Allow initial concentrations / sizes in condition table #238
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@@ Coverage Diff @@
## develop #238 +/- ##
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+ Coverage 77.94% 78.16% +0.21%
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Files 20 20
Lines 1424 1424
Branches 313 313
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+ Hits 1110 1113 +3
+ Misses 249 247 -2
+ Partials 65 64 -1
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yannikschaelte
approved these changes
Jan 22, 2020
doc/documentation_data_format.md
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| Column names are global parameter IDs or IDs of constant species as given in | ||
| the SBML model. These parameters will override any parameter values specified | ||
| in the model. `parameterOrStateId`s and `conditionId`s must be unique. | ||
| Column names are global parameter IDs, IDs of species or compartments as given |
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Suggested change
| Column names are global parameter IDs, IDs of species or compartments as given | |
| Column names are global parameter IDs, or IDs of species or compartments defined |
doc/documentation_data_format.md
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| concentration/amount given in the SBML model or given by a preequilibration | ||
| condition. If `NaN` is provided for a condition, the result of the | ||
| preequilibration (or initial concentration/amount from the SBML model, if no | ||
| preequilibration is defined) is used. |
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for understanding: so when there is a species id defined, but there is also preeq. then the species value overrides whatever comes out of the preeq, s.t. the preeq does not actually need to be run?
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If you specify all initial conditions here, and if for the simulationCondition all of them are non-NaN, then you could as well skip preequlibration. This is only useful (and sometimes required, since you generally can't just preequilibrate a subset of the model) if you do not add/overwrite all initial conditions here.
doc/documentation_data_format.md
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| preequilibration (or initial concentration/amount from the SBML model, if no | ||
| preequilibration is defined) is used. | ||
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| If a compartment Id is provided, it is interpreted as the initial compartment |
doc/documentation_data_format.md
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| Values for condition parameters may be provided either as numeric values, or | ||
| as parameter IDs. In case parameter IDs are provided, they need to be defined | ||
| in the SBML model, the parameter table or both. | ||
| as IDs defined in the SBML model, the parameter table or both. |
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what would be a scenario where the id is only defined in the parameter table and it is to be overwritten in a condition-specific manner?
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You could set output parameters in a condition-specific manner, avoiding the not so aesthetic observableParameter1_observableId construct.
doc/documentation_data_format.md
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| Additional columns are *not* allowed. | ||
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| *Note 1:* Instead of adding additional columns to the condition table, they | ||
| can easily be added to a separate file, since every row of the condition table | ||
| has `parameterId` as unique key. | ||
| has `parameterOrStateId` as unique key. |
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parameterOrStateOrCompartmentId. But I still don't understand the sentence.
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Still wrong, rows are conditions. I removed the whole sentence. Doesn't really belong here, and at the time this sentence was correct, it was probably an answer to a not asked question.
doc/documentation_data_format.md
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| Row- and column-ordering are arbitrary, although specifying `parameterId` | ||
| first may improve human readability. The `conditionName` column is optional. | ||
| first may improve human readability. The `conditionName` column is optional |
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why parameterId first? you mean conditionId?
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Yes. As previous. This was from the days where the table was transposed. Never got updated...
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dweindl
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Jan 29, 2020
Release 0.1.0 Data format: * Introduce observables table instead of SBML assignment rules for defining observation model (#244) (moves observableTransformation and noiseModel from the measurement table to the observables table) * Allow initial concentrations / sizes in condition table (#238) * Fixes and clarifications in the format documentation * Changes in prior columns of the parameter table (#222) * Introduced separate version number of file format, this release being version 1 Library: * Adaptations to new file formats * Various bugfixes and clean-up, especially in visualization and validator * Parameter mapping changed to include all model parameters and not only those differing from the ones defined inside the SBML model * Introduced constants for all field names and string options, replacing most string literals in the code (#228) * Added unit tests and additional format validation steps * Optional parallelization of parameter mapping (#205) * Extended documentation (in-source and example Jupyter notebooks)
LeonardSchmiester
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Feb 11, 2020
