diff --git a/binarycpython/tests/main.py b/binarycpython/tests/main.py
index 9d7e00f632b5b42ac96c21ced287609a3d7f622f..abafd95b221ca038e06521ed47a79c4f7198e336 100755
--- a/binarycpython/tests/main.py
+++ b/binarycpython/tests/main.py
@@ -5,7 +5,6 @@ Main file for the tests. This file imports all the combined_test functions from
import unittest
-
from binarycpython.tests.test_c_bindings import *
from binarycpython.tests.test_custom_logging import *
from binarycpython.tests.test_distributions import *
@@ -18,6 +17,7 @@ from binarycpython.tests.test_spacing_functions import *
from binarycpython.tests.test_useful_funcs import *
from binarycpython.tests.test_grid_options_defaults import *
from binarycpython.tests.test_stellar_types import *
+from test_notebooks import *
if __name__ == "__main__":
unittest.main()
diff --git a/binarycpython/tests/test_custom_logging.py b/binarycpython/tests/test_custom_logging.py
index 9e9600f4105f95848ce3be951e7d2217a81a6e76..17f54545f0941c2a5dbb8db823d6e12bafb958d0 100644
--- a/binarycpython/tests/test_custom_logging.py
+++ b/binarycpython/tests/test_custom_logging.py
@@ -128,7 +128,7 @@ class test_custom_logging(unittest.TestCase):
input_2 = "version"
output_2 = from_binary_c_config(BINARY_C_CONFIG, input_2)
- self.assertIn(output_2, ["2.1.7", "2.2pre1"], msg="binary_c version doesnt match")
+ self.assertIn(output_2, ["2.1.7", "2.2pre1", "2.2.0", "2.2.1"], msg="binary_c version doesnt match")
def test_return_compilation_dict(self):
with Capturing() as output:
diff --git a/binarycpython/tests/test_functions.py b/binarycpython/tests/test_functions.py
index 432a48253585c59e4b5ae3c681d465b574cba77f..4c15060dc6682aa76dd0b9f78930347ac6deb87b 100644
--- a/binarycpython/tests/test_functions.py
+++ b/binarycpython/tests/test_functions.py
@@ -166,7 +166,7 @@ class test_return_binary_c_version_info(unittest.TestCase):
Test for the raw version_info output
"""
- version_info = return_binary_c_version_info()
+ version_info = return_binary_c_version_info(parsed=False)
self.assertTrue(isinstance(version_info, str))
self.assertIn("Build", version_info)
@@ -210,7 +210,7 @@ class test_parse_binary_c_version_info(unittest.TestCase):
Test for the parsed versio info, more detailed
"""
- info = return_binary_c_version_info()
+ info = return_binary_c_version_info(parsed=False)
parsed_info = parse_binary_c_version_info(info)
self.assertIn("isotopes", parsed_info.keys())
diff --git a/binarycpython/tests/test_grid.py b/binarycpython/tests/test_grid.py
index 5c761801ca11679d978ad55c69b1a3ba1048f1ac..ce1bda06b48be6b565a12f2ca9391a7971171578 100644
--- a/binarycpython/tests/test_grid.py
+++ b/binarycpython/tests/test_grid.py
@@ -256,17 +256,17 @@ class test_Population(unittest.TestCase):
self.assertIn("custom_options", population_settings)
self.assertTrue(population_settings["custom_options"]["data_dir"] == "/tmp")
- def test__return_binary_c_version_info(self):
+ def test_return_binary_c_version_info(self):
with Capturing() as output:
- self._test__return_binary_c_version_info()
+ self._test_return_binary_c_version_info()
- def _test__return_binary_c_version_info(self):
+ def _test_return_binary_c_version_info(self):
"""
- Unittests for the function _return_binary_c_version_info
