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Increase the usage of augmented assignment statements
:eyes: Some source code analysis tools can help to find opportunities for improving software components. :thought_balloon: I propose to increase the usage of augmented assignment statements accordingly.
diff --git a/ete3/coretype/tree.py b/ete3/coretype/tree.py
index d0d3e93c..954fb5f6 100644
--- a/ete3/coretype/tree.py
+++ b/ete3/coretype/tree.py
@@ -2176,7 +2176,7 @@ class TreeNode(object):
if ignore_missing:
found_values = set([getattr(n, target_attr) for n in n2leaves[self]])
missing_values = values - found_values
- values = values & found_values
+ values &= found_values
# Locate leaves matching requested attribute values
targets = set([leaf for leaf in n2leaves[self]
diff --git a/ete3/evol/evoltree.py b/ete3/evol/evoltree.py
index d37f5de9..e40037e9 100644
--- a/ete3/evol/evoltree.py
+++ b/ete3/evol/evoltree.py
@@ -268,7 +268,7 @@ class EvolNode(PhyloNode):
setattr(model_obj, 'run', run)
self.link_to_evol_model(os.path.join(fullpath,'out'), model_obj)
sep = '\n'
- run_model.__doc__ = run_model.__doc__ % \
+ run_model.__doc__ %= \
(sep.join([' %-8s %-27s %-15s ' % \
('%s' % (x), AVAIL[x]['evol'], AVAIL[x]['typ']) for x in sorted (sorted (AVAIL.keys()), key=lambda x: \
AVAIL[x]['typ'],
diff --git a/ete3/evol/model.py b/ete3/evol/model.py
index 8efbe0e1..bc85ceeb 100644
--- a/ete3/evol/model.py
+++ b/ete3/evol/model.py
@@ -370,7 +370,7 @@ def check_name(model):
-Model.__doc__ = Model.__doc__ % \
+Model.__doc__ %= \
('\n'.join([ ' %-8s %-27s %-15s ' % \
('%s' % (x), AVAIL[x]['evol'], AVAIL[x]['typ']) \
for x in sorted(sorted(AVAIL.keys()),key=lambda x: \
diff --git a/ete3/evol/parser/codemlparser.py b/ete3/evol/parser/codemlparser.py
index 2e2da87b..aaefce01 100644
--- a/ete3/evol/parser/codemlparser.py
+++ b/ete3/evol/parser/codemlparser.py
@@ -142,7 +142,7 @@ def divide_data(pamout, model):
for multiple dataset, divide outfile.
'''
for num in range (1, int (model.properties['params']['ndata'])):
- model.name = model.name + '_' + str(num)
+ model.name += '_' + str(num)
out = open (pamout + '_' + str(num), 'w')
copy = False
for line in open (pamout):
diff --git a/ete3/evol/utils.py b/ete3/evol/utils.py
index 92e490ac..4464de0a 100644
--- a/ete3/evol/utils.py
+++ b/ete3/evol/utils.py
@@ -307,7 +307,7 @@ def lgam(x):
if u == 2:
return log(z)
p -= 2
- x = x + p
+ x += p
p = x * polevl(x, GB)/polevl(x,GC)
return log(z) + p
if x > MAXLGM:
diff --git a/ete3/tools/ete_build_lib/seqio.py b/ete3/tools/ete_build_lib/seqio.py
index b0d8527f..55e0b54f 100644
--- a/ete3/tools/ete_build_lib/seqio.py
+++ b/ete3/tools/ete_build_lib/seqio.py
@@ -121,7 +121,7 @@ def load_sequences(args, seqtype, target_seqs, target_species, cached_seqs):
if seqname in loaded_seqs:
if fix_dups:
dupnames[seqname] += 1
- seqname = seqname + "_%d"%dupnames[seqname]
+ seqname += "_%d" % dupnames[seqname]
else:
raise DataError("Duplicated sequence name [%s] found. Fix manually or use --rename-dup-seqnames to continue" %(seqname))
diff --git a/ete3/tools/ete_build_lib/task/merger.py b/ete3/tools/ete_build_lib/task/merger.py
