Commit 86bb06e6 authored by Cristian Lalescu's avatar Cristian Lalescu
Browse files

Merge branch 'feature/documentation' into develop

parents b49f29db 6e883bcd
......@@ -65,52 +65,3 @@ Comments
compatibility should be kept since mayavi (well, vtk actually) only
works on Python 2.
===========
Development
===========
`bfps` is using `git` for version tracking (see https://git-scm.com/
for description).
The branching model described at
http://nvie.com/posts/a-successful-git-branching-model/ should be
adhered to as strictly as possible.
The usable `VERSION` number will be constructed according to semantic
versioning rules (see http://semver.org/), `MAJOR.MINOR.PATCH`.
In principle, if you use `bfps` and you've created children of the
`NavierStokes` class, you should not need to rewrite your code unless
the `MAJOR` version changes.
Versioning guidelines
---------------------
There are 2 main branches, `master` and `develop`.
`setup.py` will call `git` to read in the `VERSION`: it will get the
latest available tag.
If the active branch name contains either of the strings `develop`,
`feature` or `bugfix`, then the full output of `git describe --tags`
will be used;
otherwise, only the string before the dash (if a dash exists) will be
used.
At the moment the following rules seem adequate.
Once I get feedback from someone who actually knows how to handle bigger
projects, these may change.
1. New features are worked on in branches forked from `develop`, with
the branch name of the form `feature/bla`.
Feature branches are merged back into `develop` only after all tests
pass.
2. Whenever the `develop` branch is merged into `master`, the last
commit on the `develop` branch is tagged with `MAJOR.MINOR`.
3. Whenever a bug is discovered in version X.Y, a new branch called `vX.Y`
is forked from the corresponding `master` merge point.
A new bugfix branch is forked from `vX.Y`, the bug is fixed, and then
this bugfix branch is merged into all affected branches (this includes
`vX.Y`).
After merging, the respective merge points are tagged adequately (`vX.Y`
gets the tag X.Y.1).
4. Whenever a bug is discovered in version X.Y.Z, a bugfix branch is
forked from `vX.Y`, and then rule 3 is adapted accordingly.
......@@ -422,8 +422,9 @@ class NavierStokes(bfps.fluid_base.fluid_particle_base):
:type frozen_particles: bool
:type acc_name: str
.. warning :: if not None, kcut must be a list of decreasing
wavenumbers, since filtering is done on the same field...
.. warning:: if not None, kcut must be a list of decreasing
wavenumbers, since filtering is done sequentially
on the same complex FFTW field.
"""
if self.dtype == np.float32:
FFTW = 'fftwf'
......
......@@ -32,8 +32,29 @@ def generate_data_3D(
dtype = np.complex128,
p = 1.5,
amplitude = 0.5):
"""
generate something that has the proper shape
"""returns the Fourier representation of a Gaussian random field.
The generated field is scalar (single component), in practice a
3D `numpy` complex-valued array.
The field will use the FFTW representation, with the slowest
direction corresponding to :math:`y`, the intermediate to :math:`z`
and the fastest direction to :math:`x`.
:param n0: number of :math:`z` nodes on real-space grid
:param n1: number of :math:`y` nodes on real-space grid
:param n2: number of :math:`x` nodes on real-space grid
:param dtype: data type to use, (default=numpy.complex128)
:param p: exponent for powerlaw to use in spectrum
:param amplitude: prefactor that field is multiplied with
:type n0: int
:type n1: int
:type n2: int
:type dtype: numpy.dtype
:type p: float
:type amplitude: float
:returns: `a`, a complex valued 3D `numpy.array` that uses the FFTW
layout.
"""
assert(n0 % 2 == 0 and n1 % 2 == 0 and n2 % 2 == 0)
a = np.zeros((n1, n0, n2/2+1), dtype = dtype)
......@@ -57,6 +78,17 @@ def generate_data_3D(
return a
def randomize_phases(v):
"""randomize the phases of an FFTW complex field.
Given some `numpy.array` of dimension at least 3, with values
corresponding to the FFTW layout for the Fourier representation,
randomize the phases (assuming that the initial field is complex
valued; otherwise I'm not sure what will come out).
