diff --git a/.gitignore b/.gitignore
index fc4b5eaa0e905f92701264354a082eb56ebfe503..a1f83a92e8e0d778f8824315aa37bdfcd4603fb5 100644
--- a/.gitignore
+++ b/.gitignore
@@ -12,7 +12,6 @@ obj/
binarycpython_snippets
-1.log
-
# Standard template
*.org~
*.so
diff --git a/binarycpython/tests/example.ipynb b/binarycpython/tests/example.ipynb
new file mode 100644
index 0000000000000000000000000000000000000000..57ce0148138a19e0c9cffd6872673c3f44d627d7
--- /dev/null
+++ b/binarycpython/tests/example.ipynb
@@ -0,0 +1,95 @@
+{
+ "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
+}
diff --git a/binarycpython/tests/test_c_bindings.py b/binarycpython/tests/test_c_bindings.py
index 662a50e4654f453519aabc887758f331d5c82842..d92d449682bdded20d9e06e2e7b4fcca394a7c37 100644
--- a/binarycpython/tests/test_c_bindings.py
+++ b/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(
diff --git a/binarycpython/tests/test_custom_logging.py b/binarycpython/tests/test_custom_logging.py
index 62c5be37044f9eac622ed553924ff14005d0f6b3..9e9600f4105f95848ce3be951e7d2217a81a6e76 100644
--- a/binarycpython/tests/test_custom_logging.py
+++ b/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")
diff --git a/binarycpython/tests/test_distributions.py b/binarycpython/tests/test_distributions.py
index caeb87ffe3119f48359edd64cc4a51088d91d3a2..ba90e5d50fb9b2b4226f0588e990bea80fb3820b 100644
--- a/binarycpython/tests/test_distributions.py
+++ b/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):
"""
diff --git a/binarycpython/tests/test_functions.py b/binarycpython/tests/test_functions.py
index b576bf7f66ea5fa98a350c7a0084ab6bf79c18ee..432a48253585c59e4b5ae3c681d465b574cba77f 100644
--- a/binarycpython/tests/test_functions.py
+++ b/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)
diff --git a/binarycpython/tests/test_grid.py b/binarycpython/tests/test_grid.py
index 5eb146ff8962e2c275718f81e14a7b3e6a9c3349..5c761801ca11679d978ad55c69b1a3ba1048f1ac 100644
--- a/binarycpython/tests/test_grid.py
+++ b/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,
)
diff --git a/binarycpython/tests/test_grid_options_defaults.py b/binarycpython/tests/test_grid_options_defaults.py
index 8986e1ada77ac6f10c18e2064b31c7b46b66dc62..ae1ccb9124db5a771800078b0328d93920dc2b29 100644
--- a/binarycpython/tests/test_grid_options_defaults.py
+++ b/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)
diff --git a/binarycpython/tests/test_notebooks.py b/binarycpython/tests/test_notebooks.py
new file mode 100644
index 0000000000000000000000000000000000000000..e90d2696f7dee2e53ac3d99d2dc4882ff7fe1864
--- /dev/null
+++ b/binarycpython/tests/test_notebooks.py
@@ -0,0 +1,78 @@
+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()
diff --git a/binarycpython/tests/test_plot_functions.py b/binarycpython/tests/test_plot_functions.py
index 43b716e95d811cf78d88ca8b64a4aabdb42b391f..3e103e6b732a9ee9460b072ff700a7beb47cddd6 100644
--- a/binarycpython/tests/test_plot_functions.py
+++ b/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):
diff --git a/binarycpython/utils/grid.py b/binarycpython/utils/grid.py
index 5a5d8ec6874b89febc21df5fc936e8b8b932442d..c0bfae70ae996d079c6fc2c28fdf348d8919b333 100644
--- a/binarycpython/utils/grid.py
+++ b/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(
diff --git a/examples/notebook_individual_systems.ipynb b/examples/notebook_individual_systems.ipynb
index 19c2d29fbd316324eb39a361e897be2b835955e8..7aec69eae0a90a6d767573701958bdff340b21ec 100644
--- a/examples/notebook_individual_systems.ipynb
+++ b/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",