Add options to omit empty or default columns from v2 tables

Converting PEtab v2 tables to DataFrames or TSV files currently always
includes all standard columns, even if they are empty in every row.

Add `TableColumns` modes `all` (default, current behavior), `non_empty`,
and `non_default` to select the columns to include. Required columns
(`C.*_DF_REQUIRED_COLS`) are always included. The mode can be passed to
`to_df`, `to_tsv`, and `Problem.to_files`, or set via
`petab.v2.set_options` or temporarily via `petab.v2.option_context`,
which also applies to `Problem.*_df`.

Also add the `parameterName` column as `Parameter.name`, add
`nominalValue` to the required parameter table columns as in the spec,
and make `to_df` work for empty parameter, observable, and measurement
tables.

Closes #523.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

Author: dweindl

CHANGELOG.md

@@ -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
@@ -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
 

doc/modules.rst

@@ -38,4 +38,5 @@ API Reference
    petab.v2.extensions
    petab.v2.lint
    petab.v2.models
+   petab.v2.options
    petab.v2.petab1to2

petab/v2/C.py

@@ -45,8 +45,8 @@
 MEASUREMENT_DF_REQUIRED_COLS = [
     OBSERVABLE_ID,
     EXPERIMENT_ID,
-    MEASUREMENT,
     TIME,
+    MEASUREMENT,
 ]
 
 #: Optional columns of measurement table
@@ -91,13 +91,13 @@
     PARAMETER_ID,
     LOWER_BOUND,
     UPPER_BOUND,
+    NOMINAL_VALUE,
     ESTIMATE,
 ]
 
 #: Optional columns of parameter table
 PARAMETER_DF_OPTIONAL_COLS = [
     PARAMETER_NAME,
-    NOMINAL_VALUE,
     PRIOR_DISTRIBUTION,
     PRIOR_PARAMETERS,
 ]

petab/v2/__init__.py

@@ -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 *