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Add support for experiments (previously named timecourses) #263

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@dilpath dilpath commented May 29, 2024

  • functionality
    • read/write
    • OOP
    • methods for tools
      • to_events
      • to_sequence_of_petab
      • to_single_petab_and_sequence_of_metadata
      • optimize_metadata_to_reduce_redundant_simulations
      • optimize_metadata_to_reduce_events_or_unique_petabs_in_sequence_of_petabs
  • linter validation checks
  • test all functionality
  • docs

dilpath added 19 commits May 20, 2024 20:09
@dilpath
add timecourse.py:* to __init__
cca2cd7
@dilpath
add timecourse_df to petab.Problem
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@dilpath
add timecourse_files to yaml.py
2a5ccb2
@dilpath
add timecourse constants to C.py
56b5b9e
@dilpath
add timecourses.py
2d6dcbb
@dilpath
save timecourses in PEtab yaml; test to_files_generic; add timecour…
8714e7a 
…ses to problem tests
@dilpath
add test_timecourses.py
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@dilpath
update measurements for timecourses; add `core.time_is_at_steady_stat…
d543f1f 
…e`; add dependency
@dilpath
parameter_mapping.py: update and refactor for timecourses
815a258
@dilpath
add Timecourse and Period classes
61dea8a
@dilpath
add Timecourse.to_series
dbc210a
@dilpath
test denesting of nesting from restartEvery and nested timecourses
df2f6a9
@dilpath
rename to experiments
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@dilpath
update measurements
5cabb65
@dilpath
update test_parameter_mapping to new par_map structure
c98195b
@dilpath
update sbml get_period_model and fix tests
2e9efcf
@dilpath
update simplify and lint for experiments
350a38c
@dilpath
fix remaining nonvis tests
a7272b5
@dilpath
fix vis example petabs
e9ca0d0
@dilpath dilpath changed the title Add support for timecourses Add support for experiments (previously named timecourses) Jun 4, 2024
@m-philipps m-philipps self-assigned this Dec 3, 2024
@dweindl dweindl mentioned this pull request Dec 5, 2024
Merged
dweindl added a commit that referenced this pull request Dec 18, 2024
@dweindl @dilpath
Support for petab v2 experiments (#332)
6a433e0 
Add basic support for PEtab version 2 experiments (see also PEtab-dev/PEtab#586, and  PEtab-dev/PEtab#581). Follow-up to #334.

Partially supersedes #263, which was started before petab.v1/petab.v2 were introduced and before PEtab-dev/PEtab#586.

* updates the required fields in the measurement table
* updates some validation functions to not expect the old `simulationConditionId`s (but does not do full validation yet)
* extends PEtab v1 up-conversion to create a new experiment table.

---------

Co-authored-by: Dilan Pathirana <[email protected]>
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