diff --git a/docs/source/_static/coverage.svg b/docs/source/_static/coverage.svg
deleted file mode 100644
index e3a194825898162c01c3ad48af8208fd626e36a5..0000000000000000000000000000000000000000
--- a/docs/source/_static/coverage.svg
+++ /dev/null
@@ -1,21 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<svg xmlns="http://www.w3.org/2000/svg" width="99" height="20">
- <linearGradient id="b" x2="0" y2="100%">
- <stop offset="0" stop-color="#bbb" stop-opacity=".1"/>
- <stop offset="1" stop-opacity=".1"/>
- </linearGradient>
- <mask id="a">
- <rect width="99" height="20" rx="3" fill="#fff"/>
- </mask>
- <g mask="url(#a)">
- <path fill="#555" d="M0 0h63v20H0z"/>
- <path fill="#e05d44" d="M63 0h36v20H63z"/>
- <path fill="url(#b)" d="M0 0h99v20H0z"/>
- </g>
- <g fill="#fff" text-anchor="middle" font-family="DejaVu Sans,Verdana,Geneva,sans-serif" font-size="11">
- <text x="31.5" y="15" fill="#010101" fill-opacity=".3">coverage</text>
- <text x="31.5" y="14">coverage</text>
- <text x="80" y="15" fill="#010101" fill-opacity=".3">5%</text>
- <text x="80" y="14">5%</text>
- </g>
-</svg>
diff --git a/docs/source/binary_c_parameters.rst b/docs/source/binary_c_parameters.rst
index b24fad112973e222734f17c6c792c598d3bcb77d..31481dd7b9db0a44656c723cb8d5ff2831b31a6c 100644
--- a/docs/source/binary_c_parameters.rst
+++ b/docs/source/binary_c_parameters.rst
@@ -1,5 +1,10 @@
Binary\_c parameters
====================
+The following chapter contains all the parameters that the current version of binary\_c can handle, along with their descriptions and other properties.
+
+
+This information was obtained by the following binary_c build:
+ **binary_c git branch**: branch_david **binary_c git revision**: 5473:20210104:97f766764 **Built on**: Jan 4 2021 18:40:36
Section: stars
@@ -2330,4 +2335,5 @@ Section: misc
| **Description**: Display list of arguments with their default values. Useful for batchmode.
| **Parameter input type**: *
| **Default value**: NULL
-| **Extra**: Ignore
\ No newline at end of file
+| **Extra**: Ignore
+
diff --git a/docs/source/conf.py b/docs/source/conf.py
index ccf1ef45f4204c4f9e9c59d959033cc58178bed6..118f1a9be674429d2dd8e962f376888a81acc54d 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -3,7 +3,7 @@
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
-
+# https://brendanhasz.github.io/2019/01/05/sphinx.html
# -- Path setup --------------------------------------------------------------
# If extensions (or modules to document with autodoc) are in another directory,
@@ -13,14 +13,16 @@
import os
import sys
+import sphinx_rtd_theme
+
# https://www.sphinx-doc.org/en/1.5/ext/example_google.html
# Include paths for python code
sys.path.insert(0, os.path.abspath("."))
-sys.path.insert(0, os.path.abspath("../../binarycpython"))
-# sys.path.insert(0, os.path.abspath('../../examples'))
-sys.path.insert(0, os.path.abspath("../../"))
-sys.path.insert(0, os.path.abspath("../../binarycpython/utils"))
+# sys.path.insert(0, os.path.abspath("../../binarycpython"))
+# # sys.path.insert(0, os.path.abspath('../../examples'))
+# sys.path.insert(0, os.path.abspath("../../"))
+# sys.path.insert(0, os.path.abspath("../../binarycpython/utils"))
sys.path.insert(0, os.path.join(os.getenv("BINARY_C"), "src/API/"))
# include paths for c code
@@ -33,9 +35,6 @@ copyright = "2020, David Hendriks, Robert Izzard"
author = "David Hendriks, Robert Izzard"
-
-
-
# -- General configuration ---------------------------------------------------
# Add any Sphinx extension module names here, as strings. They can be
@@ -50,12 +49,14 @@ extensions = [
"sphinx.ext.napoleon",
"hawkmoth",
"m2r2",
+ "sphinx_rtd_theme",
+ "sphinx_autodoc_typehints", # https://mypy.readthedocs.io/en/stable/cheat_sheet_py3.html
]
# Napoleon settings
-napoleon_google_docstring = True
-napoleon_numpy_docstring = False
+napoleon_google_docstring = True # https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html
+napoleon_numpy_docstring = False
napoleon_include_init_with_doc = False
napoleon_include_private_with_doc = False
napoleon_include_special_with_doc = True
@@ -66,7 +67,6 @@ napoleon_use_ivar = False
napoleon_use_param = True
napoleon_use_rtype = True
-
source_suffix = [".rst", ".md"]
