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Importing ete3 generates many SyntaxWarnings with python 3.12
Hi,
ete3 declares many strings with escape sequences but they are not raw strings. With python 3.12, it generates a SyntaxWarning.
Here is the output
/usr/local/lib/python3.12/site-packages/ete3/coretype/tree.py:365: SyntaxWarning: invalid escape sequence '\-'
"""
/usr/local/lib/python3.12/site-packages/ete3/coretype/tree.py:436: SyntaxWarning: invalid escape sequence '\-'
"""Prunes the topology of a node to conserve only the selected list of leaf
/usr/local/lib/python3.12/site-packages/ete3/coretype/tree.py:1508: SyntaxWarning: invalid escape sequence '\-'
"""
/usr/local/lib/python3.12/site-packages/ete3/parser/newick.py:51: SyntaxWarning: invalid escape sequence '\['
_ILEGAL_NEWICK_CHARS = ":;(),\[\]\t\n\r="
/usr/local/lib/python3.12/site-packages/ete3/parser/newick.py:54: SyntaxWarning: invalid escape sequence '\['
_NHX_RE = "\[&&NHX:[^\]]*\]"
/usr/local/lib/python3.12/site-packages/ete3/parser/newick.py:55: SyntaxWarning: invalid escape sequence '\s'
_FLOAT_RE = "\s*[+-]?\d+\.?\d*(?:[eE][-+]?\d+)?\s*"
/usr/local/lib/python3.12/site-packages/ete3/parser/newick.py:402: SyntaxWarning: invalid escape sequence '\s'
matcher_str= '^\s*%s\s*%s\s*(%s)?\s*$' % (FIRST_MATCH, SECOND_MATCH, _NHX_RE)
/usr/local/lib/python3.12/site-packages/ete3/utils.py:82: SyntaxWarning: invalid escape sequence '\['
return re.sub("\\033\[[^m]+m", "", string)
/usr/local/lib/python3.12/site-packages/ete3/treeview/main.py:64: SyntaxWarning: invalid escape sequence '\d'
_COLOR_MATCH = re.compile("^#[A-Fa-f\d]{6}$")
/usr/local/lib/python3.12/site-packages/ete3/treeview/main.py:712: SyntaxWarning: invalid escape sequence '\d'
compatible_code = re.sub('font-size="(\d+)"', 'font-size="\\1pt"', compatible_code)
/usr/local/lib/python3.12/site-packages/ete3/treeview/main.py:714: SyntaxWarning: invalid escape sequence '\s'
compatible_code = re.sub('<g [^>]+>\s*</g>', '', compatible_code)
/usr/local/lib/python3.12/site-packages/ete3/treeview/faces.py:159: SyntaxWarning: invalid escape sequence '\_'
"""Base Face object. All Face types (i.e. TextFace, SeqMotifFace,
/usr/local/lib/python3.12/site-packages/ete3/parser/phylip.py:76: SyntaxWarning: invalid escape sequence '\s'
m = re.match("^\s*(\d+)\s+(\d+)",line)
/usr/local/lib/python3.12/site-packages/ete3/parser/phylip.py:108: SyntaxWarning: invalid escape sequence '\s'
SG.id2seq[id_counter] += re.sub("\s","", line)
/usr/local/lib/python3.12/site-packages/ete3/parser/phylip.py:123: SyntaxWarning: invalid escape sequence '\s'
seq = re.sub("\s","",m.groups()[1])
/usr/local/lib/python3.12/site-packages/ete3/parser/phylip.py:138: SyntaxWarning: invalid escape sequence '\s'
seq = re.sub("\s", "", line)
/usr/local/lib/python3.12/site-packages/ete3/phylo/phylotree.py:132: SyntaxWarning: invalid escape sequence '\d'
id_match = re.compile("([^0-9])?(\d+)([^0-9])?")
/usr/local/lib/python3.12/site-packages/ete3/phylo/phylotree.py:188: SyntaxWarning: invalid escape sequence '\d'
id_match = re.compile("([^0-9])(\d+)([^0-9])")
/usr/local/lib/python3.12/site-packages/ete3/evol/parser/codemlparser.py:74: SyntaxWarning: invalid escape sequence '\('
k = int(re.sub ('.* \(K=([0-9]+)\)\n', '\\1', line))
/usr/local/lib/python3.12/site-packages/ete3/evol/parser/codemlparser.py:78: SyntaxWarning: invalid escape sequence '\d'
re.match ('^[a-z]+.*(\d+\.\d{5} *){'+ str(k) +'}', line):
/usr/local/lib/python3.12/site-packages/ete3/evol/parser/codemlparser.py:82: SyntaxWarning: invalid escape sequence '\d'
classes[var] = [float(v) for v in re.findall('\d+\.\d{5}', line)]
/usr/local/lib/python3.12/site-packages/ete3/evol/parser/codemlparser.py:86: SyntaxWarning: invalid escape sequence '\d'
k = int(re.sub('.*for (\d+) classes.*\n', '\\1', line))
/usr/local/lib/python3.12/site-packages/ete3/evol/parser/codemlparser.py:92: SyntaxWarning: invalid escape sequence '\d'
k = int(re.sub('.*for (\d+) classes.*\n', '\\1', line))
