[Debian-med-packaging] Bug#1082310: python-ete3 FTBFS with Python 3.13
Stefano Rivera
stefanor at debian.org
Thu Sep 19 20:56:53 BST 2024
Source: python-ete3
Version: 3.1.3+dfsg-2
Severity: normal
User: debian-python at lists.debian.org
Usertags: python3.13
This package failed build from source when test-built against a version of
python3-defaults that includes 3.13 as a supported version.
To reproduce this issue, build against python3-defaults (python3-all-dev etc.)
from Debian experimental.
What's new in Python 3.13:
https://docs.python.org/3.13/whatsnew/3.13.html
Python 3.13 removed the cgi module.
Log snippet:
dh_auto_test
I: pybuild base:311: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ete3/build; python3.13 -m pytest -k "not test_ncbiquery and not test_ncbi_compare and not test_get_topology and not test_01tree_annotation and not test_00_update_database and not test_merged_id and not test_renderer" ete3/test/test_api.py
============================= test session starts ==============================
platform linux -- Python 3.13.0rc2, pytest-8.3.3, pluggy-1.5.0
rootdir: /<<PKGBUILDDIR>>
plugins: typeguard-4.3.0
collected 0 items / 1 error
==================================== ERRORS ====================================
___ ERROR collecting .pybuild/cpython3_3.13_ete3/build/ete3/test/test_api.py ___
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ete3/build/ete3/test/test_api.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
ete3/__init__.py:56: in <module>
from .webplugin.webapp import *
ete3/webplugin/webapp.py:44: in <module>
import cgi
E ModuleNotFoundError: No module named 'cgi'
=============================== warnings summary ===============================
ete3/coretype/tree.py:365
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ete3/build/ete3/coretype/tree.py:365: SyntaxWarning: invalid escape sequence '\-'
"""
ete3/coretype/tree.py:436
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ete3/build/ete3/coretype/tree.py:436: SyntaxWarning: invalid escape sequence '\-'
"""Prunes the topology of a node to conserve only the selected list of leaf
ete3/coretype/tree.py:1508
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ete3/build/ete3/coretype/tree.py:1508: SyntaxWarning: invalid escape sequence '\-'
"""
ete3/parser/newick.py:51
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ete3/build/ete3/parser/newick.py:51: SyntaxWarning: invalid escape sequence '\['
_ILEGAL_NEWICK_CHARS = ":;(),\[\]\t\n\r="
ete3/parser/newick.py:54
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ete3/build/ete3/parser/newick.py:54: SyntaxWarning: invalid escape sequence '\['
_NHX_RE = "\[&&NHX:[^\]]*\]"
ete3/parser/newick.py:55
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ete3/build/ete3/parser/newick.py:55: SyntaxWarning: invalid escape sequence '\s'
_FLOAT_RE = "\s*[+-]?\d+\.?\d*(?:[eE][-+]?\d+)?\s*"
ete3/parser/newick.py:402
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ete3/build/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)
ete3/utils.py:82
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ete3/build/ete3/utils.py:82: SyntaxWarning: invalid escape sequence '\['
return re.sub("\\033\[[^m]+m", "", string)
ete3/treeview/main.py:64
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ete3/build/ete3/treeview/main.py:64: SyntaxWarning: invalid escape sequence '\d'
_COLOR_MATCH = re.compile("^#[A-Fa-f\d]{6}$")
ete3/treeview/main.py:712
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ete3/build/ete3/treeview/main.py:712: SyntaxWarning: invalid escape sequence '\d'
compatible_code = re.sub('font-size="(\d+)"', 'font-size="\\1pt"', compatible_code)
ete3/treeview/main.py:714
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ete3/build/ete3/treeview/main.py:714: SyntaxWarning: invalid escape sequence '\s'
compatible_code = re.sub('<g [^>]+>\s*</g>', '', compatible_code)
ete3/treeview/faces.py:159
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ete3/build/ete3/treeview/faces.py:159: SyntaxWarning: invalid escape sequence '\_'
"""Base Face object. All Face types (i.e. TextFace, SeqMotifFace,
ete3/parser/phylip.py:76
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ete3/build/ete3/parser/phylip.py:76: SyntaxWarning: invalid escape sequence '\s'
m = re.match("^\s*(\d+)\s+(\d+)",line)
ete3/parser/phylip.py:108
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ete3/build/ete3/parser/phylip.py:108: SyntaxWarning: invalid escape sequence '\s'
SG.id2seq[id_counter] += re.sub("\s","", line)
ete3/parser/phylip.py:123
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ete3/build/ete3/parser/phylip.py:123: SyntaxWarning: invalid escape sequence '\s'
seq = re.sub("\s","",m.groups()[1])
ete3/parser/phylip.py:138
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ete3/build/ete3/parser/phylip.py:138: SyntaxWarning: invalid escape sequence '\s'
seq = re.sub("\s", "", line)
ete3/phylo/phylotree.py:132
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ete3/build/ete3/phylo/phylotree.py:132: SyntaxWarning: invalid escape sequence '\d'
id_match = re.compile("([^0-9])?(\d+)([^0-9])?")