# Add any paths that contain templates here, relative to this directory.
@@ -82,8 +82,9 @@ exclude_patterns = []
# The theme to use for HTML and HTML Help pages. See the documentation for
# a list of builtin themes.
-#
-html_theme = "alabaster"
+
+# html_theme = "alabaster"
+html_theme = "sphinx_rtd_theme"
# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
@@ -91,7 +92,6 @@ html_theme = "alabaster"
html_static_path = ["_static"]
-
"""Patching m2r2"""
import m2r2
@@ -107,4 +107,16 @@ def patched_m2r2_setup(app):
version=m2r2.__version__, parallel_read_safe=True, parallel_write_safe=True,
)
-m2r2.setup = patched_m2r2_setup
\ No newline at end of file
+m2r2.setup = patched_m2r2_setup
+
+# Generate some custom documentations for this version of binarycpython and binary_c
+from binarycpython.utils.functions import write_binary_c_parameter_descriptions_to_rst_file
+from binarycpython.utils.grid_options_defaults import write_grid_options_to_rst_file
+
+print("Generating binary_c_parameters.rst")
+write_binary_c_parameter_descriptions_to_rst_file("binary_c_parameters.rst")
+print("Done")
+
+print("Generating grid_options_descriptions.rst")
+write_grid_options_to_rst_file("grid_options_descriptions.rst")
+print("Done")
diff --git a/docs/source/coverage.svg b/docs/source/coverage.svg
deleted file mode 100644
index e3a194825898162c01c3ad48af8208fd626e36a5..0000000000000000000000000000000000000000
--- a/docs/source/coverage.svg
+++ /dev/null
@@ -1,21 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<svg xmlns="http://www.w3.org/2000/svg" width="99" height="20">
- <linearGradient id="b" x2="0" y2="100%">
- <stop offset="0" stop-color="#bbb" stop-opacity=".1"/>
- <stop offset="1" stop-opacity=".1"/>
- </linearGradient>
- <mask id="a">
- <rect width="99" height="20" rx="3" fill="#fff"/>
- </mask>
- <g mask="url(#a)">
- <path fill="#555" d="M0 0h63v20H0z"/>
- <path fill="#e05d44" d="M63 0h36v20H63z"/>
- <path fill="url(#b)" d="M0 0h99v20H0z"/>
- </g>
- <g fill="#fff" text-anchor="middle" font-family="DejaVu Sans,Verdana,Geneva,sans-serif" font-size="11">
- <text x="31.5" y="15" fill="#010101" fill-opacity=".3">coverage</text>
- <text x="31.5" y="14">coverage</text>
- <text x="80" y="15" fill="#010101" fill-opacity=".3">5%</text>
- <text x="80" y="14">5%</text>
- </g>
-</svg>
diff --git a/docs/source/custom_logging_functions.rst b/docs/source/custom_logging_functions.rst
index 84f5bcf9954aab034c5ee509f3be6038e5bf7c51..e382d4320eb4ab1546f534724b45368c7e2319a4 100644
--- a/docs/source/custom_logging_functions.rst
+++ b/docs/source/custom_logging_functions.rst
@@ -1,7 +1,7 @@
custom\_logging\_functions module
=================================
-.. automodule:: custom_logging_functions
+.. automodule:: binarycpython.utils.custom_logging_functions
:members:
:undoc-members:
:show-inheritance:
diff --git a/docs/source/distribution_functions.rst b/docs/source/distribution_functions.rst
index 0e6da4a9e8c1316096fd26270cb5aa306526dee7..5881ee38299d5af76771ac7312abd140886f99d1 100644
--- a/docs/source/distribution_functions.rst
+++ b/docs/source/distribution_functions.rst
@@ -1,7 +1,7 @@
distribution_functions module
=================================
-.. automodule:: distribution_functions
+.. automodule:: binarycpython.utils.distribution_functions
:members:
:undoc-members:
:show-inheritance:
\ No newline at end of file
diff --git a/docs/source/functions.rst b/docs/source/functions.rst
index 087d090c05d40e4c58022adbc9fb1d41b0b84507..e675cc8780c7725f698119fab7237b4adcfb8e52 100644
--- a/docs/source/functions.rst
+++ b/docs/source/functions.rst
@@ -1,7 +1,7 @@
functions module
================
-.. automodule:: functions
+.. automodule:: binarycpython.utils.functions
:members:
:undoc-members:
:show-inheritance:
diff --git a/docs/source/grid.rst b/docs/source/grid.rst
index ea842b9750a9e1d71dab567cf5670f3040907b0c..5f3347e6f42616884c86dffc98baf5da3bc8ea03 100644
--- a/docs/source/grid.rst
+++ b/docs/source/grid.rst
@@ -1,7 +1,7 @@
grid\_class module
=================================
-.. automodule:: grid
+.. automodule:: binarycpython.utils.grid
:members:
:undoc-members:
:show-inheritance:
\ No newline at end of file
