Merge branch 'main' into goodness_of_fit

Author: plakrisenko

doc/modules.rst

@@ -32,9 +32,9 @@ API Reference
    petab.v1.yaml
    petab.v2
    petab.v2.C
+   petab.v2.converters
    petab.v2.core
    petab.v2.experiments
    petab.v2.lint
    petab.v2.models
-   petab.v2.problem
    petab.v2.petab1to2

petab/__init__.py

@@ -26,7 +26,7 @@ def __getattr__(name):
         return importlib.import_module("petab.v1")
     if name == "v2":
         return importlib.import_module("petab.v2")
-    if name != "__path__":
+    if name not in ("__path__", "__all__"):
         warn(
             f"Accessing `petab.{name}` is deprecated and will be removed in "
             f"the next major release. Please use `petab.v1.{name}` instead.",
@@ -37,7 +37,7 @@ def __getattr__(name):
 
 
 def v1getattr(name, module):
-    if name != "__path__":
+    if name not in ("__path__", "__all__"):
         warn(
             f"Accessing `petab.{name}` is deprecated and will be removed in "
             f"the next major release. Please use `petab.v1.{name}` instead.",

petab/petablint.py

@@ -179,14 +179,14 @@ def main():
             logger.error(e)
             sys.exit(1)
 
-        if petab.is_composite_problem(args.yaml_file_name):
-            # TODO: further checking:
-            #  https://github.com/ICB-DCM/PEtab/issues/191
-            #  problem = petab.CompositeProblem.from_yaml(args.yaml_file_name)
-            return
-
         match get_major_version(args.yaml_file_name):
             case 1:
+                if petab.is_composite_problem(args.yaml_file_name):
+                    # TODO: further checking:
+                    #  https://github.com/ICB-DCM/PEtab/issues/191
+                    #  petab.CompositeProblem.from_yaml(args.yaml_file_name)
+                    return
+
                 problem = petab.Problem.from_yaml(args.yaml_file_name)
                 ret = petab.lint.lint_problem(problem)
                 sys.exit(ret)

petab/schemas/petab_schema.v2.0.0.yaml

@@ -23,79 +23,55 @@ properties:
       - type: integer
     description: Version of the PEtab format
 
-  parameter_file:
-    oneOf:
-    - type: string
-    - type: array
-    description: |
-      File name (absolute or relative) or URL to PEtab parameter table
-      containing parameters of all models listed in `problems`. A single
-      table may be split into multiple files and described as an array here.
-  problems:
+  parameter_files:
     type: array
     description: |
-      One or multiple PEtab problems (sets of model, condition, observable
-      and measurement files). If different model and data files are
-      independent, they can be specified as separate PEtab problems, which
-      may allow more efficient handling. Files in one problem cannot refer
-      to models entities or data specified inside another problem.
+      List of PEtab parameter files.
     items:
-
-      type: object
+      type: string
       description: |
-        A set of PEtab model, condition, observable and measurement
-        files and optional visualization files.
-      properties:
-
-        model_files:
-          type: object
-          description: One or multiple models
-
-          # the model ID
-          patternProperties:
-            "^[a-zA-Z_]\\w*$":
-              type: object
-              properties:
-                location:
-                  type: string
-                  description: Model file name or URL
-                language:
-                  type: string
-                  description: |
-                    Model language, e.g., 'sbml', 'cellml', 'bngl', 'pysb'
-              required:
-                - location
-                - language
-          additionalProperties: false
-
-        measurement_files:
-          description: List of PEtab measurement files.
-          $ref: "#/definitions/list_of_files"
-
-        condition_files:
-          description: List of PEtab condition files.
-          $ref: "#/definitions/list_of_files"
-
-        experiment_files:
-          description: List of PEtab experiment files.
-          $ref: "#/definitions/list_of_files"
-
-        observable_files:
-          description: List of PEtab observable files.
-          $ref: "#/definitions/list_of_files"
-
-        visualization_files:
-          description: List of PEtab visualization files.
-          $ref: "#/definitions/list_of_files"
-
-        mapping_file:
+        File name (absolute or relative) or URL to a PEtab parameter table.
+
+  model_files:
+    type: object
+    description: One or multiple models
+
+    # the model ID
+    patternProperties:
+      "^[a-zA-Z_]\\w*$":
+        type: object
+        properties:
+          location:
+            type: string
+            description: Model file name or URL
+          language:
             type: string
-            description: Optional PEtab mapping file name or URL.
+            description: |
+              Model language, e.g., 'sbml', 'cellml', 'bngl', 'pysb'
+        required:
+          - location
+          - language
+    additionalProperties: false
+
+  measurement_files:
+    description: List of PEtab measurement files.
+    $ref: "#/definitions/list_of_files"
+
+  condition_files:
+    description: List of PEtab condition files.
+    $ref: "#/definitions/list_of_files"
+
+  experiment_files:
+    description: List of PEtab experiment files.
+    $ref: "#/definitions/list_of_files"
+
+  observable_files:
+    description: List of PEtab observable files.
+    $ref: "#/definitions/list_of_files"
 