+ Unittests for the function return_binary_c_version_info
"""
test_pop = Population()
- binary_c_version_info = test_pop._return_binary_c_version_info(parsed=True)
+ binary_c_version_info = test_pop.return_binary_c_version_info(parsed=True)
self.assertTrue(isinstance(binary_c_version_info, dict))
self.assertIn("isotopes", binary_c_version_info)
@@ -289,17 +289,17 @@ class test_Population(unittest.TestCase):
if binary_c_version_info["macros"]["NUCSYN_ID_SOURCES"] == "on":
self.assertIsNotNone(binary_c_version_info["nucleosynthesis_sources"])
- def test__return_binary_c_defaults(self):
+ def test_return_binary_c_defaults(self):
with Capturing() as output:
- self._test__return_binary_c_defaults()
+ self._test_return_binary_c_defaults()
- def _test__return_binary_c_defaults(self):
+ def _test_return_binary_c_defaults(self):
"""
- Unittests for the function _return_binary_c_defaults
+ Unittests for the function return_binary_c_defaults
"""
test_pop = Population()
- binary_c_defaults = test_pop._return_binary_c_defaults()
+ binary_c_defaults = test_pop.return_binary_c_defaults()
self.assertIn("probability", binary_c_defaults)
self.assertIn("phasevol", binary_c_defaults)
self.assertIn("metallicity", binary_c_defaults)
diff --git a/binarycpython/utils/functions.py b/binarycpython/utils/functions.py
index c1c2379beea2d2facf824381440234b89389a138..5a1caf4cee196eed44bf03d894d5371bb0711f6b 100644
--- a/binarycpython/utils/functions.py
+++ b/binarycpython/utils/functions.py
@@ -10,6 +10,7 @@ Tasks:
import json
import os
+import gc
import tempfile
import copy
import inspect
@@ -73,6 +74,35 @@ def get_size(obj, seen=None):
size += sum([get_size(i, seen) for i in obj])
return size
+
+def format_ensemble_results(ensemble_dictionary):
+ """
+ Function to handle all the steps of formatting the ensemble output again.
+
+ Input:
+ ensemble_dictionary: dictionary containing all the ensemble results
+ """
+
+ original_ensemble_results = ensemble_dictionary
+
+ float_format_ensemble_results = recursive_change_key_to_float(original_ensemble_results)
+ del original_ensemble_results
+ gc.collect()
+
+ # Then sort the dictionary
+ sorted_ensemble_results = custom_sort_dict(float_format_ensemble_results)
+ del float_format_ensemble_results
+ gc.collect()
+
+ # Then Change the keys back to a string but with a %g format.
+ reformatted_ensemble_results = recursive_change_key_to_string(sorted_ensemble_results)
+ del sorted_ensemble_results
+ gc.collect()
+
+ # Put back in the dictionary
+ return reformatted_ensemble_results
+
+
def subtract_dicts(dict_1: dict, dict_2: dict) -> dict:
"""
Function to subtract two dictionaries.
diff --git a/binarycpython/utils/grid.py b/binarycpython/utils/grid.py
index c0bfae70ae996d079c6fc2c28fdf348d8919b333..d027b8a4cd4858ad26a06fd98fef274922f47c57 100644
--- a/binarycpython/utils/grid.py
+++ b/binarycpython/utils/grid.py
@@ -72,6 +72,7 @@ from binarycpython.utils.functions import (
custom_sort_dict,
recursive_change_key_to_string,
multiply_values_dict,
+ format_ensemble_results,
)
@@ -961,33 +962,6 @@ class Population:
for _ in range(amt_cores):
job_queue.put("STOP")
- def format_ensemble_results(self, ensemble_dictionary):
- """
- Function to handle all the steps of formatting the ensemble output again.
