PEtab COMBINE archive #271
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Codecov Report
@@ Coverage Diff @@
## develop #271 +/- ##
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+ Coverage 69.7% 71.92% +2.21%
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Files 22 22
Lines 1753 1781 +28
Branches 376 383 +7
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+ Hits 1222 1281 +59
+ Misses 450 413 -37
- Partials 81 87 +6
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yannikschaelte
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Feb 9, 2020
dweindl
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Feb 10, 2020
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| """Test COMBINE archive""" | |||
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dweindl
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Feb 10, 2020
| @@ -32,13 +32,9 @@ def minimal_sbml_model(): | |||
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| @pytest.fixture | |||
| def petab_problem(): | |||
| def petab_problem(minimal_sbml_model): | |||
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dweindl
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Feb 10, 2020
| model.setExtentUnits("mole") | ||
| model.setSubstanceUnits('mole') | ||
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| def test_create_parameter_df(minimal_sbml_model, condition_df_2_conditions): |
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dweindl
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Feb 10, 2020
| model.setExtentUnits("mole") | ||
| model.setSubstanceUnits('mole') | ||
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| def test_create_parameter_df(minimal_sbml_model, condition_df_2_conditions): |
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dweindl
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Feb 10, 2020
| """ | ||
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| with open(filename, 'w') as outfile: | ||
| yaml.dump(yaml_config, outfile, default_flow_style=False) |
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dweindl
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Feb 10, 2020
| """Test `create_combine_archive` and `Problem.from_combine`""" | ||
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| # Create test files | ||
| document, sbml_model = minimal_sbml_model |
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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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