PEtab-dev/libpetab-python

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Python package for working with PEtab files

Stars: 18
Forks: 9
Open beginner issues: 0
Indexed issues: 43

Dominant language: Python
License: MIT
Last GitHub push: Sep 7, 2026
Latest indexed: Sep 20, 2026
Contributing guide: Contributing guide
Code of conduct: No code of conduct
Beginner labels: No beginner labels indexed
PR merge metrics: No merged PRs in 30d

Beginner friendly Everything

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43 open issues indexed

Improve model abstractions Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

PEtab-dev/libpetab-python#518 · Opened Sep 7, 2026
Mapping table contributions to parameter table validation (SciML use case) Open

validation

Difficulty 5/5 Over a week Newbie friendliness 35/100

PEtab-dev/libpetab-python#494 · 1 comment · Opened Jun 26, 2026
Support for discrete noise distributions Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

PEtab-dev/libpetab-python#466 · Opened Dec 3, 2025
Add CLI for petab v1->v2 conversion Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 45/100

PEtab-dev/libpetab-python#453 · Opened Oct 29, 2025
Add goodness-of-fit and residual plots to visualization examples Open

documentation

Difficulty 3/5 1-2 days Newbie friendliness 45/100

PEtab-dev/libpetab-python#439 · Opened Sep 19, 2025
API for renaming PEtab entities Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

PEtab-dev/libpetab-python#438 · Opened Sep 19, 2025
Remove `v2.Problem.*_df` Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

PEtab-dev/libpetab-python#409 · Opened Jul 21, 2025
v2: Visualization functions Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

PEtab-dev/libpetab-python#398 · Opened Jul 2, 2025
Document release process Open

documentation

Difficulty 3/5 1-2 days Newbie friendliness 35/100

PEtab-dev/libpetab-python#396 · Opened Jul 2, 2025
v2: Handle multi-model problems Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

PEtab-dev/libpetab-python#392 · 2 comments · Opened Jun 5, 2025
v2: Update validator Open

validation

Difficulty 5/5 Over a week Newbie friendliness 30/100

PEtab-dev/libpetab-python#369 · Opened Mar 28, 2025
antlr runtime version Open

Difficulty 3/5 1-2 days Newbie friendliness 42/100

PEtab-dev/libpetab-python#344 · 4 comments · Opened Dec 18, 2024
`flatten_timepoint_specific_output_overrides` should not do anything if there are no timepoint-specific output parameters Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

PEtab-dev/libpetab-python#314 · Opened Oct 17, 2024
Add functionality for computing posteriors Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

PEtab-dev/libpetab-python#312 · 2 reactions · Opened Oct 15, 2024
Refactor priors Open

enhancement

PEtab-dev/libpetab-python#311 · 2 reactions · 1 assignee · Opened Oct 15, 2024
Feature to automate handling of replicate data Open

PEtab-dev/libpetab-python#310 · 1 comment · 1 assignee · Opened Oct 8, 2024
PEtab Simulator update_parameters Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

PEtab-dev/libpetab-python#305 · 2 reactions · Opened Aug 15, 2024
Replace individual dataframe arguments by Problem objects Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

PEtab-dev/libpetab-python#301 · 1 reaction · Opened Jul 2, 2024
v2 validation: atomize checks Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

PEtab-dev/libpetab-python#289 · 1 reaction · Opened Jun 29, 2024
Integration of extensions Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

PEtab-dev/libpetab-python#273 · 2 comments · Opened Jun 25, 2024
composite problem Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

PEtab-dev/libpetab-python#265 · 4 comments · Opened Jun 2, 2024
Wrong plot_goodness_of_fit if different order of rows in measurement_df and simulation_df Open

bug visualization

Difficulty 3/5 1-2 days Newbie friendliness 45/100

PEtab-dev/libpetab-python#247 · 1 comment · 2 reactions · Opened Feb 27, 2024
Validator does not check for required column `noiseFormula` in observables table Open

validation

PEtab-dev/libpetab-python#219 · 1 assignee · Opened Jul 25, 2023
Improve error handling in Problem.from_yaml - parameter_file Open

