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83 warnings, 3 errors in tests
==================================================================================== test session starts =====================================================================================
platform freebsd13 -- Python 3.9.13, pytest-7.1.2, pluggy-1.0.0 -- /usr/local/bin/python3.9
cachedir: .pytest_cache
hypothesis profile 'default' -> database=DirectoryBasedExampleDatabase('/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/.hypothesis/examples')
rootdir: /disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2
plugins: hypothesis-6.53.0, typeguard-2.13.3, forked-1.4.0, xdist-2.5.0
collected 177 items / 3 errors
=========================================================================================== ERRORS ===========================================================================================
____________________________________________________________________ ERROR collecting examples/evol/3_branchsite_test.py _____________________________________________________________________
examples/evol/3_branchsite_test.py:22: in <module>
tree = EvolTree("data/L_example/measuring_L_tree.nw")
ete3/evol/evoltree.py:135: in __init__
PhyloNode.__init__(self, newick=newick, format=format,
ete3/phylo/phylotree.py:391: in __init__
TreeNode.__init__(self, newick=newick, format=format, **kargs)
ete3/coretype/tree.py:212: in __init__
read_newick(newick, root_node = self, format=format,
ete3/parser/newick.py:264: in read_newick
raise NewickError('Unexisting tree file or Malformed newick tree structure.')
E ete3.parser.newick.NewickError: Unexisting tree file or Malformed newick tree structure.
E You may want to check other newick loading flags like 'format' or 'quoted_node_names'.
________________________________________________________________________ ERROR collecting examples/evol/test_hist.py _________________________________________________________________________
examples/evol/test_hist.py:23: in <module>
T = EvolTree (TREE_PATH)
ete3/evol/evoltree.py:135: in __init__
PhyloNode.__init__(self, newick=newick, format=format,
ete3/phylo/phylotree.py:391: in __init__
TreeNode.__init__(self, newick=newick, format=format, **kargs)
ete3/coretype/tree.py:212: in __init__
read_newick(newick, root_node = self, format=format,
ete3/parser/newick.py:264: in read_newick
raise NewickError('Unexisting tree file or Malformed newick tree structure.')
E ete3.parser.newick.NewickError: Unexisting tree file or Malformed newick tree structure.
E You may want to check other newick loading flags like 'format' or 'quoted_node_names'.
______________________________________________________________________ ERROR collecting examples/evol/test_protamine.py ______________________________________________________________________
/usr/local/lib/python3.9/site-packages/_pytest/python.py:608: in _importtestmodule
mod = import_path(self.path, mode=importmode, root=self.config.rootpath)
/usr/local/lib/python3.9/site-packages/_pytest/pathlib.py:533: in import_path
importlib.import_module(module_name)
/usr/local/lib/python3.9/importlib/__init__.py:127: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
<frozen importlib._bootstrap>:1030: in _gcd_import
???
<frozen importlib._bootstrap>:1007: in _find_and_load
???
<frozen importlib._bootstrap>:986: in _find_and_load_unlocked
???
<frozen importlib._bootstrap>:680: in _load_unlocked
???
/usr/local/lib/python3.9/site-packages/_pytest/assertion/rewrite.py:159: in exec_module
source_stat, co = _rewrite_test(fn, self.config)
/usr/local/lib/python3.9/site-packages/_pytest/assertion/rewrite.py:359: in _rewrite_test
tree = ast.parse(source, filename=strfn)
/usr/local/lib/python3.9/ast.py:50: in parse
return compile(source, filename, mode, flags,
E File "/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/examples/evol/test_protamine.py", line 33
E print 'pv of LRT M2 vs M1: ',
E ^
E SyntaxError: Missing parentheses in call to 'print'. Did you mean print('pv of LRT M2 vs M1: ', end=" ")?
