From 7b5c97ab1b5edb8c810fa49e30a174618ad171a0 Mon Sep 17 00:00:00 2001
From: loikki <loic.hausammann@protonmail.ch>
Date: Wed, 22 May 2019 09:38:55 +0200
Subject: [PATCH] Start doc
---
docs/Makefile | 19 ++++
docs/conf.py | 201 ++++++++++++++++++++++++++++++++++++++++
docs/index.rst | 23 +++++
docs/make.bat | 35 +++++++
docs/pyswiftsim.rst | 11 +++
docs/wrapper.rst | 11 +++
test/getCoolingTable.sh | 2 +
test/test_cooling.py | 59 ++++++++++++
test/test_cooling.yml | 20 ++++
9 files changed, 381 insertions(+)
create mode 100644 docs/Makefile
create mode 100644 docs/conf.py
create mode 100644 docs/index.rst
create mode 100644 docs/make.bat
create mode 100644 docs/pyswiftsim.rst
create mode 100644 docs/wrapper.rst
create mode 100644 test/getCoolingTable.sh
create mode 100644 test/test_cooling.py
create mode 100644 test/test_cooling.yml
diff --git a/docs/Makefile b/docs/Makefile
new file mode 100644
index 0000000..298ea9e
--- /dev/null
+++ b/docs/Makefile
@@ -0,0 +1,19 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS =
+SPHINXBUILD = sphinx-build
+SOURCEDIR = .
+BUILDDIR = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+ @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+ @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
\ No newline at end of file
diff --git a/docs/conf.py b/docs/conf.py
new file mode 100644
index 0000000..aa7b47b
--- /dev/null
+++ b/docs/conf.py
@@ -0,0 +1,201 @@
+# -*- coding: utf-8 -*-
+#
+# Configuration file for the Sphinx documentation builder.
+#
+# This file does only contain a selection of the most common options. For a
+# full list see the documentation:
+# http://www.sphinx-doc.org/en/master/config
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'PySWIFTsim'
+copyright = '2019, Loic Hausammann'
+author = 'Loic Hausammann'
+
+# The short X.Y version
+version = ''
+# The full version, including alpha/beta/rc tags
+release = ''
+
+
+# -- General configuration ---------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+ 'sphinx.ext.autodoc',
+ 'sphinx.ext.doctest',
+ 'sphinx.ext.intersphinx',
+ 'sphinx.ext.todo',
+ 'sphinx.ext.coverage',
+ 'sphinx.ext.mathjax',
+ 'sphinx.ext.viewcode',
+ 'numpydoc'
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
+
+# The master toctree document.
+master_doc = 'index'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = None
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages. See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'alabaster'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further. For a list of options available for each theme, see the
+# documentation.
+#
+# html_theme_options = {}
+
+# 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,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# The default sidebars (for documents that don't match any pattern) are
+# defined by theme itself. Builtin themes are using these templates by
+# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
+# 'searchbox.html']``.
+#
+# html_sidebars = {}
+
+
+# -- Options for HTMLHelp output ---------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'PySWIFTsimdoc'
+
+
+# -- Options for LaTeX output ------------------------------------------------
+
+latex_elements = {
+ # The paper size ('letterpaper' or 'a4paper').
+ #
+ # 'papersize': 'letterpaper',
+
+ # The font size ('10pt', '11pt' or '12pt').
+ #
+ # 'pointsize': '10pt',
+
+ # Additional stuff for the LaTeX preamble.
+ #
+ # 'preamble': '',
+
+ # Latex figure (float) alignment
+ #
+ # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+# author, documentclass [howto, manual, or own class]).
+latex_documents = [
+ (master_doc, 'PySWIFTsim.tex', 'PySWIFTsim Documentation',
+ 'Loic Hausammann', 'manual'),
+]
+
+
+# -- Options for manual page output ------------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+ (master_doc, 'pyswiftsim', 'PySWIFTsim Documentation',
+ [author], 1)
+]
+
+
+# -- Options for Texinfo output ----------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+# dir menu entry, description, category)
+texinfo_documents = [
+ (master_doc, 'PySWIFTsim', 'PySWIFTsim Documentation',
+ author, 'PySWIFTsim', 'One line description of project.',
+ 'Miscellaneous'),
+]
+
+
+# -- Options for Epub output -------------------------------------------------
+
+# Bibliographic Dublin Core info.
+epub_title = project
+
+# The unique identifier of the text. This can be a ISBN number
+# or the project homepage.
+#
+# epub_identifier = ''
+
+# A unique identification for the text.
+#
+# epub_uid = ''
+
+# A list of files that should not be packed into the epub file.
+epub_exclude_files = ['search.html']
+
+
+# -- Extension configuration -------------------------------------------------
+
+# -- Options for intersphinx extension ---------------------------------------
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {
+ 'python': ('https://docs.python.org/', None),
+ 'numpy': ('https://docs.scipy.org/doc/numpy', None),
+}
+
+# -- Options for todo extension ----------------------------------------------
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = True
+
+# -- Options for numpy extension ----------------------------------------------
+
+numpydoc_use_plots = True
diff --git a/docs/index.rst b/docs/index.rst
new file mode 100644
index 0000000..9c79e72
--- /dev/null
+++ b/docs/index.rst
@@ -0,0 +1,23 @@
+.. PySWIFTsim documentation master file, created by
+ sphinx-quickstart on Wed May 22 08:34:27 2019.
+ You can adapt this file completely to your liking, but it should at least
+ contain the root `toctree` directive.
