From f32e9c61dd68ed30193382f48d41c57ce28cca06 Mon Sep 17 00:00:00 2001
From: Miro <200482516+Mirochill@users.noreply.github.com>
Date: Sat, 23 May 2026 16:43:03 +0200
Subject: [PATCH] Fix invalid escape sequence warnings
---
ete3/coretype/tree.py | 6 +++---
ete3/evol/evoltree.py | 4 ++--
ete3/evol/model.py | 4 ++--
ete3/evol/parser/codemlparser.py | 32 ++++++++++++++++----------------
ete3/parser/newick.py | 8 ++++----
ete3/parser/phylip.py | 8 ++++----
ete3/phylo/phylotree.py | 4 ++--
ete3/phylomedb/phylomeDB3.py | 12 ++++++------
ete3/tools/common.py | 2 +-
ete3/tools/ete_view.py | 8 ++++----
ete3/tools/utils.py | 2 +-
ete3/treeview/faces.py | 2 +-
ete3/treeview/main.py | 6 +++---
ete3/utils.py | 2 +-
14 files changed, 50 insertions(+), 50 deletions(-)
diff --git a/ete3/coretype/tree.py b/ete3/coretype/tree.py
index 5fe48cea8..3978c8958 100644
--- a/ete3/coretype/tree.py
+++ b/ete3/coretype/tree.py
@@ -362,7 +362,7 @@ def remove_sister(self, sister=None):
return self.up.remove_child(sister)
def delete(self, prevent_nondicotomic=True, preserve_branch_length=False):
- """
+ r"""
Deletes node from the tree structure. Notice that this method
makes 'disappear' the node from the tree structure. This means
that children from the deleted node are transferred to the
@@ -433,7 +433,7 @@ def detach(self):
def prune(self, nodes, preserve_branch_length=False):
- """Prunes the topology of a node to conserve only the selected list of leaf
+ r"""Prunes the topology of a node to conserve only the selected list of leaf
internal nodes. The minimum number of nodes that conserve the
topological relationships among the requested nodes will be
retained. Root node is always conserved.
@@ -1487,7 +1487,7 @@ def render(self, file_name, layout=None, w=None, h=None, \
units=units, dpi=dpi)
def copy(self, method="cpickle"):
- """.. versionadded: 2.1
+ r""".. versionadded: 2.1
Returns a copy of the current node.
diff --git a/ete3/evol/evoltree.py b/ete3/evol/evoltree.py
index 824875a57..43ab2e212 100644
--- a/ete3/evol/evoltree.py
+++ b/ete3/evol/evoltree.py
@@ -465,10 +465,10 @@ def write(self, features=None, outfile=None, format=10):
from re import sub
if int(format) == 11:
nwk = ' %s 1\n' % (len(self))
- nwk += sub('\[&&NHX:mark=([ #0-9.]*)\]', r'\1',
+ nwk += sub(r'\[&&NHX:mark=([ #0-9.]*)\]', r'\1',
write_newick(self, features=['mark'], format=9))
elif int(format) == 10:
- nwk = sub('\[&&NHX:mark=([ #0-9.]*)\]', r'\1',
+ nwk = sub(r'\[&&NHX:mark=([ #0-9.]*)\]', r'\1',
write_newick(self, features=['mark'], format=9))
else:
nwk = write_newick(self, features=features, format=format)
diff --git a/ete3/evol/model.py b/ete3/evol/model.py
index 91de572c4..0e4965571 100644
--- a/ete3/evol/model.py
+++ b/ete3/evol/model.py
@@ -364,8 +364,8 @@ def check_name(model):
'''
check that model name corresponds to one of the available
'''
- if sub('\..*', '', model) in AVAIL:
- return model, AVAIL [sub('\..*', '', model)]
+ if sub(r'\..*', '', model) in AVAIL:
+ return model, AVAIL [sub(r'\..*', '', model)]
diff --git a/ete3/evol/parser/codemlparser.py b/ete3/evol/parser/codemlparser.py
index a75fe4270..ac10a24be 100644
--- a/ete3/evol/parser/codemlparser.py
+++ b/ete3/evol/parser/codemlparser.py
@@ -71,25 +71,25 @@ def parse_rst(path):
for line in open(path):
# get number of classes of sites
if line.startswith ('dN/dS '):
- k = int(re.sub ('.* \(K=([0-9]+)\)\n', '\\1', line))
+ k = int(re.sub (r'.* \(K=([0-9]+)\)\n', r'\1', line))
continue
# get values of omega and proportions
if typ is None and \
- re.match ('^[a-z]+.*(\d+\.\d{5} *){'+ str(k) +'}', line):