Difficulty 2/5 1-3 hours Newbie friendliness 48/100

PEtab-dev/libpetab-python#218 · Opened Jul 25, 2023
Improve error handling in Problem.from_yaml - format_version Open

validation

Difficulty 2/5 1-3 hours Newbie friendliness 45/100

PEtab-dev/libpetab-python#217 · Opened Jul 25, 2023
petab.get_model_for_condition may remove rateRules where it shouldn't Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 35/100

PEtab-dev/libpetab-python#197 · Opened Apr 17, 2023
Validator: Add option to warn about unused / non-standard columns Open

enhancement validation

Difficulty 5/5 Over a week Newbie friendliness 35/100

PEtab-dev/libpetab-python#128 · Opened Apr 22, 2022
Python API for linter Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 35/100

PEtab-dev/libpetab-python#35 · 2 comments · Opened Feb 16, 2021
False positive invalid condition ID. Open

PEtab-dev/libpetab-python#366 · 6 comments · 1 assignee · Opened Oct 20, 2020
single objectivePriorParameters are cast to numpy.float64 Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

PEtab-dev/libpetab-python#27 · 7 comments · Opened Aug 27, 2020
writer functions do not perform sanity checks + use misleading options for writing tsv Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

PEtab-dev/libpetab-python#26 · 11 comments · Opened Aug 24, 2020
Should unspecified optional strings be the empty string or NaN? Open

question

Difficulty 4/5 3-5 days Newbie friendliness 35/100

PEtab-dev/libpetab-python#25 · 4 comments · Opened Jun 18, 2020
Visualization of measurements without condition table and visualization table Open

visualization

PEtab-dev/libpetab-python#22 · 1 assignee · Opened May 13, 2020
Visualization: if column 'XValues' not provided and multiple conditions should be plotted automatically Open

visualization

Difficulty 4/5 3-5 days Newbie friendliness 45/100

PEtab-dev/libpetab-python#21 · 2 comments · Opened Apr 21, 2020
consistent coloring of legend entries across plots Open

visualization

Difficulty 3/5 1-2 days Newbie friendliness 30/100

PEtab-dev/libpetab-python#18 · 1 comment · Opened Feb 21, 2020
xOffset for logscale xValues Open

question visualization

Difficulty 4/5 3-5 days Newbie friendliness 35/100

PEtab-dev/libpetab-python#17 · 1 comment · Opened Feb 21, 2020
BarPlots ignore xValues Open

visualization

PEtab-dev/libpetab-python#16 · 6 comments · 2 assignees · Opened Feb 21, 2020
Parallelize plotting for large amounts of subplots (saved to files) Open

visualization

PEtab-dev/libpetab-python#11 · 1 reaction · 1 assignee · Opened Jan 24, 2020
Implement validation CompositeProblem Open

validation

Difficulty 4/5 3-5 days Newbie friendliness 35/100

PEtab-dev/libpetab-python#9 · Opened Dec 16, 2019
Add function to create joint parameter table from multiple models and measurement files Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

PEtab-dev/libpetab-python#5 · 1 comment · Opened Dec 16, 2019
Add: Allow plotting by observableID & simCondID at the same time Open

visualization

Difficulty 4/5 3-5 days Newbie friendliness 35/100

PEtab-dev/libpetab-python#4 · Opened Sep 30, 2019
add: plotting STD if the column noiseParameter has values and no replicates available Open

visualization

Difficulty 3/5 1-2 days Newbie friendliness 45/100

PEtab-dev/libpetab-python#3 · 1 comment · Opened Aug 20, 2019
add case in visualization routine: in measurementData file, if same simulationConditionId, but differing preequilibrationId etc. Open

visualization

Difficulty 3/5 1-2 days Newbie friendliness 45/100

PEtab-dev/libpetab-python#2 · Opened Jul 5, 2019

PEtab-dev/libpetab-python

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