Update bio2bel and override populate function in CLI

requirements.txt

@@ -1,5 +1,5 @@
 pybel[deployment]>=0.11.1
-bio2bel>=0.0.9
+bio2bel>=0.0.10
 tqdm
 sqlalchemy
 click

setup.py

@@ -12,7 +12,7 @@
 META_PATH = os.path.join('src', 'bio2bel_hgnc', '__init__.py')
 INSTALL_REQUIRES = [
     'pybel[deployment]>=0.11.1',
-    'bio2bel>=0.0.9',
+    'bio2bel>=0.0.10',
     'tqdm',
     'sqlalchemy',
     'click',

src/bio2bel_hgnc/manager.py

@@ -6,9 +6,10 @@
 import time
 from collections import Counter
 
+import click
 from tqdm import tqdm
 
-from bio2bel.abstractmanager import AbstractManager
+from bio2bel import AbstractManager
 from pybel import BELGraph, to_bel
 from pybel.constants import FUNCTION, GENE, IDENTIFIER, IS_A, NAME, NAMESPACE, NAMESPACE_DOMAIN_GENE, PROTEIN, RNA
 from pybel.dsl import gene as gene_dsl, protein as protein_dsl, rna as rna_dsl
@@ -809,3 +810,24 @@ def upload_bel_namespace(self):
         self._update_namespace(ns)
 
         return ns
+
+    @staticmethod
+    def _cli_add_populate(main):
+        """Overrides default method to make it possible to add more flags"""
+
+        @main.command()
+        @click.option('--reset', is_flag=True)
+        @click.option('--skip-hcop', is_flag=True)
+        @click.pass_obj
+        def populate(manager, reset, skip_hcop):
+            """Populates the database"""
+
+            if reset:
+                log.info('Deleting the previous instance of the database')
+                manager.drop_all()
+                log.info('Creating new models')
+                manager.create_all()
+
+            manager.populate(use_hcop=(not skip_hcop))
+
+        return main