-      required:
-        - model_files
-        - observable_files
-        - measurement_files
+  mapping_files:
+    description: List of PEtab mapping files.
+    $ref: "#/definitions/list_of_files"
 
   extensions:
     type: object
@@ -119,5 +95,7 @@ properties:
 
 required:
   - format_version
-  - parameter_file
-  - problems
+  - parameter_files
+  - model_files
+  - observable_files
+  - measurement_files

petab/v1/math/printer.py

@@ -37,7 +37,13 @@ def _print_BooleanFalse(self, expr):
     def _print_Pow(self, expr: sp.Pow):
         """Custom printing for the power operator"""
         base, exp = expr.as_base_exp()
-        return f"{self._print(base)} ^ {self._print(exp)}"
+        str_base = self._print(base)
+        str_exp = self._print(exp)
+        if not base.is_Atom:
+            str_base = f"({str_base})"
+        if not exp.is_Atom:
+            str_exp = f"({str_exp})"
+        return f"{str_base} ^ {str_exp}"
 
     def _print_Infinity(self, expr):
         """Custom printing for infinity"""

petab/v1/priors.py

@@ -277,9 +277,11 @@ def from_par_dict(
             at the bounds. **deprecated**.
         :return: A distribution object.
         """
-        dist_type = d.get(f"{type_}PriorType", C.PARAMETER_SCALE_UNIFORM)
-        if not isinstance(dist_type, str) and np.isnan(dist_type):
-            dist_type = C.PARAMETER_SCALE_UNIFORM
+        dist_type = C.PARAMETER_SCALE_UNIFORM
+        if (_table_dist_type := d.get(f"{type_}PriorType")) and (
+            isinstance(_table_dist_type, str) or not np.isnan(_table_dist_type)
+        ):
+            dist_type = _table_dist_type
 
         pscale = d.get(C.PARAMETER_SCALE, C.LIN)
         params = d.get(f"{type_}PriorParameters", None)

petab/v1/yaml.py

@@ -242,7 +242,7 @@ def write_yaml(yaml_config: dict[str, Any], filename: str | Path) -> None:
     """
     Path(filename).parent.mkdir(parents=True, exist_ok=True)
     with open(filename, "w") as outfile:
-        yaml.dump(
+        yaml.safe_dump(
             yaml_config, outfile, default_flow_style=False, sort_keys=False
         )
 

petab/v2/C.py

@@ -38,6 +38,9 @@
 #: Replicate ID column in the measurement table
 REPLICATE_ID = "replicateId"
 
+#: The model ID column in the measurement table
+MODEL_ID = "modelId"
+
 #: Mandatory columns of measurement table
 MEASUREMENT_DF_REQUIRED_COLS = [
     OBSERVABLE_ID,
@@ -52,6 +55,7 @@
     NOISE_PARAMETERS,
     DATASET_ID,
     REPLICATE_ID,
+    MODEL_ID,
 ]
 
 #: Measurement table columns
@@ -69,8 +73,6 @@
 PARAMETER_ID = "parameterId"
 #: Parameter name column in the parameter table
 PARAMETER_NAME = "parameterName"
-#: Parameter scale column in the parameter table
-PARAMETER_SCALE = "parameterScale"
 #: Lower bound column in the parameter table
 LOWER_BOUND = "lowerBound"
 #: Upper bound column in the parameter table
@@ -87,7 +89,6 @@
 #: Mandatory columns of parameter table
 PARAMETER_DF_REQUIRED_COLS = [
     PARAMETER_ID,
-    PARAMETER_SCALE,
     LOWER_BOUND,
     UPPER_BOUND,
     ESTIMATE,
@@ -233,119 +234,11 @@
 #: 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"
-#: Parameter file key in the YAML file
-PARAMETER_FILE = "parameter_file"
+#: Parameter files key in the YAML file
+PARAMETER_FILES = "parameter_files"
 #: Problems key in the YAML file
 PROBLEMS = "problems"
 #: Model files key in the YAML file
@@ -388,8 +281,6 @@
 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/__init__.py

@@ -37,10 +37,10 @@
     models,  # noqa: F401, E402
 )
 from .conditions import *  # noqa: F403, F401, E402
+from .core import *  # noqa: F401, E402
 from .experiments import (  # noqa: F401, E402
     get_experiment_df,
     write_experiment_df,
 )
 from .lint import lint_problem  # noqa: F401, E402
 from .models import MODEL_TYPE_PYSB, MODEL_TYPE_SBML, Model  # noqa: F401, E402
-from .problem import Problem, ProblemConfig  # noqa: F401, E402