Refactoring tests (#123)

* removing dummy parser * fix typing * fixes * fixes * fixes * tests refactoring * moving example JSON to tests resources * tests fixing * fixing TOPAS * fixing tests * missing files added * refactor: Autofix issues in 4 files Resolved issues in the following files with DeepSource Autofix: 1. tests/shieldhit/test_shieldhit_converter.py 2. tests/shieldhit/test_zones.py 3. tests/topas/conftest.py 4. tests/topas/test_topas_converter.py * readme added * fixes * fixes * fixes * refactor: Autofix issues in 1 file Resolved issues in converter/topas/parser.py with DeepSource Autofix * deepsource * Apply suggestions from code review Co-authored-by: Dominik Hendzel <[email protected]> * review * review * Apply suggestions from code review Co-authored-by: Mateusz Wronka <[email protected]> * Apply suggestions from code review Co-authored-by: Mateusz Wronka <[email protected]> --------- Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com> Co-authored-by: Dominik Hendzel <[email protected]> Co-authored-by: Mateusz Wronka <[email protected]>
yaptide · May 14, 2023 · 7a12210 · 7a12210
1 parent 2a1ff47
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diff --git a/.github/workflows/test-run.yml b/.github/workflows/test-run.yml
@@ -28,7 +28,7 @@ jobs:
           pip3 install -r test_requirements.txt
 
       - name: Run main tests
-        run: python -m pytest tests/
+        run: python -m pytest
 
 
   build-and-test:
@@ -61,7 +61,7 @@ jobs:
 
       - name: Run main tests
         # when triggering tests with `python -m pytest` (instead of simply calling `pytest`) we add current directory to sys.path
-        run: python -m pytest tests/
+        run: python -m pytest
 
   make-package:
     runs-on: ubuntu-latest
@@ -87,7 +87,7 @@ jobs:
           name: packages
           path: |
             ./dist
-            ./input_examples
+            ./tests/shieldhit/resources
 
   test-package:
     runs-on: ubuntu-latest
@@ -117,6 +117,6 @@ jobs:
       - name: Test package
         run: |
          yaptide-converter -h
-         yaptide-converter ./input_examples/sh_parser_test.json
+         yaptide-converter ./tests/shieldhit/resources/project.json
          python3 -m converter.main -h
-         python3 -m converter.main ./input_examples/sh_parser_test.json
+         python3 -m converter.main ./tests/shieldhit/resources/project.json
diff --git a/.gitignore b/.gitignore
@@ -266,4 +266,4 @@ cython_debug/
 # End of https://www.toptal.com/developers/gitignore/api/python,visualstudiocode,pycharm
 
 **/*.dat
-!input_examples/expected_shieldhit_output/*.dat
+!tests/shieldhit/resources/expected_shieldhit_output/*.dat
diff --git a/README.md b/README.md
@@ -3,6 +3,7 @@
 The Converter of the project file (JSON file generated by frontend part) into a set of input files for particle transport simulators:
  - SHIELD-HIT12A (beam.dat, mat.dat, geo.dat and detect.dat).
  - TOPAS
+ - Fluka
 
 ## Requirements
 - Python 3.9+
@@ -28,7 +29,7 @@ It is capable of transforming JSON project file (generated in the yaptide web in
 To run the converter use the following command:
 
 ```bash
-python converter/main.py editor.json workspace
+python converter/main.py tests/shieldhit/resources/project.json workspace
 ```
 
 ## Testing

diff --git a/converter/api.py b/converter/api.py
@@ -1,6 +1,6 @@
 from pathlib import Path
 from typing import Union
-from converter.shieldhit.parser import DummmyParser as SHDummyParser, ShieldhitParser
+from converter.shieldhit.parser import ShieldhitParser
 from converter.topas.parser import TopasParser
 from converter.common import Parser
 from converter.fluka.parser import FlukaParser
@@ -9,8 +9,6 @@
 def get_parser_from_str(parser_type: str) -> Parser:
     """Get a converter object based on the provided type."""
     # This is temporary, suggestions on how to do this better appreciated.
-    if parser_type.lower() == 'sh_dummy':
-        return SHDummyParser()
     if parser_type.lower() == 'shieldhit':
         return ShieldhitParser()
     if parser_type.lower() == 'topas':
@@ -19,7 +17,7 @@ def get_parser_from_str(parser_type: str) -> Parser:
         return FlukaParser()
 
     print(f"Invalid parser type \"{parser_type}\".")
-    raise ValueError("Parser type must be either 'sh_dummy', 'shieldhit', 'topas' or 'fluka'.")
+    raise ValueError("Parser type must be either 'shieldhit', 'topas' or 'fluka'.")
 
 
 def run_parser(parser: Parser, input_data: dict, output_dir: Union[Path, None] = None, silent: bool = True) -> dict:

diff --git a/converter/common.py b/converter/common.py
@@ -1,24 +1,38 @@
-from abc import ABC, abstractmethod
 from pathlib import Path
 
 
-class Parser(ABC):
+class Parser:
     """Abstract parser, the template for implementing other parsers."""
 
