Merge branch 'docs'

.readthedocs.yaml

@@ -0,0 +1,12 @@
+version: 2
+
+sphinx:
+  configuration: docs/conf.py
+
+formats: all
+
+python:
+   version: 3.7
+   install:
+      - method: pip
+        path: .

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

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)

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:

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 -------------------------------------------------

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`