* Add pylint config * Fixes ys (#237) * fix merge error * add petablint yaml test * add parameters test * Parameter mapping should include all model parameters (#235) Closes #103 * Parameter mapping should include all model parameters * Known values should be filled in * Extend and update tests * Refactor parameter mapping * properly handle estimated and non-estimated parameters * Fix wrong parameter scale returned from mapping * ... * Allow initial concentrations / sizes in condition table (#238) * Allow species and compartments in condition table * Updated doc allowing for states etc in condition file * Update pylint: allow lower-case constants * Export __format_version__ * Fix returning floats as strings in case there are parameter names in the condition table Co-authored-by: LeonardSchmiester <leonard.schmiester@helmholtz-muenchen.de> * Barplots and Replicates with Simulation data (#214) Fixes #196, fixes #210, fixes #213 * Cleanup visualization (#240) * Add constants for visualization field IDs * .. and some others * start using them * formatting, ... * Observables table instead of SBML assignment rules (#244) Closes #201, closes #241 * Update data format doc for observable table * Add field name constants for observable table * Add observables table to petab.Problem * Update YAML schema and CompositeProblem * Add functions for writing PEtab dataframes to files * Deprecate SBML-observable functions * Implement validation for observable table * Add function for converting SBML-observable models to observable table * Use costants for PEtab table fields * Update PEtab files illustration * Fix most pylint issues (Closes #234) * Update vis to observalble table (Closes #246) No need to check for equal NOISE_DISTRIBUTION and OBSERVABLE_TRANSFORMATION anymore, so they are no longer included in the measurement table, and cannot differ for the same observableId * Fix and update flatten_timepoint_specific_output_overrides Closes #247 Was creating wrong observables before * Address review comments Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Release 0.1.0; file format version 1 * Fix parameter mapping: include output parameters not present in SBML model * Add convenience functions to petab.Problem * get_optimization_parameter_scales * get_optimization_to_simulation_scale_mapping * add tests * Fix petab/petab_schema.yaml missing in pypi package * Update pylint ignorelist * Update README * Remove obsolete functions ... related to hierarchical optimization, which should be kept outside PEtab * Let get_placeholders return an (ordered) list of placeholders because it is much more useful * Add check for valid identifiers (Closes #179) (#253) Co-authored-by: Polina Lakrisenko <p.lakrisenko@gmail.com> * Deprecate petab.problem.from_folder (Closes #245) ... as well as get_default_*_file_name * Release 0.1.1 * Barplot uniform coloring & yScale=log fix #196 (#255) * resolves #197 * small fix * change all barplot colors to blue * allow to extract only estimate parameters (#256) * allow to extract only estimate parameters * add docstrings * Visu callobs par (#262) * fix #261 * corrected flake8 error - line too long * deleted white space * add F403 to falke8 tests * Fix handling of numeric observable/noiseFormula in observable table (Fixes #264) * Add properties for fixed/free and scaled values (#268) * allow to extract only estimate parameters * add docstrings * return scaled versions of arrays * Update petab/problem.py Co-Authored-By: Daniel Weindl <dweindl@users.noreply.github.com> Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com> * Observables function (#269) * allow to extract only estimate parameters * add docstrings * return scaled versions of arrays * Update petab/problem.py Co-Authored-By: Daniel Weindl <dweindl@users.noreply.github.com> * add get_observables function * add observables test; use observables file in petab test * fix typo * move get_observables to ..._ids * remove unused arg * add docstring * fix lint * fix pylint * fix flake8 Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com> * Fix documentation hierarchy * Add functions to get all of fixed|free, scaled parameter values (#273) * allow to extract only estimate parameters * add docstrings * return scaled versions of arrays * Update petab/problem.py Co-Authored-By: Daniel Weindl <dweindl@users.noreply.github.com> * add get_observables function * add observables test; use observables file in petab test * fix typo * move get_observables to ..._ids * remove unused arg * add docstring * fix lint * fix pylint * fix flake8 * fix typo * streamline fixed|free|all, and scaled values * fix default args * fix codacy * address reviewer comment: return empty list * add docstring# * add more docstrings * fix var type error * address reviewer comments Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com> * Default column to look for simulation results should be 'simulation' * PEtab COMBINE archives (#271) * Add create_combine_archive for generation of COMBINE archives * Add support for reading PEtab COMBINE archives * Add tests for COMBINE archive r/w * Fix sbml_observables_to_table - got broken in eb5453 * Increase test coverage (#278) * allow to extract only estimate parameters * add docstrings * return scaled versions of arrays * Update petab/problem.py Co-Authored-By: Daniel Weindl <dweindl@users.noreply.github.com> * add get_observables function * add observables test; use observables file in petab test * fix typo * move get_observables to ..._ids * remove unused arg * add docstring * fix lint * fix pylint * fix flake8 * fix typo * streamline fixed|free|all, and scaled values * fix default args * fix codacy * address reviewer comment: return empty list * add docstring# * add more docstrings * fix var type error * address reviewer comments * add parameter properties test * add tests for get/write_parameter_df * add measurements tests * add conditions tests * fix conditions create function * add parameter tests * add observables tests * fixup * add docstrings * address reviewer comments * random edit to see if codacy is happy * random stuff to annoy codecov Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com> Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com> Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> Co-authored-by: LeonardSchmiester <leonard.schmiester@helmholtz-muenchen.de> Co-authored-by: Simon Merkt <49190262+MerktSimon@users.noreply.github.com> Co-authored-by: Polina Lakrisenko <p.lakrisenko@gmail.com> Co-authored-by: LaraFuhrmann <55209716+LaraFuhrmann@users.noreply.github.com>
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@LeonardSchmiester:
@dweindl:
- [ ] Add something likeget_initial_states()- [ ] .. add test case