Temporarily removes pathway organizer related entities for the merge into main

erikhuck · erikhuck · commit 557f17ddd829 · 2023-03-23T17:44:09.000-05:00
diff --git a/dev/test_main.py b/dev/test_main.py
@@ -9,7 +9,6 @@
 import kegg_pull.rest_cli as r_cli
 import kegg_pull.pull_cli as p_cli
 import kegg_pull.map_cli as map_cli
-import kegg_pull.pathway_organizer_cli as po_cli
 import dev.utils as u
 
 
@@ -20,7 +19,7 @@ def test_help(mocker):
     delimiter: str = '-'*80
     expected_print_call_args = [
         (m.__doc__,), (delimiter,), (p_cli.__doc__,), (delimiter,), (ei_cli.__doc__,), (delimiter,), (map_cli.__doc__,),
-        (delimiter,), (po_cli.__doc__,), (delimiter,), (r_cli.__doc__,)]
+        (delimiter,), (r_cli.__doc__,)]
     u.assert_call_args(function_mock=print_mock, expected_call_args_list=expected_print_call_args, do_kwargs=False)
     for help_arg in (['--help'], ['-h'], []):
         help_args = ['kegg_pull']
@@ -199,10 +198,3 @@ def test_map(mocker, print_output: bool, args: list, stdin_mock_str: str, expect
         json_output=True)
     if stdin_mock:
         stdin_mock.assert_called_once_with()
-
-
-def test_pathway_organizer(mocker, print_output: bool):
-    args = ['kegg_pull', 'pathway-organizer', '--tln=Metabolism', '--fn=Global and overview maps']
-    _test_output(
-        mocker=mocker, args=args, expected_output='dev/test_data/pathway-organizer/metabolic-pathways.json',
-        print_output=print_output, json_output=True)
diff --git a/dev/test_pathway_organizer.py b/dev/test_pathway_organizer.py
diff --git a/dev/test_pathway_organizer_cli.py b/dev/test_pathway_organizer_cli.py
diff --git a/dev/test_utils.py b/dev/test_utils.py
@@ -5,7 +5,6 @@
 import dev.utils as u
 import kegg_pull.pull as p
 import kegg_pull.rest as r
-import kegg_pull.pathway_organizer as po
 
 
 @pt.mark.parametrize('comma_separated_list', [',,', ',', ''])
@@ -34,7 +33,7 @@ def test_get_range_values_exception():
 
 
 @pt.mark.parametrize(
-    'NonInstantiable,kwargs', [(p.PullResult, {}), (r.KEGGresponse, {'status': None, 'kegg_url': None}), (po.PathwayOrganizer, {})])
+    'NonInstantiable,kwargs', [(p.PullResult, {}), (r.KEGGresponse, {'status': None, 'kegg_url': None})])
 def test_non_instantiable(NonInstantiable: type, kwargs: dict):
     expected_error_message = f'The class "{NonInstantiable.__name__}" cannot be instantiated outside of its module.'
     with pt.raises(RuntimeError) as error:
diff --git a/docs/api.rst b/docs/api.rst
@@ -16,10 +16,6 @@ API
     :members:
     :undoc-members:
 
-.. automodule:: kegg_pull.pathway_organizer
-    :members:
-    :undoc-members:
-
 .. automodule:: kegg_pull.rest
     :members:
     :undoc-members:
diff --git a/docs/cli.rst b/docs/cli.rst
@@ -76,15 +76,6 @@ If the ``--unsuccessful-threshold`` option is set and surpassed, an ``aborted-pu
     :end-before: """
     :language: none
 
-.. include:: ../src/kegg_pull/pathway_organizer.py
-    :start-after: """
-    :end-before: """
-
-.. literalinclude:: ../src/kegg_pull/pathway_organizer_cli.py
-    :start-at: Usage:
-    :end-before: """
-    :language: none
-
 .. include:: ../src/kegg_pull/rest.py
     :start-after: """
     :end-before: """
diff --git a/docs/conf.py b/docs/conf.py
@@ -43,7 +43,7 @@ def setup(app):
 
 templates_path = ['_templates']
 exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
-
+latex_elements = {'preamble': r'\usepackage{pmboxdraw}'}
 
