[Doc] Add Documentation/ stub

Documentation/.gitignore

@@ -0,0 +1 @@
+_build

Documentation/Doxyfile

@@ -0,0 +1,26 @@
+PROJECT_NAME = "Graphene"
+OUTPUT_DIRECTORY = _build/doxygen
+
+GENERATE_XML = YES
+XML_PROGRAMLISTING = NO
+XML_OUTPUT = xml
+
+GENERATE_HTML = NO
+GENERATE_LATEX = NO
+
+RECURSIVE = YES
+INPUT = \
+    ../Pal \
+    ../LibOS/shim/include \
+    ../LibOS/shim/src
+
+EXCLUDE = \
+    ../Pal/lib \
+    ../Pal/regression \
+    ../Pal/test
+#EXCLUDE_PATTERNS =
+
+WARN_NO_PARAMDOC = YES
+WARN_AS_ERROR = NO
+OPTIMIZE_OUTPUT_FOR_C = YES
+EXTRACT_STATIC = YES

Documentation/Makefile

@@ -0,0 +1,22 @@
+# 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)
+
+clean:
+	$(RM) -r "$(BUILDDIR)"
+
+.PHONY: help Makefile Doxyfile clean
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile Doxyfile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

Documentation/conf.py

@@ -0,0 +1,139 @@
+# -*- 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('.'))
+
+import collections
+import pathlib
+import subprocess
+
+import recommonmark.parser
+
+# -- Project information -----------------------------------------------------
+
+project = 'Graphene'
+copyright = '2019, Graphene Contributors'
+author = 'Graphene Contributors'
+
+# 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.todo',
+    'breathe',
+    'recommonmark',
+    'sphinx_rtd_theme',
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+source_suffix = {
+    '.rst': 'restructuredtext',
+    '.md': 'markdown',
+    '.markdown': 'markdown',
+}
+
+# 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
+
+rst_prolog = '''
+.. |nbsp| unicode:: 0xa0
+   :trim:
+'''
+
+breathe_default_project = 'graphene'
+breathe_projects = {breathe_default_project: '_build/doxygen/xml'}
+
+def generate_doxygen(app):
+    subprocess.check_call(['doxygen', 'Doxyfile'])
+def setup(app):
+    app.connect('builder-inited', generate_doxygen)
+
+todo_include_todos = True
+
+# -- 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 manual page output ------------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    ('manpages/pal_loader', 'pal_loader', 'FIXME Loader', [author], 1),
+]
+
+# barf if a page is not included
+assert (collections.Counter(str(p.with_suffix(''))
+        for p in pathlib.Path().glob('manpages/*.rst')
+        if not p.stem == 'index')
+    == collections.Counter(source
+        for source, *_ in man_pages))

Documentation/glossary.rst

@@ -0,0 +1,15 @@
+Glossary
+========
+
+.. keep this file sorted lexicographically
+
+.. glossary::
+
+   PAL
+      Platform Adaption Layer
+
+      .. todo:: Is this really correct?
+
+   SGX
+      Software Guard Extensions is a set of instructions on Intel processors.
+      See https://en.wikipedia.org/wiki/Software_Guard_Extensions.