+ re.match (r'^[a-z]+.*(\d+\.\d{5} *){'+ str(k) +'}', line):
var = re.sub (':', '', line.split(' ')[0])
if var.startswith ('p'):
var = 'proportions'
- classes[var] = [float(v) for v in re.findall('\d+\.\d{5}', line)]
+ classes[var] = [float(v) for v in re.findall(r'\d+\.\d{5}', line)]
continue
# parse NEB and BEB tables
if '(BEB)' in line :
- k = int(re.sub('.*for (\d+) classes.*\n', '\\1', line))
+ k = int(re.sub(r'.*for (\d+) classes.*\n', r'\1', line))
typ = 'BEB'
sites[typ] = {}
n_classes[typ] = k
continue
if '(NEB)' in line :
- k = int(re.sub('.*for (\d+) classes.*\n', '\\1', line))
+ k = int(re.sub(r'.*for (\d+) classes.*\n', r'\1', line))
typ = 'NEB'
sites[typ] = {}
n_classes[typ] = k
@@ -214,7 +214,7 @@ def parse_paml (pamout, model):
# if we do not have tree, load it
if model._tree is None:
from ..evol import EvolTree
- model._tree = EvolTree (re.findall ('\(.*\);', ''.join(all_lines))[2])
+ model._tree = EvolTree (re.findall (r'\(.*\);', ''.join(all_lines))[2])
model._tree._label_as_paml()
# starts parsing
for i, line in enumerate (all_lines):
@@ -224,7 +224,7 @@ def parse_paml (pamout, model):
if line.startswith('Codon frequencies under model'):
model.stats ['codonFreq'] = []
for j in range (16):
- line = list(map (float, re.findall ('\d\.\d+', all_lines [i+j+1])))
+ line = list(map (float, re.findall (r'\d\.\d+', all_lines [i+j+1])))
model.stats ['codonFreq'] += [line]
continue
if line.startswith('Nei & Gojobori 1986'):
@@ -237,32 +237,32 @@ def parse_paml (pamout, model):
# lnL and number of parameters
if line.startswith ('lnL'):
try:
- line = re.sub ('.* np: *(\d+)\): +(-\d+\.\d+).*',
- '\\1 \\2', line)
+ line = re.sub (r'.* np: *(\d+)\): +(-\d+\.\d+).*',
+ r'\1 \2', line)
model.stats ['np' ] = int (line.split()[0])
model.stats ['lnL'] = float (line.split()[1])
except ValueError:
- line = re.sub ('.* np: *(\d+)\): +(nan).*',
- '\\1 \\2', line)
+ line = re.sub (r'.* np: *(\d+)\): +(nan).*',
+ r'\1 \2', line)
model.stats ['np' ] = int (line.split()[0])
model.stats ['lnL'] = float ('-inf')
continue
# get labels of internal branches
if line.count('..') >= 2:
- labels = re.findall ('\d+\.\.\d+', line + ' ')
+ labels = re.findall (r'\d+\.\.\d+', line + ' ')
_check_paml_labels (model._tree, labels, pamout, model)
continue
# retrieve kappa
if line.startswith ('kappa '):
try:
- model.stats ['kappa'] = float (re.sub ('.*(\d+\.\d+).*',
- '\\1', line))
+ model.stats ['kappa'] = float (re.sub (r'.*(\d+\.\d+).*',
+ r'\1', line))
except ValueError:
model.stats ['kappa'] = 'nan'
# retrieve dS dN t w N S and if present, errors. from summary table
if line.count('..') == 1 and line.startswith (' '):
- if not re.match (' +\d+\.\.\d+ +\d+\.\d+ ', line):
- if re.match (' +( +\d+\.\d+){8}', all_lines [i+1]):
+ if not re.match (r' +\d+\.\.\d+ +\d+\.\d+ ', line):
+ if re.match (r' +( +\d+\.\d+){8}', all_lines [i+1]):
_get_values (model, line.split ()[0]+' '+all_lines [i+1])
continue
_get_values (model, line)
diff --git a/ete3/parser/newick.py b/ete3/parser/newick.py
index 6f16890eb..704d2041d 100644
--- a/ete3/parser/newick.py
+++ b/ete3/parser/newick.py
@@ -48,11 +48,11 @@
ITERABLE_TYPES = set([list, set, tuple, frozenset])
# Regular expressions used for reading newick format
-_ILEGAL_NEWICK_CHARS = ":;(),\[\]\t\n\r="
+_ILEGAL_NEWICK_CHARS = ":;(),\\[\\]\t\n\r="
_NON_PRINTABLE_CHARS_RE = "[\x00-\x1f]+"
-_NHX_RE = "\[&&NHX:[^\]]*\]"
-_FLOAT_RE = "\s*[+-]?\d+\.?\d*(?:[eE][-+]?\d+)?\s*"
+_NHX_RE = r"\[&&NHX:[^\]]*\]"
+_FLOAT_RE = r"\s*[+-]?\d+\.?\d*(?:[eE][-+]?\d+)?\s*"
#_FLOAT_RE = "[+-]?\d+\.?\d*"
#_NAME_RE = "[^():,;\[\]]+"
_NAME_RE = "[^():,;]+?"