-
- Input:
- ensemble_dictionary: dictionary containing all the ensemble results
- """
-
- original_ensemble_results = ensemble_dictionary
-
- float_format_ensemble_results = recursive_change_key_to_float(original_ensemble_results)
- del original_ensemble_results
- gc.collect()
-
- # Then sort the dictionary
- sorted_ensemble_results = custom_sort_dict(float_format_ensemble_results)
- del float_format_ensemble_results
- gc.collect()
-
- # Then Change the keys back to a string but with a %g format.
- reformatted_ensemble_results = recursive_change_key_to_string(sorted_ensemble_results)
- del sorted_ensemble_results
- gc.collect()
-
- # Put back in the dictionary
- return reformatted_ensemble_results
-
def _evolve_population_grid(self):
"""
Function that handles running the population using multiprocessing.
@@ -1049,7 +1023,7 @@ class Population:
break
# Extra ensemble result manipulation:
- combined_output_dict['ensemble_results']['ensemble'] = self.format_ensemble_results(combined_output_dict['ensemble_results'].get('ensemble', {}))
+ combined_output_dict['ensemble_results']['ensemble'] = format_ensemble_results(combined_output_dict['ensemble_results'].get('ensemble', {}))
gc.collect()
# Take into account that we run this on multiple cores
@@ -1421,10 +1395,11 @@ class Population:
),
)
+ # TODO: consider writing this in a formatted structure
# Write to file
- ensemble_output = extract_ensemble_json_from_string(ensemble_raw_output)
with open(output_file, "w") as f:
- f.write(json.dumps(self.format_ensemble_results(ensemble_output)))
+ 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 7aec69eae0a90a6d767573701958bdff340b21ec..21d49016f3b2826d6f9d5ec87a1f6d8bb18df7af 100644
--- a/examples/notebook_individual_systems.ipynb
+++ b/examples/notebook_individual_systems.ipynb
@@ -27,7 +27,7 @@
},
{
"cell_type": "code",
- "execution_count": 16,
+ "execution_count": 1,
"id": "e32dcdee",
"metadata": {},
"outputs": [],
@@ -39,7 +39,7 @@
},
{
"cell_type": "code",
- "execution_count": 17,
+ "execution_count": 2,
"id": "425efed3-d8e3-432d-829e-41d8ebe05162",
"metadata": {},
"outputs": [],
@@ -50,7 +50,7 @@
},
{
"cell_type": "code",
- "execution_count": 18,
+ "execution_count": 3,
"id": "b2abab48-433d-4936-8434-14804c52c9f6",
"metadata": {},
"outputs": [
@@ -78,7 +78,7 @@
},
{
"cell_type": "code",
- "execution_count": 19,
+ "execution_count": 4,
"id": "029fc3f2-f09a-49af-a32b-248505738f2e",
"metadata": {},
"outputs": [
@@ -86,7 +86,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- " TIME M1 M2 K1 K2 SEP PER ECC R1/ROL1 R2/ROL2 TYPE RANDOM_SEED=9935 RANDOM_COUNT=0\n",
+ " TIME M1 M2 K1 K2 SEP PER ECC R1/ROL1 R2/ROL2 TYPE RANDOM_SEED=17089 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",
@@ -118,7 +118,7 @@
},
{
"cell_type": "code",
- "execution_count": 20,
+ "execution_count": 5,
"id": "e6a23b55-ca42-440d-83ac-e76a24a83a67",
"metadata": {
"tags": []
@@ -167,7 +167,7 @@
},
{
"cell_type": "code",
- "execution_count": 21,
+ "execution_count": 6,
"id": "3822721f-217a-495b-962e-d57137b9e290",
"metadata": {},
"outputs": [
@@ -217,7 +217,7 @@
},
{
"cell_type": "code",
- "execution_count": 22,
+ "execution_count": 7,
"id": "654a07ed-2a88-46ff-9da0-b7759580f9f3",
"metadata": {},
