mcell/libmcell/definition/submodules.yaml

geometry_utils:
  doc: | 
     Submodule geometry_utils provides several functions to define 
     model geometry. Rather limited for now.  
  type: submodule  # default type is class
  methods:
  - name: create_box
    doc: Creates a GeometryObject in the shape of a cube whose center is at (0, 0, 0).
    return_type: GeometryObject*
    examples: tests/pymcell4/1400_rel_site_for_each_it/model.py tests/pymcell4/1105_point_release_w_create_box_not_cube/model.py
    params:
    - name: name
      type: str
      doc: Name of the created geometry object.

    - name: edge_dimension
      type: float
      default: unset
      doc: | 
         Specifies length of each edge of the box in um. 
         None of x/y/z dimensions can be set.

    - name: xyz_dimensions
      type: List[float]
      default: unset
      doc: Specifies x/y/z sizes of the box in um. Parameter edge_dimension must not be set.
      
  - name: create_icosphere
    doc: Creates a GeometryObject in the shape of an icosphere whose center is at (0, 0, 0).
    return_type: GeometryObject*
    examples: tests/pymcell4/1110_point_release_w_create_icosphere/model.py
    params:
    - name: name
      type: str
      doc: Name of the created geometry object.

    - name: radius
      type: float
      doc: Specifies radius of the sphere.

    - name: subdivisions
      type: int
      min: 1
      max: 8
      doc: | 
         Number of subdivisions from the initial icosphere. 
         The higher this value will be the smoother the icosphere will be.
         Allowed range is between 1 and 8.
    
  - name: validate_volumetric_mesh
    doc: | 
       Checks that the mesh was correctly analyzed, that it has volume and 
       all edges have neighboring walls.
       Must be called after model initialization. 
       Throws exception with detained message if validation did not pass. 
    params:
    - name: model
      type: Model*
      doc: Model object after initialization.

    - name: geometry_object
      type: GeometryObject*
      doc: Geometry object to be checked.
             
bngl_utils:
  doc: | 
     Submodule bngl_utils provides a function to load parameters from a BNGL file. 
  type: submodule 
  methods:
  - name: load_bngl_parameters
    return_type: Dict[str, float]
    doc: Load parameters section from a BNGL file and return it as a dictionary name->value.
    examples: tests/pymcell4_positive/2010_bng_parameter_override/model.py
    
    params:
    - name: file_name
      type: str
      doc: Path to the BNGL file to be loaded.

    - name: parameter_overrides
      type: Dict[str, float]
      default: empty
      doc: |
         For each key k in the parameter_overrides, if it is defined in the BNGL's parameters section,
         its value is ignored and instead value parameter_overrides[k] is used.
      
      
run_utils:
  doc: | 
     Submodule run_utils provides functions used by checkpointing. 
  type: submodule
  methods:
  - name: get_last_checkpoint_dir
    doc: | 
       Searches the directory checkpoints for the last checkpoint for the given 
       parameters and returns the directory name if such a directory exists. 
       Returns empty string if no checkpoint directory was found.
       Currently supports only the seed argument.
    todo: extend to handle additional parameters, not just seed
    return_type: str
    params:
    - name: seed
      type: int

  - name: remove_cwd
    doc: |
       Removes all directory names items pointing to the current working directory from a list and 
       returns a new list.
    return_type: List[str]
    params:
    - name: paths
      type: List[str]
    
data_utils:
   doc: |
      Submodule data_utils provides data loading and manipulation functions.
   type: submodule
   methods:
   - name: load_dat_file
     doc: | 
        Loads a two-column file where the first column is usually time and the second is a 
        floating point value. Returns a two-column list. 
        Can be used to load a file with variable rate constants. 
     return_type: List[List[float]]
     params:
     - name: file_name
       type: str      
       doc: Path to the .dat file to be loaded.