@@ -399,7 +399,7 @@ def compile_matchers(formatcode):
SECOND_MATCH += "?"
- matcher_str= '^\s*%s\s*%s\s*(%s)?\s*$' % (FIRST_MATCH, SECOND_MATCH, _NHX_RE)
+ matcher_str= r'^\s*%s\s*%s\s*(%s)?\s*$' % (FIRST_MATCH, SECOND_MATCH, _NHX_RE)
compiled_matcher = re.compile(matcher_str)
matchers[node_type] = [container1, container2, converterFn1, converterFn2, compiled_matcher]
diff --git a/ete3/parser/phylip.py b/ete3/parser/phylip.py
index ba62b13e7..5f8728cd5 100644
--- a/ete3/parser/phylip.py
+++ b/ete3/parser/phylip.py
@@ -73,7 +73,7 @@ def read_phylip(source, interleaved=True, obj=None,
continue
# Reads head
if not nchar or not ntax:
- m = re.match("^\s*(\d+)\s+(\d+)",line)
+ m = re.match(r"^\s*(\d+)\s+(\d+)",line)
if m:
ntax = int (m.groups()[0])
nchar = int (m.groups()[1])
@@ -105,7 +105,7 @@ def read_phylip(source, interleaved=True, obj=None,
line = m.groups()[1]
else:
raise Exception("Wrong phylip sequencial format.")
- SG.id2seq[id_counter] += re.sub("\s","", line)
+ SG.id2seq[id_counter] += re.sub(r"\s","", line)
if len(SG.id2seq[id_counter]) == nchar:
id_counter += 1
name = None
@@ -120,7 +120,7 @@ def read_phylip(source, interleaved=True, obj=None,
if m:
name = m.groups()[0].strip()
- seq = re.sub("\s","",m.groups()[1])
+ seq = re.sub(r"\s","",m.groups()[1])
SG.id2seq[id_counter] = seq
SG.id2name[id_counter] = name
if fix_duplicates and name in SG.name2id:
@@ -135,7 +135,7 @@ def read_phylip(source, interleaved=True, obj=None,
else:
raise Exception("Unexpected number of sequences.")
else:
- seq = re.sub("\s", "", line)
+ seq = re.sub(r"\s", "", line)
if id_counter == len(SG):
id_counter = 0
SG.id2seq[id_counter] += seq
diff --git a/ete3/phylo/phylotree.py b/ete3/phylo/phylotree.py
index d0b68fc2c..72a55cef9 100644
--- a/ete3/phylo/phylotree.py
+++ b/ete3/phylo/phylotree.py
@@ -129,7 +129,7 @@ def _nodereplacer(match):
return ''.join([pre, node.name, fstring, post])
if newick_only:
- id_match = re.compile("([^0-9])?(\d+)([^0-9])?")
