added verbosity options and reformatted the code

binarycpython/utils/custom_logging_functions.py

@@ -8,7 +8,7 @@ import random
 import uuid
 
 
-def autogen_C_logging_code(logging_dict):
+def autogen_C_logging_code(logging_dict, verbose=0):
     """
     Function that autogenerates PRINTF statements for binaryc. intput is a dictionary where the key is the header of that logging line and items which are lists of parameters\
     that will be put in that logging line
@@ -33,6 +33,12 @@ def autogen_C_logging_code(logging_dict):
     code = ""
     # Loop over dict keys
     for key in logging_dict:
+        if verbose > 0:
+            print(
+                "Generating Print statement for custom logging code with {} as a header".format(
+                    key
+                )
+            )
         logging_dict_entry = logging_dict[key]
 
         # Check if item is of correct type:
@@ -54,16 +60,20 @@ def autogen_C_logging_code(logging_dict):
                 "Error: please use a list for the list of parameters that you want to have logged"
             )
     code = code.strip()
-    # print("MADE AUTO CODE\n\n{}\n\n{}\n\n{}\n".format('*'*60, repr(code), '*'*60))
 
     return code
 
 
 ####################################################################################
-def binary_c_log_code(code):
+def binary_c_log_code(code, verbose):
     """
     Function to construct the code to construct the custom logging function
     """
+
+    if verbose > 0:
+        print("Creating the code for the shared library for the custom logging")
+
+    # Create code
     custom_logging_function_string = """\
 #pragma push_macro(\"MAX\")
 #pragma push_macro(\"MIN\")
@@ -91,7 +101,7 @@ void binary_c_API_function custom_output_function(struct stardata_t * stardata)
     return textwrap.dedent(custom_logging_function_string)
 
 
-def binary_c_write_log_code(code, filename):
+def binary_c_write_log_code(code, filename, verbose=0):
     """
     Function to write the generated logging code to a file
     """
@@ -105,6 +115,8 @@ def binary_c_write_log_code(code, filename):
         except:
             print("Error while deleting file {}".format(filePath))
 
+    if verbose > 0:
+        print("Writing the custom logging code to {}".format(filePath))
     with open(filePath, "w") as f:
         f.write(code)
 
@@ -125,7 +137,7 @@ def from_binary_c_config(config_file, flag):
     return res
 
 
-def return_compilation_dict(verbose=False):
+def return_compilation_dict(verbose=0):
     """
     Function to build the compile command for the shared library
 
@@ -139,6 +151,10 @@ def return_compilation_dict(verbose=False):
      - string containing the command to build the shared library
     """
 
+    if verbose > 0:
+        print(
+            "Calling the binary_c config code to get the info to build the shared library"
+        )
     # use binary_c-config to get necessary flags
     BINARY_C_DIR = os.getenv("BINARY_C")
     if BINARY_C_DIR:
@@ -209,12 +225,7 @@ def return_compilation_dict(verbose=False):
     ]
     libs = "{} {}".format(" ".join(library_paths), " ".join(non_library_paths))
 
-    if verbose:
-        print(
-            "Building shared library for custom logging with (binary_c.h) at {} on {}\n".format(
-                BINARY_C_SRC_DIR, socket.gethostname()
-            )
-        )
+    if verbose > 0:
         print(
             "With options:\n\tcc = {cc}\n\tccflags = {ccflags}\n\tld = {ld}\n\tlibs = {libs}\n\tinc = {inc}\n\n".format(
                 cc=cc, ccflags=ccflags, ld=ld, libs=libs, inc=inc
@@ -224,13 +235,13 @@ def return_compilation_dict(verbose=False):
     return {"cc": cc, "ld": ld, "ccflags": ccflags, "libs": libs, "inc": inc}
 
 
-def compile_shared_lib(code, sourcefile_name, outfile_name, verbose=False):
+def compile_shared_lib(code, sourcefile_name, outfile_name, verbose=0):
     """
     Function to write the custom logging code to a file and then compile it.
     """
 