====================================================================================== warnings summary ======================================================================================
ete3/coretype/tree.py:365
/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/ete3/coretype/tree.py:365: DeprecationWarning: invalid escape sequence \-
"""
ete3/coretype/tree.py:436
/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/ete3/coretype/tree.py:436: DeprecationWarning: invalid escape sequence \-
"""Prunes the topology of a node to conserve only the selected list of leaf
ete3/coretype/tree.py:1508
/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/ete3/coretype/tree.py:1508: DeprecationWarning: invalid escape sequence \-
"""
ete3/parser/newick.py:51
/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/ete3/parser/newick.py:51: DeprecationWarning: invalid escape sequence \[
_ILEGAL_NEWICK_CHARS = ":;(),\[\]\t\n\r="
ete3/parser/newick.py:54
/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/ete3/parser/newick.py:54: DeprecationWarning: invalid escape sequence \[
_NHX_RE = "\[&&NHX:[^\]]*\]"
ete3/parser/newick.py:55
/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/ete3/parser/newick.py:55: DeprecationWarning: invalid escape sequence \s
_FLOAT_RE = "\s*[+-]?\d+\.?\d*(?:[eE][-+]?\d+)?\s*"
ete3/parser/newick.py:402
/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/ete3/parser/newick.py:402: DeprecationWarning: invalid escape sequence \s
matcher_str= '^\s*%s\s*%s\s*(%s)?\s*$' % (FIRST_MATCH, SECOND_MATCH, _NHX_RE)
ete3/utils.py:82
/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/ete3/utils.py:82: DeprecationWarning: invalid escape sequence \[
return re.sub("\\033\[[^m]+m", "", string)
ete3/treeview/main.py:64
/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/ete3/treeview/main.py:64: DeprecationWarning: invalid escape sequence \d
_COLOR_MATCH = re.compile("^#[A-Fa-f\d]{6}$")
ete3/treeview/main.py:710
/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/ete3/treeview/main.py:710: DeprecationWarning: invalid escape sequence \d
compatible_code = re.sub('font-size="(\d+)"', 'font-size="\\1pt"', compatible_code)
ete3/treeview/main.py:712
/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/ete3/treeview/main.py:712: DeprecationWarning: invalid escape sequence \s
compatible_code = re.sub('<g [^>]+>\s*</g>', '', compatible_code)
ete3/treeview/faces.py:159
/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/ete3/treeview/faces.py:159: DeprecationWarning: invalid escape sequence \_
"""Base Face object. All Face types (i.e. TextFace, SeqMotifFace,
ete3/parser/phylip.py:76
/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/ete3/parser/phylip.py:76: DeprecationWarning: invalid escape sequence \s
m = re.match("^\s*(\d+)\s+(\d+)",line)
ete3/parser/phylip.py:108
/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/ete3/parser/phylip.py:108: DeprecationWarning: invalid escape sequence \s
SG.id2seq[id_counter] += re.sub("\s","", line)
ete3/parser/phylip.py:123
/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/ete3/parser/phylip.py:123: DeprecationWarning: invalid escape sequence \s
seq = re.sub("\s","",m.groups()[1])
ete3/parser/phylip.py:138
/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/ete3/parser/phylip.py:138: DeprecationWarning: invalid escape sequence \s
seq = re.sub("\s", "", line)
ete3/phylo/phylotree.py:132
/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/ete3/phylo/phylotree.py:132: DeprecationWarning: invalid escape sequence \d
id_match = re.compile("([^0-9])?(\d+)([^0-9])?")
