Merge branch 'development' into development_version/2.2.1

.gitignore

@@ -12,7 +12,6 @@ obj/
 binarycpython_snippets
 -1.log
 
-
 # Standard template
 *.org~
 *.so

binarycpython/tests/example.ipynb

+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "fd5b1a83-7212-4aca-b317-991bf289fba8",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def add(a, b):\n",
+    "    return a + b"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "4d842395-3e17-48e8-b613-9856365e9796",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "11"
+      ]
+     },
+     "execution_count": 2,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "add(5, 6)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "f2afc967-a66a-4a47-bfc5-0d6c17826794",
+   "metadata": {},
+   "outputs": [
+    {
+     "ename": "ZeroDivisionError",
+     "evalue": "division by zero",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mZeroDivisionError\u001b[0m                         Traceback (most recent call last)",
+      "\u001b[0;32m<ipython-input-3-bc757c3fda29>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0;36m1\u001b[0m \u001b[0;34m/\u001b[0m \u001b[0;36m0\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
+      "\u001b[0;31mZeroDivisionError\u001b[0m: division by zero"
+     ]
+    }
+   ],
+   "source": [
+    "1 / 0"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "8491b29d-375d-458f-8a46-fc822422d8f3",
+   "metadata": {},
+   "source": [
+    "hello"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "601a89e6-5ca6-4725-8834-5e975ba76726",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.6.4"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

binarycpython/tests/test_c_bindings.py

@@ -24,9 +24,7 @@ from binarycpython.utils.functions import (
     Capturing,
 )
 
-# https://docs.python.org/3/library/unittest.html
-TMP_DIR = temp_dir()
-os.makedirs(os.path.join(TMP_DIR, "test"), exist_ok=True)
+TMP_DIR = temp_dir("tests", "test_c_bindings")
 
 #### some useful functions
 def return_argstring(

binarycpython/tests/test_custom_logging.py

@@ -7,8 +7,7 @@ import unittest
 from binarycpython.utils.custom_logging_functions import *
 from binarycpython.utils.functions import Capturing
 
-binary_c_temp_dir = temp_dir()
-
+TMP_DIR = temp_dir("tests", "test_custom_logging")
 
 class test_custom_logging(unittest.TestCase):
     """
@@ -26,7 +25,7 @@ class test_custom_logging(unittest.TestCase):
         """
 
         input_dict_1 = None
-        output_1 = autogen_C_logging_code(input_dict_1, verbose=1)
+        output_1 = autogen_C_logging_code(input_dict_1, verbosity=1)
         self.assertEqual(output_1, None, msg="Error. return value should be None")
 
         input_dict_2 = {
@@ -37,7 +36,7 @@ class test_custom_logging(unittest.TestCase):
                 "model.dt",
             ]
         }
-        output_2 = autogen_C_logging_code(input_dict_2, verbose=1)
+        output_2 = autogen_C_logging_code(input_dict_2, verbosity=1)
 
         test_output_2 = 'Printf("MY_STELLAR_DATA %g %g %g %g\\n",((double)stardata->model.time),((double)stardata->star[0].mass),((double)stardata->model.probability),((double)stardata->model.dt));'
         self.assertEqual(
@@ -45,7 +44,7 @@ class test_custom_logging(unittest.TestCase):
         )
 
         input_dict_3 = {"MY_STELLAR_DATA": 2}
-        output_3 = autogen_C_logging_code(input_dict_3, verbose=1)
+        output_3 = autogen_C_logging_code(input_dict_3, verbosity=1)
         self.assertEqual(output_3, None, msg="Output should be None")
 
     def test_binary_c_log_code(self):
@@ -59,11 +58,11 @@ class test_custom_logging(unittest.TestCase):
         """
 
         input_1 = "None"
-        output_1 = binary_c_log_code(input_1, verbose=1)
+        output_1 = binary_c_log_code(input_1, verbosity=1)
         self.assertEqual(output_1, None, msg="Output should be None")
 
         input_2 = 'Printf("MY_STELLAR_DATA %g %g %g %g\\n",((double)stardata->model.time),((double)stardata->star[0].mass),((double)stardata->model.probability),((double)stardata->model.dt));'
-        output_2 = binary_c_log_code(input_2, verbose=1)
+        output_2 = binary_c_log_code(input_2, verbosity=1)
         test_value_2 = '#pragma push_macro("Max")\n#pragma push_macro("Min")\n#undef Max\n#undef Min\n#include "binary_c.h"\n\n// add visibility __attribute__ ((visibility ("default"))) to it \nvoid binary_c_API_function custom_output_function(struct stardata_t * stardata);\nvoid binary_c_API_function custom_output_function(struct stardata_t * stardata)\n{\n    // struct stardata_t * stardata = (struct stardata_t *)x;\n    Printf("MY_STELLAR_DATA %g %g %g %g\\n",((double)stardata->model.time),((double)stardata->star[0].mass),((double)stardata->model.probability),((double)stardata->model.dt));;\n}\n\n#undef Max \n#undef Min\n#pragma pop_macro("Min")\n#pragma pop_macro("Max")    '
 