/usr/local/lib/python3.12/site-packages/ete3/evol/parser/codemlparser.py:217: SyntaxWarning: invalid escape sequence '\('
model._tree = EvolTree (re.findall ('\(.*\);', ''.join(all_lines))[2])
/usr/local/lib/python3.12/site-packages/ete3/evol/parser/codemlparser.py:227: SyntaxWarning: invalid escape sequence '\d'
line = list(map (float, re.findall ('\d\.\d+', all_lines [i+j+1])))
/usr/local/lib/python3.12/site-packages/ete3/evol/parser/codemlparser.py:240: SyntaxWarning: invalid escape sequence '\d'
line = re.sub ('.* np: *(\d+)\): +(-\d+\.\d+).*',
/usr/local/lib/python3.12/site-packages/ete3/evol/parser/codemlparser.py:245: SyntaxWarning: invalid escape sequence '\d'
line = re.sub ('.* np: *(\d+)\): +(nan).*',
/usr/local/lib/python3.12/site-packages/ete3/evol/parser/codemlparser.py:252: SyntaxWarning: invalid escape sequence '\d'
labels = re.findall ('\d+\.\.\d+', line + ' ')
/usr/local/lib/python3.12/site-packages/ete3/evol/parser/codemlparser.py:258: SyntaxWarning: invalid escape sequence '\d'
model.stats ['kappa'] = float (re.sub ('.*(\d+\.\d+).*',
/usr/local/lib/python3.12/site-packages/ete3/evol/parser/codemlparser.py:264: SyntaxWarning: invalid escape sequence '\d'
if not re.match (' +\d+\.\.\d+ +\d+\.\d+ ', line):
/usr/local/lib/python3.12/site-packages/ete3/evol/parser/codemlparser.py:265: SyntaxWarning: invalid escape sequence '\d'
if re.match (' +( +\d+\.\d+){8}', all_lines [i+1]):
/usr/local/lib/python3.12/site-packages/ete3/evol/evoltree.py:468: SyntaxWarning: invalid escape sequence '\['
nwk += sub('\[&&NHX:mark=([ #0-9.]*)\]', r'\1',
/usr/local/lib/python3.12/site-packages/ete3/evol/evoltree.py:471: SyntaxWarning: invalid escape sequence '\['
nwk = sub('\[&&NHX:mark=([ #0-9.]*)\]', r'\1',
/usr/local/lib/python3.12/site-packages/ete3/tools/utils.py:28: SyntaxWarning: invalid escape sequence '\['
return re.sub("\\033\[[^m]+m", "", string)
/usr/local/lib/python3.12/site-packages/ete3/evol/model.py:367: SyntaxWarning: invalid escape sequence '\.'
if sub('\..*', '', model) in AVAIL:
/usr/local/lib/python3.12/site-packages/ete3/evol/model.py:368: SyntaxWarning: invalid escape sequence '\.'
return model, AVAIL [sub('\..*', '', model)]
/usr/local/lib/python3.12/site-packages/ete3/phylomedb/phylomeDB3.py:75: SyntaxWarning: invalid escape sequence '\w'
ID_PATTERN = re.compile("^[Pp][Hh][Yy]\w{7}(_\w{2,7})?$")
/usr/local/lib/python3.12/site-packages/ete3/phylomedb/phylomeDB3.py:153: SyntaxWarning: invalid escape sequence '\w'
m = re.search("Phy(\w{7})_[\w\d]+", name)
/usr/local/lib/python3.12/site-packages/ete3/phylomedb/phylomeDB3.py:500: SyntaxWarning: invalid escape sequence '\w'
QUERY_OLD_REGEXP_FILTER = "^\w{3}\d{1,}$"
/usr/local/lib/python3.12/site-packages/ete3/phylomedb/phylomeDB3.py:756: SyntaxWarning: invalid escape sequence '\w'
QUERY_GEN_REGEXP_FILTER = "^[\w\d\-_,;:.|#@\/\\\()'<>!]+$"
/usr/local/lib/python3.12/site-packages/ete3/phylomedb/phylomeDB3.py:757: SyntaxWarning: invalid escape sequence '\w'
QUERY_OLD_REGEXP_FILTER = "^\w{3}\d{1,}$"
/usr/local/lib/python3.12/site-packages/ete3/phylomedb/phylomeDB3.py:758: SyntaxWarning: invalid escape sequence '\w'
QUERY_INT_REGEXP_FILTER = "^[Pp][Hh][Yy]\w{7}(_\w{2,7})?$"
/usr/local/lib/python3.12/site-packages/ete3/tools/common.py:158: SyntaxWarning: invalid escape sequence '\w'
func_match = re.search("(\w+)\(([^)]*)\)", fvalue)
/usr/local/lib/python3.12/site-packages/ete3/tools/ete_view.py:209: SyntaxWarning: invalid escape sequence '\d'
nw = re.sub(":(\d+\.\d+)\[(\d+)\]", ":\\1[&&NHX:support=\\2]", open(tfile).read())
/usr/local/lib/python3.12/site-packages/ete3/tools/ete_view.py:275: SyntaxWarning: invalid escape sequence '\d'
nw = re.sub(":(\d+\.\d+)\[(\d+)\]", ":\\1[&&NHX:support=\\2]", open(tfile).read())
/usr/local/lib/python3.12/site-packages/ete3/tools/ete_view.py:372: SyntaxWarning: invalid escape sequence '\('
auto_m = re.search("auto\(([^)]*)\)", fcolor)
/usr/local/lib/python3.12/site-packages/ete3/tools/ete_view.py:392: SyntaxWarning: invalid escape sequence '\('
auto_m = re.search("auto\(([^)]*)\)", fbgcolor)
Could you fix it?