Documentation/howto-doc.rst

@@ -0,0 +1,47 @@
+.. _doc-howto:
+
+How to write documentation
+==========================
+
+Documentation is generally written as `reStructuredText`_ files and processed
+using `Sphinx`_. See `Sphinx' reST primer`_ for short introduction into syntax.
+:ref:`Old Wiki <old-wiki>` is imported as it was, in Markdown, but new
+documentation should be written in reST.
+
+API documentation of C |nbsp| language should be written as Doxygen comments
+(prefer Qt-style ``/*!`` and ``\param``) and then included in one of the
+``.rst`` files (with appropriate description) using one of the `Breathe
+directives`_, like :rst:dir:`doxygenfunction` or :rst:dir:`doxygenstruct`. See
+`Breathe`_ documentation for more info. Do not use ``autodoxygen`` directives,
+and especially do not use ``.. doxygenfile::``, because documentation should be
+written as prose, not a |nbsp| coredump.
+
+In ``.rst`` files use 3-space tab. This is an uncommon value, but good value
+because intended blocks usually follow explicit markup, which begins with
+``..``). Wrap the paragraphs at 80th character, but don't wrap verbatim text
+like logs and use applicable style when wrapping code examples. Use Python
+convention for header hierarchy: ``#`` with overline, ``*`` with overline,
+``=``, ``-``, ``^``, ``"``. This means most documents use only ``=`` and ``-``
+underlines. Those underlines are easy to enter in :command:`vim` using the
+combination ``yypVr-``.
+
+Documentation of the code should be organized into files by logical concepts,
+as they fit into programmers mind. Ideally, this should match the source files,
+if those files were organised correctly in the first place, but the reality may
+be different. In case of doubt, place them as they fit the narration of the
+document, not as they are placed in the source files.
+
+Documents should be grouped by general areas and presented using
+:rst:dir:`toctree` directive in :file:`index.rst` file. This causes them to be
+included in TOC in the main document and also in sidebar on RTD.
+
+The documentation targets ``html`` output of Sphinx. The :file:`manpages/`
+subdirectory also targets ``manpage`` builder. Other formats (like ``latex``)
+may be considered in the future, but for now their output is neither published
+not cared for.
+
+.. _reStructuredText: https://en.wikipedia.org/wiki/ReStructuredText
+.. _Sphinx: https://www.sphinx-doc.org/
+.. _Sphinx' reST primer: https://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html
+.. _Breathe: https://breathe.readthedocs.io/en/latest/
+.. _Breathe directives: https://breathe.readthedocs.io/en/latest/directives.html

Documentation/index.rst

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+.. include:: ../README.rst
+
+.. toctree::
+   :caption: Introduction
+   :maxdepth: 2
+
+   glossary
+   howto-doc
+
+.. toctree::
+   :caption: LibOS
+
+   libos/shim-init
+
+.. toctree::
+   :caption: Manual pages
+   :maxdepth: 1
+   :glob:
+
+   manpages/*
+
+.. _old-wiki:
+
+.. toctree::
+   :caption: Old Wiki (to be rewritten)
+   :maxdepth: 1
+   :glob:
+
+   oldwiki/*
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

Documentation/libos/shim-init.rst

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+A random file documentation
+===========================
+
+.. note::
+
+   This file is more like a |nbsp| stub, not yet a |nbsp| real documentation.
+
+There is a |nbsp| random function:
+
+.. doxygenfunction:: parse_int

Documentation/manpages/pal_loader.rst

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+.. program:: pal_loader
+
+======================================
+:program:`pal_loader` -- Run something
+======================================
+
+.. note::
+
+   This page is a stub.
+
+Synopsis
+========
+
+:command:`pal_loader` [SGX] [GDB] {<*MANIFEST*> | <*EXECUTABLE*>} [<*ARGS*> ...]
+
+Description
+===========
+
+Command line arguments
+======================
+
+.. option:: SGX
+
+   Enable :term:`SGX`.
+
+   .. seealso::
+
+      :envvar:`SGX environment variable <SGX>`
+         For an equivalent.
+
+Environment variables
+=====================
+
+.. envvar:: SGX
+
+   If not empty and not ``0``, enable :term:`SGX`. Could be used instead of
+   :option:`SGX option <SGX>`. This has some unexplained interaction with
+   :envvar:`SGX_RUN`.
+
+.. envvar:: SGX_RUN
+
+   This is a mystery to me. It cannot be set together with :envvar:`SGX`.

Documentation/requirements.txt

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+breathe
+recommonmark

LibOS/shim/src/shim_init.c

@@ -14,8 +14,8 @@
    You should have received a copy of the GNU Lesser General Public License
    along with this program.  If not, see <http://www.gnu.org/licenses/>.  */
 
-/*
- * shim_init.c
+/*!
+ * \file shim_init.c
  *
  * This file contains entry and exit functions of library OS.
  */
@@ -110,6 +110,15 @@ long convert_pal_errno (long err)
            pal_errno_to_unix_errno[err] : 0;
 }
 
+/*!
+ * \brief Parse a number into an unsigned long.
+ *
+ * \param str A string containing a non-negative number.
+ *
+ * By default the number should be decimal, but if it starts with 0x it is
+ * parsed as hexadecimal and if it otherwise starts with 0, it is parsed as
+ * octal.
+ */
 unsigned long parse_int (const char * str)
 {
     unsigned long num = 0;