         self.assertEqual(
@@ -86,18 +85,18 @@ class test_custom_logging(unittest.TestCase):
 
         binary_c_write_log_code(
             input_1,
-            os.path.join(binary_c_temp_dir, "test_binary_c_write_log_code.txt"),
-            verbose=1,
+            os.path.join(TMP_DIR, "test_binary_c_write_log_code.txt"),
+            verbosity=1,
         )
 
         self.assertTrue(
             os.path.isfile(
-                os.path.join(binary_c_temp_dir, "test_binary_c_write_log_code.txt")
+                os.path.join(TMP_DIR, "test_binary_c_write_log_code.txt")
             ),
             msg="File not created",
         )
         with open(
-            os.path.join(binary_c_temp_dir, "test_binary_c_write_log_code.txt")
+            os.path.join(TMP_DIR, "test_binary_c_write_log_code.txt")
         ) as f:
             content_file = repr(f.read())
         self.assertEqual(repr(input_1), content_file, msg="Contents are not similar")
@@ -144,7 +143,7 @@ class test_custom_logging(unittest.TestCase):
         # Just going to check whether the dictionary has the components it needs
         # TODO: check whether we need to make this better
 
-        output = return_compilation_dict(verbose=1)
+        output = return_compilation_dict(verbosity=1)
 
         self.assertTrue("cc" in output)
         self.assertTrue("ld" in output)
@@ -164,7 +163,7 @@ class test_custom_logging(unittest.TestCase):
 
         #
         input_1 = '#pragma push_macro("MAX")\n#pragma push_macro("MIN")\n#undef MAX\n#undef MIN\n#include "binary_c.h"\n\n// add visibility __attribute__ ((visibility ("default"))) to it \nvoid binary_c_API_function custom_output_function(struct stardata_t * stardata);\nvoid binary_c_API_function custom_output_function(struct stardata_t * stardata)\n{\n    // struct stardata_t * stardata = (struct stardata_t *)x;\n    Printf("MY_STELLAR_DATA %g %g %g %g\\n",((double)stardata->model.time),((double)stardata->star[0].mass),((double)stardata->model.probability),((double)stardata->model.dt));;\n}\n\n#undef MAX \n#undef MIN\n#pragma pop_macro("MIN")\n#pragma pop_macro("MAX")    '
-        output_1 = create_and_load_logging_function(input_1, verbose=1)
+        output_1 = create_and_load_logging_function(input_1, verbosity=1)
 
         self.assertTrue(isinstance(output_1[0], int), msg="memaddr is not an int")
         self.assertTrue(output_1[0] > 0, msg="memaddr is an int but not set correctly")

binarycpython/tests/test_distributions.py

@@ -6,8 +6,12 @@ import unittest
 
 from binarycpython.utils.distribution_functions import *
 from binarycpython.utils.useful_funcs import calc_sep_from_period
-from binarycpython.utils.functions import Capturing
+from binarycpython.utils.functions import (
+    Capturing,
+    temp_dir
+)
 
+TMP_DIR = temp_dir("tests", "test_distributions")
 
 class TestDistributions(unittest.TestCase):
     """

binarycpython/tests/test_functions.py

@@ -8,19 +8,7 @@ from binarycpython.utils.functions import *
 from binarycpython.utils.custom_logging_functions import binary_c_log_code
 from binarycpython.utils.run_system_wrapper import run_system
 
-binary_c_temp_dir = temp_dir()
-
-#############################
-# Script that contains unit tests for functions from the binarycpython.utils.functions file
-
-# class test_(unittest.TestCase):
-#     """
-#     Unittests for function
-#     """
-
-#     def test_1(self):
-#         pass
-
+TMP_DIR = temp_dir("tests", "test_functions")
 
 class dummy:
     """
@@ -82,11 +70,11 @@ class test_remove_file(unittest.TestCase):
         """
 
         with open(
-            os.path.join(binary_c_temp_dir, "test_remove_file_file.txt"), "w"
+            os.path.join(TMP_DIR, "test_remove_file_file.txt"), "w"
         ) as f:
             f.write("test")
 
-        remove_file(os.path.join(binary_c_temp_dir, "test_remove_file_file.txt"))
+        remove_file(os.path.join(TMP_DIR, "test_remove_file_file.txt"))
 
     def test_remove_nonexisting_file(self):
         with Capturing() as output:
@@ -97,7 +85,7 @@ class test_remove_file(unittest.TestCase):
         Test to try to remove a nonexistant file
         """
 