:param v: `numpy.array` of dimension at least 3.
:returns: `v` with randomized phases (i.e. a Gaussian random field).
"""
phi = np.random.random(v.shape[:3])*(2*np.pi)
phi[0, 0, 0] = 0.0
for ky in range(1, phi.shape[0]//2):
......
# Makefile for Sphinx documentation
#
# You can set these variables from the command line.
SPHINXOPTS =
SPHINXBUILD = sphinx-build
PAPER =
BUILDDIR = _build
# User-friendly check for sphinx-build
ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
endif
# Internal variables.
PAPEROPT_a4 = -D latex_paper_size=a4
PAPEROPT_letter = -D latex_paper_size=letter
ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
# the i18n builder cannot share the environment and doctrees with the others
I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest coverage gettext
help:
@echo "Please use \`make <target>' where <target> is one of"
@echo " html to make standalone HTML files"
@echo " dirhtml to make HTML files named index.html in directories"
@echo " singlehtml to make a single large HTML file"
@echo " pickle to make pickle files"
@echo " json to make JSON files"
@echo " htmlhelp to make HTML files and a HTML help project"
@echo " qthelp to make HTML files and a qthelp project"
@echo " applehelp to make an Apple Help Book"
@echo " devhelp to make HTML files and a Devhelp project"
@echo " epub to make an epub"
@echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
@echo " latexpdf to make LaTeX files and run them through pdflatex"
@echo " latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
@echo " text to make text files"
@echo " man to make manual pages"
@echo " texinfo to make Texinfo files"
@echo " info to make Texinfo files and run them through makeinfo"
@echo " gettext to make PO message catalogs"
@echo " changes to make an overview of all changed/added/deprecated items"
@echo " xml to make Docutils-native XML files"
@echo " pseudoxml to make pseudoxml-XML files for display purposes"
@echo " linkcheck to check all external links for integrity"
@echo " doctest to run all doctests embedded in the documentation (if enabled)"
@echo " coverage to run coverage check of the documentation (if enabled)"
clean:
rm -rf $(BUILDDIR)/*
html:
$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
@echo
@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
dirhtml:
$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
@echo
@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
singlehtml:
$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
@echo
@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
pickle:
$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
@echo
@echo "Build finished; now you can process the pickle files."
json:
$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
@echo
@echo "Build finished; now you can process the JSON files."
htmlhelp:
$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
@echo
@echo "Build finished; now you can run HTML Help Workshop with the" \
".hhp project file in $(BUILDDIR)/htmlhelp."
qthelp:
$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
@echo
@echo "Build finished; now you can run "qcollectiongenerator" with the" \
".qhcp project file in $(BUILDDIR)/qthelp, like this:"
@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/bfps.qhcp"
@echo "To view the help file:"
@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/bfps.qhc"
applehelp:
$(SPHINXBUILD) -b applehelp $(ALLSPHINXOPTS) $(BUILDDIR)/applehelp
@echo
@echo "Build finished. The help book is in $(BUILDDIR)/applehelp."
@echo "N.B. You won't be able to view it unless you put it in" \
"~/Library/Documentation/Help or install it in your application" \
"bundle."
devhelp:
$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
@echo
@echo "Build finished."
@echo "To view the help file:"
@echo "# mkdir -p $$HOME/.local/share/devhelp/bfps"
@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/bfps"
@echo "# devhelp"
epub:
$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
@echo
@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
latex:
$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
@echo
@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
@echo "Run \`make' in that directory to run these through (pdf)latex" \
"(use \`make latexpdf' here to do that automatically)."
latexpdf:
$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
@echo "Running LaTeX files through pdflatex..."
$(MAKE) -C $(BUILDDIR)/latex all-pdf
@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
latexpdfja:
$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
@echo "Running LaTeX files through platex and dvipdfmx..."
