Merge branch 'develop' into 330_truncated

doc/example/example_petablint.ipynb

@@ -16,75 +16,26 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "usage: petablint [-h] [-v] [-s SBML_FILE_NAME] [-m MEASUREMENT_FILE_NAME]\r\n",
-      "                 [-c CONDITION_FILE_NAME] [-p PARAMETER_FILE_NAME]\r\n",
-      "                 [-y YAML_FILE_NAME | -n MODEL_NAME] [-d DIRECTORY]\r\n",
-      "\r\n",
-      "Check if a set of files adheres to the PEtab format.\r\n",
-      "\r\n",
-      "optional arguments:\r\n",
-      "  -h, --help            show this help message and exit\r\n",
-      "  -v, --verbose         More verbose output\r\n",
-      "  -s SBML_FILE_NAME, --sbml SBML_FILE_NAME\r\n",
-      "                        SBML model filename\r\n",
-      "  -m MEASUREMENT_FILE_NAME, --measurements MEASUREMENT_FILE_NAME\r\n",
-      "                        Measurement table\r\n",
-      "  -c CONDITION_FILE_NAME, --conditions CONDITION_FILE_NAME\r\n",
-      "                        Conditions table\r\n",
-      "  -p PARAMETER_FILE_NAME, --parameters PARAMETER_FILE_NAME\r\n",
-      "                        Parameter table\r\n",
-      "  -y YAML_FILE_NAME, --yaml YAML_FILE_NAME\r\n",
-      "                        PEtab YAML problem filename\r\n",
-      "  -n MODEL_NAME, --model-name MODEL_NAME\r\n",
-      "                        Model name where all files are in the working\r\n",
-      "                        directory and follow PEtab naming convention.\r\n",
-      "                        Specifying -[smcp] will override defaults\r\n",
-      "  -d DIRECTORY, --directory DIRECTORY\r\n"
-     ]
-    }
-   ],
    "source": [
     "!petablint -h"
-   ]
+   ],
+   "outputs": [],
+   "execution_count": null
   },
   {
    "cell_type": "markdown",
    "metadata": {},
-   "source": [
-    "Let's look at an example: In the example_Fujita folder, we have a PEtab configuration file `Fujita.yaml` telling which files belong to the Fujita model:"
-   ]
+   "source": "Let's look at an example: In the `example_Fujita/` directory, we have a PEtab problem configuration file `Fujita.yaml` telling which files belong to the \"Fujita\" problem:"
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "parameter_file: Fujita_parameters.tsv\r\n",
-      "petab_version: 0.0.0a17\r\n",
-      "problems:\r\n",
-      "- condition_files:\r\n",
-      "  - Fujita_experimentalCondition.tsv\r\n",
-      "  measurement_files:\r\n",
-      "  - Fujita_measurementData.tsv\r\n",
-      "  sbml_files:\r\n",
-      "  - Fujita_model.xml\r\n"
-     ]
-    }
-   ],
    "source": [
     "!cat example_Fujita/Fujita.yaml"
-   ]
+   ],
+   "outputs": [],
+   "execution_count": null
   },
   {
    "cell_type": "markdown",
@@ -95,20 +46,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "\u001b[0m"
-     ]
-    }
-   ],
-   "source": [
-    "!petablint -y example_Fujita/Fujita.yaml"
-   ]
+   "source": "!petablint example_Fujita/Fujita.yaml",
+   "outputs": [],
+   "execution_count": null
   },
   {
    "cell_type": "markdown",

petab/petablint.py

@@ -12,9 +12,8 @@
 
 import petab.v1 as petab
 from petab.v1.C import FORMAT_VERSION
-from petab.v2.lint import lint_problem
+from petab.v1.yaml import validate
 from petab.versions import get_major_version
-from petab.yaml import validate
 
 logger = logging.getLogger(__name__)
 