-        file = os.path.join(binary_c_temp_dir, "test_remove_nonexistingfile_file.txt")
+        file = os.path.join(TMP_DIR, "test_remove_nonexistingfile_file.txt")
 
         remove_file(file)
 
@@ -141,7 +129,7 @@ class test_create_hdf5(unittest.TestCase):
         Test that creates files, packs them in a hdf5 file and checks the contents
         """
 
-        testdir = os.path.join(binary_c_temp_dir, "test_create_hdf5")
+        testdir = os.path.join(TMP_DIR, "test_create_hdf5")
         os.makedirs(testdir, exist_ok=True)
 
         # Create dummy settings file:
@@ -600,7 +588,7 @@ class test_write_binary_c_parameter_descriptions_to_rst_file(unittest.TestCase):
         """
 
         output_name = os.path.join(
-            binary_c_temp_dir,
+            TMP_DIR,
             "test_write_binary_c_parameter_descriptions_to_rst_file_test_1.txt",
         )
         output_1 = write_binary_c_parameter_descriptions_to_rst_file(output_name)
@@ -616,7 +604,7 @@ class test_write_binary_c_parameter_descriptions_to_rst_file(unittest.TestCase):
         """
 
         output_name = os.path.join(
-            binary_c_temp_dir,
+            TMP_DIR,
             "test_write_binary_c_parameter_descriptions_to_rst_file_test_1.rst",
         )
         output_1 = write_binary_c_parameter_descriptions_to_rst_file(output_name)

binarycpython/tests/test_grid.py

@@ -22,8 +22,7 @@ from binarycpython.utils.functions import (
 )
 from binarycpython.utils.custom_logging_functions import binary_c_log_code
 
-binary_c_temp_dir = temp_dir()
-
+TMP_DIR = temp_dir("tests", "test_grid")
 TEST_VERBOSITY = 1
 
 def parse_function_test_grid_evolve_2_threads_with_custom_logging(self, output):
@@ -342,7 +341,7 @@ class test_Population(unittest.TestCase):
         test_pop.set(metallicity=0.02, verbosity=TEST_VERBOSITY)
         test_pop.set(M_1=10)
         test_pop.set(amt_cores=2)
-        test_pop.set(data_dir=binary_c_temp_dir)
+        test_pop.set(data_dir=TMP_DIR)
 
         # datadir
         settings_filename = test_pop.export_all_info(use_datadir=True)
@@ -366,7 +365,7 @@ class test_Population(unittest.TestCase):
         # datadir
         settings_filename = test_pop.export_all_info(
             use_datadir=False,
-            outfile=os.path.join(binary_c_temp_dir, "example_settings.json"),
+            outfile=os.path.join(TMP_DIR, "example_settings.json"),
         )
         self.assertTrue(os.path.isfile(settings_filename))
         with open(settings_filename, "r") as f:
@@ -389,7 +388,7 @@ class test_Population(unittest.TestCase):
             ValueError,
             test_pop.export_all_info,
             use_datadir=False,
-            outfile=os.path.join(binary_c_temp_dir, "example_settings.txt"),
+            outfile=os.path.join(TMP_DIR, "example_settings.txt"),
         )
 
     def test__cleanup_defaults(self):
@@ -440,7 +439,7 @@ class test_Population(unittest.TestCase):
         Unittests for the function _dict_from_line_source_file
         """
 
-        source_file = os.path.join(binary_c_temp_dir, "example_source_file.txt")
+        source_file = os.path.join(TMP_DIR, "example_source_file.txt")
 
         # write
         with open(source_file, "w") as f:
@@ -602,7 +601,7 @@ class test_grid_evolve(unittest.TestCase):
         Unittests to see if multiple threads do the custom logging correctly
         """
 
-        data_dir_value = os.path.join(binary_c_temp_dir, "grid_tests")
+        data_dir_value = os.path.join(TMP_DIR, "grid_tests")
         amt_cores_value = 2
         custom_logging_string = 'Printf("MY_STELLAR_DATA_TEST_EXAMPLE %g %g %g %g\\n",((double)stardata->model.time),((double)stardata->star[0].mass),((double)stardata->model.probability),((double)stardata->model.dt));'
 
@@ -784,7 +783,7 @@ Printf("TEST_CUSTOM_LOGGING_1 %30.12e %g %g %g %g\\n",
         Unittests to see if multiple threads output the ensemble information to files correctly
         """
 
