libpetab-python v0.10.0

This release focuses on PEtab v2: a more faithful v1-to-v2 conversion, support for multi-model problems, conversion of time-dependent model assignments to experiments, log-scale reparametrization, and cleaner table output.

Note: the deprecated top-level petab.* aliases for petab.v1 are gone (use import petab.v1 as petab), and pandas>=2.3 is now required.

Breaking changes

• Removed the deprecated top-level aliases for petab.v1 (deprecated since 0.4.0). Accessing petab.<name> or importing petab.<module> for anything other than petab.v1, petab.v2, petab.ENV_NUM_THREADS and petab.__version__ now raises AttributeError / ModuleNotFoundError. Use petab.v1.<name> instead, e.g., import petab.v1 as petab. import petab no longer imports petab.v1. (by @dweindl in #538)
• Require pandas>=2.3. get_{condition,observable,parameter,mapping}_df no longer modify DataFrames passed by the caller (by @dweindl in #571)
• Removed the tests, doc and quality extras. Development dependencies are now dependency groups. New all extra for all optional features (by @dweindl in #564)
• petab.v2.Parameter has a new name field for the parameterName column, which was previously stored as an extra attribute parameterName. BaseTable subclasses now implement _to_df instead of to_df. (by @dweindl in #543)

Fixes

petablint:

• petablint no longer fails for PEtab v2 problems with only warnings, consistent with PEtab v1. Warnings are still reported. The previous behavior can be restored via --fail-on-warnings (currently only effective for PEtab v2) (by @dweindl in #569)

v1:

• Raise a clear error for a PEtab YAML file with an empty problems section (by @dweindl in #521)
• petab.v1.sbml.get_model_for_condition no longer turns rate-rule targets that are overridden in the condition table into constants (by @dweindl in #520)

v2 tables and files:

• Loading and saving v2 tables no longer adds a spurious index column (by @dweindl in #542)
• to_df no longer fails for empty v2 parameter, observable and measurement tables (by @dweindl in #543)
• petab.v2.ConditionTable.from_df no longer stores the condition ID on each Change, which caused renamed conditions to be written with their old ID (by @dweindl in #551)
• petab.v2.ProblemConfig.to_yaml no longer writes empty optional entries (condition_files, experiment_files, mapping_files, extensions) (by @dweindl in #547)

v1-to-v2 conversion (petab1to2):

• Keep pre-equilibration for conditions that set nothing, order placeholders by index instead of lexicographically, rescale noise and priors when converting log10 to log, and fix the conversion of logNormal, logLaplace and parameterScaleUniform priors (by @FFroehlich in #532, #533, #535, and #536)
• No longer add default uniform priors to non-estimated parameters, or if no estimated parameter has an objective prior (by @dweindl in #539)
• No longer write condition tables without any condition-specific changes (by @dweindl in #554)
• Rename a pre-existing experimentId column in the measurement table to experimentId_v1* instead of a random name, and warn about it (by @dweindl in #572)

v2 converters:

• petab.v2.converters.ExperimentsToSbmlConverter now creates flat initial assignments, which previously were nested once per experiment and failed for problems with many experiments (by @FFroehlich in #546)
• petab.v2.converters.ExperimentsToSbmlConverter now assigns a priority to a pre-existing event without priority if it is the only such event, so that PEtab condition changes are applied before its assignments. Previously, their order was undefined (by @dweindl in #562)

Math:

• petab_math_str now produces valid PEtab math expressions for boolean operators, (in)equality, min/max, powers with negative bases, and pi/e, and prints floats without loss of precision. PEtab v2 condition and measurement tables now write expressions in PEtab syntax (by @dweindl in #545)

Features

v2 problems and tables:

• petab.v2.Problem.split_by_model splits a multi-model problem into single-model problems. petab.v2.Problem.validate now supports multi-model problems (by @FFroehlich in #537)
• petab.v2.Problem.get_unused_id returns an identifier that is not yet used in the problem or its model (by @dweindl in #561)
• PEtab v2 tables can omit empty columns or columns at their default values via to_df(columns=...), to_tsv(columns=...) and Problem.to_files(columns=...), or globally via petab.v2.set_options and petab.v2.option_context (by @dweindl in #543)
• Added petab.v2.C.PROBLEM_CONFIG_REQUIRED_KEYS and petab.v2.C.PROBLEM_CONFIG_OPTIONAL_KEYS (by @dweindl in #547)

v1-to-v2 conversion (petab1to2):

• petab1to2 and petab_files_1to2 can skip validation via validate=False (by @FFroehlich in #534)
• petab1to2 and petab_files_1to2 can preserve the objective function of log-scaled parameters with parameterScale* priors via reparametrize="priors" or reparametrize="all" (by @dweindl in #539)

v2 converters:

• petab.v2.reparametrize_log estimates parameters on log scale by replacing them with new log-transformed parameters (by @dweindl in #560)
• petab.v2.converters.assignments_to_experiments converts time-dependent piecewise assignment rules in the model to experiment periods. Supported are step changes at fixed switching times, including sums and nested piecewise functions, and values that change linearly with time, which are implemented via a rate rule (by @BSnelling and @FFroehlich in #527, #556, #557, #559, #573, and #574)

Math:

• petab.v1.math.petab_symbol (also in petab.v2.math) creates sympy symbols with the same assumptions as sympify_petab (by @dweindl in #563)

Full Changelog: v0.9.0...v0.10.0

🤖 Drafted with AI assistance (Claude Code)