ete3/phylo/phylotree.py:188
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ete3/build/ete3/phylo/phylotree.py:188: SyntaxWarning: invalid escape sequence '\d'
id_match = re.compile("([^0-9])(\d+)([^0-9])")
ete3/evol/parser/codemlparser.py:74
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ete3/build/ete3/evol/parser/codemlparser.py:74: SyntaxWarning: invalid escape sequence '\('
k = int(re.sub ('.* \(K=([0-9]+)\)\n', '\\1', line))
ete3/evol/parser/codemlparser.py:78
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ete3/build/ete3/evol/parser/codemlparser.py:78: SyntaxWarning: invalid escape sequence '\d'
re.match ('^[a-z]+.*(\d+\.\d{5} *){'+ str(k) +'}', line):
ete3/evol/parser/codemlparser.py:82
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ete3/build/ete3/evol/parser/codemlparser.py:82: SyntaxWarning: invalid escape sequence '\d'
classes[var] = [float(v) for v in re.findall('\d+\.\d{5}', line)]
ete3/evol/parser/codemlparser.py:86
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ete3/build/ete3/evol/parser/codemlparser.py:86: SyntaxWarning: invalid escape sequence '\d'
k = int(re.sub('.*for (\d+) classes.*\n', '\\1', line))
ete3/evol/parser/codemlparser.py:92
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ete3/build/ete3/evol/parser/codemlparser.py:92: SyntaxWarning: invalid escape sequence '\d'
k = int(re.sub('.*for (\d+) classes.*\n', '\\1', line))
ete3/evol/parser/codemlparser.py:217
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ete3/build/ete3/evol/parser/codemlparser.py:217: SyntaxWarning: invalid escape sequence '\('
model._tree = EvolTree (re.findall ('\(.*\);', ''.join(all_lines))[2])
ete3/evol/parser/codemlparser.py:227
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ete3/build/ete3/evol/parser/codemlparser.py:227: SyntaxWarning: invalid escape sequence '\d'
line = list(map (float, re.findall ('\d\.\d+', all_lines [i+j+1])))
ete3/evol/parser/codemlparser.py:240
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ete3/build/ete3/evol/parser/codemlparser.py:240: SyntaxWarning: invalid escape sequence '\d'
line = re.sub ('.* np: *(\d+)\): +(-\d+\.\d+).*',
ete3/evol/parser/codemlparser.py:245
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ete3/build/ete3/evol/parser/codemlparser.py:245: SyntaxWarning: invalid escape sequence '\d'
line = re.sub ('.* np: *(\d+)\): +(nan).*',
ete3/evol/parser/codemlparser.py:252
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ete3/build/ete3/evol/parser/codemlparser.py:252: SyntaxWarning: invalid escape sequence '\d'
labels = re.findall ('\d+\.\.\d+', line + ' ')
ete3/evol/parser/codemlparser.py:258
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ete3/build/ete3/evol/parser/codemlparser.py:258: SyntaxWarning: invalid escape sequence '\d'
model.stats ['kappa'] = float (re.sub ('.*(\d+\.\d+).*',
ete3/evol/parser/codemlparser.py:264
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ete3/build/ete3/evol/parser/codemlparser.py:264: SyntaxWarning: invalid escape sequence '\d'
if not re.match (' +\d+\.\.\d+ +\d+\.\d+ ', line):
ete3/evol/parser/codemlparser.py:265
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ete3/build/ete3/evol/parser/codemlparser.py:265: SyntaxWarning: invalid escape sequence '\d'
if re.match (' +( +\d+\.\d+){8}', all_lines [i+1]):
ete3/evol/evoltree.py:468
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ete3/build/ete3/evol/evoltree.py:468: SyntaxWarning: invalid escape sequence '\['
nwk += sub('\[&&NHX:mark=([ #0-9.]*)\]', r'\1',
ete3/evol/evoltree.py:471
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ete3/build/ete3/evol/evoltree.py:471: SyntaxWarning: invalid escape sequence '\['
nwk = sub('\[&&NHX:mark=([ #0-9.]*)\]', r'\1',
ete3/tools/utils.py:28
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ete3/build/ete3/tools/utils.py:28: SyntaxWarning: invalid escape sequence '\['
return re.sub("\\033\[[^m]+m", "", string)
ete3/evol/model.py:367
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ete3/build/ete3/evol/model.py:367: SyntaxWarning: invalid escape sequence '\.'
