refactor

petabtests/core.py

@@ -5,6 +5,7 @@
 import re
 import sys
 from pathlib import Path
+from collections.abc import Iterable
 
 from petab.v1.calculate import calculate_chi2, calculate_llh
 
@@ -18,7 +19,7 @@
     write_solution,
 )
 
-__all__ = ["get_cases", "create", "clear", "get_cases_dir"]
+__all__ = ["get_cases", "create_all", "clear", "get_cases_dir"]
 
 test_formats = ("sbml", "pysb")
 test_versions = ("v1.0.0", "v2.0.0")
@@ -27,10 +28,14 @@
 
 
 def get_cases_dir(format_: str, version: str) -> Path:
+    """Get the directory of the test cases for the given PEtab version and
+    model format."""
     return CASES_DIR / version / format_
 
 
-def get_cases(format_: str, version: str):
+def get_cases(format_: str, version: str) -> Iterable[str]:
+    """Get the list of test case IDs for the given PEtab version and model
+    format."""
     cases_dir = get_cases_dir(format_=format_, version=version)
     if not cases_dir.exists():
         return []
@@ -41,13 +46,15 @@ def get_cases(format_: str, version: str):
     )
 
 
-def create():
+def create_all():
     """Create all test files."""
     for version, format_ in itertools.product(test_versions, test_formats):
         case_list = get_cases(format_=format_, version=version)
         if not case_list:
             continue
 
+        # Table of contents markdown string for the current format x version
+        #  directory README
         toc = ""
 
         for case_id in case_list:
@@ -58,55 +65,12 @@ def create():
                 f"Processing {version}/{format_} #{case_id} at {case_dir}"
             )
 
-            # load test case module
-            #  directory needs to be removed from path again and the module
-            #  has to be unloaded, as modules from different model format
-            #  suites have the same name
-            sys.path.append(str(case_dir))
-            case_module = importlib.import_module(case_id)
-            sys.path.pop()
-            # noinspection PyUnresolvedReferences
-            case: PetabTestCase = case_module.case
-            del sys.modules[case_id]
+            case = load_case(case_dir, case_id)
 
             id_str = test_id_str(case.id)
             toc += f"# [{id_str}]({id_str}/)\n\n{case.brief}\n\n"
 
-            write_info(case, format_, version=version)
-
-            write_problem(
-                test_id=case.id,
-                parameter_df=case.parameter_df,
-                condition_dfs=case.condition_dfs,
-                experiment_dfs=case.experiment_dfs,
-                observable_dfs=case.observable_dfs,
-                measurement_dfs=case.measurement_dfs,
-                model_files=case.model,
-                format_=format_,
-                version=version,
-                mapping_df=case.mapping_df,
-            )
-
-            chi2 = calculate_chi2(
-                case.measurement_dfs,
-                case.simulation_dfs,
-                case.observable_dfs,
-                case.parameter_df,
-            )
-            llh = calculate_llh(
-                case.measurement_dfs,
-                case.simulation_dfs,
-                case.observable_dfs,
-                case.parameter_df,
-            )
-            write_solution(
-                test_id=case.id,
-                chi2=chi2,
-                llh=llh,
-                simulation_dfs=case.simulation_dfs,
-                format_=format_,
-                version=version,
-            )
+            create_case(format_, version, case_id)
 
         toc_path = (
             get_cases_dir(format_=format_, version=version) / "README.md"
@@ -115,7 +79,60 @@ def create():
             f.write(toc)
 
 
-def clear():
+def load_case(case_dir: Path, case_id: str) -> PetabTestCase:
+    """Load a test case definition module."""
+    sys.path.append(str(case_dir))
+    case_module = importlib.import_module(case_id)
+    sys.path.pop()
+    # noinspection PyUnresolvedReferences
+    case: PetabTestCase = case_module.case
+    del sys.modules[case_id]
+    return case
+
+
+def create_case(format_: str, version: str, id_: str) -> None:
+    """Create a single test case."""
+    case_dir = get_case_dir(format_=format_, version=version, id_=id_)
+    case = load_case(case_dir, id_)
+
+    write_info(case, format_, version=version)
+
+    write_problem(
+        test_id=case.id,
+        parameter_df=case.parameter_df,
+        condition_dfs=case.condition_dfs,
+        experiment_dfs=case.experiment_dfs,
+        observable_dfs=case.observable_dfs,
+        measurement_dfs=case.measurement_dfs,
+        model_files=case.model,
+        format_=format_,
+        version=version,
+        mapping_df=case.mapping_df,
+    )
+
+    chi2 = calculate_chi2(
+        case.measurement_dfs,
+        case.simulation_dfs,
+        case.observable_dfs,
+        case.parameter_df,
+    )
+    llh = calculate_llh(
+        case.measurement_dfs,
+        case.simulation_dfs,
+        case.observable_dfs,
+        case.parameter_df,
+    )
+    write_solution(
+        test_id=case.id,
+        chi2=chi2,
+        llh=llh,
+        simulation_dfs=case.simulation_dfs,
+        format_=format_,
+        version=version,
+    )
+
+
+def clear() -> None:
     """Clear all model folders."""
     for version, format_ in itertools.product(test_versions, test_formats):
         case_list = get_cases(format_=format_, version=version)
@@ -134,4 +151,4 @@ def _cli_create():
     """`petabtests_create` entry point."""
     # initialize logging
     logging.basicConfig(level=logging.INFO)
-    create()
+    create_all()

petabtests/file.py

@@ -49,25 +49,29 @@ class PetabTestCase:
 
 
 def get_case_dir(id_: int | str, format_: str, version: str) -> Path:
+    """Get the directory of a test case."""
     id_str = test_id_str(id_)
     dir_ = CASES_DIR / version / format_ / id_str
     dir_.mkdir(parents=True, exist_ok=True)
     return dir_
 
 
 def problem_yaml_name(_id: int | str) -> str:
+    """Get the name of the problem yaml file."""
     return "_" + test_id_str(_id) + ".yaml"
 
 
 def solution_yaml_name(_id: int | str) -> str:
+    """Get the name of the solution yaml file."""
     return "_" + test_id_str(_id) + "_solution.yaml"
 
 
 def test_id_str(_id: int | str) -> str:
+    """Get the test id as a string."""
     return f"{_id:0>4}"
 
 
-def write_info(case: PetabTestCase, format_: str, version: str):
+def write_info(case: PetabTestCase, format_: str, version: str) -> None:
     """Write test info markdown file"""
     # id to string
     dir_ = get_case_dir(id_=case.id, format_=format_, version=version)
@@ -91,7 +95,7 @@ def write_problem(
     mapping_df: pd.DataFrame = None,
     format_: str = "sbml",
 ) -> None:
-    """Write problem to files.
+    """Write the PEtab problem for a given test to files.
 
     Parameters
     ----------

test/test_generate.py

@@ -1,4 +1,4 @@
-from petabtests.core import create
+from petabtests.core import create_all
 from petabtests.C import CASES_DIR
 
 import sys
@@ -7,7 +7,7 @@
 
 def test_check_cases_up_to_date():
     sys.path.insert(0, CASES_DIR)
-    create()
+    create_all()
     res = subprocess.run(
         ["git", "diff", "--exit-code", CASES_DIR], capture_output=True
     )