it might be best, to just add the commits to the current PR. In anycase. I cann now add new conditions. |
# Conflicts: # src/petab_gui/models/pandas_table_model.py
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|
while trying I have the following error: Traceback (most recent call last):
File "~/pyPESTO_GUI/src/petab_gui/controllers/mother_controller.py", line 635, in check_model
failed = self.model.test_consistency()
File "~/pyPESTO_GUI/src/petab_gui/models/petab_model.py", line 112, in test_consistency
return petab.lint.lint_problem(self.current_petab_problem)
~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/frank/env-penguin/lib/python3.13/site-packages/petab/v1/lint.py", line 910, in lint_problem
check_measurement_df(problem.measurement_df, problem.observable_df)
~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/frank/env-penguin/lib/python3.13/site-packages/petab/v1/lint.py", line 200, in check_measurement_df
if measurement <= 0.0 and trafo in [LOG, LOG10]:
^^^^^^^^^^^^^^^^^^
TypeError: '<=' not supported between instances of 'str' and 'float'
Traceback (most recent call last):
File "~/pyPESTO_GUI/src/petab_gui/controllers/mother_controller.py", line 635, in check_model
failed = self.model.test_consistency()
File "~/pyPESTO_GUI/src/petab_gui/models/petab_model.py", line 112, in test_consistency
return petab.lint.lint_problem(self.current_petab_problem)
~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/frank/env-penguin/lib/python3.13/site-packages/petab/v1/lint.py", line 910, in lint_problem
check_measurement_df(problem.measurement_df, problem.observable_df)
~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/frank/env-penguin/lib/python3.13/site-packages/petab/v1/lint.py", line 200, in check_measurement_df
if measurement <= 0.0 and trafo in [LOG, LOG10]:
^^^^^^^^^^^^^^^^^^
TypeError: '<=' not supported between instances of 'str' and 'float' |
# Conflicts: # src/petab_gui/app.py # src/petab_gui/controllers/mother_controller.py # src/petab_gui/controllers/table_controllers.py # src/petab_gui/controllers/utils.py # src/petab_gui/models/pandas_table_model.py # src/petab_gui/utils.py # src/petab_gui/views/main_view.py
…ond tables. Allow defaults for meas table
fbergmann
approved these changes
Apr 10, 2025
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Handles default values. No default values for measurement table so far, as condition is too specific. Condition is separately asked in a dialogue when uploading.