fixing tests and docs

binarycpython/utils/custom_logging_functions.py

@@ -85,30 +85,29 @@ def binary_c_log_code(code: str, verbose: int=0) -> str:
     Function to construct the code to construct the custom logging function
     
     Example:
-        Code to log and terminate evolution when the primary star becomes a NS
+        Code to log and terminate evolution when the primary star becomes a NS::
 
-        ::
-        if(stardata->star[0].stellar_type>=NS)
-        {
-            if (stardata->model.time < stardata->model.max_evolution_time)
+            if(stardata->star[0].stellar_type>=NS)
             {
-                Printf("EXAMPLE_LOG_CO %30.12e %g %g %g %g %d %d\\n",
-                    // 
-                    stardata->model.time, // 1
-
-                    stardata->star[0].mass, //2
-                    stardata->previous_stardata->star[0].mass, //3
-
-                    stardata->star[0].radius, //4
-                    stardata->previous_stardata->star[0].radius, //5
-
-                    stardata->star[0].stellar_type, //6
-                    stardata->previous_stardata->star[0].stellar_type //7
-              );
+                if (stardata->model.time < stardata->model.max_evolution_time)
+                {
+                    Printf("EXAMPLE_LOG_CO %30.12e %g %g %g %g %d %d\\n",
+                        // 
+                        stardata->model.time, // 1
+
+                        stardata->star[0].mass, //2
+                        stardata->previous_stardata->star[0].mass, //3
+
+                        stardata->star[0].radius, //4
+                        stardata->previous_stardata->star[0].radius, //5
+
+                        stardata->star[0].stellar_type, //6
+                        stardata->previous_stardata->star[0].stellar_type //7
+                  );
+                };
+                /* Kill the simulation to save time */
+                stardata->model.max_evolution_time = stardata->model.time - stardata->model.dtm;
             };
-            /* Kill the simulation to save time */
-            stardata->model.max_evolution_time = stardata->model.time - stardata->model.dtm;
-        };
 
     Args:
         code: Exact c-statement to output information in binary_c. Can be wrapped in logical statements. 
@@ -116,7 +115,6 @@ def binary_c_log_code(code: str, verbose: int=0) -> str:
 
     Returns:
         string containing the custom logging code. This includes all the includes and other definitions. This code will be used as the shared library
-
     """
 
     verbose_print("Creating the code for the shared library for the custom logging", verbose, 0)

binarycpython/utils/plot_functions.py

@@ -102,21 +102,21 @@ def plot_HR_diagram(
     log temperature on x axis (reversed)
 
     requires:
-        time
-        stellar_type_1
-        stellar_type_2
-        radius_1
-        radius_2
-        luminosity_1
-        luminosity_2
+        - time
+        - stellar_type_1
+        - stellar_type_2
+        - radius_1
+        - radius_2
+        - luminosity_1
+        - luminosity_2
 
     Plots:
-        luminosity_1 vs teff_1
-        luminosity_2 vs teff_2
+        - luminosity_1 vs teff_1
+        - luminosity_2 vs teff_2
     
     Tasks:
-        TODO: add HD limit
-        TODO: add lines of constant radius
+        - TODO: add HD limit
+        - TODO: add lines of constant radius
 
     Args:
         df: pandas dataframe with the required columns
@@ -296,7 +296,7 @@ def plot_masses(df, show_stellar_types: bool=False, show_plot: bool=True):
         - Pms mass 1
         - pms mass 2
         - pms total mass
-        (maybe?) core and env masses
+        - (maybe?) core and env masses
 
     Args:
         df: pandas dataframe with the required columns
@@ -500,30 +500,31 @@ def plot_system(plot_type, **kwargs):
         - a preset custom logging for a specific plotting routine is loaded, depending on the choice of plot_type
         - This is used for the run_system call
         - The output of this run_system is loaded into a dataframe by
-            parsing it with a corresponding parsing function
+        parsing it with a corresponding parsing function
         - The dataframe is passed to the plotting routine
         - plot is shown or returned.
 
     There are several pre-set plots to choose from:
-        mass_evolution
-        orbit_evolution
-        hr_diagram
+        - mass_evolution
+        - orbit_evolution
+        - hr_diagram
 
     Tasks:
-        TODO: Complex Function!
-        TODO: make sure this way of passing args works correctly.
-        TODO: make the plotting specific keywords available via the inspect stuff
+        - TODO: Complex Function!
+        - TODO: make sure this way of passing args works correctly.
+        - TODO: make the plotting specific keywords available via the inspect stuff
 
     All keywords are considered kwargs, except for plot_type
     Args:
-        plot_type: string input should be one of the following types:
-            ['mass_evolution', 'orbit_evolution', 'hr_diagram'].
-            Input will be matched against this,
-            and then go through a dictionary to pick the correct plotting function.
+        plot_type: string input should be one of ['mass_evolution', 'orbit_evolution', 'hr_diagram'].
+            Input will be matched against this, and then go through a dictionary to pick the correct plotting function.
+        
         return_fig: boolean whether to return the fig object instead of plotting the plot
             (makes so that you can customize it)
+        
         show_stellar_types: whether to plot the stellar type evolution on a second pane.
             This is not included in all the plotting routines.
+        
         Other input: other kwargs that are passed to run_system
             (inspect the docstring of run_system for more info)
 

binarycpython/utils/run_system_wrapper.py

@@ -20,18 +20,19 @@ def run_system(**kwargs):
     Function that runs a system.
     Mostly as a useful utility function that handles all the setup of argument lists etc.
 
-    examples:
-        * run_system(M_1=10): will run a system with ZAMS mass 1 = 10
-        * run_system(M_1=10, log_filename="~/example_log.txt"): Will run a system
+    Examples:
+        - run_system(M_1=10): will run a system with ZAMS mass 1 = 10
+        - run_system(M_1=10, log_filename="~/example_log.txt"): Will run a system
             and write the logfile too
-        * run_system(M_1=10, parse_function=fancy_parsing_function)
+        - run_system(M_1=10, parse_function=fancy_parsing_function)
 
     Tasks:
-        TODO: Expand functionality.
-        TODO: Notify user when an unknown keyword is passed.
+        - TODO: Expand functionality.
+        - TODO: Notify user when an unknown keyword is passed.
 
     All~ the arguments known to binary_c can be passed to this function as kwargs.
     Several extra arguments can be passed through the kwargs:
+    Kwargs:
         custom_logging_code (string):
             Should contain a string containing the c-code for the shared library.
             If this is provided binary_c will use that custom logging code to output its data