Merge pull request #32 from OpenFreeEnergy/docs

[WIP] Docs

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+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/index.rst

@@ -0,0 +1,9 @@
+.. _api:
+
+Exorcist API Reference
+======================
+
+.. toctree::
+   :maxdepth: 2
+
+   taskstatusdb

docs/api/taskstatusdb.rst

@@ -0,0 +1,10 @@
+Task Status Database
+====================
+
+.. module:: exorcist.taskdb
+
+.. autosummary::
+   :toctree: generated/
+
+   AbstractTaskStatusDB
+   TaskStatusDB

docs/conf.py

@@ -0,0 +1,29 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = 'Exorcist'
+copyright = '2023, Open Free Energy'
+author = 'Open Free Energy'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.napoleon",
+]
+
+templates_path = ['_templates']
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'alabaster'
+html_static_path = ['_static']

docs/guide/index.rst

@@ -0,0 +1,17 @@
+User Guide
+==========
+
+This guide is designed to introduce developers to the ideas, architecture,
+and terminology used by Exorcist. We will use the term "client" to refer to
+developers who use Exorcist in their own projects, in order to distinguish
+from the "users" of the client application.
+
+Exorcist is designed to be directly used by client code developers. It is
+not intended for direct usage by end users, although we provide several
+conveniences that client developers can use in their code to improve the end
+user experience.
+
+
+.. toctree::
+
+    intro

docs/guide/intro.rst

@@ -0,0 +1,73 @@
+Introduction to Exorcist
+========================
+
+Tasks form a directed acyclic graph (DAG)
+-----------------------------------------
+
+Any large-scale campaign can be described as a directed acyclic graph of
+tasks, where edges represent the flow of information from an earlier stage
+to a later stage. This graph is directed because the outputs of one task can
+be the inputs of a future task, and it is acyclic because it is not possible
+for a task to require its own outputs as an input.
+
+Task-based frameworks, like Exorcist, implement efficient methods for
+executing these task graphs.
+
+Three databases in Exorcist
+---------------------------
+
+The central idea of Exorcist is to separate three types of data storage:
+
+* **Task Status Database**: The task status database is the core of
+  Exorcist, and fully implemented in Exorcist. This database contains the
+  task identifiers, and information on the execution status of those tasks.
+  It is intentionally small and simple, to enable better concurrency.
+* **Task Details Database**: The task details database is a key-value store
+  that describes the tasks to be performed; this is specific to the
+  client application. The client must define how these tasks are serialized
+  and deserialized into the database.
+* **Results Store**: The results store is a generic storage of result data
+  from the specific application. The only thing Exorcist needs to know is
+  whether the received result was a success or a failure (in which case,
+  Exorcist can take responsibility for ensuring that it gets retried).
+
+Some aspects that distinguish Exorcist from similar tools are the separation
+of task status from task descriptions, and the ability for the user to
+customize how task descriptions or task status are stored.
+
+Practical usage for users
+-------------------------
+
+When thinking about the end user's experience, Exorcist tends to assume that
+this occurs in two stages: planning the initial campaign, and the running
+the campaign. The general assumption is that these will beqtwo different
+software tools (typically two executables) with different user experiences.
+
+Preparing the campaign: the planner
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+For many use cases, planning the campaign happens on the user's workstation
+or on the head node of a cluster. While this can, in principle, be a stage
+that must run on a compute node, it is more frequently something that is
+done interactively by the user.
+
+The "campaign planner" tool must have write access to the *task status
+database* and to the *task details database*.
+
+
+Running a campaign: the worker
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The second tool that the user interacts with is the worker. Typically, the
+user will launch many identical workers through jobs submitted to their
+queueing system.
+
+The worker is the workhorse of the campaign. It does the real computational
+effort. It needs read/write access to the *task status database*, read access
+to the *task details database*, and write access to the *results store*.
+
+In most cases, it will also have read access to the results store, which
+allows things like analysis as a separate task. If it can also have write
+access to the the task details database, this allows on-the-fly creation of
+new tasks, e.g., focusing simulation effort in a different direction based
+on the results of the campaign so far.

docs/index.rst

@@ -0,0 +1,33 @@
+Exorcist
+========
+
+*Task execution/orchestration, without the daemons*
+
+Exorcist is a tool for execution and orchestration of many-task
+computing/high-throughput computing.  It is specifically designed for a
+common case in the world of simulation, where a large simulation campaign
+may include many loosely coupled individual simulations, each of which may
+require hours to days to run, and the results need to be gathered into a
+large storage backend.
+
+At small to moderate scale, Exorcist can run without setting up any
+long-running daemon. At larger scales, Exorcist can interface with standard
+database backends, e.g. PostgreSQL. In this way, Exorcist offers the easy
+set-up procedure of a daemonless solution, while offering a smooth
+transition to a highly scalable solution when needed.
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   guide/index
+   api/index
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

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
+
+%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.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

exorcist/taskdb.py

@@ -136,7 +136,7 @@ class TaskStatusDB(AbstractTaskStatusDB):
     """Database for managing execution and orchestration of tasks.
 
     This implementation is built on SQLAlchemy. For simple usage, the
-    recommendation is to use the :method:`.from_filename` method to create
+    recommendation is to use the :meth:`.from_filename` method to create
     this object, rather than its ``__init__``. The ``__init__`` method takes
     a SQLAlchemy engine, which provides much more flexibility in choice of
     backend.