-        data_dir_value = binary_c_temp_dir
+        data_dir_value = TMP_DIR
         amt_cores_value = 2
 
         test_pop = Population()
@@ -800,7 +799,7 @@ Printf("TEST_CUSTOM_LOGGING_1 %30.12e %g %g %g %g\\n",
             ensemble_dt=1000,
         )
         test_pop.set(
-            data_dir=binary_c_temp_dir,
+            data_dir=TMP_DIR,
             ensemble_output_name="ensemble_output.json",
             combine_ensemble_with_thread_joining=False,
         )
@@ -858,7 +857,7 @@ Printf("TEST_CUSTOM_LOGGING_1 %30.12e %g %g %g %g\\n",
         Unittests to see if multiple threads correclty combine the ensemble data and store them in the grid
         """
 
-        data_dir_value = binary_c_temp_dir
+        data_dir_value = TMP_DIR
         amt_cores_value = 2
 
         test_pop = Population()
@@ -874,7 +873,7 @@ Printf("TEST_CUSTOM_LOGGING_1 %30.12e %g %g %g %g\\n",
             ensemble_dt=1000,
         )
         test_pop.set(
-            data_dir=binary_c_temp_dir,
+            data_dir=TMP_DIR,
             combine_ensemble_with_thread_joining=True,
             ensemble_output_name="ensemble_output.json",
         )
@@ -915,7 +914,7 @@ Printf("TEST_CUSTOM_LOGGING_1 %30.12e %g %g %g %g\\n",
         Unittests to compare the method of storing the combined ensemble data in the object and writing them to files and combining them later. they have to be the same
         """
 
-        data_dir_value = binary_c_temp_dir
+        data_dir_value = TMP_DIR
         amt_cores_value = 2
 
         # First
@@ -932,7 +931,7 @@ Printf("TEST_CUSTOM_LOGGING_1 %30.12e %g %g %g %g\\n",
             ensemble_dt=1000,
         )
         test_pop_1.set(
-            data_dir=binary_c_temp_dir,
+            data_dir=TMP_DIR,
             combine_ensemble_with_thread_joining=True,
             ensemble_output_name="ensemble_output.json",
         )
@@ -971,7 +970,7 @@ Printf("TEST_CUSTOM_LOGGING_1 %30.12e %g %g %g %g\\n",
             ensemble_dt=1000,
         )
         test_pop_2.set(
-            data_dir=binary_c_temp_dir,
+            data_dir=TMP_DIR,
             ensemble_output_name="ensemble_output.json",
             combine_ensemble_with_thread_joining=False,
         )

binarycpython/tests/test_grid_options_defaults.py

@@ -14,8 +14,7 @@ from binarycpython.utils.grid_options_defaults import (
     grid_options_description_checker,
 )
 
-binary_c_temp_dir = temp_dir()
-
+TMP_DIR = temp_dir("tests", "test_grid_options_defaults")
 
 class test_grid_options_defaults(unittest.TestCase):
     """
@@ -79,13 +78,13 @@ class test_grid_options_defaults(unittest.TestCase):
         """
 
         input_1 = os.path.join(
-            binary_c_temp_dir, "test_write_grid_options_to_rst_file_1.txt"
+            TMP_DIR, "test_write_grid_options_to_rst_file_1.txt"
         )
         output_1 = write_grid_options_to_rst_file(input_1)
         self.assertIsNone(output_1)
 
         input_2 = os.path.join(
-            binary_c_temp_dir, "test_write_grid_options_to_rst_file_2.rst"
+            TMP_DIR, "test_write_grid_options_to_rst_file_2.rst"
         )
         output_2 = write_grid_options_to_rst_file(input_2)
 