$(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
text:
$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
@echo
@echo "Build finished. The text files are in $(BUILDDIR)/text."
man:
$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
@echo
@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
texinfo:
$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
@echo
@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
@echo "Run \`make' in that directory to run these through makeinfo" \
"(use \`make info' here to do that automatically)."
info:
$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
@echo "Running Texinfo files through makeinfo..."
make -C $(BUILDDIR)/texinfo info
@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
gettext:
$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
@echo
@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
changes:
$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
@echo
@echo "The overview file is in $(BUILDDIR)/changes."
linkcheck:
$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
@echo
@echo "Link check complete; look for any errors in the above output " \
"or in $(BUILDDIR)/linkcheck/output.txt."
doctest:
$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
@echo "Testing of doctests in the sources finished, look at the " \
"results in $(BUILDDIR)/doctest/output.txt."
coverage:
$(SPHINXBUILD) -b coverage $(ALLSPHINXOPTS) $(BUILDDIR)/coverage
@echo "Testing of coverage in the sources finished, look at the " \
"results in $(BUILDDIR)/coverage/python.txt."
xml:
$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
@echo
@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
pseudoxml:
$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
@echo
@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."
../../README.rst
\ No newline at end of file
API
===
bfps
----
.. automodule:: bfps
:members:
:undoc-members:
:inherited-members:
:show-inheritance:
bfps.NavierStokes
-----------------
.. automodule:: bfps.NavierStokes
:members:
:undoc-members:
:inherited-members:
:show-inheritance:
bfps.tools
----------
.. automodule:: bfps.tools
:members:
:undoc-members:
:inherited-members:
:show-inheritance:
Development
===========
Versioning guidelines
---------------------
Version tracking for `bfps` is done with `git` (see https://git-scm.com/
for description).
The branching model described at
http://nvie.com/posts/a-successful-git-branching-model/ should be
adhered to as strictly as possible.
The usable `VERSION` number will be constructed according to semantic
versioning rules (see http://semver.org/), `MAJOR.MINOR.PATCH`.
In principle, if you use `bfps` and you've created children of the
`NavierStokes` class, you should not need to rewrite your code unless
the `MAJOR` version changes.
There are 2 main branches, `master` and `develop`.
`setup.py` will call `git` to read in the `VERSION`: it will get the
latest available tag.
If the active branch name contains either of the strings `develop`,
`feature` or `bugfix`, then the full output of `git describe --tags`
will be used;
otherwise, only the string before the dash (if a dash exists) will be
used.
At the moment the following rules seem adequate.
Once I get feedback from someone who actually knows how to handle bigger
projects, these may change.
1. New features are worked on in branches forked from `develop`, with
the branch name of the form `feature/bla`.
Feature branches are merged back into `develop` only after all tests
pass.
2. Whenever the `develop` branch is merged into `master`, the last
commit on the `develop` branch is tagged with `MAJOR.MINOR`.
3. Whenever a bug is discovered in version X.Y, a new branch called `vX.Y`
is forked from the corresponding `master` merge point.
A new bugfix branch is forked from `vX.Y`, the bug is fixed, and then
this bugfix branch is merged into all affected branches (this includes
`vX.Y`).
After merging, the respective merge points are tagged adequately (`vX.Y`
gets the tag X.Y.1).
4. Whenever a bug is discovered in version X.Y.Z, a bugfix branch is
forked from `vX.Y`, and then rule 3 is adapted accordingly.
Code testing
------------
Testing for `bfps` is done with `tox`.
Overview and Tutorial
=====================
Equations
---------
The code uses a fairly standard pseudo-spectral algorithm to solve fluid
equations.
The incompressible Navier Stokes equations in velocity form are as
follows:
.. math::
\partial_t \mathbf{u} + \mathbf{u} \cdot \nabla \mathbf{u} =
- \nabla p + \nu \Delta \mathbf{u} + \mathbf{f}
In fact, the code solves the vorticity formulation of these equations:
.. math::
\partial_t \mathbf{\omega} +
\mathbf{u} \cdot \nabla \mathbf{\omega} =
\mathbf{\omega} \cdot \nabla \mathbf{u} +
\nu \Delta \mathbf{\omega} + \nabla \times \mathbf{f}
Tutorial
--------
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# bfps documentation build configuration file, created by
# sphinx-quickstart on Thu Jan 21 20:53:27 2016.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All configuration values have a default; values that are commented out
# serve to show the default.
import sys
import os
import shlex
# 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.
#sys.path.insert(0, os.path.abspath('.'))
