feat: add measurement grouping based on initial conditions; fix circular imports

- Introduced `group_id` assignment for measurements in an EnzymeMLDocument based on shared initial conditions (species concentration, pH, temperature).
- Refactored import structure to avoid circular imports caused by top-level references, improving compatibility with third-party usage.

Author: haeussma

README.md

@@ -1,6 +1,6 @@
 <h1 align="center">
   PyEnzyme<br>
-  <img src="https://img.shields.io/badge/PyEnzyme-1.1.5-blue" alt="v2.0.0">
+  <img alt="PyPI - Version" src="https://img.shields.io/pypi/v/pyenzyme">
   <img src="https://github.com/EnzymeML/PyEnzyme/actions/workflows/unit-tests.yaml/badge.svg" alt="Build Badge"> 
 </a>
 <a href="https://www.codacy.com/gh/EnzymeML/PyEnzyme/dashboard?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=EnzymeML/PyEnzyme&amp;utm_campaign=Badge_Grade"><img src="https://app.codacy.com/project/badge/Grade/4ceb8d010e7b456c926c8b18737ff102"/></a>

pyenzyme/__init__.py

@@ -2,13 +2,14 @@
 
 from mdmodels.units.unit_definition import UnitDefinition, UnitType
 
-from .versions.v2 import *  # noqa: F403
-from .versions.io import EnzymeMLHandler
-from .fetcher import *  # noqa: F403
 from .composer import compose
-from .suite import EnzymeMLSuite
+from .fetcher import *  # noqa: F403
 from .plotting import plot, plot_interactive
 from .pretty import summary
+from .suite import EnzymeMLSuite
+from .tools import group_measurements
+from .versions.io import EnzymeMLHandler
+from .versions.v2 import *  # noqa: F403
 
 # Input functions
 from_csv = EnzymeMLHandler.from_csv
@@ -41,6 +42,7 @@
     "plot",
     "plot_interactive",
     "summary",
+    "group_measurements",
 ]
 
-__version__ = "2.0.0"
+__version__ = "2.1.0"

pyenzyme/petab/io.py

@@ -7,11 +7,11 @@
 from pyenzyme.sbml.serializer import to_sbml
 from pyenzyme.versions import v2
 
-from .petab import PEtab, Problem
 from .conditions import ConditionRow
-from .observables import ObservableRow
 from .measurements import MeasurementRow
+from .observables import ObservableRow
 from .parameters import ParameterRow
+from .petab import PEtab, Problem
 
 # Default filenames for PEtab format components
 PARAMETER_FILENAME = "parameters.tsv"

pyenzyme/sbml/serializer.py

@@ -10,15 +10,13 @@
 
 import pyenzyme as pe
 import pyenzyme.tools as tools
-
-from pyenzyme import rdf
+from pyenzyme import UnitDefinition, rdf
 from pyenzyme import xmlutils as _xml
 from pyenzyme.logging import add_logger
 from pyenzyme.sbml import create_sbml_omex
 from pyenzyme.sbml.validation import validate_sbml_export
 from pyenzyme.sbml.versions import v2
 from pyenzyme.tabular import to_pandas
-from pyenzyme import UnitDefinition
 
 NSMAP = {"enzymeml": "https://www.enzymeml.org/v2"}
 CELSIUS_CONVERSION_FACTOR = 273.15

pyenzyme/sbml/validation.py

@@ -1,10 +1,17 @@
 from loguru import logger
+from mdmodels.units.unit_definition import UnitDefinition
 
-import pyenzyme as pe
 import pyenzyme.tools as tools
+from pyenzyme.versions.v2 import (
+    EnzymeMLDocument,
+    EquationType,
+    MeasurementData,
+    Parameter,
+    ReactionElement,
+)
 
 
-def validate_sbml_export(doc: pe.EnzymeMLDocument) -> bool:
+def validate_sbml_export(doc: EnzymeMLDocument) -> bool:
     """This function validates the SBML export of an EnzymeML document.
 
     Args:
@@ -26,7 +33,7 @@ def validate_sbml_export(doc: pe.EnzymeMLDocument) -> bool:
     return result
 
 
-def _check_consistent_vessel_ids(doc: pe.EnzymeMLDocument) -> bool:
+def _check_consistent_vessel_ids(doc: EnzymeMLDocument) -> bool:
     """This validator checks whether all species have a vessel id that exists in the document.
 
     SBML documents require that all species have a vessel id that exists in the document and
@@ -62,7 +69,7 @@ def _check_consistent_vessel_ids(doc: pe.EnzymeMLDocument) -> bool:
     return all(result)
 
 
-def _check_equation_either_rule_or_reaction(doc: pe.EnzymeMLDocument) -> bool:
+def _check_equation_either_rule_or_reaction(doc: EnzymeMLDocument) -> bool:
     """This validator checks whether there are either rules or reactions in the document.
 