"outputs": [
@@ -268,7 +268,7 @@
},
{
"cell_type": "code",
- "execution_count": 23,
+ "execution_count": 8,
"id": "4a98ffca-1b72-4bb8-8df1-3bf3187d882f",
"metadata": {},
"outputs": [],
@@ -287,7 +287,7 @@
},
{
"cell_type": "code",
- "execution_count": 24,
+ "execution_count": 9,
"id": "bff1cc2e-6b32-4ba0-879f-879ffbabd223",
"metadata": {},
"outputs": [
@@ -333,7 +333,7 @@
},
{
"cell_type": "code",
- "execution_count": 25,
+ "execution_count": 10,
"id": "dd748bab-b57e-4129-8350-9ea11fa179d0",
"metadata": {
"scrolled": true,
@@ -358,7 +358,7 @@
"Creating and loading custom logging functionality\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_491813c1f1184f97951202e364eb3b55.so\n",
+ "Removed /tmp/binary_c_python/custom_logging/libcustom_logging_8967553693ac4e11a49c42d4eef773e8.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",
@@ -398,7 +398,7 @@
},
{
"cell_type": "code",
- "execution_count": 26,
+ "execution_count": 11,
"id": "fec39154-cce6-438c-8c2c-509d76b00f34",
"metadata": {},
"outputs": [],
@@ -449,7 +449,7 @@
},
{
"cell_type": "code",
- "execution_count": 27,
+ "execution_count": 12,
"id": "57347512-fd4a-434b-b13c-5e6dbd3ac415",
"metadata": {
"scrolled": true,
@@ -460,13 +460,13 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "adding: parse_function=<function object_parse_function at 0x7fa3136e5378> to grid_options\n",
+ "adding: parse_function=<function object_parse_function at 0x7fb4d41ebbf8> 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 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_83729c10ca52451cb773d29d6b28ea96.so\n",
+ "Removed /tmp/binary_c_python/custom_logging/libcustom_logging_5d7779e8190e4b79b10c7e6a44cb0e7e.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"
]
@@ -511,7 +511,7 @@
},
{
"cell_type": "code",
- "execution_count": 28,
+ "execution_count": 13,
"id": "ec48125c-6bf5-48f4-9357-8261800b5d8b",
"metadata": {},
"outputs": [
diff --git a/examples/notebook_population.ipynb b/examples/notebook_population.ipynb
index 56f3b153c23064e82863f188906d50243e795715..b6a37baa8d90a2f36c0fd19311548ed49e77f173 100644
--- a/examples/notebook_population.ipynb
+++ b/examples/notebook_population.ipynb
@@ -3,7 +3,9 @@
{
"cell_type": "markdown",
"id": "bbbaafbb-fd7d-4b73-a970-93506ba35d71",
- "metadata": {},
+ "metadata": {
+ "tags": []
+ },
"source": [
"# Running populations with binarycpython\n",
"This notebook will show you how to evolve a population of stars\n",
@@ -27,15 +29,6 @@
"# help(Population) # Uncomment to see the public functions of this object"
]
},
- {
- "cell_type": "markdown",
- "id": "a081ab23-7822-4971-aa82-991548534714",
- "metadata": {},
- "source": [
- "- running ensemble\n",
- "- using M&S grid"
- ]
- },
{
"cell_type": "markdown",
"id": "f268eff3-4e08-4f6b-8b59-f22dba4d2074",
@@ -329,7 +322,7 @@
],
"source": [
"# Add grid variables\n",
- "resolution = {\"M_1\": 20, \"q\": 20, \"per\": 40}\n",
+ "resolution = {\"M_1\": 20}\n",
"\n",
"# Mass\n",
"example_pop.add_grid_variable(\n",
@@ -1125,7 +1118,7 @@
")\n",
"\n",
"# Add grid variables\n",
- "resolution = {\"M_1\": 5, \"q\": 5, \"per\": 5}\n",
+ "resolution = {\"M_1\": 3, \"q\": 3, \"per\": 3}\n",
"\n",
"# Mass\n",
"example_pop.add_grid_variable(\n",