binarycpython/tests/test_notebooks.py

+import unittest
+
+
+import nbformat
+import os
+
+from nbconvert.preprocessors import ExecutePreprocessor
+
+from binarycpython.utils.functions import temp_dir
+
+TMP_DIR = temp_dir('testing', 'test_notebooks')
+NOTEBOOKS_DIR = os.path.abspath(os.path.join(os.path.abspath(__file__), '../../../examples'))
+
+def run_notebook(notebook_path):
+    """
+    Function to run notebooks and get the errors
+    """
+
+    # https://www.blog.pythonlibrary.org/2018/10/16/testing-jupyter-notebooks/
+    nb_name, _ = os.path.splitext(os.path.basename(notebook_path))
+    dirname = os.path.dirname(notebook_path)
+
+    with open(notebook_path) as f:
+        nb = nbformat.read(f, as_version=4)
+
+    proc = ExecutePreprocessor(timeout=600, kernel_name='python3')
+    proc.allow_errors = True
+
+    proc.preprocess(nb, {'metadata': {'path': '/'}})
+
+    output_path = os.path.join(TMP_DIR, '{}_all_output.ipynb'.format(nb_name))
+
+    with open(output_path, mode='wt') as f:
+        nbformat.write(nb, f)
+    errors = []
+    for cell in nb.cells:
+        if 'outputs' in cell:
+            for output in cell['outputs']:
+                if output.output_type == 'error':
+                    errors.append(output)
+
+    return nb, errors
+
+class TestNotebook(unittest.TestCase):
+    """
+    Class that contains the notebook test calls
+    """
+
+    def test_notebook_api_functionality(self):
+        notebook_name = 'notebook_api_functionality.ipynb'
+        full_notebook_path = os.path.join(NOTEBOOKS_DIR, notebook_name)
+        nb, errors = run_notebook(full_notebook_path)
+        msg = "\nNotebook: {}\n\n".format(notebook_name) + "\n".join(["{}: {}\n{}".format(el['ename'], el['evalue'], '\n'.join(el['traceback'])) for el in errors])
+        self.assertEqual(errors, [], msg=msg)
+
+    def test_notebook_population(self):
+        notebook_name = 'notebook_population.ipynb'
+        full_notebook_path = os.path.join(NOTEBOOKS_DIR, notebook_name)
+        nb, errors = run_notebook(full_notebook_path)
+        msg = "\nNotebook: {}\n\n".format(notebook_name) + "\n".join(["{}: {}\n{}".format(el['ename'], el['evalue'], '\n'.join(el['traceback'])) for el in errors])
+        self.assertEqual(errors, [], msg=msg)
+
+    def test_notebook_individual_systems(self):
+        notebook_name = 'notebook_individual_systems.ipynb'
+        full_notebook_path = os.path.join(NOTEBOOKS_DIR, notebook_name)
+        nb, errors = run_notebook(full_notebook_path)
+        msg = "\nNotebook: {}\n\n".format(notebook_name) + "\n".join(["{}: {}\n{}".format(el['ename'], el['evalue'], '\n'.join(el['traceback'])) for el in errors])
+        self.assertEqual(errors, [], msg=msg)
+
+    def test_notebook_extra_features(self):
+        notebook_name = 'notebook_extra_features.ipynb'
+        full_notebook_path = os.path.join(NOTEBOOKS_DIR, notebook_name)
+        nb, errors = run_notebook(full_notebook_path)
+        msg = "\nNotebook: {}\n\n".format(notebook_name) + "\n".join(["{}: {}\n{}".format(el['ename'], el['evalue'], '\n'.join(el['traceback'])) for el in errors])
+        self.assertEqual(errors, [], msg=msg)
+
+if __name__ == '__main__':
+    unittest.main()

binarycpython/tests/test_plot_functions.py

@@ -9,13 +9,7 @@ import matplotlib.pyplot as plt
 from binarycpython.utils.plot_functions import *
 from binarycpython.utils.functions import Capturing
 
-# class test_(unittest.TestCase):
-#     """
-#     Unittests for function
-#     """
 
-#     def test_1(self):
-#         pass
 
 
 class test_color_by_index(unittest.TestCase):

binarycpython/utils/grid.py

@@ -1411,11 +1411,6 @@ class Population:
                 ensemble_json["ensemble"] = extract_ensemble_json_from_string(
                     ensemble_raw_output
                 )  # Load this into a dict so that we can combine it later
-
-                # Extra ensemble result manipulation:
-                # We need to reformat and multiply by a factor
-                ensemble_json["ensemble"] = self.format_ensemble_results(ensemble_json["ensemble"])
-                gc.collect()
             else:
                 # If we do not allow this, automatically we will export this to the data_dir, in
                 # some formatted way
@@ -1427,8 +1422,9 @@ class Population:
                 )
 
                 # Write to file
+                ensemble_output = extract_ensemble_json_from_string(ensemble_raw_output)
                 with open(output_file, "w") as f:
-                    f.write(ensemble_raw_output)
+                    f.write(json.dumps(self.format_ensemble_results(ensemble_output)))
 
                 print(
                     "Thread {}: Wrote ensemble results directly to file: {}".format(

