Commit 7d30dc17 authored by David Hendriks's avatar David Hendriks
Browse files

adding functionality to load binary_c calls from a sourcefile

parent 2fd73538

binarycpython/utils/functions.py

+1 −1
Original line number Diff line number Diff line
@@ -727,7 +727,7 @@ def inspect_dict(dict_1, indent=0, print_structure=True): 
        if print_structure:

            print("\t" * indent, key, type(value))

        if isinstance(value, dict):

            structure_dict[key] = inspect_dict(value, indent=indent + 1)

            structure_dict[key] = inspect_dict(value, indent=indent + 1, print_structure=print_structure)

    return structure_dict

binarycpython/utils/grid.py

+173 −30
Original line number Diff line number Diff line
@@ -521,6 +521,85 @@ class Population: 
                custom_logging_code, verbose=self.grid_options["verbosity"]

            )



    ###################################################

    # Sourcefile functions

    ###################################################



    def load_source_file(self, check=False):

        """

        Function that loads the source_file that contains a binary_c calls

        """



        if not os.path.isfile(self.grid_options["source_file_filename"]):

            verbose_print("Source file doesnt exist", self.grid_options["verbosity"], 0)



        verbose_print(

            message="Loading source file from {}".format(

                self.grid_options["gridcode_filename"]

            ),

            verbosity=self.grid_options["verbosity"],

            minimal_verbosity=1,

        )



        # We can choose to perform a check on the sourcefile, which checks if the lines start with 'binary_c'

        if check:

            source_file_check_filehandle = open(self.grid_options["source_file_filename"], 'r')

            for line in source_file_check_filehandle:

                if not line.startswith('binary_c')

                    failed = True

                    break

            if failed:

                verbose_print("Error, sourcefile contains lines that do not start with binary_c", self.grid_options["verbosity"], 0)

                raise ValueError



        source_file_filehandle = open(self.grid_options["source_file_filename"], 'r')



        self.grid_options["system_generator"] = source_file_filehandle



        verbose_print("Source file loaded", self.grid_options["verbosity"], 1)



    def dict_from_line_source_file(self):

        """

        Function that creates a dict from a binary_c argline 

        """



        if line.startswith("binary_c "):

            line = line.replace("binary_c ", "")



        split_line = line.split()

        arg_dict = {}



        for i in range(0, len(split_line), 2):

            if "." in split_line[i+1]:

                arg_dict[split_line[i]] = float(split_line[i + 1])

            else: 

                arg_dict[split_line[i]] = int(split_line[i + 1])



        return arg_dict



    def dry_run_source_file(self):

        """

        Function to go through the source_file and count the amount of lines and the total probability

        """



        system_generator = self.grid_options["system_generator"]



        total_starcount = 0

        total_probability = 0



        contains_probability = False



        for line in system_generator:

            





            total_starcount += 1





        total_starcount = system_generator(self)

        self.grid_options["total_starcount"] = total_starcount





    ###################################################

    # Ensemble functions

    ###################################################
@@ -637,6 +716,8 @@ class Population: 
                )

                raise ValueError



        # Check which type of population generation

        if grid_options["population_type_options"] == "grid":

            #######################

            # Dry run and getting starcount

            self.grid_options["probtot"] = 0
@@ -676,6 +757,43 @@ class Population: 
            #

            self.load_grid_function()



        # Source file

        elif grid_options["population_type_options"] == "source_file":

            #######################

            # Dry run and getting starcount

            self.grid_options["probtot"] = 0



            # Load the grid code

            self.load_source_file_function()



            # Do a dry run

            self.dry_run_source_file()



            print(

                "Total starcount for this run will be: {}".format(

                    self.grid_options["total_starcount"]

                )

            )



            #######################

            # Reset values and prepare the grid function

            self.grid_options[

                "probtot"

            ] = 0  # To make sure that the values are reset. TODO: fix this in a cleaner way

            self.grid_options[

                "start_time_evolution"

            ] = time.time()  # Setting start time of grid



            #

            self.load_source_file_function(dry_run=False)



            #

            self.load_grid_function()











        #######



    def cleanup(self):
@@ -1391,6 +1509,31 @@ class Population: 
        # warning; dont use yet. not fully tested.