+ id_match = re.compile(r"([^0-9])?(\d+)([^0-9])?")
for nw in sp_trees:
yield re.sub(id_match, _nodereplacer, str(nw)+";")
else:
@@ -185,7 +185,7 @@ def _nodereplacer(match):
return ''.join([pre, node.name, fstring, post])
if newick_only:
- id_match = re.compile("([^0-9])(\d+)([^0-9])")
+ id_match = re.compile(r"([^0-9])(\d+)([^0-9])")
for nw in sptrees:
yield re.sub(id_match, _nodereplacer, str(nw)+";")
else:
diff --git a/ete3/phylomedb/phylomeDB3.py b/ete3/phylomedb/phylomeDB3.py
index 52e0f7c16..df04b4ce1 100644
--- a/ete3/phylomedb/phylomeDB3.py
+++ b/ete3/phylomedb/phylomeDB3.py
@@ -72,7 +72,7 @@
def extract_species_name(name):
return name.split("_")[1]
-ID_PATTERN = re.compile("^[Pp][Hh][Yy]\w{7}(_\w{2,7})?$")
+ID_PATTERN = re.compile(r"^[Pp][Hh][Yy]\w{7}(_\w{2,7})?$")
ITERABLE_TYPES = set([list, set, tuple, frozenset])
__all__ = ["PhylomeDB3Connector"]
@@ -150,7 +150,7 @@ def load_trees(self, seqnames=None, model="best_lk", anotate_trees = True):
"""
def clean_name(name):
quote = lambda x: '"%s"' %x
- m = re.search("Phy(\w{7})_[\w\d]+", name)
+ m = re.search(r"Phy(\w{7})_[\w\d]+", name)
if m:
return quote(m.groups()[0])
@@ -497,7 +497,7 @@ def get_new_phylomedb_id(self, old_id):
"""
# Check whether the input code is a valid former phylomeDB id or not
- QUERY_OLD_REGEXP_FILTER = "^\w{3}\d{1,}$"
+ QUERY_OLD_REGEXP_FILTER = r"^\w{3}\d{1,}$"
if not re.match(QUERY_OLD_REGEXP_FILTER, old_id):
return None
@@ -753,9 +753,9 @@ def search_id(self, id):
query = id.strip()
# To avoid weird queries which creates slow or invalid MYSQL queries
- QUERY_GEN_REGEXP_FILTER = "^[\w\d\-_,;:.|#@\/\\\()'<>!]+$"
- QUERY_OLD_REGEXP_FILTER = "^\w{3}\d{1,}$"
- QUERY_INT_REGEXP_FILTER = "^[Pp][Hh][Yy]\w{7}(_\w{2,7})?$"
+ QUERY_GEN_REGEXP_FILTER = r"^[\w\d\-_,;:.|#@/\\()'<>!]+$"
+ QUERY_OLD_REGEXP_FILTER = r"^\w{3}\d{1,}$"
+ QUERY_INT_REGEXP_FILTER = r"^[Pp][Hh][Yy]\w{7}(_\w{2,7})?$"
phylomeDB_matches = {}
# First, check if it is a current phylomeDB ID
diff --git a/ete3/tools/common.py b/ete3/tools/common.py
index eb75766b9..e831efcbe 100644
--- a/ete3/tools/common.py
+++ b/ete3/tools/common.py
@@ -155,7 +155,7 @@ def shorten_str(string, l, reverse=False):
return string
def parse_value(fvalue):
- func_match = re.search("(\w+)\(([^)]*)\)", fvalue)
+ func_match = re.search(r"(\w+)\(([^)]*)\)", fvalue)
if func_match:
func_name = func_match.groups()[0]
func_arg = func_match.groups()[1]
diff --git a/ete3/tools/ete_view.py b/ete3/tools/ete_view.py
index 35667c617..ccbde0aa1 100644
--- a/ete3/tools/ete_view.py
+++ b/ete3/tools/ete_view.py
@@ -206,7 +206,7 @@ def run(args):
for tindex, tfile in enumerate(src_tree_iterator(args)):
#print tfile
if args.raxml:
- nw = re.sub(":(\d+\.\d+)\[(\d+)\]", ":\\1[&&NHX:support=\\2]", open(tfile).read())
+ nw = re.sub(r":(\d+\.\d+)\[(\d+)\]", r":\1[&&NHX:support=\2]", open(tfile).read())
t = Tree(nw, format=args.src_newick_format)
else:
t = Tree(tfile, format=args.src_newick_format)
@@ -272,7 +272,7 @@ def run(args):
for tindex, tfile in enumerate(src_tree_iterator(args)):
#print tfile
if args.raxml:
- nw = re.sub(":(\d+\.\d+)\[(\d+)\]", ":\\1[&&NHX:support=\\2]", open(tfile).read())
+ nw = re.sub(r":(\d+\.\d+)\[(\d+)\]", r":\1[&&NHX:support=\2]", open(tfile).read())