examples/notebook_individual_systems.ipynb

@@ -27,7 +27,19 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 16,
+   "id": "e32dcdee",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import os\n",
+    "from binarycpython.utils.functions import temp_dir\n",
+    "TMP_DIR = temp_dir(\"notebooks\", \"notebook_individual_systems\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 17,
    "id": "425efed3-d8e3-432d-829e-41d8ebe05162",
    "metadata": {},
    "outputs": [],
@@ -38,7 +50,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 18,
    "id": "b2abab48-433d-4936-8434-14804c52c9f6",
    "metadata": {},
    "outputs": [
@@ -46,7 +58,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "SINGLE_STAR_LIFETIME 1 12462\n",
+      "SINGLE_STAR_LIFETIME 1 12461.9\n",
       "\n"
      ]
     }
@@ -66,7 +78,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 19,
    "id": "029fc3f2-f09a-49af-a32b-248505738f2e",
    "metadata": {},
    "outputs": [
@@ -74,24 +86,25 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "      TIME      M1       M2   K1  K2           SEP   ECC  R1/ROL1 R2/ROL2  TYPE RANDOM_SEED=67365 RANDOM_COUNT=0\n",
-      "     0.0000    1.000    0.000  1  15            -1 -1.00   0.000   0.000  \"INITIAL \"\n",
-      " 11003.1302    1.000    0.000  2  15            -1 -1.00   0.000   0.000  \"OFF_MS\"\n",
-      " 11003.1302    1.000    0.000  2  15            -1 -1.00   0.000   0.000  \"TYPE_CHNGE\"\n",
-      " 11582.2424    1.000    0.000  3  15            -1 -1.00   0.000   0.000  \"TYPE_CHNGE\"\n",
-      " 12325.1085    0.817    0.000  4  15            -1 -1.00   0.000   0.000  \"TYPE_CHNGE\"\n",
-      " 12457.1300    0.783    0.000  5  15            -1 -1.00   0.000   0.000  \"TYPE_CHNGE\"\n",
-      " 12460.8955    0.774    0.000  6  15            -1 -1.00   0.000   0.000  \"TYPE_CHNGE\"\n",
-      " 12460.8955    0.774    0.000  6  15            -1 -1.00   0.000   0.000  \"shrinkAGB\"\n",
-      " 12461.9514    0.523    0.000 11  15            -1 -1.00   0.000   0.000  \"TYPE_CHNGE\"\n",
-      " 15000.0000    0.523    0.000 11  15            -1 -1.00   0.000   0.000  \"MAX_TIME\"\n",
+      "      TIME      M1       M2   K1  K2           SEP      PER    ECC  R1/ROL1 R2/ROL2  TYPE RANDOM_SEED=9935 RANDOM_COUNT=0\n",
+      "     0.0000    1.000    0.000  1  15            -1       -1  -1.00   0.000   0.000  \"INITIAL \"\n",
+      " 11003.1302    1.000    0.000  2  15            -1       -1  -1.00   0.000   0.000  \"OFF_MS\"\n",
+      " 11003.1302    1.000    0.000  2  15            -1       -1  -1.00   0.000   0.000  \"TYPE_CHNGE\"\n",
+      " 11582.2424    1.000    0.000  3  15            -1       -1  -1.00   0.000   0.000  \"TYPE_CHNGE\"\n",
+      " 12325.1085    0.817    0.000  4  15            -1       -1  -1.00   0.000   0.000  \"TYPE_CHNGE\"\n",
+      " 12457.1301    0.783    0.000  5  15            -1       -1  -1.00   0.000   0.000  \"TYPE_CHNGE\"\n",
+      " 12460.9983    0.716    0.000  6  15            -1       -1  -1.00   0.000   0.000  \"TYPE_CHNGE\"\n",
+      " 12460.9983    0.716    0.000  6  15            -1       -1  -1.00   0.000   0.000  \"shrinkAGB\"\n",
+      " 12461.9458    0.518    0.000 11  15            -1       -1  -1.00   0.000   0.000  \"TYPE_CHNGE\"\n",
+      " 15000.0000    0.518    0.000 11  15            -1       -1  -1.00   0.000   0.000  \"MAX_TIME\"\n",
       "\n"
      ]
     }
    ],
    "source": [
-    "output = run_system(M_1=1, log_filename='/tmp/test_logfile.txt')\n",
-    "with open('/tmp/test_logfile.txt', 'r') as f:\n",
+    "log_filename = os.path.join(TMP_DIR, 'test_logfile.txt')\n",
+    "output = run_system(M_1=1, log_filename=log_filename, api_log_filename_prefix=TMP_DIR)\n",
+    "with open(log_filename, 'r') as f:\n",
     "    print(f.read())"
    ]
   },
@@ -105,7 +118,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 20,
    "id": "e6a23b55-ca42-440d-83ac-e76a24a83a67",
    "metadata": {
     "tags": []
@@ -115,7 +128,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "['EXAMPLE_MASSLOSS             0.000000000000e+00 1 1 1', 'EXAMPLE_MASSLOSS             0.000000000000e+00 1 1 1', 'EXAMPLE_MASSLOSS             1.000000000000e-06 1 1 1', 'EXAMPLE_MASSLOSS             2.000000000000e-06 1 1 1']\n"