        """



        # Check if there is no compiled grid yet. If not, lets try to build it first.

        if not self.grid_options["system_generator"]:



            ## check the settings:

            if self.bse_options.get("ensemble", None):

                if self.bse_options['ensemble'] == 1:

                    if not self.bse_options["ensemble_defer"] == 1:

                        verbose_print(

                            "Error, if you want to run an ensemble in a population, the output needs to be deferred",

                            self.grid_options["verbosity"],

                            0,

                        )

                        raise ValueError



            # Put in check

            if len(self.grid_options["grid_variables"]) == 0:

                print("Error: you havent defined any grid variables! Aborting")

                raise ValueError



            #

            self.generate_grid_code(dry_run=False)



            #

            self.load_grid_function()



        if self.grid_options["system_generator"]:

            # Check if there is an output dir configured

            if self.custom_options.get("data_dir", None):
@@ -1435,7 +1578,7 @@ class Population: 
                    file.write(binary_cmdline_string + "\n")

        else:

            print("Error. No grid function found!")

            raise KeyError

            raise ValueError



    def cleanup_defaults(self):

        """

binarycpython/utils/grid_options_defaults.py

+4 −2
Original line number Diff line number Diff line
@@ -27,7 +27,7 @@ grid_options_defaults_dict = { 
    # binary_c files

    ##########################

    "binary_c_executable": os.path.join(

        os.environ["BINARY_C"], "binary_c-config"

        os.environ["BINARY_C"], "binary_c"

    ),  # TODO: make this more robust

    "binary_c_shared_library": os.path.join(

        os.environ["BINARY_C"], "src", "libbinary_c.so"
@@ -69,7 +69,9 @@ grid_options_defaults_dict = { 
    "population_type": "grid",  #

    "population_type_options": [

        "grid",

    ],  # Available choices for type of population generation # TODO: fill later with monte carlo, source file etc

        "source_file",

    ],  # Available choices for type of population generation # TODO: fill later with monte carlo etc

    "source_file_filename": None # filename for the source

    "count": 0,  # total count of systems

    "probtot": 0,  # total probability

    "weight": 1.0,  # weighting for the probability

tests/core/test_persistent_data.py

+20 −4
Original line number Diff line number Diff line
@@ -65,6 +65,8 @@ def test_return_persistent_data_memaddr(): 
    print("Binary_c output:")

    print(textwrap.indent(str(output), "\t"))



    assert isinstance(output, int), "memory adress has to be an integer"

    assert output != 0, "memory adress seems not to have a correct value"



def test_passing_persistent_data_to_run_system():

    # Function to test the passing of the persistent data memoery adress, and having ensemble_defer = True
@@ -286,6 +288,12 @@ def test_adding_ensemble_output(): 
    and output on the second run

    """



    #

    # print(json.dumps(test_1_merged_dict, indent=4))

    # print(json.dumps(test_2_json, indent=4))







    #

    assert inspect_dict(test_1_merged_dict, print_structure=False) == inspect_dict(

        test_2_json, print_structure=False
@@ -293,7 +301,7 @@ def test_adding_ensemble_output(): 
    # assert inspect_dict(test_1_merged_dict, print_structure=False) == inspect_dict(test_3_json, print_structure=False), assert_message_2





def combine_with_empty_json():

def test_combine_with_empty_json():

    argstring_1 = return_argstring(defer_ensemble=0)

    output_1 = binary_c_python_api.run_system(argstring=argstring_1)

    ensemble_jsons_1 = [
@@ -351,12 +359,20 @@ def test_free_and_json_output(): 
    # ensemble_jsons_1 = [line for line in output_1.splitlines() if line.startswith("ENSEMBLE_JSON")]

    # json_1 = json.loads(ensemble_jsons_1[0][len("ENSEMBLE_JSON "):], cls=binarycDecoder)



def test_all():

    test_return_persistent_data_memaddr()

    test_passing_persistent_data_to_run_system()

    test_full_ensemble_output()

    test_adding_ensemble_output()

    test_free_and_json_output()

    test_combine_with_empty_json()



####

if __name__ == "__main__":

    # test_return_persistent_data_memaddr()

    # test_passing_persistent_data_to_run_system()

    # test_full_ensemble_output()

    # test_adding_ensemble_output()

    test_free_and_json_output()

    # combine_with_empty_json()
 
    test_adding_ensemble_output()

    # test_free_and_json_output()

    # test_combine_with_empty_json()

    print("Done")