+
+Welcome to PySWIFTsim's documentation!
+======================================
+
+.. toctree::
+ :maxdepth: 2
+ :caption: Contents:
+
+ pyswiftsim.rst
+ wrapper.rst
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
diff --git a/docs/make.bat b/docs/make.bat
new file mode 100644
index 0000000..27f573b
--- /dev/null
+++ b/docs/make.bat
@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+ set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+ echo.
+ echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+ echo.installed, then set the SPHINXBUILD environment variable to point
+ echo.to the full path of the 'sphinx-build' executable. Alternatively you
+ echo.may add the Sphinx directory to PATH.
+ echo.
+ echo.If you don't have Sphinx installed, grab it from
+ echo.http://sphinx-doc.org/
+ exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+
+:end
+popd
diff --git a/docs/pyswiftsim.rst b/docs/pyswiftsim.rst
new file mode 100644
index 0000000..0e77bb5
--- /dev/null
+++ b/docs/pyswiftsim.rst
@@ -0,0 +1,11 @@
+PySWIFTsim
+==========
+
+.. automodule:: pyswiftsim
+ :members:
+ :undoc-members:
+ :private-members:
+ :special-members:
+ :show-inheritance:
+ :inherited-members:
+
diff --git a/docs/wrapper.rst b/docs/wrapper.rst
new file mode 100644
index 0000000..ed4f2fe
--- /dev/null
+++ b/docs/wrapper.rst
@@ -0,0 +1,11 @@
+Wrapper
+=======
+
+.. automodule:: pyswiftsim.wrapper
+ :members:
+ :undoc-members:
+ :private-members:
+ :special-members:
+ :show-inheritance:
+ :inherited-members:
+
diff --git a/test/getCoolingTable.sh b/test/getCoolingTable.sh
new file mode 100644
index 0000000..809958b
--- /dev/null
+++ b/test/getCoolingTable.sh
@@ -0,0 +1,2 @@
+#!/bin/bash
+wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/CoolingTables/CloudyData_UVB=HM2012.h5
diff --git a/test/test_cooling.py b/test/test_cooling.py
new file mode 100644
index 0000000..8623c51
--- /dev/null
+++ b/test/test_cooling.py
@@ -0,0 +1,59 @@
+#!/usr/bin/env python3
+
+from pyswiftsim.wrapper import coolingRate
+import numpy as np
+from astropy import units, constants
+import yaml
+
+# define parameters
+filename = "test_cooling.yml"
+# adiabatic index
+gamma = 5. / 3.
+
+# Read parameter file
+f = open(filename, "r")
+data = yaml.load(f)
+f.close()
+
+# Get the units
+swift_units = data["InternalUnitSystem"]
+# length unit
+u_l = float(swift_units["UnitLength_in_cgs"])
+# velocity unit
+u_v = float(swift_units["UnitVelocity_in_cgs"])
+# mass unit
+u_m = float(swift_units["UnitMass_in_cgs"])
+# time unit
+u_t = u_l / u_v
+# energy unit
+u_e = u_m * u_l**2 / u_t**2
+
+# boltzman constant
+k_B = constants.k_B.to("{} J / K".format(u_e))
+# proton mass
+m_p = constants.m_p.to("{} g".format(u_l))
+
+
+def internalEnergy(T):
+ u = k_B * T
+ u /= (gamma - 1.) * m_p
+ return u
+
+
+# generates data
+# density in atom / cm3
+density = np.array([1.], dtype=np.float32)
+density *= float(constants.m_p.to("g") / units.g) / u_m
+density *= u_l**3
+
+# Temperature in K
+T = np.array([100], dtype=np.float32)
+u = internalEnergy(T)
+
+# compute the cooling rate
+rate = coolingRate(filename, density, u)
+
+# go back to cgs
+rate /= u_e / u_t
+
+print("Cooling done: {} erg/s".format(rate))
diff --git a/test/test_cooling.yml b/test/test_cooling.yml
new file mode 100644
index 0000000..067bf3a
--- /dev/null
+++ b/test/test_cooling.yml
@@ -0,0 +1,20 @@
+# Define the system of units to use internally.
+InternalUnitSystem:
+ UnitMass_in_cgs: 1000 # Grams
+ UnitLength_in_cgs: 1 # Centimeters
+ UnitVelocity_in_cgs: 1 # Centimeters per second
+ UnitCurrent_in_cgs: 1 # Amperes
+ UnitTemp_in_cgs: 1 # Kelvin
+
+# Cooling with Grackle 3.0
+GrackleCooling:
+ CloudyTable: CloudyData_UVB=HM2012.h5 # Name of the Cloudy Table (available on the grackle bitbucket repository)
+ WithUVbackground: 1 # Enable or not the UV background
+ Redshift: 0 # Redshift to use (-1 means time based redshift)
+ WithMetalCooling: 1 # Enable or not the metal cooling
+ ProvideVolumetricHeatingRates: 0 # (optional) User provide volumetric heating rates
+ ProvideSpecificHeatingRates: 0 # (optional) User provide specific heating rates
+ SelfShieldingMethod: 0 # (optional) Grackle (<= 3) or Gear self shielding method
+ OutputMode: 0 # (optional) Write in output corresponding primordial chemistry mode
+ MaxSteps: 10000 # (optional) Max number of step when computing the initial composition
+ ConvergenceLimit: 1e-2 # (optional) Convergence threshold (relative) for initial composition
--
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