Updates to setup.py and setup.cfg prior to release. Addition of docs …

…folder (Sphinx rst)

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     = source
+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/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+if "%1" == "" goto help
+
+%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.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/source/about.rst

@@ -0,0 +1,96 @@
+
+=====
+About
+=====
+
+A Python library for writing SciData_ JSON-LD_ files.
+
+.. _SciData: http://stuchalk.github.io/scidata/
+.. _JSON-LD: https://json-ld.org/
+
+SciData and JSON-LD
+-------------------
+
+JSON-LD is a convenient (human-readable) encoding of Resource
+Desctiption Framework (RDF) triples.  However, unlike traditional
+relational databases (e.g., MySQL), the graph has no schema. This
+is problematic as including data from different sources results
+in a system with no common way to search across the data.  The
+SciData framework is a structure for users to add data and its metadata
+that are organized in the graph through the associated SciData ontology.
+
+There are three main sections of the SciData framework:
+
+* the methodology section (describing how the research was done)
+* the system section (describing what the research studied and the conditions)
+* the dataset section (the experimental data, plus any derived or supplemental
+  data)
+
+The methodology and system sections are generic and users can add any data
+they need to contextualize the dataset.  However, in addition they must
+provide a JSON-LD context file to semantically describe the data elements
+included.  The dataset section has predefined data structures (dataseries,
+datagroup, and datapoint) although other strudtures can be included
+if needed.
+
+Translating the content in JSON-LD.  Referencing the JSON-LD below:
+
+*  '@context': provides resources that define the context (meaning) of
+   data elements in the document (as a JSON array). It consists of
+   three sections:
+
+   - a list of one or more 'context' files
+   - a JSON object containing one or more definitions of namespaces
+     used in the document
+   - a JSON object with one entry '@base' that defines the base URL
+     to be prepended to all internal references (i.e. '@id' entries)
+*  root level '@id': the 'name' of the file and where ingested into a
+   graph database, the graph name
+*  '@graph': the definition of content that will be represented as triples
+   and identified by the graph name (this is therfore a 'quad')
+*  '@id' under '@graph': the identifier for the graph.  The scidatalib
+   code uses the '@base' to populate this, so they are consistent. As a result,
+   all node identifiers '@id's in the document are globally unique because the
+   '@base' is unique.
+
+Example JSON-LD::
+
+  {
+    "@context": [
+      "https://stuchalk.github.io/scidata/contexts/scidata.jsonld",
+      {
+        "sci": "https://stuchalk.github.io/scidata/ontology/scidata.owl#"
+      },
+      {
+        "@base": "https://my.research.edu/<uniqueid>/"
+      }
+    ],
+    "@id": "file_identifier",
+    "generatedAt": "<automatically added",
+    "version": "1",
+    "@graph": {
+      "@id": "https://my.research.edu/<uniqueid>/",
+      "@type": "sdo:scidataFramework",
+      "uid": "<uniqueid>",
+      "scidata": {
+        "@type": "sdo:scientificData",
+        "methodology": {
+          "@id": "methodology/",
+          "@type": "sdo:methodology",
+          "aspects": []
+        },
+        "system": {
+          "@id": "system/",
+          "@type": "sdo:system",
+          "facets": []
+        },
+        "dataset": {
+          "@id": "dataset/",
+          "@type": "sdo:dataset",
+          "dataseries": [],
+          "datagroup": [],
+          "datapoint": []
+        }
+      }
+    }
+  }

docs/source/conf.py

@@ -0,0 +1,79 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- 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 = 'SciDataLib'
+copyright = '2021, Dylan Johnson, Marshall McDonnell, and Stuart Chalk'
+author = 'Dylan Johnson, Marshall McDonnell, and Stuart Chalk'
+
+# The short X.Y version
+version = '0.2'
+# The full version, including alpha/beta/rc tags
+release = '0.2'
+
+# -- General configuration ---------------------------------------------------
+
+# 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.doctest',
+    'sphinx.ext.todo',
+    'sphinx.ext.coverage',
+    'sphinx.ext.imgmath',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.githubpages',
+]
+
+# 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'
+
+# 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 = []
+
+# 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 = 'alabaster'
+
+# 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']

docs/source/index.rst

@@ -0,0 +1,20 @@
+.. SciDataLib documentation master file, created by
+   sphinx-quickstart on Tue Apr 13 11:39:44 2021.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to SciDataLib's documentation!
+======================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

setup.cfg

@@ -1,15 +1,15 @@
 [metadata]
 # replace with your username:
 name = SciDataLib
-version = 0.1.0
+version = 0.2
 url = https://github.com/ChalkLab/SciDataLib
-author = 'Dylan Johnson, Stuart Chalk'
-author_email = '[email protected], [email protected]'
+author = 'Dylan Johnson, Marshall McDonnell, Stuart Chalk'
+author_email = '[email protected], [email protected], [email protected]'
 classifiers =
     Programming Language :: Python :: 3
     License :: OSI Approved :: MIT License
     Operating System :: OS Independent
-description = Python library for development of SciData JSON-LD files
+description = Python library for creation of SciData JSON-LD files
 long_description = file: README.md
 long_description_content_type = text/markdown
 

setup.py

@@ -6,9 +6,9 @@
 
 setuptools.setup(
     name="SciDataLib",
-    version="0.1.0",
-    author="Dylan Johnson, Stuart Chalk",
-    author_email="[email protected], [email protected]",
+    version="0.2",
+    author="Dylan Johnson, Marshall McDonnell, Stuart Chalk",
+    author_email="[email protected], [email protected], [email protected]",
     description="Python library for development of SciData JSON-LD files",
     long_description=long_description,
     long_description_content_type="text/markdown",