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
diff --git a/docs/tutorial.rst b/docs/tutorial.rst
@@ -320,24 +320,6 @@ operation or “conv” operation into dictionaries usable in python code.
     {'cpd:C00001': {'pubchem:3303'}, 'cpd:C00002': {'pubchem:3304'}}
 
 
-Pathway Organizer
-~~~~~~~~~~~~~~~~~
-
-The ``pathway_organizer`` module flattens a brite hierarchy into a
-mapping of the IDs of its nodes to information about those nodes.
-
-.. code:: python3
-
-    import kegg_pull.pathway_organizer as po
-    pathway_org = po.PathwayOrganizer.load_from_kegg()
-    print(pathway_org.hierarchy_nodes['Metabolism'])
-
-
-.. parsed-literal::
-
-    {'name': 'Metabolism', 'level': 1, 'parent': None, 'children': ['Amino acid metabolism', 'Biosynthesis of other secondary metabolites', 'Carbohydrate metabolism', 'Chemical structure transformation maps', 'Energy metabolism', 'Global and overview maps', 'Glycan biosynthesis and metabolism', 'Lipid metabolism', 'Metabolism of cofactors and vitamins', 'Metabolism of other amino acids', 'Metabolism of terpenoids and polyketides', 'Nucleotide metabolism', 'Xenobiotics biodegradation and metabolism'], 'entry_id': None}
-
-
 Rest API
 ~~~~~~~~
 
@@ -703,29 +685,6 @@ map
         "cpd:C00084",
 
 
-pathway-organizer
-~~~~~~~~~~~~~~~~~
-
-.. code:: none
-
-    % kegg_pull pathway-organizer --tln=Metabolism --fn="Global and overview maps,Carbohydrate metabolism" --output=hierarchy-nodes.json
-    % head hierarchy-nodes.json
-
-
-.. parsed-literal::
-
-    {
-      "path:map00190": {
-        "name": "00190  Oxidative phosphorylation",
-        "level": 3,
-        "parent": "Energy metabolism",
-        "children": null,
-        "entry_id": "path:map00190"
-      },
-      "path:map00195": {
-        "name": "00195  Photosynthesis",
-
-
 rest
 ~~~~
 
diff --git a/src/kegg_pull/__init__.py b/src/kegg_pull/__init__.py
@@ -7,8 +7,6 @@
 
 ``map``
 
-``pathway_organizer``
-
 ``rest``
 
 ``kegg_url``
diff --git a/src/kegg_pull/__main__.py b/src/kegg_pull/__main__.py
@@ -6,15 +6,13 @@
     kegg_pull pull ...              Pull, separate, and store an arbitrary number of KEGG entries to the local file system.
     kegg_pull entry-ids ...         Obtain a list of KEGG entry IDs.
     kegg_pull map ...               Obtain a mapping of entry IDs (KEGG or outside databases) to the IDs of related entries.
-    kegg_pull pathway-organizer ... Creates a flattened version of a pathways Brite hierarchy.
     kegg_pull rest ...              Executes one of the KEGG REST API operations.
 """
 import sys
 from . import __version__
 from . import pull_cli as p_cli
 from . import entry_ids_cli as ei_cli
 from . import map_cli as map_cli
-from . import pathway_organizer_cli as po_cli
 from . import rest_cli as r_cli
 
 
@@ -26,8 +24,6 @@ def main() -> None:
         ei_cli.main()
     elif first_arg == 'map':
         map_cli.main()
-    elif first_arg == 'pathway-organizer':
-        po_cli.main()
     elif first_arg == 'rest':
         r_cli.main()
     elif first_arg == '--full-help':
@@ -40,8 +36,6 @@ def main() -> None:
         print(separator)
         print(map_cli.__doc__)
         print(separator)
-        print(po_cli.__doc__)
-        print(separator)
         print(r_cli.__doc__)
     elif first_arg == '--version' or first_arg == '-v':
         print(__version__)
diff --git a/src/kegg_pull/pathway_organizer.py b/src/kegg_pull/pathway_organizer.py
diff --git a/src/kegg_pull/pathway_organizer_cli.py b/src/kegg_pull/pathway_organizer_cli.py
