diff --git a/.readthedocs.yaml b/.readthedocs.yaml new file mode 100644 index 00000000..7d9db4c4 --- /dev/null +++ b/.readthedocs.yaml @@ -0,0 +1,12 @@ +version: 2 + +sphinx: + configuration: docs/conf.py + +formats: all + +python: + version: 3.7 + install: + - method: pip + path: . diff --git a/daisy/__init__.py b/daisy/__init__.py index 4a313457..e50c89e9 100644 --- a/daisy/__init__.py +++ b/daisy/__init__.py @@ -1,6 +1,7 @@ from __future__ import absolute_import from . import persistence # noqa from .array import Array # noqa +from .block import Block # noqa from .blocks import create_dependency_graph # noqa from .blocks import expand_roi_to_grid # noqa from .blocks import expand_write_roi_to_grid # noqa @@ -14,7 +15,7 @@ from .processes import call # noqa from .roi import Roi # noqa from .scheduler import Scheduler # noqa +from .scheduler import _NO_SPAWN_STATUS_THREAD # noqa from .scheduler import distribute # noqa from .scheduler import run_blockwise # noqa -from .scheduler import _NO_SPAWN_STATUS_THREAD # noqa from .task import Task # noqa diff --git a/docs/Makefile b/docs/Makefile new file mode 100644 index 00000000..298ea9e2 --- /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/api.rst b/docs/api.rst new file mode 100644 index 00000000..a6c38b50 --- /dev/null +++ b/docs/api.rst @@ -0,0 +1,65 @@ +.. _sec_api: + +API Reference +============= + +.. automodule:: daisy + +Convenience API +--------------- + + .. autofunction:: run_blockwise + +Block-wise Task Scheduling +-------------------------- + + .. autoclass:: Block + + .. autoclass:: Scheduler + + .. autoclass:: Client + + .. autoclass:: Context + + .. autoclass:: Task + + .. autoclass:: DependencyGraph + +Geometry +-------- + +Coordinate +^^^^^^^^^^ + .. autoclass:: Coordinate + :members: + +Roi +^^^ + .. autoclass:: Roi + :members: + +Arrays +------ + + .. autoclass:: Array + + .. autofunction:: open_ds + + .. autofunction:: prepare_ds + +Graphs +------ + +Graph +^^^^^ + + .. autoclass:: Graph + :members: + +MongoDbGraphProvider +^^^^^^^^^^^^^^^^^^^^ + + .. automodule:: daisy.persistence + + .. autoclass:: MongoDbGraphProvider + :members: diff --git a/docs/conf.py b/docs/conf.py new file mode 100644 index 00000000..59459d62 --- /dev/null +++ b/docs/conf.py @@ -0,0 +1,179 @@ +# -*- 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 = 'daisy' +copyright = '2019, Jan Funke, Tri Nguyen, Carolin Malin-Mayor, Arlo Sheridan, Philipp Hanslovsky, Chris Barnes' +author = 'Jan Funke, Tri Nguyen, Carolin Malin-Mayor, Arlo Sheridan, Philipp Hanslovsky, Chris Barnes' + +# The short X.Y version +version = '' +# The full version, including alpha/beta/rc tags +release = 'v0.2' + + +# -- 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 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 = 'sphinx_rtd_theme' + +# 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 = 'daisydoc' + + +# -- 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, 'daisy.tex', 'daisy Documentation', + 'Jan Funke, Tri Nguyen, Carolin Malin-Mayor, Arlo Sheridan, Philipp Hanslovsky, Chris Barnes', '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, 'daisy', 'daisy 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, 'daisy', 'daisy Documentation', + author, 'daisy', '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 ------------------------------------------------- diff --git a/docs/index.rst b/docs/index.rst new file mode 100644 index 00000000..a0f76431 --- /dev/null +++ b/docs/index.rst @@ -0,0 +1,13 @@ +.. daisy documentation master file, created by + sphinx-quickstart on Mon Mar 25 14:53:44 2019. + +Daisy: Block-wise Task Scheduling +================================= + +.. toctree:: + :maxdepth: 2 + + api + release + +* :ref:`search` diff --git a/release.rst b/docs/release.rst similarity index 100% rename from release.rst rename to docs/release.rst