Merge branch 'master' into pretty-defline-formatting

merenlab · Sep 25, 2024 · 2e67baa · 2e67baa
2 parents b461f29 + aa73ca2
commit 2e67baa
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diff --git a/anvio/__init__.py b/anvio/__init__.py
@@ -3168,6 +3168,22 @@ def TABULATE(table, header, numalign="right", max_width=0):
              'action': 'store_true',
              'help': "Use this flag to skip using BRITE hierarchies, which we don't recommend but let you do anyways."}
                 ),
+    'skip-binary-relations': (
+            ['--skip-binary-relations'],
+            {'default': False,
+             'action': 'store_true',
+             'help': "Use this flag to skip setting up KEGG binary relation files, which we don't "
+                     "recommend, since they are necessary for running `anvi-reaction-network`, but "
+                     "let you do anyways."}
+                ),
+    'skip-map-images': (
+            ['--skip-map-images'],
+            {'default': False,
+             'action': 'store_true',
+             'help': "Use this flag to skip setting up KEGG pathway map image files, which we don't "
+                     "recommend, since they are used in visualizing pathway membership, but let you "
+                     "do anyways."}
+                ),
     'heuristic-e-value': (
             ['-E', '--heuristic-e-value'],
             {'default': 1.0e-5,

diff --git a/anvio/biochemistry/__init__.py b/anvio/biochemistry/__init__.py