+      "EXAMPLE_MASSLOSS             0.000000000000e+00 1 1 1\n",
+      "EXAMPLE_MASSLOSS             0.000000000000e+00 1 1 1\n",
+      "EXAMPLE_MASSLOSS             1.000000000000e-06 1 1 1\n",
+      "EXAMPLE_MASSLOSS             2.000000000000e-06 1 1 1\n"
      ]
     }
    ],
@@ -137,8 +153,8 @@
     "# Generate entire shared lib code around logging lines\n",
     "custom_logging_code = binary_c_log_code(custom_logging_print_statement)\n",
     "\n",
-    "output = run_system(M_1=1, custom_logging_code=custom_logging_code)\n",
-    "print(output.splitlines()[:4])"
+    "output = run_system(M_1=1, custom_logging_code=custom_logging_code, api_log_filename_prefix=TMP_DIR)\n",
+    "print('\\n'.join(output.splitlines()[:4]))"
    ]
   },
   {
@@ -151,7 +167,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 21,
    "id": "3822721f-217a-495b-962e-d57137b9e290",
    "metadata": {},
    "outputs": [
@@ -201,7 +217,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 22,
    "id": "654a07ed-2a88-46ff-9da0-b7759580f9f3",
    "metadata": {},
    "outputs": [
@@ -216,13 +232,13 @@
       "4       2e-06         1            1            1\n",
       "5       3e-06         1            1            1\n",
       "...       ...       ...          ...          ...\n",
-      "1612  12461.8  0.577754            1            6\n",
-      "1613    12462  0.522806            1           11\n",
-      "1614    13462  0.522806            1           11\n",
-      "1615    14462  0.522806            1           11\n",
-      "1616    15000  0.522806            1           11\n",
+      "1617  12461.8  0.546683            1            6\n",
+      "1618  12461.9  0.517749            1           11\n",
+      "1619  13461.9  0.517749            1           11\n",
+      "1620  14461.9  0.517749            1           11\n",
+      "1621    15000  0.517749            1           11\n",
       "\n",
-      "[1616 rows x 4 columns]\n"
+      "[1621 rows x 4 columns]\n"
      ]
     }
    ],
@@ -252,7 +268,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 23,
    "id": "4a98ffca-1b72-4bb8-8df1-3bf3187d882f",
    "metadata": {},
    "outputs": [],
@@ -271,7 +287,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 24,
    "id": "bff1cc2e-6b32-4ba0-879f-879ffbabd223",
    "metadata": {},
    "outputs": [
@@ -279,11 +295,12 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
+      "adding: api_log_filename_prefix=/tmp/binary_c_python/notebooks/notebook_individual_systems to BSE_options\n",
       "adding: M_1=10 to BSE_options\n",
       "Creating and loading custom logging functionality\n",
-      "Running binary_c M_1 10\n",
+      "Running binary_c M_1 10 api_log_filename_prefix /tmp/binary_c_python/notebooks/notebook_individual_systems\n",
       "Cleaning up the custom logging stuff. type: single\n",
-      "SINGLE_STAR_LIFETIME 10 27.7358\n",
+      "SINGLE_STAR_LIFETIME 10 28.4838\n",
       "\n"
      ]
     }
@@ -294,7 +311,8 @@
     "\n",
     "# Set some parameters\n",
     "example_pop.set(\n",
-    "    verbosity=1\n",
+    "    verbosity=1,\n",
+    "    api_log_filename_prefix=TMP_DIR\n",
     ")\n",
     "example_pop.set(\n",
     "    M_1=10\n",
@@ -315,7 +333,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": 25,
    "id": "dd748bab-b57e-4129-8350-9ea11fa179d0",
    "metadata": {
     "scrolled": true,
@@ -338,10 +356,13 @@
       ");\n",
       " to grid_options\n",
       "Creating and loading custom logging functionality\n",
-      "Running binary_c M_1 10\n",
+      "Running binary_c M_1 10 api_log_filename_prefix /tmp/binary_c_python/notebooks/notebook_individual_systems\n",
       "Cleaning up the custom logging stuff. type: single\n",
-      "Removed /tmp/binary_c_python/custom_logging/libcustom_logging_eac2dfc438a14e5a9f5be98b1b6b4294.so\n",
-      "['EXAMPLE_MASSLOSS             0.000000000000e+00 10 0 10 1', 'EXAMPLE_MASSLOSS             0.000000000000e+00 10 10 10 1', 'EXAMPLE_MASSLOSS             1.000000000000e-06 10 10 10 1', 'EXAMPLE_MASSLOSS             2.000000000000e-06 10 10 10 1']\n"
