Add petab.v2.C (#299)

For now, mostly a copy of v1. The be updated as petab v2 development progresses.

Also adds some missing documentation.

Use of PEtab v2-related constants from `petab.v1.C` is deprecated.

Author: dweindl

doc/modules.rst

@@ -28,5 +28,6 @@ API Reference
    petab.v1.visualize
    petab.v1.yaml
    petab.v2
+   petab.v2.C
    petab.v2.lint
    petab.v2.problem

petab/v1/C.py

@@ -7,34 +7,34 @@
 
 # MEASUREMENTS
 
-#:
+#: Observable ID column in the observable and measurement tables
 OBSERVABLE_ID = "observableId"
 
-#:
+#: Preequilibration condition ID column in the measurement table
 PREEQUILIBRATION_CONDITION_ID = "preequilibrationConditionId"
 
-#:
+#: Simulation condition ID column in the measurement table
 SIMULATION_CONDITION_ID = "simulationConditionId"
 
-#:
+#: Measurement value column in the measurement table
 MEASUREMENT = "measurement"
 
-#:
+#: Time column in the measurement table
 TIME = "time"
 
 #: Time value that indicates steady-state measurements
 TIME_STEADY_STATE = _math.inf
 
-#:
+#: Observable parameters column in the measurement table
 OBSERVABLE_PARAMETERS = "observableParameters"
 
-#:
+#: Noise parameters column in the measurement table
 NOISE_PARAMETERS = "noiseParameters"
 
-#:
+#: Dataset ID column in the measurement table
 DATASET_ID = "datasetId"
 
-#:
+#: Replicate ID column in the measurement table
 REPLICATE_ID = "replicateId"
 
 #: Mandatory columns of measurement table
@@ -65,27 +65,27 @@
 
 # PARAMETERS
 
-#:
+#: Parameter ID column in the parameter table
 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
 UPPER_BOUND = "upperBound"
-#:
+#: Nominal value column in the parameter table
 NOMINAL_VALUE = "nominalValue"
-#:
+#: Estimate column in the parameter table
 ESTIMATE = "estimate"
-#:
+#: Initialization prior type column in the parameter table
 INITIALIZATION_PRIOR_TYPE = "initializationPriorType"
-#:
+#: Initialization prior parameters column in the parameter table
 INITIALIZATION_PRIOR_PARAMETERS = "initializationPriorParameters"
-#:
+#: Objective prior type column in the parameter table
 OBJECTIVE_PRIOR_TYPE = "objectivePriorType"
-#:
+#: Objective prior parameters column in the parameter table
 OBJECTIVE_PRIOR_PARAMETERS = "objectivePriorParameters"
 
 #: Mandatory columns of parameter table
@@ -115,31 +115,31 @@
     *PARAMETER_DF_OPTIONAL_COLS[1:],
 ]
 
-#:
+#: Initialization-type prior
 INITIALIZATION = "initialization"
-#:
+#: Objective-type prior
 OBJECTIVE = "objective"
 
 
 # CONDITIONS
 
-#:
+#: Condition ID column in the condition table
 CONDITION_ID = "conditionId"
-#:
+#: Condition name column in the condition table
 CONDITION_NAME = "conditionName"
 
 
 # OBSERVABLES
 
-#:
+#: Observable name column in the observables table
 OBSERVABLE_NAME = "observableName"
-#:
+#: Observable formula column in the observables table
 OBSERVABLE_FORMULA = "observableFormula"
-#:
+#: Noise formula column in the observables table
 NOISE_FORMULA = "noiseFormula"
-#:
+#: Observable transformation column in the observables table
 OBSERVABLE_TRANSFORMATION = "observableTransformation"
-#:
+#: Noise distribution column in the observables table
 NOISE_DISTRIBUTION = "noiseDistribution"
 