diff --git a/docs/source/grid_options_defaults.rst b/docs/source/grid_options_defaults.rst
index 185893b362605acab15f229763846bbf9c5820f2..c66555ac9989dff3ad956f893683dc34c4dc4c46 100644
--- a/docs/source/grid_options_defaults.rst
+++ b/docs/source/grid_options_defaults.rst
@@ -1,7 +1,7 @@
-grid\_options\_defaults module
-=================================
+Grid options and descriptions
+=============================
-.. automodule:: grid_options_defaults
+.. automodule:: binarycpython.utils.grid_options_defaults
:members:
:undoc-members:
:show-inheritance:
\ No newline at end of file
diff --git a/docs/source/grid_options_descriptions.rst b/docs/source/grid_options_descriptions.rst
index db86452ceafe504bd31d52e7460da162d3f5ca26..5cef435708da72fe78b6838571fbd91a8c6880b2 100644
--- a/docs/source/grid_options_descriptions.rst
+++ b/docs/source/grid_options_descriptions.rst
@@ -1,7 +1,156 @@
-grid\_options\_descriptions module
-==================================
+Population grid code options
+============================
+The following chapter contains all grid code options, along with their descriptions
+There are 27 options that are not described yet.
+
+
+Public options
+--------------
+The following options are meant to be changed by the user.
+
+
+| **C_auto_logging**: Dictionary containing parameters to be logged by binary_c. The structure of this dictionary is as follows: the key is used as the headline which the user can then catch. The value at that key is a list of binary_c system parameters (like star[0].mass)
+
+| **C_logging_code**: Variable to store the exact code that is used for the custom_logging. In this way the user can do more complex logging, as well as putting these logging strings in files.
+
+| **amt_cores**: The amount of cores that the population grid will use. The multiprocessing is useful but make sure to figure out how many logical cores the machine has. The core is multiprocessed, not multithreaded, and will gain no extra speed when amt_cores exceeds the amount of logical cores. Input: int
+
+| **binary**: Set this to 1 if the population contains binaries. Input: int
+
+| **condor**: Int flag whether to use a condor type population evolution.
+
+| **condor_command**: No description available yet
+
+| **condor_dir**: No description available yet
+
+| **condor_extra_settings**: No description available yet
+
+| **condor_jobid**: No description available yet
+
+| **condor_join_pwd**: No description available yet
+
+| **condor_memory**: No description available yet
+
+| **condor_njobs**: No description available yet
+
+| **condor_postpone_join**: No description available yet
+
+| **condor_universe**: No description available yet
+
+| **custom_logging_func_memaddr**: Memory adress where the custom_logging_function is stored. Input: int
+
+| **evolution_type**: Variable containing the type of evolution used of the grid. Multiprocessing or linear processing
+
+| **failed_systems_threshold**: Variable storing the maximum amount of systems that are allowed to fail before logging their commandline arguments to failed_systems log files
+
+| **gridcode_filename**: Filename for the grid code. Set and used by the population object. TODO: allow the user to provide their own function, rather than only a generated function.
+
+| **log_args**: Boolean to log the arguments. Unused
+
+| **log_args_dir**: Directory to log the arguments to. Unused
+
+| **log_file**: Log file for the population object. Unused
+
+| **modulo**: No description available yet
+
+| **parse_function**: Function that the user can provide to handle the output the binary_c. This function has to take the arguments (self, output). Its best not to return anything in this function, and just store stuff in the grid_options['results'] dictionary, or just output results to a file
+
+| **population_type**: variable storing what kind of population type should be evolved. See population_type_options for the options.
+
+| **results**: Dictionary in which the user can place their results. This dictionary gets merged at the end of a mulitprocessing simulation.
+
+| **slurm**: Int flag whether to use a slurm type population evolution.