     # Write code to file
-    binary_c_write_log_code(code, sourcefile_name)
+    binary_c_write_log_code(code, sourcefile_name, verbose)
 
     # Remove the library if present:
     if os.path.exists(outfile_name):
@@ -241,7 +252,7 @@ def compile_shared_lib(code, sourcefile_name, outfile_name, verbose=False):
             print("Error while deleting file {}".format(outfile_name))
 
     # create compilation command
-    compilation_dict = return_compilation_dict()
+    compilation_dict = return_compilation_dict(verbose)
 
     # Construct full command
     command = "{cc} {ccflags} {libs} -o {outfile_name} {sourcefile_name} {inc}".format(
@@ -257,11 +268,22 @@ def compile_shared_lib(code, sourcefile_name, outfile_name, verbose=False):
     command = " ".join(command.split())
 
     # Execute compilation and create the library
-    if verbose:
-        print("Executing following command:\n{command}".format(command=command))
+    if verbose > 0:
+        BINARY_C_DIR = os.getenv("BINARY_C")
+        BINARY_C_SRC_DIR = os.path.join(BINARY_C_DIR, "src")
+        print(
+            "Building shared library for custom logging with (binary_c.h) at {} on {}\n".format(
+                BINARY_C_SRC_DIR, socket.gethostname()
+            )
+        )
+        print(
+            "Executing following command to compile the shared library:\n{command}".format(
+                command=command
+            )
+        )
     res = subprocess.check_output("{command}".format(command=command), shell=True)
 
-    if verbose:
+    if verbose > 0:
         if res:
             print("Output of compilation command:\n{}".format(res))
 
@@ -282,7 +304,7 @@ def temp_dir():
     return path
 
 
-def create_and_load_logging_function(custom_logging_code):
+def create_and_load_logging_function(custom_logging_code, verbose):
     """
     Function to automatically compile the shared library with the given custom logging code and load it with ctypes
 
@@ -300,9 +322,12 @@ def create_and_load_logging_function(custom_logging_code):
         custom_logging_code,
         sourcefile_name=os.path.join(temp_dir(), "custom_logging.c"),
         outfile_name=library_name,
-        # verbose=True
+        verbose=verbose,
     )
 
+    if verbose > 0:
+        print("loading shared library for custom logging")
+
     # Loading library
     dll1 = ctypes.CDLL("libgslcblas.so", mode=ctypes.RTLD_GLOBAL)
     dll2 = ctypes.CDLL("libgsl.so", mode=ctypes.RTLD_GLOBAL)
@@ -316,4 +341,11 @@ def create_and_load_logging_function(custom_logging_code):
         libcustom_logging.custom_output_function, ctypes.c_void_p
     ).value
 
+    if verbose > 0:
+        print(
+            "loaded shared library for custom logging. custom_output_function is loaded in memory at {}".format(
+                func_memaddr
+            )
+        )
+
     return func_memaddr

binarycpython/utils/functions.py

@@ -112,9 +112,10 @@ def create_hdf5(data_dir):
     content_data_dir = os.listdir(data_dir)
 
     # Settings
-    settings_file = os.path.join(data_dir, [
-        file for file in content_data_dir if file.endswith("_settings.json")
-    ][0])
+    settings_file = os.path.join(
+        data_dir,
+        [file for file in content_data_dir if file.endswith("_settings.json")][0],
+    )
     with open(settings_file, "r") as f:
         settings_json = json.load(f)
 