if sub('\..*', '', model) in AVAIL:
ete3/evol/model.py:368
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ete3/build/ete3/evol/model.py:368: SyntaxWarning: invalid escape sequence '\.'
return model, AVAIL [sub('\..*', '', model)]
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=========================== short test summary info ============================
ERROR ete3/test/test_api.py
!!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!!!!!!!!
======================== 36 warnings, 1 error in 0.71s =========================
E: pybuild pybuild:389: test: plugin distutils failed with: exit code=2: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ete3/build; python3.13 -m pytest -k "not test_ncbiquery and not test_ncbi_compare and not test_get_topology and not test_01tree_annotation and not test_00_update_database and not test_merged_id and not test_renderer" ete3/test/test_api.py
I: pybuild base:311: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build; python3.12 -m pytest -k "not test_ncbiquery and not test_ncbi_compare and not test_get_topology and not test_01tree_annotation and not test_00_update_database and not test_merged_id and not test_renderer" ete3/test/test_api.py
============================= test session starts ==============================
platform linux -- Python 3.12.6, pytest-8.3.3, pluggy-1.5.0
rootdir: /<<PKGBUILDDIR>>
plugins: typeguard-4.3.0
collected 53 items / 7 deselected / 46 selected
ete3/test/test_api.py .............................................. [100%]
=============================== warnings summary ===============================
ete3/coretype/tree.py:365
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/coretype/tree.py:365: SyntaxWarning: invalid escape sequence '\-'
"""
ete3/coretype/tree.py:436
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/coretype/tree.py:436: SyntaxWarning: invalid escape sequence '\-'
"""Prunes the topology of a node to conserve only the selected list of leaf
ete3/coretype/tree.py:1508
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/coretype/tree.py:1508: SyntaxWarning: invalid escape sequence '\-'
"""
ete3/parser/newick.py:51
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/parser/newick.py:51: SyntaxWarning: invalid escape sequence '\['
_ILEGAL_NEWICK_CHARS = ":;(),\[\]\t\n\r="
ete3/parser/newick.py:54
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/parser/newick.py:54: SyntaxWarning: invalid escape sequence '\['
_NHX_RE = "\[&&NHX:[^\]]*\]"
ete3/parser/newick.py:55
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/parser/newick.py:55: SyntaxWarning: invalid escape sequence '\s'
_FLOAT_RE = "\s*[+-]?\d+\.?\d*(?:[eE][-+]?\d+)?\s*"
ete3/parser/newick.py:402
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/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)
ete3/utils.py:82
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/utils.py:82: SyntaxWarning: invalid escape sequence '\['
return re.sub("\\033\[[^m]+m", "", string)
ete3/treeview/main.py:64
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/treeview/main.py:64: SyntaxWarning: invalid escape sequence '\d'
_COLOR_MATCH = re.compile("^#[A-Fa-f\d]{6}$")
ete3/treeview/main.py:712
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/treeview/main.py:712: SyntaxWarning: invalid escape sequence '\d'
compatible_code = re.sub('font-size="(\d+)"', 'font-size="\\1pt"', compatible_code)
ete3/treeview/main.py:714
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/treeview/main.py:714: SyntaxWarning: invalid escape sequence '\s'
compatible_code = re.sub('<g [^>]+>\s*</g>', '', compatible_code)
ete3/treeview/faces.py:159
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/treeview/faces.py:159: SyntaxWarning: invalid escape sequence '\_'
"""Base Face object. All Face types (i.e. TextFace, SeqMotifFace,
ete3/parser/phylip.py:76
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/parser/phylip.py:76: SyntaxWarning: invalid escape sequence '\s'
m = re.match("^\s*(\d+)\s+(\d+)",line)
ete3/parser/phylip.py:108
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/parser/phylip.py:108: SyntaxWarning: invalid escape sequence '\s'
SG.id2seq[id_counter] += re.sub("\s","", line)
ete3/parser/phylip.py:123
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/parser/phylip.py:123: SyntaxWarning: invalid escape sequence '\s'
seq = re.sub("\s","",m.groups()[1])
ete3/parser/phylip.py:138
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/parser/phylip.py:138: SyntaxWarning: invalid escape sequence '\s'
seq = re.sub("\s", "", line)
ete3/phylo/phylotree.py:132
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/phylo/phylotree.py:132: SyntaxWarning: invalid escape sequence '\d'
id_match = re.compile("([^0-9])?(\d+)([^0-9])?")