+
+| **slurm_array**: No description available yet
+
+| **slurm_command**: No description available yet
+
+| **slurm_control_CPUs**: No description available yet
+
+| **slurm_dir**: No description available yet
+
+| **slurm_extra_settings**: No description available yet
+
+| **slurm_jobarrayindex**: No description available yet
+
+| **slurm_jobid**: No description available yet
+
+| **slurm_jobname**: No description available yet
+
+| **slurm_memory**: No description available yet
+
+| **slurm_njobs**: No description available yet
+
+| **slurm_ntasks**: No description available yet
+
+| **slurm_partition**: No description available yet
+
+| **slurm_postpone_join**: No description available yet
+
+| **slurm_postpone_sbatch**: No description available yet
+
+| **slurm_time**: No description available yet
+
+| **slurm_use_all_node_CPUs**: No description available yet
+
+| **slurm_warn_max_memory**: No description available yet
+
+| **source_file_filename**: Variable containing the source file containing lines of binary_c commandline calls. These all have to start with binary_c.
+
+| **tmp_dir**: Directory where certain types of output are stored. The grid code is stored in that directory, as well as the custom logging libraries. Log files and other diagnostics will usually be written to this location, unless specified otherwise
+
+| **verbosity**: Verbosity of the population code. Default is 0, by which only errors will be printed. Higher values will show more output, which is good for debugging.
+
+Private options
+---------------
+The following options are not meant to be changed by the user, as these options are used and set internally by the object itself. The description still is provided, but just for documentation purposes.
+| **_binary_c_config_executable**: Full path of the binary_c-config executable. This options is not used in the population object.
+
+| **_binary_c_dir**: Director where binary_c is stored. This options are not really used
+
+| **_binary_c_executable**: Full path to the binary_c executable. This options is not used in the population object.
+
+| **_binary_c_shared_library**: Full path to the libbinary_c file. This options is not used in the population object
+
+| **_commandline_input**: String containing the arguments passed to the population object via the command line. Set and used by the population object.
+
+| **_count**: Counter tracking which system the generator is on.
+
+| **_custom_logging_shared_library_file**: filename for the custom_logging shared library. Used and set by the population object
+
+| **_end_time_evolution**: Variable storing the end timestamp of the population evolution. Set by the object itself
+
+| **_errors_exceeded**: Variable storing a boolean flag whether the amount of errors was higher than the set threshold (failed_systems_threshold). If True, then the commandline arguments of the failing systems will not be stored in the failed_system_log files.
+
+| **_errors_found**: Variable storing a boolean flag whether errors by binary_c are encountered.
+
+| **_evolution_type_options**: List containing the evolution type options.
+
+| **_failed_count**: Variable storing the amount of failed systems.
+
+| **_failed_prob**: Variable storing the total probability of all the failed systems
+
+| **_failed_systems_error_codes**: List storing the unique error codes raised by binary_c of the failed systems
+
+| **_grid_variables**: Dictionary storing the grid_variables. These contain properties which are accessed by the _generate_grid_code function
+
+| **_main_pid**: Main process ID of the master process. Used and set by the population object.
+
+| **_population_id**: Variable storing a unique 32-char hex string.
+
+| **_population_type_options**: List storing the population_type options.
+
+| **_probtot**: Total probability of the population.
+
+| **_repeat**: Factor of how many times a system should be repeated. Consider the evolution splitting binary_c argument for supernovae kick repeating.
+
+| **_start_time_evolution**: Variable storing the start timestamp of the population evolution. Set by the object itself.
+
+| **_store_memaddr**: Memory adress of the store object for binary_c.
+
+| **_system_generator**: Function object that contains the system generator function. This can be from a grid, or a source file, or a montecarlo grid.
+
+| **_total_starcount**: Variable storing the total amount of systems in the generator. Used and set by the population object.
+
+| **_weight**: Weight factor for each system. The calculated probability is mulitplied by this. If the user wants each system to be repeated several times, then this variable should not be changed, rather change the _repeat variable instead, as that handles the reduction in probability per system. This is useful for systems that have a process with some random element in it.
