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Release 0.0.1 #200

Merged
merged 15 commits into from
Dec 17, 2019
Merged

Release 0.0.1 #200

merged 15 commits into from
Dec 17, 2019

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dweindl
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@dweindl dweindl commented Dec 17, 2019

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MerktSimon and others added 13 commits December 9, 2019 14:05
@MerktSimon
fixes #142
2d95849
@dweindl
Update format documentation with respect to data and parameter scales… (
38396a4 
#169)

* Update format documentation with respect to data and parameter scales (Closes #154)

Fix formatting

* Assert bound positivity for log-scaled parameters + add test case

* Check for positive measurements for log-transformed observables

* Update changelog
@dweindl @yannikschaelte @MerktSimon
Reorganize PEtab library (#177)
17fac2c 
* Reorganize PEtab library

* Update CHANGELOG.md

* Address review comments

* fixup

* Extend and clean-up documentation (1)

* Extend and clean-up documentation (Closes #163)

* Add optional RNG seed to sample_parameter_startpoints

* Update petab/parameters.py

Co-Authored-By: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com>
@dweindl
Remove deprecated function petab.sbml.constant_species_to_parameters
ab8fb7c
@dweindl
Remove deprecated function petab.Problem.get_constant_parameters
db37dc5
@dweindl
YAML file for grouping PEtab files (#183) (Closes 49)
54c526a 
* Validation of contents (e.g. files exist)
* petab.Problem from yaml
* Adapt schema to multiple measurement files
* Use in petablint
* Implement petab.CompositeProblem
* Multiple measurement files for petab.Problem (only in from_files, merge during loading)
@dweindl
Fix: Can't pass list to os.path.join
ed18247
@dweindl
Fix warning: 'YAMLLoadWarning: calling yaml.load() without Loader=...…
a3f8f99 
… is deprecated'
@dweindl
Add missing file, fixes documentation link
50498cd
@dweindl
Fix validation: Don't access non-existing column observableTransforma…
16b4ede 
…tion (Closes #174)
@dweindl
Add petab.parameter_mapping.merge_preeq_and_sim_pars (from pypesto.pe…
ed24599 
…tab_import._merge_preeq_and_sim_pars which actually belongs here)
@dweindl
Add Problem properties to retrieve scaled parameters; add function to…
6736411 
… scale parameters
@dweindl
Enable missing assert_noise_distributions_valid in petablint
636abeb
yannikschaelte
yannikschaelte reviewed Dec 17, 2019
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yannikschaelte
yannikschaelte approved these changes Dec 17, 2019
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not gonna look through everything again, but seems sound. good job!
some changes still to be expected, in particular to the visualization routines and the problem merging.

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codecov-io commented Dec 17, 2019 •
edited

Codecov Report

Merging #200 into master will decrease coverage by 2.28%.
The diff coverage is 68.58%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #200      +/-   ##
==========================================
- Coverage   70.65%   68.37%   -2.29%     
==========================================
  Files          11       18       +7     
  Lines        1152     1271     +119     
  Branches      267      288      +21     
==========================================
+ Hits          814      869      +55     
- Misses        290      354      +64     
  Partials       48       48
Impacted Files Coverage Δ
petab/visualize/plotting_config.py 50% <ø> (ø) ⬆️
petab/petablint.py 0% <0%> (ø) ⬆️
petab/version.py 100% <100%> (ø) ⬆️
petab/core.py 90.9% <100%> (+10.9%) ⬆️
petab/sbml.py 67.96% <100%> (+2.12%) ⬆️
petab/composite_problem.py 43.47% <43.47%> (ø)
petab/conditions.py 46.15% <46.15%> (ø)
petab/visualize/helper_functions.py 95.8% <50%> (ø) ⬆️
petab/yaml.py 52.63% <52.63%> (ø)
petab/problem.py 63.55% <63.55%> (ø)
... and 14 more

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@dweindl dweindl merged commit ea121dc into master Dec 17, 2019
@dweindl dweindl deleted the release_0.0.1 branch December 17, 2019 11:39
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@dweindl @codecov-io @yannikschaelte @MerktSimon