ete3/phylo/phylotree.py:188
/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/ete3/phylo/phylotree.py:188: DeprecationWarning: invalid escape sequence \d
id_match = re.compile("([^0-9])(\d+)([^0-9])")
ete3/evol/parser/codemlparser.py:74
/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/ete3/evol/parser/codemlparser.py:74: DeprecationWarning: invalid escape sequence \(
k = int(re.sub ('.* \(K=([0-9]+)\)\n', '\\1', line))
ete3/evol/parser/codemlparser.py:78
/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/ete3/evol/parser/codemlparser.py:78: DeprecationWarning: invalid escape sequence \d
re.match ('^[a-z]+.*(\d+\.\d{5} *){'+ str(k) +'}', line):
ete3/evol/parser/codemlparser.py:82
/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/ete3/evol/parser/codemlparser.py:82: DeprecationWarning: invalid escape sequence \d
classes[var] = [float(v) for v in re.findall('\d+\.\d{5}', line)]
ete3/evol/parser/codemlparser.py:86
/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/ete3/evol/parser/codemlparser.py:86: DeprecationWarning: invalid escape sequence \d
k = int(re.sub('.*for (\d+) classes.*\n', '\\1', line))
ete3/evol/parser/codemlparser.py:92
/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/ete3/evol/parser/codemlparser.py:92: DeprecationWarning: invalid escape sequence \d
k = int(re.sub('.*for (\d+) classes.*\n', '\\1', line))
ete3/evol/parser/codemlparser.py:217
/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/ete3/evol/parser/codemlparser.py:217: DeprecationWarning: invalid escape sequence \(
model._tree = EvolTree (re.findall ('\(.*\);', ''.join(all_lines))[2])
ete3/evol/parser/codemlparser.py:227
/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/ete3/evol/parser/codemlparser.py:227: DeprecationWarning: invalid escape sequence \d
line = list(map (float, re.findall ('\d\.\d+', all_lines [i+j+1])))
ete3/evol/parser/codemlparser.py:240
/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/ete3/evol/parser/codemlparser.py:240: DeprecationWarning: invalid escape sequence \d
line = re.sub ('.* np: *(\d+)\): +(-\d+\.\d+).*',
ete3/evol/parser/codemlparser.py:245
/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/ete3/evol/parser/codemlparser.py:245: DeprecationWarning: invalid escape sequence \d
line = re.sub ('.* np: *(\d+)\): +(nan).*',
ete3/evol/parser/codemlparser.py:252
/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/ete3/evol/parser/codemlparser.py:252: DeprecationWarning: invalid escape sequence \d
labels = re.findall ('\d+\.\.\d+', line + ' ')
ete3/evol/parser/codemlparser.py:258
/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/ete3/evol/parser/codemlparser.py:258: DeprecationWarning: invalid escape sequence \d
model.stats ['kappa'] = float (re.sub ('.*(\d+\.\d+).*',
ete3/evol/parser/codemlparser.py:264
/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/ete3/evol/parser/codemlparser.py:264: DeprecationWarning: invalid escape sequence \d
if not re.match (' +\d+\.\.\d+ +\d+\.\d+ ', line):
ete3/evol/parser/codemlparser.py:265
/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/ete3/evol/parser/codemlparser.py:265: DeprecationWarning: invalid escape sequence \d
if re.match (' +( +\d+\.\d+){8}', all_lines [i+1]):
ete3/evol/parser/codemlparser.py:221
/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/ete3/evol/parser/codemlparser.py:221: SyntaxWarning: "is" with a literal. Did you mean "=="?
if line is '\n':
ete3/evol/evoltree.py:470
/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/ete3/evol/evoltree.py:470: DeprecationWarning: invalid escape sequence \[
nwk += sub('\[&&NHX:mark=([ #0-9.]*)\]', r'\1', \
ete3/evol/evoltree.py:473
/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/ete3/evol/evoltree.py:473: DeprecationWarning: invalid escape sequence \[
nwk = sub('\[&&NHX:mark=([ #0-9.]*)\]', r'\1', \
ete3/evol/model.py:368
/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/ete3/evol/model.py:368: DeprecationWarning: invalid escape sequence \.
if sub('\..*', '', model) in AVAIL:
ete3/evol/model.py:369
/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/ete3/evol/model.py:369: DeprecationWarning: invalid escape sequence \.