index a7b50a73..93c1c658 100644
--- a/ete3/tools/ete_build_lib/task/merger.py
+++ b/ete3/tools/ete_build_lib/task/merger.py
@@ -236,13 +236,13 @@ def dump_tree_debug(msg, taskdir, mtree, ttree, target_seqs, out_seqs):
if ttree:
for n in ttree.get_leaves():
if n.name in out_seqs:
- n.name = n.name + " *__OUTGROUP__*"
+ n.name += " *__OUTGROUP__*"
if mtree:
for n in mtree.get_leaves():
if n.name in out_seqs:
- n.name = n.name + " *__OUTGROUP__*"
+ n.name += " *__OUTGROUP__*"
if n.name in target_seqs:
- n.name = n.name + " [ TARGET ]"
+ n.name += " [ TARGET ]"
OUT = open(pjoin(taskdir, "__debug__"), "w")
print(msg, file=OUT)
diff --git a/ete3/tools/ete_evol.py b/ete3/tools/ete_evol.py
index 354bad7c..2749cdd7 100644
--- a/ete3/tools/ete_evol.py
+++ b/ete3/tools/ete_evol.py
@@ -983,7 +983,7 @@ def run(args):
if args.histface:
if len(args.histface) != len(site_models):
if len(args.histface) == 1:
- args.histface = args.histface * len(site_models)
+ args.histface *= len(site_models)
elif len(args.histface) <= len(site_models):
args.histface.extend([args.histface[-1]] * (
len(site_models) - len(args.histface)))
diff --git a/ete3/tools/ete_maptrees.py b/ete3/tools/ete_maptrees.py
index f1963d83..51b6c4c7 100644
--- a/ete3/tools/ete_maptrees.py
+++ b/ete3/tools/ete_maptrees.py
@@ -112,8 +112,8 @@ def get_splits(tree, min_support=None, target_attr="name", discard_root=False, i
b1 = set([getattr(_c, target_attr) for _c in node2content[node.children[0]]])
b2 = set([getattr(_c, target_attr) for _c in node2content[node.children[1]]])
if target_species:
- b1 = b1 & target_species
- b2 = b2 & target_species
+ b1 &= target_species
+ b2 &= target_species
if b1 and b2:
branches.append([node, b1, b2])
return all_species, branches
diff --git a/ete3/treeview/main.py b/ete3/treeview/main.py
index 1c930fa9..274228ec 100644
--- a/ete3/treeview/main.py
+++ b/ete3/treeview/main.py
@@ -664,14 +664,14 @@ def save(scene, imgName, w=None, h=None, dpi=90,\
# Adjust to resolution
if units == "mm":
if w:
- w = w * 0.0393700787 * dpi
+ w *= 0.0393700787 * dpi
if h:
- h = h * 0.0393700787 * dpi
+ h *= 0.0393700787 * dpi
elif units == "in":
if w:
- w = w * dpi
+ w *= dpi
if h:
- h = h * dpi
+ h *= dpi
elif units == "px":
pass
else:
diff --git a/ete3/treeview/qt4_gui.py b/ete3/treeview/qt4_gui.py
index b33bacea..cc1181af 100644
--- a/ete3/treeview/qt4_gui.py
+++ b/ete3/treeview/qt4_gui.py
@@ -429,7 +429,7 @@ class _GUI(QMainWindow):
else:
self.showMaximized()
elif key >= 49 and key <= 58:
- key = key - 48
+ key -= 48
m = self.view.transform()
m.reset()
self.view.setTransform(m)
diff --git a/examples/webplugin/wsgi/webplugin_example.py b/examples/webplugin/wsgi/webplugin_example.py
index a9daa88b..6b4d7abd 100755
--- a/examples/webplugin/wsgi/webplugin_example.py
+++ b/examples/webplugin/wsgi/webplugin_example.py
@@ -345,7 +345,7 @@ def tree_renderer(tree, treeid, application):
for f in l.features:
if not f.startswith("_"):
text_features_avail.setdefault(f, 0)
- text_features_avail[f] = text_features_avail[f] + 1
+ text_features_avail[f] += 1
html_features = """
<div id="tree_features_box">