# -- 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.mathjax',
'sphinx.ext.viewcode',
]
# 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 encoding of source files.
#source_encoding = 'utf-8-sig'
# The master toctree document.
master_doc = 'index'
# General information about the project.
project = 'bfps'
copyright = '2016, Cristian C Lalescu'
author = 'Cristian C Lalescu'
### package versioning
# get current time
import datetime
import shutil
import subprocess
now = datetime.datetime.now()
# obtain version
try:
git_branch = subprocess.check_output(['git',
'rev-parse',
'--abbrev-ref',
'HEAD']).strip().split()[-1].decode()
git_revision = subprocess.check_output(['git', 'rev-parse', 'HEAD']).strip()
git_date = datetime.datetime.fromtimestamp(int(subprocess.check_output(['git', 'log', '-1', '--format=%ct']).strip()))
except:
git_revision = ''
git_branch = ''
git_date = now
if git_branch == '':
# there's no git available or something
release = '{0:0>4}{1:0>2}{2:0>2}.{3:0>2}{4:0>2}{5:0>2}'.format(
git_date.year, git_date.month, git_date.day,
git_date.hour, git_date.minute, git_date.second)
else:
if (('develop' in git_branch) or
('feature' in git_branch) or
('bugfix' in git_branch)):
release = subprocess.check_output(['git', 'describe', '--tags']).strip().decode()
else:
release = subprocess.check_output(['git', 'describe', '--tags']).strip().decode().split('-')[0]
# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
# built documents.
#
# release is the full version, including alpha/beta/rc tags.
# version is supposed to be the short X.Y version.
version = release
# 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
# There are two options for replacing |today|: either, you set today to some
# non-false value, then it is used:
#today = ''
# Else, today_fmt is used as the format for a strftime call.
#today_fmt = '%B %d, %Y'
# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
exclude_patterns = ['_build']
# The reST default role (used for this markup: `text`) to use for all
# documents.
#default_role = None
# If true, '()' will be appended to :func: etc. cross-reference text.
#add_function_parentheses = True
# If true, the current module name will be prepended to all description
# unit titles (such as .. function::).
#add_module_names = True
# If true, sectionauthor and moduleauthor directives will be shown in the
# output. They are ignored by default.
#show_authors = False
# The name of the Pygments (syntax highlighting) style to use.
pygments_style = 'sphinx'
# A list of ignored prefixes for module index sorting.
#modindex_common_prefix = []
# If true, keep warnings as "system message" paragraphs in the built documents.
#keep_warnings = False
# If true, `todo` and `todoList` produce output, else they produce nothing.
todo_include_todos = False
# -- 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 themes here, relative to this directory.
#html_theme_path = []
# The name for this set of Sphinx documents. If None, it defaults to
# "<project> v<release> documentation".
#html_title = None
# A shorter title for the navigation bar. Default is the same as html_title.
#html_short_title = None
# The name of an image file (relative to this directory) to place at the top
# of the sidebar.
#html_logo = None
# The name of an image file (within the static path) to use as favicon of the
# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
# pixels large.
#html_favicon = None
# 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']
# Add any extra paths that contain custom files (such as robots.txt or
# .htaccess) here, relative to this directory. These files are copied
# directly to the root of the documentation.
#html_extra_path = []
# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
# using the given strftime format.
#html_last_updated_fmt = '%b %d, %Y'
# If true, SmartyPants will be used to convert quotes and dashes to
# typographically correct entities.
#html_use_smartypants = True
# Custom sidebar templates, maps document names to template names.
#html_sidebars = {}
# Additional templates that should be rendered to pages, maps page names to
# template names.
#html_additional_pages = {}
# If false, no module index is generated.
#html_domain_indices = True
# If false, no index is generated.
#html_use_index = True
# If true, the index is split into individual pages for each letter.
#html_split_index = False
# If true, links to the reST sources are added to the pages.
#html_show_sourcelink = True
# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
#html_show_sphinx = True
# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
#h