Updated documentation build

belbio · Jan 2, 2018 · 4a1bce4 · 4a1bce4
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diff --git a/bel/scripts.py b/bel/scripts.py
@@ -5,17 +5,16 @@
 import re
 
 import bel.db
+import bel.utils as utils
+import bel.Config
+from bel.Config import config
 
 from bel.lang.bel import BEL
 
 import bel.nanopub.nanopubs as bnn
 import bel.nanopub.files as bnf
-import bel.nanopub.utils as utils
 import bel.nanopub.belscripts
 
-import bel.Config
-from bel.Config import config
-
 import logging
 import logging.config
 
@@ -36,6 +35,7 @@ def bel():
     """ BEL commands
 
     Uses first file found to load in default configuration:
+
         ./belbio_conf.yaml
         ./.belbio_conf
         ~/.belbio_conf
@@ -291,7 +291,7 @@ def canonicalize(ctx, statement, namespace_targets, version, api, config_fn):
 
     Target namespaces can be provided in the following manner:
 
-        belstmt canonicalize "<BELStmt>" --namespace_targets '{"HGNC": ["EG", "SP"], "CHEMBL": ["CHEBI"]}'
+        bel stmt canonicalize "<BELStmt>" --namespace_targets '{"HGNC": ["EG", "SP"], "CHEMBL": ["CHEBI"]}'
             the value of target_namespaces must be JSON and embedded in single quotes
             reserving double quotes for the dictionary elements
     """
@@ -339,7 +339,7 @@ def canonicalize(ctx, statement, namespace_targets, version, api, config_fn):
 @click.argument('statement')
 @pass_context
 def orthologize(ctx, statement, species_id, version, api, config_fn):
-    """Canonicalize statement
+    """Orthologize statement
 
     Species ID needs to be the NCBI Taxonomy ID in this format: TAX:<tax_id_number>
     You can use the following common names for species_id: human, mouse, rat
@@ -387,7 +387,7 @@ def orthologize(ctx, statement, species_id, version, api, config_fn):
 @click.argument('statement')
 @pass_context
 def edges(ctx, statement, rules, species_id, namespace_targets, version, api, config_fn):
-    """Create BEL Edges"""
+    """Create BEL Edges from BEL Statement"""
 
     if config_fn:
         config = bel.db.Config.merge_config(ctx.config, override_config_fn=config_fn)

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -8,11 +8,21 @@ Introduction
 
 Welcome to bel's documentation.
 
+.. image:: https://api.codeclimate.com/v1/badges/3fdfec7ee96fc639bb09/maintainability
+   :target: https://codeclimate.com/github/belbio/bel/maintainability
+   :alt: Maintainability
+
+.. image:: https://api.codeclimate.com/v1/badges/3fdfec7ee96fc639bb09/test_coverage
+   :target: https://codeclimate.com/github/belbio/bel/test_coverage
+   :alt: Test Coverage
+
+
 .. toctree::
    :maxdepth: 2
    :caption: Contents:
 
    overview
-   scripts
+   script
+   modules
    lang
 
diff --git a/docs/source/lang.rst b/docs/source/lang.rst
@@ -1,123 +1,123 @@
-bel\_lang package
+bel package
 =================
 
 Classes
 -------
 
-.. autoclass:: bel.lang.bel.BEL
-    :members:
+.. .. autoclass:: bel.lang.bel.BEL
+..     :members:
 
-.. autoclass:: bel.lang.ast.BELAst
-    :members:
+.. .. autoclass:: bel.lang.ast.BELAst
+..     :members:
 
-.. autoclass:: bel.lang.ast.Function
-    :members:
+.. .. autoclass:: bel.lang.ast.Function
+..     :members:
 
-.. autoclass:: bel.lang.ast.Arg
-    :members:
+.. .. autoclass:: bel.lang.ast.Arg
+..     :members:
 
-.. autoclass:: bel.lang.ast.NSArg
-    :members:
+.. .. autoclass:: bel.lang.ast.NSArg
+..     :members:
 
-.. autoclass:: bel.lang.ast.StrArg
-    :members:
+.. .. autoclass:: bel.lang.ast.StrArg
+..     :members:
 
-Submodules
-----------
+.. Submodules
+.. ----------
 
-bel\.lang\.ast module
----------------------
+.. bel\.lang\.ast module
+.. ---------------------
 
-.. automodule:: bel.lang.ast
-    :members:
-    :undoc-members:
-    :show-inheritance:
+.. .. automodule:: bel.lang.ast
+..     :members:
+..     :undoc-members:
+..     :show-inheritance:
 
-bel\.lang\.bel module
----------------------
+.. bel\.lang\.bel module
+.. ---------------------
 
-.. automodule:: bel.lang.bel
-    :members:
-    :undoc-members:
-    :show-inheritance:
+.. .. automodule:: bel.lang.bel
+..     :members:
+..     :undoc-members:
+..     :show-inheritance:
 