-    @abstractmethod
+    def __init__(self) -> None:
+        self.info = {
+            "version": "",
+            "label": "",
+            "simulator": "",
+        }
+
     def parse_configs(self, json: dict) -> None:
         """Convert the json dict to the 4 config dataclasses."""
+        raise NotImplementedError
 
-    @abstractmethod
-    def save_configs(self, target_dir: Path) -> None:
+    def save_configs(self, target_dir: str):
         """
         Save the configs as text files in the target_dir.
         The files are: beam.dat, mat.dat, detect.dat and geo.dat.
         """
+        if not Path(target_dir).exists():
+            raise ValueError("Target directory does not exist.")
+
+        for file_name, content in self.get_configs_json().items():
+            with open(Path(target_dir, file_name), 'w') as conf_f:
+                conf_f.write(content)
 
-    @abstractmethod
     def get_configs_json(self) -> dict:
         """
         Return a dict representation of the config files. Each element has
         the config files name as key and its content as value.
         """
+        configs_json = {
+            "info.json": str(self.info),
+        }
+        return configs_json
diff --git a/converter/fluka/parser.py b/converter/fluka/parser.py
@@ -1,7 +1,5 @@
-from pathlib import Path
 from converter.common import Parser
 
-
 DEFAULT_CONFIG = """TITLE
 proton beam simulation
 * default physics settings for hadron therapy
@@ -67,32 +65,19 @@ class FlukaParser(Parser):
     """A simple placeholder that ignores the json input and prints example (default) configs."""
 
     def __init__(self) -> None:
-        version = "unknown"
-        self.info = {
-            "version": version,
-            "label": "development",
-            "simulator": "fluka",
-        }
+        super().__init__()
+        self.info['simulator'] = 'fluka'
+        self.info['version'] = 'unknown'
 
     def parse_configs(self, json: dict) -> None:
         """Basicaly do nothing since we work on defaults in this parser."""
 
-    def save_configs(self, target_dir: Path) -> None:
-        """
-        This will save the Fluka Configuration to a file named fl_sim.imp
-        in the target_dir directory.
-        """
-        if not Path(target_dir).exists():
-            raise FileNotFoundError("Target directory doest not exist.")
-        for file_name, content in self.get_configs_json().items():
-            with open(Path(target_dir, file_name), "w") as conf_f:
-                conf_f.write(content)
-
     def get_configs_json(self) -> dict:
         """
         Return a dict representation of the config files. Each element has
         the config files name as key and its content as value.
         """
-        configs_json = {"info.json": str(self.info), "fl_sim.inp": DEFAULT_CONFIG}
+        configs_json = super().get_configs_json()
+        configs_json["fl_sim.inp"] = DEFAULT_CONFIG
 
         return configs_json
diff --git a/converter/shieldhit/beam.py b/converter/shieldhit/beam.py
@@ -71,7 +71,8 @@ class BeamConfig:
     energy_cutoff_template = "TCUT0 {energy_low_cutoff} {energy_high_cutoff}  ! energy cutoffs [MeV]"
     sad_template = "BEAMSAD {sad_x} {sad_y}  ! BEAMSAD value [cm]"
     beam_source_type: BeamSourceType = BeamSourceType.SIMPLE
-    beam_source_file: Optional[str] = None
+    beam_source_filename: Optional[str] = None
+    beam_source_file_content: Optional[str] = None
 
     beam_dat_template: str = """
 RNDSEED      	89736501     ! Random seed

diff --git a/converter/shieldhit/detect.py b/converter/shieldhit/detect.py
@@ -1,4 +1,5 @@
 from dataclasses import dataclass, field
+from typing import Optional
 from converter.shieldhit.scoring_geometries import ScoringGeometry, ScoringCylinder, ScoringMesh
 