binarycpython/utils/grid_options_defaults.py

@@ -28,10 +28,9 @@ grid_options_defaults_dict = {
     "binary_c_dir": os.environ["BINARYC_DIR"],
     "tmp_dir": temp_dir(),
     # Probability:
-    "weight": 1.0, # weighting for the probability
-    "repeat": 1.0, # number of times to repeat each system (probability is adjusted to be 1/repeat)
+    "weight": 1.0,  # weighting for the probability
+    "repeat": 1.0,  # number of times to repeat each system (probability is adjusted to be 1/repeat)
     ##
-
     # return_array_refs=>1, # quicker data parsing mode
     # sort_args=>1,
     # save_args=>1,
@@ -89,7 +88,6 @@ grid_options_defaults_dict = {
     # merge_datafiles=>'',
     # merge_datafiles_filelist=>'',
     # # parameter space options
-
     # binary=>0, # set to 0 for single stars, 1 for binaries
     #     # if use_full_resolution is 1, then run a dummy grid to
     #     # calculate the resolution. this could be slow...

setup.py

@@ -8,9 +8,11 @@ import re
 import sys
 
 # TODO: make this clean
-GSL_DIR = os.getenv('GSL_DIR', None)
+GSL_DIR = os.getenv("GSL_DIR", None)
 if not GSL_DIR:
-    print("Warning: GSL_DIR is not set, this might lead to errors along the installation if there is no other version of GSL in the include dirs")
+    print(
+        "Warning: GSL_DIR is not set, this might lead to errors along the installation if there is no other version of GSL in the include dirs"
+    )
 
 
 # TODO: write code to know exact parent directory of this file.
@@ -63,27 +65,30 @@ for x in defines:
 API_h = os.environ["BINARY_C"] + "/src/API/binary_c_API.h"
 binary_c_define_macros.extend([("BINARY_C_API_H", API_h)])
 
-# 
-include_dirs = [
-        os.environ["BINARY_C"] + "/src",
-        os.environ["BINARY_C"] + "/src/API",
-        "include", ] + binary_c_incdirs + [os.path.join(GSL_DIR,'include')] if GSL_DIR else []
+#
+include_dirs = (
+    [os.environ["BINARY_C"] + "/src", os.environ["BINARY_C"] + "/src/API", "include",]
+    + binary_c_incdirs
+    + [os.path.join(GSL_DIR, "include")]
+    if GSL_DIR
+    else []
+)
 
 libraries = ["binary_c"] + binary_c_libs + ["binary_c_api"]
 
 library_dirs = [
-        os.environ["BINARY_C"] + "/src",
-        "./",
-        os.path.join(CWD, "lib/"),
-        # os.path.join(CWD, "binarycpython/core/"),
-    ] + binary_c_libdirs
+    os.environ["BINARY_C"] + "/src",
+    "./",
+    os.path.join(CWD, "lib/"),
+    # os.path.join(CWD, "binarycpython/core/"),
+] + binary_c_libdirs
 
 runtime_library_dirs = [
-        os.environ["BINARY_C"] + "/src",
-        "./",
-        os.path.join(CWD, "lib/"),
-        # os.path.join(CWD, "binarycpython/core/"),
-    ] + binary_c_libdirs
+    os.environ["BINARY_C"] + "/src",
+    "./",
+    os.path.join(CWD, "lib/"),
+    # os.path.join(CWD, "binarycpython/core/"),
+] + binary_c_libdirs
 
 # TODO: move the creeation of all the include stuff to here so its easier to print everything
 # print('\n')
@@ -102,7 +107,7 @@ binary_c_python_api_module = Extension(
     # name="binarycpython.core.binary_c",
     name="binary_c_python_api",
     sources=["src/binary_c_python.c"],
-    include_dirs= include_dirs,
+    include_dirs=include_dirs,
     libraries=libraries,
     library_dirs=library_dirs,
     runtime_library_dirs=runtime_library_dirs,
@@ -112,6 +117,7 @@ binary_c_python_api_module = Extension(
     language="C",
 )
 
+
 def readme():
     with open("README.md") as f:
         return f.read()

tests/population/multiprocessing_via_population_comparison.py

@@ -13,22 +13,17 @@ from binarycpython.utils.functions import get_help_all, get_help, create_hdf5
 import argparse
 
