Added API theme, tests for misc functions, and comments for docs

docs/source/API.rst

@@ -6,191 +6,11 @@ common.analyzer Module
 
 .. automodule:: common.analyzer
  :members:
-
-check_model Function
---------------------
-
-.. automethod:: common.analyzer.check_model(model_str: str, rate_law_classifications_path: str=None, abort_on_complicated_rate_laws: bool=True, excluded_codes: List[int]=[])
-
- Checks the SBML model for rate law errors and warnings.
-
- **Parameters:**
-
- - **model_str** (*str*): Path to the model file, or the string representation of model.
- - **rate_law_classifications_path** (*str*): Path to the rate law classification file.
- - **abort_on_complicated_rate_laws** (*bool*): If True, the check will abort if the rate law is too complicated to process.
- - **excluded_codes** (*List[int]*): List of codes of the checks to exclude. If None, all checks are performed.
-
- **Returns:**
-
- The results of the checks as a result object, can be printed or converted to string.
-
-Analyzer
---------
-
-.. autoclass:: common.analyzer.Analyzer
- :members:
  :noindex:
- :undoc-members:
- :show-inheritance:
-
- .. automethod:: list_all_checks()
-
- Returns a string representation of all the checks.
-
- **Returns:**
-
- A string listing all error and warning checks.
-
- .. automethod:: list_check(code: int)
-
- Returns a string representation of the check corresponding to the provided code.
-
- **Parameters:**
-
- - **code** (*int*): The code of the check.
-
- **Returns:**
-
- A string describing the check corresponding to the provided code.
-
- .. automethod:: __init__(model_str: str, rate_law_classifications_path: str=None, abort_on_complicated_rate_laws: bool=True)
-
- Initializes the Analyzer class.
-
- **Parameters:**
-
- - **model_str** (*str*): Path to the model file, or the string representation of model.
- - **rate_law_classifications_path** (*str*): Path to the rate law classification file.
- - **abort_on_complicated_rate_laws** (*bool*): If True, the check will abort if the rate law is too complicated to process.
-
- **Examples:**
-
- ::
-
- from ratesb_python import Analyzer
- analyzer = Analyzer("path/to/biomodel.xml", "path/to/rate_laws.json")
- analyzer.check_all()
- results = analyzer.results
- print(str(results))
- str(results)
-
- .. automethod:: check_except(excluded_codes: Optional[List[int]]=[])
-
- Performs all checks except the ones corresponding to the provided list of error or warning codes.
-
- **Parameters:**
-
- - **excluded_codes** (*Optional[List[int]]*): List of codes of the checks to exclude. If None, all checks are performed.
-
- **Updates:**
-
- The results of the check(s) to self.results.
-
- .. automethod:: check_all()
-
- Performs all checks.
-
- **Updates:**
-
- The results of the check_all to self.results.
-
- .. automethod:: checks(codes: List[int])
-
- Performs multiple checks based on the provided list of error or warning codes. If no codes are provided, all checks are performed.
-
- **Parameters:**
-
- - **codes** (*List[int]*): List of codes of the checks to perform.
-
- **Updates:**
-
- The results of the checks to self.results.
 
 Results
 -------
 
 .. autoclass:: common.results.Results
  :members:
- :noindex:
- :undoc-members:
- :show-inheritance:
-
- .. automethod:: __init__()
-
- Initializes the Results class.
-
- .. automethod:: add_message(reaction_name: str, code: int, message: str, is_warning=True)
-
- Adds a new result to the results list.
-
- **Parameters:**
-
- - **reaction_name** (*str*): Name of the reaction.
- - **code** (*int*): Code of the message.
- - **message** (*str*): The message to be added.
- - **is_warning** (*bool*): If the message is a warning message.
-
- .. automethod:: clear_results()
-
- Clears all results from the results list.
-
- .. automethod:: get_all_warnings()
-
- Returns all the warnings as a list of strings.
-
- **Returns:**
-
- A list of warnings.
-
- .. automethod:: get_all_errors()
-
- Returns all the errors.
-
- **Returns:**
-
- A list of errors.
-
- .. automethod:: get_messages_by_reaction(reaction_name: str)
-
- Returns all the messages for a specific reaction.
-
- **Parameters:**
-
- - **reaction_name** (*str*): Name of the reaction.
-
- **Returns:**
-
- A list of messages for the specified reaction.
-
- .. automethod:: remove_messages_by_reaction(reaction_name: str)
-
- Removes all the messages for a specific reaction.
-
- **Parameters:**
-
- - **reaction_name** (*str*): Name of the reaction.
-
- .. automethod:: count_messages()
-
- Returns the total number of errors and warnings.
-
- **Returns:**
-
- The total count of errors and warnings.
-
- .. automethod:: count_errors()
-
- Returns the total number of errors.
-
- **Returns:**
-
- The total count of errors.
-
- .. automethod:: count_warnings()
-
- Returns the total number of warnings.
-
- **Returns:**
-
- The total count of warnings.
+ :noindex:

docs/source/conf.py

@@ -1,5 +1,6 @@
 import os
 import sys
+import sphinx_rtd_theme
 sys.path.insert(0, os.path.abspath('../../ratesb_python'))
 
 
@@ -37,9 +38,15 @@
 # ones.
 extensions = [
  'sphinx.ext.autodoc',
+ 'sphinx.ext.mathjax',
+ 'sphinx.ext.viewcode',
  'sphinx.ext.napoleon'
 ]
 
+html_theme = "sphinx_rtd_theme"
+
+html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
+
 napoleon_google_docstring = True
 napoleon_numpy_docstring = True
 

ratesb_python/common/analyzer.py

@@ -144,6 +144,10 @@ class Analyzer:
  some rules. It uses sympy for processing mathematical symbol expressions, libsbmlpython 
  for processing SBML models, and SBMLKinetics for analyzing SBML models and classifying 
  rate laws. The class can return errors and warnings based on the specified checks.
+ 
+ Attributes:
+ results (Results): An instance of the Results class used to store and retrieve 
+ analysis results. For more details, refer to the documentation of the Results class.
  """
 
  @staticmethod