return model, AVAIL [sub('\..*', '', model)]
ete3/tools/utils.py:28
/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/ete3/tools/utils.py:28: DeprecationWarning: invalid escape sequence \[
return re.sub("\\033\[[^m]+m", "", string)
ete3/phylomedb/phylomeDB3.py:75
/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/ete3/phylomedb/phylomeDB3.py:75: DeprecationWarning: invalid escape sequence \w
ID_PATTERN = re.compile("^[Pp][Hh][Yy]\w{7}(_\w{2,7})?$")
ete3/phylomedb/phylomeDB3.py:153
/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/ete3/phylomedb/phylomeDB3.py:153: DeprecationWarning: invalid escape sequence \w
m = re.search("Phy(\w{7})_[\w\d]+", name)
ete3/phylomedb/phylomeDB3.py:500
/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/ete3/phylomedb/phylomeDB3.py:500: DeprecationWarning: invalid escape sequence \w
QUERY_OLD_REGEXP_FILTER = "^\w{3}\d{1,}$"
ete3/phylomedb/phylomeDB3.py:756
/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/ete3/phylomedb/phylomeDB3.py:756: DeprecationWarning: invalid escape sequence \w
QUERY_GEN_REGEXP_FILTER = "^[\w\d\-_,;:.|#@\/\\\()'<>!]+$"
ete3/phylomedb/phylomeDB3.py:757
/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/ete3/phylomedb/phylomeDB3.py:757: DeprecationWarning: invalid escape sequence \w
QUERY_OLD_REGEXP_FILTER = "^\w{3}\d{1,}$"
ete3/phylomedb/phylomeDB3.py:758
/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/ete3/phylomedb/phylomeDB3.py:758: DeprecationWarning: invalid escape sequence \w
QUERY_INT_REGEXP_FILTER = "^[Pp][Hh][Yy]\w{7}(_\w{2,7})?$"
ete3/tools/common.py:158
/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/ete3/tools/common.py:158: DeprecationWarning: invalid escape sequence \w
func_match = re.search("(\w+)\(([^)]*)\)", fvalue)
ete3/tools/ete_view.py:209
/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/ete3/tools/ete_view.py:209: DeprecationWarning: invalid escape sequence \d
nw = re.sub(":(\d+\.\d+)\[(\d+)\]", ":\\1[&&NHX:support=\\2]", open(tfile).read())
ete3/tools/ete_view.py:275
/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/ete3/tools/ete_view.py:275: DeprecationWarning: invalid escape sequence \d
nw = re.sub(":(\d+\.\d+)\[(\d+)\]", ":\\1[&&NHX:support=\\2]", open(tfile).read())
ete3/tools/ete_view.py:372
/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/ete3/tools/ete_view.py:372: DeprecationWarning: invalid escape sequence \(
auto_m = re.search("auto\(([^)]*)\)", fcolor)
ete3/tools/ete_view.py:392
/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/ete3/tools/ete_view.py:392: DeprecationWarning: invalid escape sequence \(
auto_m = re.search("auto\(([^)]*)\)", fbgcolor)
ete3/treeview/qt4_gui.py:172
/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/ete3/treeview/qt4_gui.py:172: DeprecationWarning: an integer is required (got type float). Implicit conversion to integers using __int__ is deprecated, and may be removed in a future version of Python.
splitter.setSizes([self.scene.sceneRect().width(), 10])
ete3/treeview/qt4_gui.py:75: 32 warnings
/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/ete3/treeview/qt4_gui.py:75: DeprecationWarning: an integer is required (got type float). Implicit conversion to integers using __int__ is deprecated, and may be removed in a future version of Python.
p.drawRect(self.rect().x(),self.rect().y(),self.rect().width(),self.rect().height())
examples/evol/test_hist.py:20
/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/examples/evol/test_hist.py:20: DeprecationWarning: invalid escape sequence \.
TREE_PATH = MY_PATH + re.sub('\./', '', TREE_PATH)
examples/evol/test_hist.py:21
/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/examples/evol/test_hist.py:21: DeprecationWarning: invalid escape sequence \.
ALG_PATH = MY_PATH + re.sub('\./', '', ALG_PATH )
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 3 errors during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
========================================================================= 83 warnings, 3 errors in 66.95s (0:01:06) ==========================================================================
*** Error code 2
Version: 3.1.2 Python 3.9 FreeBSD 13.1