 
-
-
 parser = argparse.ArgumentParser()
 parser.add_argument(
-    "amt_systems",
-    help='the amount of systems',
+    "amt_systems", help="the amount of systems",
 )
 
 parser.add_argument(
-    "amt_nodes",
-    help='the amount of nodes that are used for the multiprocessing',
+    "amt_nodes", help="the amount of nodes that are used for the multiprocessing",
 )
 
 parser.add_argument(
-    "name_testcase",
-    help='The name of the testcase (e.g. laptop, cluster etc)',
+    "name_testcase", help="The name of the testcase (e.g. laptop, cluster etc)",
 )
 
 
@@ -46,13 +41,14 @@ def output_lines(output):
     """
     return output.splitlines()
 
+
 def parse_function(self, output):
     # extract info from the population instance
     # TODO: think about whether this is smart. Passing around this object might be an overkill
 
-    # Get some information from the 
-    data_dir = self.custom_options['data_dir']
-    base_filename = self.custom_options['base_filename']
+    # Get some information from the
+    data_dir = self.custom_options["data_dir"]
+    base_filename = self.custom_options["base_filename"]
 
     # Check directory, make if necessary
     os.makedirs(data_dir, exist_ok=True)
@@ -65,17 +61,19 @@ def parse_function(self, output):
         headerline = el.split()[0]
 
         # CHeck the header and act accordingly
-        if (headerline=='DAVID_SN'):
-            parameters = ['time', 'mass_1', 'prev_mass_1', 'zams_mass_1', 'SN_type']
+        if headerline == "DAVID_SN":
+            parameters = ["time", "mass_1", "prev_mass_1", "zams_mass_1", "SN_type"]
             values = el.split()[1:]
-            seperator='\t'
+            seperator = "\t"
 
             if not os.path.exists(outfilename):
-                with open(outfilename, 'w') as f:
-                    f.write(seperator.join(parameters)+'\n')
+                with open(outfilename, "w") as f:
+                    f.write(seperator.join(parameters) + "\n")
+
+            with open(outfilename, "a") as f:
+                f.write(seperator.join(values) + "\n")
+
 
-            with open(outfilename, 'a') as f:
-                f.write(seperator.join(values)+'\n')
 ## Set values
 test_pop = Population()
 test_pop.set(
@@ -96,20 +94,29 @@ if(stardata->star[0].SN_type != SN_NONE)
     /* Kill the simulation to save time */
     stardata->model.max_evolution_time = stardata->model.time - stardata->model.dtm;
 };
-""")
-
-test_pop.set(separation=1000000000, 
-    orbital_period=400000000, 
-    metallicity=0.002, 
-    data_dir=os.path.join(os.environ['BINARYC_DATA_ROOT'], 'testing_python', 'multiprocessing2', name_testcase))
+"""
+)
 
-res = test_pop.evolve_population_comparison(parse_function, amt=int(amt_systems), nodes=int(amt_nodes))
-with open('comparison_result.dat', 'a') as f:
-    f.write(str(res)+'\n')
+test_pop.set(
+    separation=1000000000,
+    orbital_period=400000000,
+    metallicity=0.002,
+    data_dir=os.path.join(
+        os.environ["BINARYC_DATA_ROOT"],
+        "testing_python",
+        "multiprocessing2",
+        name_testcase,
+    ),
+)
 
+res = test_pop.evolve_population_comparison(
+    parse_function, amt=int(amt_systems), nodes=int(amt_nodes)
+)
+with open("comparison_result.dat", "a") as f:
+    f.write(str(res) + "\n")
 
 
 mass_distribution = np.arange(1, 200)
 
 
-# evolve_population_mp(parse_function, mass_distribution)
\ No newline at end of file
+# evolve_population_mp(parse_function, mass_distribution)

tests/python_API_test.py

@@ -155,6 +155,7 @@ def test_run_system():
     out = binary_c_python_api.run_system(argstring, -1, -1)
     print(out)
 
+
 ####
 if __name__ == "__main__":
     # test_run_binary()