     SBML documents require that there are either rules or reactions in the document. For instance,
@@ -78,10 +85,10 @@ def _check_equation_either_rule_or_reaction(doc: pe.EnzymeMLDocument) -> bool:
     """
 
     species_w_rate = {
-        eq.species_id for eq in doc.equations if eq.equation_type == pe.EquationType.ODE
+        eq.species_id for eq in doc.equations if eq.equation_type == EquationType.ODE
     }
 
-    all_reaction_elements = tools.extract(obj=doc, target=pe.ReactionElement)
+    all_reaction_elements = tools.extract(obj=doc, target=ReactionElement)
     result, validated = [], set()
 
     for element in all_reaction_elements:
@@ -98,7 +105,7 @@ def _check_equation_either_rule_or_reaction(doc: pe.EnzymeMLDocument) -> bool:
     return all(result)
 
 
-def _check_units_exist(doc: pe.EnzymeMLDocument) -> bool:
+def _check_units_exist(doc: EnzymeMLDocument) -> bool:
     """This validator checks whether all units in the document are defined in the SBML standard.
 
     Args:
@@ -109,26 +116,26 @@ def _check_units_exist(doc: pe.EnzymeMLDocument) -> bool:
     """
 
     mandatory_unit_objects = [
-        *tools.extract(obj=doc, target=pe.MeasurementData),
+        *tools.extract(obj=doc, target=MeasurementData),
     ]
 
     optional_unit_objects = [
-        *tools.extract(obj=doc, target=pe.Parameter),
+        *tools.extract(obj=doc, target=Parameter),
     ]
 
     result = []
 
     for unit_obj in mandatory_unit_objects:
-        units = tools.extract(obj=unit_obj, target=pe.UnitDefinition)
+        units = tools.extract(obj=unit_obj, target=UnitDefinition)
 
         if len(units) == 0:
             logger.error(
-                f"Object of type '{type(unit_obj).__name__}' with id '{unit_obj.id}' does not have a unit defined."
+                f"Object of type '{type(unit_obj).__name__}' with id '{unit_obj.species_id}' does not have a unit defined."
             )
             result.append(False)
 
     for unit_obj in optional_unit_objects:
-        units = tools.extract(obj=unit_obj, target=pe.UnitDefinition)
+        units = tools.extract(obj=unit_obj, target=UnitDefinition)
 
         if len(units) == 0:
             logger.warning(
@@ -140,7 +147,7 @@ def _check_units_exist(doc: pe.EnzymeMLDocument) -> bool:
     return all(result)
 
 
-def _check_assigned_params_are_not_constant(doc: pe.EnzymeMLDocument) -> bool:
+def _check_assigned_params_are_not_constant(doc: EnzymeMLDocument) -> bool:
     """This validator checks whether all assigned parameters are not constant.
 
     If a parameter is assigned a value through an assignment rule, it should not be constant.
@@ -154,7 +161,7 @@ def _check_assigned_params_are_not_constant(doc: pe.EnzymeMLDocument) -> bool:
         bool: True if all assigned parameters are valid, False otherwise.
     """
 
-    assignments = doc.filter_equations(equation_type=pe.EquationType.ASSIGNMENT)
+    assignments = doc.filter_equations(equation_type=EquationType.ASSIGNMENT)
     result = []
 
     for assignment in assignments:

pyenzyme/sbml/versions/v1.py

@@ -1,12 +1,13 @@
 from __future__ import annotations
 
 import pandas as pd
+from mdmodels.units.unit_definition import UnitDefinition
 from pydantic import computed_field
-from pydantic_xml import element, BaseXmlModel, attr, wrapped
+from pydantic_xml import BaseXmlModel, attr, element, wrapped
 
-from pyenzyme import Measurement, UnitDefinition, DataTypes
 from pyenzyme.sbml.utils import _get_unit
 from pyenzyme.sbml.versions.v2 import VariableAnnot
+from pyenzyme.versions.v2 import DataTypes, Measurement
 
 
 class V1Annotation(

pyenzyme/sbml/versions/v2.py

@@ -13,11 +13,12 @@
 from __future__ import annotations
 
 import pandas as pd
+from mdmodels.units.unit_definition import UnitDefinition
 from pydantic import field_validator
-from pydantic_xml import element, attr, BaseXmlModel
+from pydantic_xml import BaseXmlModel, attr, element
 
-from pyenzyme import DataTypes, Measurement, UnitDefinition
 from pyenzyme.sbml.utils import _get_unit
+from pyenzyme.versions.v2 import DataTypes, Measurement
 
 
 class BaseAnnot(BaseXmlModel):

pyenzyme/suite.py

@@ -3,7 +3,8 @@
 import httpx
 import rich
 
-import pyenzyme as pe
+from pyenzyme.versions.io import EnzymeMLHandler
+from pyenzyme.versions.v2 import EnzymeMLDocument
 
 
 class EnzymeMLSuite:
@@ -20,7 +21,7 @@ def __init__(self, url: str = "http://localhost:13452"):
         """
         self.client = httpx.Client(base_url=url)
 
-    def get_current(self) -> pe.EnzymeMLDocument:
+    def get_current(self) -> EnzymeMLDocument:
         """
         Retrieves the current EnzymeML document from the service.
 
@@ -42,9 +43,9 @@ def get_current(self) -> pe.EnzymeMLDocument:
 
         content = response.json()["data"]["content"]
 
-        return pe.read_enzymeml_from_string(content)
+        return EnzymeMLHandler.read_enzymeml_from_string(content)
 
-    def update_current(self, doc: pe.EnzymeMLDocument):
+    def update_current(self, doc: EnzymeMLDocument):
         """
         Updates the current EnzymeML document on the service.