 
@@ -28,10 +29,10 @@ class OutputQuantity:
 
     detector_type: str
     filter_name: str = ""
-    diff1: tuple[float, float, float, str] = None
-    diff1_t: str = None
-    diff2: tuple[float, float, float, str] = None
-    diff2_t: str = None
+    diff1: Optional[tuple[float, float, float, str]] = None
+    diff1_t: Optional[str] = None
+    diff2: Optional[tuple[float, float, float, str]] = None
+    diff2_t: Optional[str] = None
 
     quantity_template: str = """
     Quantity {detector_type} {filter_name}"""
@@ -52,14 +53,14 @@ def __str__(self) -> str:
 class ScoringOutput:
     """Dataclass storing information about shieldhit scoring outputs."""
 
-    filename: str = None
-    fileformat: str = None
-    geometry: str = None
-    medium: str = None
-    offset: float = None
-    primaries: float = None
+    filename: Optional[str] = None
+    fileformat: Optional[str] = None
+    geometry: Optional[str] = None
+    medium: Optional[str] = None
+    offset: Optional[float] = None
+    primaries: Optional[int] = None
     quantities: list[OutputQuantity] = field(default_factory=lambda: [])
-    rescale: float = None
+    rescale: Optional[float] = None
 
     filename_str_template: str = """
     Filename {filename}"""

diff --git a/converter/shieldhit/geo.py b/converter/shieldhit/geo.py
@@ -1,3 +1,4 @@
+from typing import Optional
 from converter.solid_figures import SolidFigure, BoxFigure, CylinderFigure, SphereFigure
 from dataclasses import dataclass, field
 from math import log10, ceil, isclose
@@ -17,7 +18,7 @@ class DefaultMaterial(IntEnum):
 
     @staticmethod
     def is_default_material(material_value: int) -> bool:
-        """Check if the material is one of the predefined materials."""
+        """Check if the material is one of the predefined default materials."""
         return material_value in DefaultMaterial._value2member_map_
 
 
@@ -29,7 +30,7 @@ def format_float(number: float, n: int) -> float:
     """
     result = number
     # If number is zero we just want to get 0.0 (it would mess up the log10 operation below)
-    if isclose(result, 0.):
+    if isclose(result, 0., rel_tol=1e-9):
         return 0.
 
     length = n
@@ -68,14 +69,14 @@ def format_float(number: float, n: int) -> float:
 
     # Formatting negative numbers smaller than the desired precission could result in -0.0 or 0.0 randomly.
     # To avoid this we catch -0.0 and return 0.0.
-    if isclose(result, 0.):
+    if isclose(result, 0., rel_tol=1e-9):
         return 0.
 
     return result
 
 
 def parse_figure(figure: SolidFigure, number: int) -> str:
-    """Parse a SolidFigure into a str representation of SH12A input file."""
+    """Parse a SolidFigure into a string representation of SH12A input file."""
     if type(figure) is BoxFigure:
         return _parse_box(figure, number)
     if type(figure) is CylinderFigure:
@@ -161,7 +162,7 @@ class Material:
 
     uuid: str
     icru: int
-    density: float = None
+    density: Optional[float] = None
     idx: int = 0
 
     property_template = """{name} {value}\n"""
@@ -184,7 +185,7 @@ class Zone:
 
     id: int = 1
     figures_operators: list[set[int]] = field(default_factory=lambda: [{1}])
-    material: str = "0"
+    material: int = 0
     material_override: dict[str, str] = field(default_factory=dict)
 
     zone_template: str = """
@@ -214,19 +215,19 @@ class GeoMatConfig:
             figures_operators=[{
                 1,
             }],
-            material="1",
+            material=1,
         ),
         Zone(
             uuid="",
             id=2,
             figures_operators=[{-1, 2}],
-            material="1000",
+            material=1000,
         ),
         Zone(
             uuid="",
             id=3,
             figures_operators=[{-2, 3}],
-            material="0",
+            material=0,
         ),
     ])
     materials: list[Material] = field(default_factory=lambda: [Material('', 276)])
@@ -244,7 +245,7 @@ class GeoMatConfig:
 """
 
     @staticmethod
-    def _split_zones_to_rows(zones: list[Zone], max_size=14) -> list[list[Zone]]:
+    def _split_zones_to_rows(zones: list[int], max_size=14) -> list[list[int]]:
         """Split list of Zones into rows of not more than 14 elements"""
         return [zones[i:min(i + max_size, len(zones))] for i in range(0, len(zones), max_size)]