 #: Mandatory columns of observables table
@@ -165,33 +165,33 @@
 
 # TRANSFORMATIONS
 
-#:
+#: Linear transformation
 LIN = "lin"
-#:
+#: Logarithmic transformation
 LOG = "log"
-#:
+#: Logarithmic base 10 transformation
 LOG10 = "log10"
 #: Supported observable transformations
 OBSERVABLE_TRANSFORMATIONS = [LIN, LOG, LOG10]
 
 
 # NOISE MODELS
 
-#:
+#: Uniform distribution
 UNIFORM = "uniform"
-#:
+#: Uniform distribution on the parameter scale
 PARAMETER_SCALE_UNIFORM = "parameterScaleUniform"
-#:
+#: Normal distribution
 NORMAL = "normal"
-#:
+#: Normal distribution on the parameter scale
 PARAMETER_SCALE_NORMAL = "parameterScaleNormal"
-#:
+#: Laplace distribution
 LAPLACE = "laplace"
-#:
+#: Laplace distribution on the parameter scale
 PARAMETER_SCALE_LAPLACE = "parameterScaleLaplace"
-#:
+#: Log-normal distribution
 LOG_NORMAL = "logNormal"
-#:
+#: Log-Laplace distribution
 LOG_LAPLACE = "logLaplace"
 
 #: Supported prior types
@@ -212,31 +212,31 @@
 
 # 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
@@ -287,11 +287,11 @@
     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]
@@ -303,65 +303,76 @@
 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"
-#:
+#: Problems key in the YAML file
 PROBLEMS = "problems"
-#:
+#: SBML files key in the YAML file
 SBML_FILES = "sbml_files"
-#:
+#: Model files key in the YAML file
+#  (PEtab v2.0 -- DEPRECATED: use value from petab.v2.C)
 MODEL_FILES = "model_files"
-#:
+#: Model location key in the YAML file
+#  (PEtab v2.0 -- DEPRECATED: use value from petab.v2.C)
 MODEL_LOCATION = "location"
-#:
+#: Model language key in the YAML file
+#  (PEtab v2.0 -- DEPRECATED: use value from petab.v2.C)
 MODEL_LANGUAGE = "language"
-#:
+#: Condition files key in the YAML file
 CONDITION_FILES = "condition_files"
-#:
+#: Measurement files key in the YAML file
 MEASUREMENT_FILES = "measurement_files"
-#:
+#: Observable files key in the YAML file
 OBSERVABLE_FILES = "observable_files"
-#:
+#: Visualization files key in the YAML file
 VISUALIZATION_FILES = "visualization_files"
-#:
+#: Mapping files key in the YAML file
+#  (PEtab v2.0 -- DEPRECATED: use value from petab.v2.C)
 MAPPING_FILES = "mapping_files"
-#:
+#: Extensions key in the YAML file
+#  (PEtab v2.0 -- DEPRECATED: use value from petab.v2.C)
 EXTENSIONS = "extensions"
 
 
 # MAPPING
-#:
+
+#: PEtab entity ID column in the mapping table
+#  (PEtab v2.0 -- DEPRECATED: use value from petab.v2.C)
 PETAB_ENTITY_ID = "petabEntityId"
-#:
+#: Model entity ID column in the mapping table
+#  (PEtab v2.0 -- DEPRECATED: use value from petab.v2.C)
 MODEL_ENTITY_ID = "modelEntityId"
-#:
+#: Required columns of the mapping table
+#  (PEtab v2.0 -- DEPRECATED: use value from petab.v2.C)
 MAPPING_DF_REQUIRED_COLS = [PETAB_ENTITY_ID, MODEL_ENTITY_ID]
 
 # MORE
 
-#:
+#: Simulated value column in the simulation table
 SIMULATION = "simulation"
-#:
+#: Residual value column in the residuals table
 RESIDUAL = "residual"
-#:
+#: ???
 NOISE_VALUE = "noiseValue"
 
-# separator for multiple parameter values (bounds, observableParameters, ...)
+#: separator for multiple parameter values (bounds, observableParameters, ...)
 PARAMETER_SEPARATOR = ";"