Update docs

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = Bio2BELCHEBI
+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/source/conf.py

@@ -0,0 +1,64 @@
+# -*- coding: utf-8 -*-
+
+import os
+import re
+import sys
+
+sys.path.insert(0, os.path.abspath('../../src'))
+
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.todo',
+    'sphinx.ext.coverage',
+    'sphinx.ext.viewcode'
+]
+templates_path = ['_templates']
+source_suffix = '.rst'
+master_doc = 'index'
+project = 'Bio2BEL ChEBI'
+copyright = '2017-2018, Charles Tapley Hoyt'
+author = 'Charles Tapley Hoyt'
+
+release = '0.0.1-dev'
+
+parsed_version = re.match(
+    '(?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(?:-(?P<release>[0-9A-Za-z-]+(?:\.[0-9A-Za-z-]+)*))?(?:\+(?P<build>[0-9A-Za-z-]+(?:\.[0-9A-Za-z-]+)*))?',
+    release
+)
+version = parsed_version.expand('\g<major>.\g<minor>.\g<patch>')
+
+if parsed_version.group('release'):
+    tags.add('prerelease')
+
+language = None
+exclude_patterns = []
+pygments_style = 'sphinx'
+todo_include_todos = True
+html_theme = 'sphinx_rtd_theme'
+html_static_path = []
+htmlhelp_basename = 'bioebel_chebidoc'
+latex_elements = {}
+latex_documents = [
+    (master_doc, 'bio2bel_chebi.tex', 'Bio2BEL ChEBI Documentation', 'Charles Tapley Hoyt', 'manual'),
+]
+man_pages = [
+    (master_doc, 'Bio2BEL ChEBI', 'Bio2BEL ChEBI Documentation', [author], 1)
+]
+texinfo_documents = [
+    (master_doc, 'Bio2BEL ChEBI', 'Bio2BEL ChEBI Documentation', author, 'Bio2BEL ChEBI', 'Serialize ChEBI to BEL', 'Miscellaneous'),
+]
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {
+    'python': ('https://docs.python.org/3', None),
+    'networkx': ('https://networkx.github.io/', None),
+    'sqlalchemy': ('https://docs.sqlalchemy.org/en/latest', None),
+    'pybel': ('https://pybel.readthedocs.io/en/latest/', None),
+}
+
+autodoc_member_order = 'bysource'
+autoclass_content = 'both'
+
+if os.environ.get('READTHEDOCS'):
+    tags.add('readthedocs')

docs/source/constants.rst

@@ -0,0 +1,4 @@
+Constants
+=========
+.. automodule:: bio2bel_chebi.constants
+   :members:

docs/source/enrichment.rst

@@ -0,0 +1,4 @@
+Enrichment
+==========
+.. automodule:: bio2bel_chebi.enrich
+   :members:

docs/source/index.rst

@@ -0,0 +1,18 @@
+Bio2BEL ChEBI
+=============
+.. automodule:: bio2bel_chebi
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   enrichment
+   manager
+   constants
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/source/manager.rst

@@ -0,0 +1,4 @@
+Manager
+==========
+.. automodule:: bio2bel_chebi.manager
+   :members:

requirements.txt

@@ -5,3 +5,5 @@ tqdm
 pybel>=0.9.5
 pybel_tools>=0.4.5
 bio2bel
+flask[web]
+flask_admin[web]

src/bio2bel_chebi/__init__.py

@@ -1,7 +1,11 @@
 # -*- coding: utf-8 -*-
 
-from . import models
-from .manager import Manager
+from . import enrich, manager, models
+from .enrich import *
+from .manager import *
+from .models import *
+
+__all__ = (manager.__all__ + enrich.__all__ + models.__all__)
 
 __version__ = '0.0.1'
 

src/bio2bel_chebi/enrich.py

@@ -0,0 +1,46 @@
+# -*- coding: utf-8 -*-
+
+import logging
+
+from pybel import to_database
+from .manager import Manager
+
+__all__ = [
+    'enrich_chemical_hierarchy',
+    'to_bel',
+    'upload_bel'
+]
+
+log = logging.getLogger(__name__)
+
+
+def enrich_chemical_hierarchy(graph, manager=None):
+    """Enriches the biological processses in a BEL graph
+
+    :type graph: pybel.BELGraph
+    :type manager: Optional[bio2bel_chebi.Manager]
+    """
+    manager = manager or Manager()
+    manager.enrich_chemical_hierarchy(graph)
+
+
+def to_bel(manager=None):
+    """Creates a BEL graph from the Gene Ontology
+
+    :type manager: Optional[bio2bel_chebi.Manager]
+    """
+    manager = manager or Manager()
+    return manager.to_bel()
+
+
+def upload_bel(manager=None, pybel_manager=None):
+    """Creates a BEL graph from the Gene Ontology and uplopads it to the PyBEL edge store
+
+    :type manager: Optional[bio2bel_chebi.Manager]
+    :type pybel_manager: Optional[pybel.Manager]
+    :rtype: pybel.manager.models.Network
+    """
+    log.info('converting bel')
+    graph = to_bel(manager=manager)
+    log.info('storing')
+    return to_database(graph, connection=pybel_manager)

src/bio2bel_chebi/manager.py

@@ -16,6 +16,8 @@
 from .parser.inchis import get_inchis_df
 from .parser.names import get_names_df
 
+__all__ = ['Manager']
+
 log = logging.getLogger(__name__)
 
 
@@ -222,3 +224,6 @@ def enrich_chemical_hierarchy(self, graph):
                 parent.as_bel(),
                 IS_A
             )
+
+    def to_bel(self):
+        raise NotImplementedError

src/bio2bel_chebi/models.py

@@ -5,8 +5,16 @@
 from sqlalchemy import Column, ForeignKey, Integer, String, Text
 from sqlalchemy.ext.declarative import declarative_base
 from sqlalchemy.orm import backref, relationship
+
 from pybel.dsl import abundance
 
+__all__ = [
+    'Base',
+    'Chemical',
+    'Synonym',
+    'Accession',
+]
+
 Base = declarative_base()
 
 TABLE_PREFIX = 'chebi'