-bel\.lang\.bel\_specification module
-------------------------------------
+.. bel\.lang\.bel\_specification module
+.. ------------------------------------
 
-.. automodule:: bel.lang.bel_specification
-    :members:
-    :undoc-members:
-    :show-inheritance:
+.. .. automodule:: bel.lang.bel_specification
+..     :members:
+..     :undoc-members:
+..     :show-inheritance:
 
-bel\.lang\.bel\_utils module
-----------------------------
+.. bel\.lang\.bel\_utils module
+.. ----------------------------
 
-.. automodule:: bel.lang.bel_utils
-    :members:
-    :undoc-members:
-    :show-inheritance:
+.. .. automodule:: bel.lang.bel_utils
+..     :members:
+..     :undoc-members:
+..     :show-inheritance:
 
-bel\.lang\.computed\_edges module
----------------------------------
+.. bel\.lang\.computed\_edges module
+.. ---------------------------------
 
-.. automodule:: bel.lang.computed_edges
-    :members:
-    :undoc-members:
-    :show-inheritance:
+.. .. automodule:: bel.lang.computed_edges
+..     :members:
+..     :undoc-members:
+..     :show-inheritance:
 
-bel\lang\.defaults module
---------------------------
+.. bel\lang\.defaults module
+.. --------------------------
 
-.. automodule:: bel.lang.defaults
-    :members:
-    :undoc-members:
-    :show-inheritance:
+.. .. automodule:: bel.lang.defaults
+..     :members:
+..     :undoc-members:
+..     :show-inheritance:
 
-bel\.lang\.exceptions module
-----------------------------
+.. bel\.lang\.exceptions module
+.. ----------------------------
 
-.. automodule:: bel.lang.exceptions
-    :members:
-    :undoc-members:
-    :show-inheritance:
+.. .. automodule:: bel.lang.exceptions
+..     :members:
+..     :undoc-members:
+..     :show-inheritance:
 
-bel\.lang\.migrate\_bel module
-------------------------------
+.. bel\.lang\.migrate\_bel module
+.. ------------------------------
 
-.. automodule:: bel.lang.migrate_bel
-    :members:
-    :undoc-members:
-    :show-inheritance:
+.. .. automodule:: bel.lang.migrate_bel
+..     :members:
+..     :undoc-members:
+..     :show-inheritance:
 
-bel\.lang\.scripts module
--------------------------
+.. bel\.lang\.scripts module
+.. -------------------------
 
-.. automodule:: bel.lang.scripts
-    :members:
-    :undoc-members:
-    :show-inheritance:
+.. .. automodule:: bel.lang.scripts
+..     :members:
+..     :undoc-members:
+..     :show-inheritance:
 
-bel\.lang\.semantics module
----------------------------
+.. bel\.lang\.semantics module
+.. ---------------------------
 
-.. automodule:: bel.lang.semantics
-    :members:
-    :undoc-members:
-    :show-inheritance:
+.. .. automodule:: bel.lang.semantics
+..     :members:
+..     :undoc-members:
+..     :show-inheritance:
 
-bel\.lang\.tools module
------------------------
+.. bel\.lang\.tools module
+.. -----------------------
 
-.. automodule:: bel.lang.tools
-    :members:
-    :undoc-members:
-    :show-inheritance:
+.. .. automodule:: bel.lang.tools
+..     :members:
+..     :undoc-members:
+..     :show-inheritance:
 
 
-Module contents
----------------
+.. Module contents
+.. ---------------
 
-.. automodule:: bel.lang
-    :members:
-    :undoc-members:
-    :show-inheritance:
+.. .. automodule:: bel.lang
+..     :members:
+..     :undoc-members:
+..     :show-inheritance:
diff --git a/docs/source/modules.rst b/docs/source/modules.rst
@@ -4,4 +4,4 @@ bel
 .. toctree::
    :maxdepth: 4
 
-   bel
+
diff --git a/docs/source/script.rst b/docs/source/script.rst
@@ -1,2 +1,17 @@
+BEL CLI
+==========
+
+The BEL CLI commands are installed by pip install bel. These are nested commands
+for which you can review the help at each nested level by:
+
+.. code-block:: bash
+
+    bel --help
+    bel stmt --help
+    bel stmt canonicalize --help
+
 
 .. click:: bel.scripts:bel
+   :prog: bel
+   :show-nested:
+
diff --git a/requirements.txt b/requirements.txt
@@ -24,3 +24,4 @@ TatSu==4.2.5
 twine==1.9.1
 typing==3.6.2
 ulid-py==0.0.6
+
diff --git a/setup.py b/setup.py
@@ -98,7 +98,7 @@ def run(self):
 
     entry_points={
         'console_scripts': [
-            'bel=bel.nanopub.scripts:bel',
+            'bel=bel.scripts:bel',
             'belspec_yaml2json=bel.lang.bel_specification:belspec_yaml2json',
         ],
     },