From 3fc08171d42ea687971b3f2b50f0cfb560f49027 Mon Sep 17 00:00:00 2001
From: Christian Diener <ch.diener@gmail.com>
Date: Wed, 31 Mar 2021 18:11:52 -0700
Subject: [PATCH] fix iffy biomass exchanges in some models

---
 docs/source/conf.py | 2 --
 micom/community.py  | 4 ++++
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/docs/source/conf.py b/docs/source/conf.py
index 8525d113..2def393b 100755
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -21,8 +21,6 @@
 # import sys
 # sys.path.insert(0, os.path.abspath('.'))
 import micom
-from os.path import dirname, join
-import sys
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
diff --git a/micom/community.py b/micom/community.py
index 97711a20..7cdf1ad8 100755
--- a/micom/community.py
+++ b/micom/community.py
@@ -310,6 +310,10 @@ def __add_exchanges(
                     "Reaction %s seems to be an exchange " % r.id
                     + "reaction but its ID does not start with 'EX_'..."
                 )
+            # Some AGORA models label the biomass demand as exchange
+            if any(bm in r.id.lower() for bm in ["biomass", "bm"]):
+                r.id = r.id.replace("EX_", "DM_")
+                continue
 
             export = len(r.reactants) == 1
             if export: