Remove vis info from petab.v2 (PEtab-dev#407)

Remove visualization tables until there is progress on PEtab-dev#398.

Author: dweindl

petab/v2/C.py

@@ -233,114 +233,6 @@
 #: Supported noise distributions
 NOISE_DISTRIBUTIONS = [NORMAL, LAPLACE, LOG_NORMAL, LOG_LAPLACE]
 
-
-# VISUALIZATION
-
-#: Plot ID column in the visualization table
-PLOT_ID = "plotId"
-#: Plot name column in the visualization table
-PLOT_NAME = "plotName"
-#: Value for plot type 'simulation' in the visualization table
-PLOT_TYPE_SIMULATION = "plotTypeSimulation"
-#: Value for plot type 'data' in the visualization table
-PLOT_TYPE_DATA = "plotTypeData"
-#: X values column in the visualization table
-X_VALUES = "xValues"
-#: X offset column in the visualization table
-X_OFFSET = "xOffset"
-#: X label column in the visualization table
-X_LABEL = "xLabel"
-#: X scale column in the visualization table
-X_SCALE = "xScale"
-#: Y values column in the visualization table
-Y_VALUES = "yValues"
-#: Y offset column in the visualization table
-Y_OFFSET = "yOffset"
-#: Y label column in the visualization table
-Y_LABEL = "yLabel"
-#: Y scale column in the visualization table
-Y_SCALE = "yScale"
-#: Legend entry column in the visualization table
-LEGEND_ENTRY = "legendEntry"
-
-#: Mandatory columns of visualization table
-VISUALIZATION_DF_REQUIRED_COLS = [PLOT_ID]
-
-#: Optional columns of visualization table
-VISUALIZATION_DF_OPTIONAL_COLS = [
-    PLOT_NAME,
-    PLOT_TYPE_SIMULATION,
-    PLOT_TYPE_DATA,
-    X_VALUES,
-    X_OFFSET,
-    X_LABEL,
-    X_SCALE,
-    Y_VALUES,
-    Y_OFFSET,
-    Y_LABEL,
-    Y_SCALE,
-    LEGEND_ENTRY,
-    DATASET_ID,
-]
-
-#: Visualization table columns
-VISUALIZATION_DF_COLS = [
-    *VISUALIZATION_DF_REQUIRED_COLS,
-    *VISUALIZATION_DF_OPTIONAL_COLS,
-]
-
-#: Visualization table columns that contain subplot specifications
-VISUALIZATION_DF_SUBPLOT_LEVEL_COLS = [
-    PLOT_ID,
-    PLOT_NAME,
-    PLOT_TYPE_SIMULATION,
-    PLOT_TYPE_DATA,
-    X_LABEL,
-    X_SCALE,
-    Y_LABEL,
-    Y_SCALE,
-]
-
-#: Visualization table columns that contain single plot specifications
-VISUALIZATION_DF_SINGLE_PLOT_LEVEL_COLS = [
-    X_VALUES,
-    X_OFFSET,
-    Y_VALUES,
-    Y_OFFSET,
-    LEGEND_ENTRY,
-    DATASET_ID,
-]
-
-#: Plot type value in the visualization table for line plot
-LINE_PLOT = "LinePlot"
-#: Plot type value in the visualization table for bar plot
-BAR_PLOT = "BarPlot"
-#: Plot type value in the visualization table for scatter plot
-SCATTER_PLOT = "ScatterPlot"
-#: Supported plot types
-PLOT_TYPES_SIMULATION = [LINE_PLOT, BAR_PLOT, SCATTER_PLOT]
-
-#: Supported xScales
-X_SCALES = [LIN, LOG, LOG10]
-
-#: Supported yScales
-Y_SCALES = [LIN, LOG, LOG10]
-
-
-#: Plot type "data" value in the visualization table for mean and standard
-#  deviation
-MEAN_AND_SD = "MeanAndSD"
-#: Plot type "data" value in the visualization table for mean and standard
-#  error
-MEAN_AND_SEM = "MeanAndSEM"
-#: Plot type "data" value in the visualization table for replicates
-REPLICATE = "replicate"
-#: Plot type "data" value in the visualization table for provided noise values
-PROVIDED = "provided"
-#: Supported settings for handling replicates
-PLOT_TYPES_DATA = [MEAN_AND_SD, MEAN_AND_SEM, REPLICATE, PROVIDED]
-
-
 # YAML
 #: PEtab version key in the YAML file
 FORMAT_VERSION = "format_version"
@@ -388,8 +280,6 @@
 SIMULATION = "simulation"
 #: Residual value column in the residual table
 RESIDUAL = "residual"
-#: ???
-NOISE_VALUE = "noiseValue"
 
 #: separator for multiple parameter values (bounds, observableParameters, ...)
 PARAMETER_SEPARATOR = ";"

petab/v2/lint.py

@@ -35,7 +35,6 @@
     "CheckExperimentConditionsExist",
     "CheckAllParametersPresentInParameterTable",
     "CheckValidParameterInConditionOrParameterTable",
-    "CheckVisualizationTable",
     "CheckUnusedExperiments",
     "CheckObservablesDoNotShadowModelEntities",
     "CheckUnusedConditions",
@@ -711,24 +710,6 @@ def run(self, problem: Problem) -> ValidationIssue | None:
         return None
 
 
-class CheckVisualizationTable(ValidationTask):
-    """A task to validate the visualization table of a PEtab problem."""
-
-    def run(self, problem: Problem) -> ValidationIssue | None:
-        if problem.visualization_df is None:
-            return None
-
-        from ..v1.visualize.lint import validate_visualization_df
-
-        if validate_visualization_df(problem):
-            return ValidationIssue(
-                level=ValidationIssueSeverity.ERROR,
-                message="Visualization table is invalid.",
-            )
-
-        return None
-
-
 class CheckPriorDistribution(ValidationTask):
     """A task to validate the prior distribution of a PEtab problem."""
 