+      "Removed /tmp/binary_c_python/custom_logging/libcustom_logging_491813c1f1184f97951202e364eb3b55.so\n",
+      "EXAMPLE_MASSLOSS             0.000000000000e+00 10 0 10 1\n",
+      "EXAMPLE_MASSLOSS             0.000000000000e+00 10 10 10 1\n",
+      "EXAMPLE_MASSLOSS             1.000000000000e-06 10 10 10 1\n",
+      "EXAMPLE_MASSLOSS             2.000000000000e-06 10 10 10 1\n"
      ]
     }
    ],
@@ -362,7 +383,7 @@
     "\n",
     "# get output and print\n",
     "output = example_pop.evolve_single()\n",
-    "print(output.splitlines()[:4])"
+    "print('\\n'.join(output.splitlines()[:4]))"
    ]
   },
   {
@@ -377,7 +398,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 14,
+   "execution_count": 26,
    "id": "fec39154-cce6-438c-8c2c-509d76b00f34",
    "metadata": {},
    "outputs": [],
@@ -428,7 +449,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": 27,
    "id": "57347512-fd4a-434b-b13c-5e6dbd3ac415",
    "metadata": {
     "scrolled": true,
@@ -439,12 +460,13 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "adding: parse_function=<function object_parse_function at 0x7f9265091598> to grid_options\n",
-      "<<<< Warning: Key does not match previously known parameter:                     adding: output_dir=/tmp/ to custom_options >>>>\n",
+      "adding: parse_function=<function object_parse_function at 0x7fa3136e5378> to grid_options\n",
+      "<<<< Warning: Key does not match previously known parameter:                     adding: output_dir=/tmp/binary_c_python/notebooks/notebook_individual_systems to custom_options >>>>\n",
+      "adding: api_log_filename_prefix=/tmp/binary_c_python/notebooks/notebook_individual_systems to BSE_options\n",
       "Creating and loading custom logging functionality\n",
-      "Running binary_c M_1 10\n",
+      "Running binary_c M_1 10 api_log_filename_prefix /tmp/binary_c_python/notebooks/notebook_individual_systems\n",
       "Cleaning up the custom logging stuff. type: single\n",
-      "Removed /tmp/binary_c_python/custom_logging/libcustom_logging_e9c2bec7f15541eb847fc6013e48e7ed.so\n",
+      "Removed /tmp/binary_c_python/custom_logging/libcustom_logging_83729c10ca52451cb773d29d6b28ea96.so\n",
       "[['time', 'mass', 'initial_mass', 'stellar_type'], [0.0, 10.0, 0.0, 10.0, 1.0], [0.0, 10.0, 10.0, 10.0, 1.0], [1e-06, 10.0, 10.0, 10.0, 1.0]]\n",
       "dict_keys(['time', 'mass', 'initial_mass', 'stellar_type'])\n"
      ]
@@ -453,7 +475,8 @@
    "source": [
     "example_pop.set(\n",
     "    parse_function=object_parse_function,\n",
-    "    output_dir='/tmp/'\n",
+    "    output_dir=TMP_DIR,\n",
+    "    api_log_filename_prefix=TMP_DIR\n",
     ")\n",
     "output = example_pop.evolve_single()\n",
     "print(output[:4])\n",
@@ -488,7 +511,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": 28,
    "id": "ec48125c-6bf5-48f4-9357-8261800b5d8b",
    "metadata": {},
    "outputs": [
@@ -496,7 +519,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "SINGLE_STAR_LIFETIME 15 14.2383\n",
+      "SINGLE_STAR_LIFETIME 15 14.9947\n",
       "\n"
      ]
     }
@@ -510,10 +533,11 @@
     "eccentricity = 0.0\n",
     "metallicity = 0.02\n",
     "max_evolution_time = 15000  # Myr. You need to include this argument.\n",
+    "api_log_filename_prefix = TMP_DIR\n",
     "\n",
     "# Here we set up the argument string that is passed to the bindings\n",
     "argstring = \"\"\"\n",
-    "binary_c M_1 {M_1} M_2 {M_2} separation {separation} orbital_period {orbital_period} eccentricity {eccentricity} metallicity {metallicity} max_evolution_time {max_evolution_time}\n",
+    "binary_c M_1 {M_1} M_2 {M_2} separation {separation} orbital_period {orbital_period} eccentricity {eccentricity} metallicity {metallicity} max_evolution_time {max_evolution_time} api_log_filename_prefix {api_log_filename_prefix}\n",
     "\"\"\".format(\n",
     "    M_1=M_1,\n",
     "    M_2=M_2,\n",
@@ -522,6 +546,7 @@
     "    eccentricity=eccentricity,\n",
     "    metallicity=metallicity,\n",
     "    max_evolution_time=max_evolution_time,\n",
+    "    api_log_filename_prefix=TMP_DIR\n",
     ").strip()\n",
     "\n",
     "from binarycpython import _binary_c_bindings\n",