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dweindl merged 2 commits into from
Oct 15, 2026
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Add options to omit empty or default columns from v2 tables #543

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Add options to omit empty or default columns from v2 tables
dweindl Oct 14, 2026
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Apply suggestion from @dilpath
dweindl Oct 15, 2026
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12 changes: 12 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -12,6 +12,10 @@
Use `petab.v1.<name>` instead, e.g., `import petab.v1 as petab`.
`import petab` no longer imports `petab.v1`.
(by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/538)
* `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 https://github.com/PEtab-dev/libpetab-python/pull/543)

**Fixes**
* `get_model_for_condition` no longer turns rate-rule targets that are
Expand All @@ -37,13 +41,21 @@
* `petab.v2.ProblemConfig.to_yaml` no longer writes empty optional entries
(`condition_files`, `experiment_files`, `mapping_files`, `extensions`)
(by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/547)
* `to_df` no longer fails for empty v2 parameter, observable and measurement
tables
(by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/543)

**Features**
* `petab1to2` and `petab_files_1to2` can skip validation via `validate=False`
(by @FFroehlich in https://github.com/PEtab-dev/libpetab-python/pull/534)
* Added `petab.v2.C.PROBLEM_CONFIG_REQUIRED_KEYS` and
`petab.v2.C.PROBLEM_CONFIG_OPTIONAL_KEYS`
(by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/547)
* 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 https://github.com/PEtab-dev/libpetab-python/pull/543)

## 0.9 series

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1 change: 1 addition & 0 deletions doc/modules.rst
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Expand Up @@ -38,4 +38,5 @@ API Reference
petab.v2.extensions
petab.v2.lint
petab.v2.models
petab.v2.options
petab.v2.petab1to2
4 changes: 2 additions & 2 deletions petab/v2/C.py
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MEASUREMENT_DF_REQUIRED_COLS = [
OBSERVABLE_ID,
EXPERIMENT_ID,
MEASUREMENT,
TIME,
MEASUREMENT,
]

#: Optional columns of measurement table
Expand Down Expand Up @@ -91,13 +91,13 @@
PARAMETER_ID,
LOWER_BOUND,
UPPER_BOUND,
NOMINAL_VALUE,

@dilpath dilpath Oct 15, 2026

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nominalValue was added to C.PARAMETER_DF_REQUIRED_COLS, as the spec requires the column to be present.

It is optional if estimate is true. Might be problematic to expect it always.

@dweindl dweindl Oct 15, 2026

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It's not marked [nominalValue] in the specs, so my understanding is that the column is mandatory, but the respective field may be empty. Other columns, such as observableParameters, explicitly state the if all-empty, the column can be omitted. For nominalValue this isn't the case. While I'd say your interpretation is desirable, I don't think this what the specs say.

@dilpath dilpath Oct 15, 2026

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Ah yes, I see your point. Also applies to upper and lower bound.

Do you know whether your description is the intended interpretation while writing the spec, or just a grey area we forgot to clarify? If the latter then I think it's fine to update the spec now, just like we updated the v1 spec when we realized some things were unclear.

@dweindl dweindl Oct 15, 2026

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I will add that to PEtab-dev/PEtab#681, so it can be discussed. Generally, I am in favor of dropping it if all-empty. For the bounds it's unlikely that they would ever be all-empty, because that would mean there is no parameter to estimate at all. Allowed, I guess. Useful? Not sure.

@dilpath dilpath Oct 15, 2026

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Since multiple parameter tables are supported, one could keep their fixed parameters in a separate table to their estimated ones. Then it's slightly nicer to not have columns related to estimation, in the fixed parameters table.

@dweindl dweindl Oct 15, 2026

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True, I didn't consider this use case.

ESTIMATE,
]

#: Optional columns of parameter table
PARAMETER_DF_OPTIONAL_COLS = [
PARAMETER_NAME,
NOMINAL_VALUE,
PRIOR_DISTRIBUTION,
PRIOR_PARAMETERS,
]
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1 change: 1 addition & 0 deletions petab/v2/__init__.py
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Expand Up @@ -37,3 +37,4 @@
)
from .lint import lint_problem # noqa: F401
from .models import MODEL_TYPE_PYSB, MODEL_TYPE_SBML, Model # noqa: F401
from .options import *
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