-.. automodule:: grid_options_descriptions
- :members:
- :undoc-members:
- :show-inheritance:
\ No newline at end of file
diff --git a/docs/source/hpc_functions.rst b/docs/source/hpc_functions.rst
index bb7f5b3503383e6cb0e0213e0c587ea70405db6a..d336a0be090ee3eac23c4342286fe8895e0aea6f 100644
--- a/docs/source/hpc_functions.rst
+++ b/docs/source/hpc_functions.rst
@@ -1,7 +1,7 @@
hpc\_functions module
=================================
-.. automodule:: hpc_functions
+.. automodule:: binarycpython.utils.hpc_functions
:members:
:undoc-members:
:show-inheritance:
\ No newline at end of file
diff --git a/docs/source/index.rst b/docs/source/index.rst
index 2cc0b56d9d1dffc2d2b6e4b9f0da1bdb53f89ed7..bf0ccf76e20c9344a43d7345dd40a3d377bc2f68 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -13,8 +13,9 @@ Welcome to binary_c-python's documentation!
readme_link
modules
examples
- tutorials
binary_c_parameters
+ grid_options_descriptions
+
Indices and tables
==================
diff --git a/docs/source/modules.rst b/docs/source/modules.rst
index c3304001b567c72b00229415882dc867bc69fd7c..d4aaac5025cbb089f2754ed01ef8bd92f70bf81c 100644
--- a/docs/source/modules.rst
+++ b/docs/source/modules.rst
@@ -10,7 +10,6 @@ This chapter contains the (auto)documentation for all the functions and modules
functions
grid
grid_options_defaults
- grid_options_descriptions
hpc_functions
plot_functions
run_system_wrapper
diff --git a/docs/source/plot_functions.rst b/docs/source/plot_functions.rst
index 9eef3f7f864cad7a21b73b050af2701f5d611b8c..6af374e53223ea93532fcd50ced89130f6f917d7 100644
--- a/docs/source/plot_functions.rst
+++ b/docs/source/plot_functions.rst
@@ -1,7 +1,7 @@
plot\_functions module
=================================
-.. automodule:: plot_functions
+.. automodule:: binarycpython.utils.plot_functions
:members:
:undoc-members:
:show-inheritance:
\ No newline at end of file
diff --git a/docs/source/run_system_wrapper.rst b/docs/source/run_system_wrapper.rst
index 44020176e8a9dca366b30a41931b088fb0cca6df..388b6878c2394eed9020aa4e3a48a9d531287ff2 100644
--- a/docs/source/run_system_wrapper.rst
+++ b/docs/source/run_system_wrapper.rst
@@ -1,7 +1,7 @@
run\_system\_wrapper module
=================================
-.. automodule:: run_system_wrapper
+.. automodule:: binarycpython.utils.run_system_wrapper
:members:
:undoc-members:
:show-inheritance:
\ No newline at end of file
diff --git a/docs/source/spacing_functions.rst b/docs/source/spacing_functions.rst
index 22af7e645b221c7db9166638f690aa8bb4079a5c..be0cf254dd52aafbde7404c588be65abcc46493e 100644
--- a/docs/source/spacing_functions.rst
+++ b/docs/source/spacing_functions.rst
@@ -1,7 +1,7 @@
spacing\_functions module
=================================
-.. automodule:: spacing_functions
+.. automodule:: binarycpython.utils.spacing_functions
:members:
:undoc-members:
:show-inheritance:
\ No newline at end of file
diff --git a/docs/source/stellar_types.rst b/docs/source/stellar_types.rst
index 4fbcab371f65b4e07137de53ecf0d7c10923cd0e..1254b3d55209d3450c07013224ca39e2866941d5 100644
--- a/docs/source/stellar_types.rst
+++ b/docs/source/stellar_types.rst
@@ -1,7 +1,7 @@
stellar\_types module
=====================
-.. automodule:: stellar_types
+.. automodule:: binarycpython.utils.stellar_types
:members:
:undoc-members:
:show-inheritance:
diff --git a/docs/source/tutorials.rst b/docs/source/tutorials.rst
deleted file mode 100644
index ec639385c16adfdd23371baf56de0b3a805235a0..0000000000000000000000000000000000000000
--- a/docs/source/tutorials.rst
+++ /dev/null
@@ -1,3 +0,0 @@
-Tutorials
-=========
-This chapter contains some tutorials for some problems
\ No newline at end of file
diff --git a/docs/source/useful_funcs.rst b/docs/source/useful_funcs.rst
index 0c0e9d99a4999b94344d7d1c3bdc86ecc399c5ff..2b8b9d26a6b16af7bd581a2d3a42fc746da039a3 100644
--- a/docs/source/useful_funcs.rst
+++ b/docs/source/useful_funcs.rst
@@ -1,7 +1,7 @@
useful\_funcs module
=================================
-.. automodule:: useful_funcs
+.. automodule:: binarycpython.utils.useful_funcs
:members:
:undoc-members:
:show-inheritance:
\ No newline at end of file