@@ -1039,7 +1020,6 @@ def get_placeholders(
     CheckUnusedExperiments(),
     CheckUnusedConditions(),
     # TODO: atomize checks, update to long condition table, re-enable
-    # CheckVisualizationTable(),
     # TODO validate mapping table
     CheckValidParameterInConditionOrParameterTable(),
     CheckAllParametersPresentInParameterTable(),

petab/v2/petab1to2.py

@@ -5,7 +5,6 @@
 import re
 import shutil
 from contextlib import suppress
-from itertools import chain
 from pathlib import Path
 from tempfile import TemporaryDirectory
 from urllib.parse import urlparse
@@ -100,11 +99,9 @@ def petab_files_1to2(yaml_config: Path | str, output_dir: Path | str):
         parameter_df, get_dest_path(new_yaml_config.parameter_files[0])
     )
 
-    # copy files that don't need conversion
-    #  (models, visualizations)
-    for file in chain(
-        (model.location for model in new_yaml_config.model_files.values()),
-        new_yaml_config.visualization_files,
+    # copy files that don't need conversion: models
+    for file in (
+        model.location for model in new_yaml_config.model_files.values()
     ):
         _copy_file(get_src_path(file), Path(get_dest_path(file)))
 
@@ -290,7 +287,6 @@ def _update_yaml(yaml_config: dict) -> dict:
             v1.C.CONDITION_FILES,
             v1.C.MEASUREMENT_FILES,
             v1.C.OBSERVABLE_FILES,
-            v1.C.VISUALIZATION_FILES,
         ):
             if file_type in problem:
                 yaml_config[file_type] = problem[file_type]

petab/v2/problem.py

@@ -24,7 +24,6 @@
     validate_yaml_syntax,
     yaml,
 )
-from ..v1.core import concat_tables, get_visualization_df
 from ..v1.distributions import Distribution
 from ..v1.models.model import Model, model_factory
 from ..v1.yaml import get_path_prefix
@@ -53,8 +52,6 @@ class Problem:
     - observable table
     - mapping table
 
-    Optionally, it may contain visualization tables.
-
     See also :doc:`petab:v2/documentation_data_format`.
     """
 
@@ -67,8 +64,6 @@ def __init__(
         measurement_tables: list[core.MeasurementTable] = None,
         parameter_tables: list[core.ParameterTable] = None,
         mapping_tables: list[core.MappingTable] = None,
-        # TODO: remove
-        visualization_df: pd.DataFrame = None,
         config: ProblemConfig = None,
     ):
         from ..v2.lint import default_validation_tasks
@@ -98,8 +93,6 @@ def __init__(
             core.ParameterTable(parameters=[])
         ]
 
-        self.visualization_df = visualization_df
-
     def __str__(self):
         model = f"with model ({self.model})" if self.model else "without model"
 
@@ -262,15 +255,6 @@ def get_path(filename):
             else None
         )
 
-        # TODO: remove in v2?!
-        visualization_files = [get_path(f) for f in config.visualization_files]
-        # If there are multiple tables, we will merge them
-        visualization_df = (
-            concat_tables(visualization_files, get_visualization_df)
-            if visualization_files
-            else None
-        )
-
         observable_tables = (
             [
                 core.ObservableTable.from_tsv(get_path(f))
@@ -298,7 +282,6 @@ def get_path(filename):
             measurement_tables=measurement_tables,
             parameter_tables=parameter_tables,
             mapping_tables=mapping_tables,
-            visualization_df=visualization_df,
         )
 
     @staticmethod
@@ -308,7 +291,6 @@ def from_dfs(
         experiment_df: pd.DataFrame = None,
         measurement_df: pd.DataFrame = None,
         parameter_df: pd.DataFrame = None,
-        visualization_df: pd.DataFrame = None,
         observable_df: pd.DataFrame = None,
         mapping_df: pd.DataFrame = None,
         config: ProblemConfig = None,
@@ -322,7 +304,6 @@ def from_dfs(
             measurement_df: PEtab measurement table
             parameter_df: PEtab parameter table
             observable_df: PEtab observable table
-            visualization_df: PEtab visualization table
             mapping_df: PEtab mapping table
             model: The underlying model
             config: The PEtab problem configuration
@@ -343,7 +324,6 @@ def from_dfs(
             measurement_tables=[measurement_table],
             parameter_tables=[parameter_table],
             mapping_tables=[mapping_table],
-            visualization_df=visualization_df,
             config=config,
         )
 
@@ -1227,8 +1207,7 @@ def model_dump(self, **kwargs) -> dict[str, Any]:
                     'measurement_files': [],
                     'model_files': {},
                     'observable_files': [],
-                    'parameter_file': [],
-                    'visualization_files': []},
+                    'parameter_file': []},
          'experiments': [],
          'mappings': [],
          'measurements': [],
@@ -1307,7 +1286,6 @@ class ProblemConfig(BaseModel):
     condition_files: list[str | AnyUrl] = []
     experiment_files: list[str | AnyUrl] = []
     observable_files: list[str | AnyUrl] = []
-    visualization_files: list[str | AnyUrl] = []
     mapping_files: list[str | AnyUrl] = []
 
     #: Extensions used by the problem.