@@ -178,6 +177,8 @@ def main():
                 ret = petab.lint.lint_problem(problem)
                 sys.exit(ret)
             case 2:
+                from petab.v2.lint import lint_problem
+
                 validation_issues = lint_problem(args.yaml_file_name)
                 if validation_issues:
                     validation_issues.log(logger=logger)

petab/v1/calculate.py

@@ -97,6 +97,9 @@ def calculate_residuals_for_table(
     Calculate residuals for a single measurement table.
     For the arguments, see `calculate_residuals`.
     """
+    # below, we rely on a unique index
+    measurement_df = measurement_df.reset_index(drop=True)
+
     # create residual df as copy of measurement df, change column
     residual_df = measurement_df.copy(deep=True).rename(
         columns={MEASUREMENT: RESIDUAL}
@@ -120,6 +123,10 @@ def calculate_residuals_for_table(
             for col in compared_cols
         ]
         mask = reduce(lambda x, y: x & y, masks)
+        if mask.sum() == 0:
+            raise ValueError(
+                f"Could not find simulation for measurement {row}."
+            )
         simulation = simulation_df.loc[mask][SIMULATION].iloc[0]
         if scale:
             # apply scaling

petab/v1/problem.py

@@ -1149,8 +1149,8 @@ def add_measurement(
         sim_cond_id: str,
         time: float,
         measurement: float,
-        observable_parameters: Sequence[str] = None,
-        noise_parameters: Sequence[str] = None,
+        observable_parameters: Sequence[str | float] = None,
+        noise_parameters: Sequence[str | float] = None,
         preeq_cond_id: str = None,
     ):
         """Add a measurement to the problem.
@@ -1172,11 +1172,11 @@ def add_measurement(
         }
         if observable_parameters is not None:
             record[OBSERVABLE_PARAMETERS] = [
-                PARAMETER_SEPARATOR.join(observable_parameters)
+                PARAMETER_SEPARATOR.join(map(str, observable_parameters))
             ]
         if noise_parameters is not None:
             record[NOISE_PARAMETERS] = [
-                PARAMETER_SEPARATOR.join(noise_parameters)
+                PARAMETER_SEPARATOR.join(map(str, noise_parameters))
             ]
         if preeq_cond_id is not None:
             record[PREEQUILIBRATION_CONDITION_ID] = [preeq_cond_id]

petab/v2/C.py

@@ -13,14 +13,6 @@
 #: Experiment ID column in the measurement table
 EXPERIMENT_ID = "experimentId"
 
-# TODO: remove
-#: Preequilibration condition ID column in the measurement table
-PREEQUILIBRATION_CONDITION_ID = "preequilibrationConditionId"
-
-# TODO: remove
-#: Simulation condition ID column in the measurement table
-SIMULATION_CONDITION_ID = "simulationConditionId"
-
 #: Measurement value column in the measurement table
 MEASUREMENT = "measurement"
 
@@ -30,6 +22,9 @@
 #: Time value that indicates steady-state measurements
 TIME_STEADY_STATE = _math.inf
 
+#: Time value that indicates pre-equilibration in the experiments table
+TIME_PREEQUILIBRATION = -_math.inf
+
 #: Observable parameters column in the measurement table
 OBSERVABLE_PARAMETERS = "observableParameters"
 
@@ -45,17 +40,13 @@
 #: Mandatory columns of measurement table
 MEASUREMENT_DF_REQUIRED_COLS = [
     OBSERVABLE_ID,
-    # TODO: add
-    # EXPERIMENT_ID,
-    SIMULATION_CONDITION_ID,
+    EXPERIMENT_ID,
     MEASUREMENT,
     TIME,
 ]
 
 #: Optional columns of measurement table
 MEASUREMENT_DF_OPTIONAL_COLS = [
-    # TODO: remove
-    PREEQUILIBRATION_CONDITION_ID,
     OBSERVABLE_PARAMETERS,
     NOISE_PARAMETERS,
     DATASET_ID,

petab/v2/__init__.py

@@ -27,7 +27,10 @@
 
 # import after v1
 from ..version import __version__  # noqa: F401, E402
-from . import models  # noqa: F401, E402
+from . import (  # noqa: F401, E402
+    C,  # noqa: F401, E402
+    models,  # noqa: F401, E402
+)
 from .conditions import *  # noqa: F403, F401, E402
 from .experiments import (  # noqa: F401, E402
     get_experiment_df,