t = PhyloTree(nw, format=args.src_newick_format)
else:
t = PhyloTree(tfile, format=args.src_newick_format)
@@ -369,7 +369,7 @@ def hls2hex(h, l, s):
if fcolor:
# Parse color options
- auto_m = re.search("auto\(([^)]*)\)", fcolor)
+ auto_m = re.search(r"auto\(([^)]*)\)", fcolor)
if auto_m:
target_attr = auto_m.groups()[0].strip()
if not target_attr :
@@ -389,7 +389,7 @@ def hls2hex(h, l, s):
if fbgcolor:
# Parse color options
- auto_m = re.search("auto\(([^)]*)\)", fbgcolor)
+ auto_m = re.search(r"auto\(([^)]*)\)", fbgcolor)
if auto_m:
target_attr = auto_m.groups()[0].strip()
if not target_attr :
diff --git a/ete3/tools/utils.py b/ete3/tools/utils.py
index 5947726c4..fc1205879 100644
--- a/ete3/tools/utils.py
+++ b/ete3/tools/utils.py
@@ -25,7 +25,7 @@ def colorify(string, color):
return "%s%s%s" %(COLORS[color], string, COLORS[None])
def clear_color(string):
- return re.sub("\\033\[[^m]+m", "", string)
+ return re.sub(r"\033\[[^m]+m", "", string)
def which(program):
def is_exe(fpath):
diff --git a/ete3/treeview/faces.py b/ete3/treeview/faces.py
index fb8839a61..ef944bcea 100644
--- a/ete3/treeview/faces.py
+++ b/ete3/treeview/faces.py
@@ -156,7 +156,7 @@
"RectFace", "StackedBarFace", "SVGFace", "DiamondFace"]
class Face(object):
- """Base Face object. All Face types (i.e. TextFace, SeqMotifFace,
+ r"""Base Face object. All Face types (i.e. TextFace, SeqMotifFace,
etc.) inherit the following options:
:param 0 margin_left: in pixels
diff --git a/ete3/treeview/main.py b/ete3/treeview/main.py
index 1255b291b..ce55b897e 100644
--- a/ete3/treeview/main.py
+++ b/ete3/treeview/main.py
@@ -61,7 +61,7 @@ def a_wrapper_accepting_arguments(*args, **kargs):
_LINE_TYPE_CHECKER = lambda x: x in (0,1,2)
_SIZE_CHECKER = lambda x: isinstance(x, int)
-_COLOR_MATCH = re.compile("^#[A-Fa-f\d]{6}$")
+_COLOR_MATCH = re.compile(r"^#[A-Fa-f\d]{6}$")
_COLOR_CHECKER = lambda x: x.lower() in SVG_COLORS or re.match(_COLOR_MATCH, x)
_NODE_TYPE_CHECKER = lambda x: x in ["sphere", "circle", "square"]
_BOOL_CHECKER = lambda x: isinstance(x, bool) or x in (0,1)
@@ -713,9 +713,9 @@ def save(scene, imgName, w=None, h=None, dpi=90,\
# Fix a very annoying problem with Radial gradients in
# inkscape and browsers...
compatible_code = compatible_code.replace("xml:id=", "id=")
- compatible_code = re.sub('font-size="(\d+)"', 'font-size="\\1pt"', compatible_code)
+ compatible_code = re.sub(r'font-size="(\d+)"', r'font-size="\1pt"', compatible_code)
compatible_code = compatible_code.replace('\n', ' ')
- compatible_code = re.sub(']+>\s*', '', compatible_code)
+ compatible_code = re.sub(r']+>\s*', '', compatible_code)
# End of fix
if ipython_inline:
from IPython.core.display import SVG
diff --git a/ete3/utils.py b/ete3/utils.py
index d4748c0e3..cccd1f4b6 100644
--- a/ete3/utils.py
+++ b/ete3/utils.py
@@ -79,7 +79,7 @@ def color(string, color):
return "%s%s%s" %(SHELL_COLORS[color], string, SHELL_COLORS[None])
def clear_color(string):
- return re.sub("\\033\[[^m]+m", "", string)
+ return re.sub(r"\033\[[^m]+m", "", string)
def print_table(items, header=None, wrap=True, max_col_width=20,
wrap_style="wrap", row_line=False, fix_col_width=False, title=None):