Make centering cytosim fibers optional

.github/workflows/ci.yml

@@ -39,7 +39,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.8, 3.9]
+        python-version: [3.9, "3.10"]
         os: [ubuntu-latest]
 
     steps:

README.md

@@ -119,7 +119,7 @@ Rendering capabilities planned for future:
 ## Installation
 **Install Requires:** 
 
-* Requires Python 3.7, 3.8, or 3.9
+* Requires Python 3.9 or 3.10
 
 * If ReaDDy trajectories will be converted, the ReaDDy python package must be installed:
 (add conda forge channel if it's not already: `conda config --add channels conda-forge`)

environment.yml

@@ -2,5 +2,5 @@ name: anaconda-client-env
 channels:
   - conda-forge
 dependencies:
-  - readdy==2.0.9
+  - readdy
   - numpy>=1.20

simulariumio/cytosim/cytosim_converter.py

@@ -192,6 +192,7 @@ def _parse_objects(
         overall_line: int,
         total_lines: int,
         scale_factor: float = None,
+        center_fibers: bool = False,
     ) -> Tuple[Dict[str, Any], List[int], int]:
         """
         Parse a Cytosim output file containing objects
@@ -277,7 +278,8 @@ def _parse_objects(
         result, scale_factor = TrajectoryConverter.scale_agent_data(
             result, scale_factor
         )
-        result = TrajectoryConverter.center_fiber_positions(result)
+        if center_fibers:
+            result = TrajectoryConverter.center_fiber_positions(result)
         result.n_timesteps = time_index + 1
         return (result, used_unique_IDs, overall_line, scale_factor)
 
@@ -319,6 +321,7 @@ def _read(self, input_data: CytosimData) -> TrajectoryData:
                     overall_line,
                     total_lines,
                     input_data.meta_data.scale_factor,
+                    input_data.center_fibers,
                 )
             except Exception as e:
                 raise InputDataError(f"Error reading input cytosim data: {e}")

simulariumio/cytosim/cytosim_data.py

@@ -19,13 +19,15 @@ class CytosimData:
     meta_data: MetaData
     draw_fiber_points: bool
     plots: List[Dict[str, Any]]
+    center_fibers: bool
 
     def __init__(
         self,
         object_info: Dict[str, CytosimObjectInfo],
         meta_data: MetaData = None,
         draw_fiber_points: bool = False,
         plots: List[Dict[str, Any]] = None,
+        center_fibers: bool = False,
     ):
         """
         This object holds simulation trajectory outputs
@@ -50,8 +52,12 @@ def __init__(
         plots : List[Dict[str, Any]] (optional)
             An object containing plot data already
             in Simularium format
+        center_fibers : bool
+            Set the position of each fiber as the center of its points?
+            Otherwise set it to zero.
         """
         self.object_info = object_info
         self.meta_data = meta_data if meta_data is not None else MetaData()
         self.draw_fiber_points = draw_fiber_points
         self.plots = plots if plots is not None else []
+        self.center_fibers = center_fibers

simulariumio/tests/converters/test_cytosim_converter.py

@@ -30,6 +30,7 @@
             ),
         )
     },
+    center_fibers=True,
 )
 converter = CytosimConverter(data)
 results = JsonWriter.format_trajectory_data(converter._data)
@@ -93,6 +94,7 @@ def test_typeMapping_default(typeMapping, expected_typeMapping):
             ),
         )
     },
+    center_fibers=True,
 )
 converter_meta_data = CytosimConverter(data_with_metadata)
 results_meta_data = JsonWriter.format_trajectory_data(converter_meta_data._data)
@@ -144,6 +146,7 @@ def test_box_size_provided(box_size, expected_box_size):
             },
         )
     },
+    center_fibers=True,
 )
 converter_display_data = CytosimConverter(data_with_display_data)
 results_display_data = JsonWriter.format_trajectory_data(converter_display_data._data)
@@ -328,6 +331,7 @@ def test_agent_ids():
             ),
         ),
     },
+    center_fibers=True,
 )
 # load the data from Cytosim output .txt files
 cytosim_data = {}
@@ -358,6 +362,7 @@ def test_input_file_error():
                 ),
             )
         },
+        center_fibers=True,
     )
     with pytest.raises(InputDataError):
         CytosimConverter(malformed_data)
@@ -374,6 +379,7 @@ def test_input_file_error():
                 ),
             )
         },
+        center_fibers=True,
     )
     with pytest.raises(InputDataError):
         CytosimConverter(wrong_file)