ete3/phylo/phylotree.py:188
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/phylo/phylotree.py:188: SyntaxWarning: invalid escape sequence '\d'
id_match = re.compile("([^0-9])(\d+)([^0-9])")
ete3/evol/parser/codemlparser.py:74
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/evol/parser/codemlparser.py:74: SyntaxWarning: invalid escape sequence '\('
k = int(re.sub ('.* \(K=([0-9]+)\)\n', '\\1', line))
ete3/evol/parser/codemlparser.py:78
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/evol/parser/codemlparser.py:78: SyntaxWarning: invalid escape sequence '\d'
re.match ('^[a-z]+.*(\d+\.\d{5} *){'+ str(k) +'}', line):
ete3/evol/parser/codemlparser.py:82
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/evol/parser/codemlparser.py:82: SyntaxWarning: invalid escape sequence '\d'
classes[var] = [float(v) for v in re.findall('\d+\.\d{5}', line)]
ete3/evol/parser/codemlparser.py:86
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/evol/parser/codemlparser.py:86: SyntaxWarning: invalid escape sequence '\d'
k = int(re.sub('.*for (\d+) classes.*\n', '\\1', line))
ete3/evol/parser/codemlparser.py:92
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/evol/parser/codemlparser.py:92: SyntaxWarning: invalid escape sequence '\d'
k = int(re.sub('.*for (\d+) classes.*\n', '\\1', line))
ete3/evol/parser/codemlparser.py:217
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/evol/parser/codemlparser.py:217: SyntaxWarning: invalid escape sequence '\('
model._tree = EvolTree (re.findall ('\(.*\);', ''.join(all_lines))[2])
ete3/evol/parser/codemlparser.py:227
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/evol/parser/codemlparser.py:227: SyntaxWarning: invalid escape sequence '\d'
line = list(map (float, re.findall ('\d\.\d+', all_lines [i+j+1])))
ete3/evol/parser/codemlparser.py:240
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/evol/parser/codemlparser.py:240: SyntaxWarning: invalid escape sequence '\d'
line = re.sub ('.* np: *(\d+)\): +(-\d+\.\d+).*',
ete3/evol/parser/codemlparser.py:245
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/evol/parser/codemlparser.py:245: SyntaxWarning: invalid escape sequence '\d'
line = re.sub ('.* np: *(\d+)\): +(nan).*',
ete3/evol/parser/codemlparser.py:252
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/evol/parser/codemlparser.py:252: SyntaxWarning: invalid escape sequence '\d'
labels = re.findall ('\d+\.\.\d+', line + ' ')
ete3/evol/parser/codemlparser.py:258
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/evol/parser/codemlparser.py:258: SyntaxWarning: invalid escape sequence '\d'
model.stats ['kappa'] = float (re.sub ('.*(\d+\.\d+).*',
ete3/evol/parser/codemlparser.py:264
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/evol/parser/codemlparser.py:264: SyntaxWarning: invalid escape sequence '\d'
if not re.match (' +\d+\.\.\d+ +\d+\.\d+ ', line):
ete3/evol/parser/codemlparser.py:265
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/evol/parser/codemlparser.py:265: SyntaxWarning: invalid escape sequence '\d'
if re.match (' +( +\d+\.\d+){8}', all_lines [i+1]):
ete3/evol/evoltree.py:468
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/evol/evoltree.py:468: SyntaxWarning: invalid escape sequence '\['
nwk += sub('\[&&NHX:mark=([ #0-9.]*)\]', r'\1',
ete3/evol/evoltree.py:471
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/evol/evoltree.py:471: SyntaxWarning: invalid escape sequence '\['
nwk = sub('\[&&NHX:mark=([ #0-9.]*)\]', r'\1',
ete3/tools/utils.py:28
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/tools/utils.py:28: SyntaxWarning: invalid escape sequence '\['
return re.sub("\\033\[[^m]+m", "", string)
ete3/evol/model.py:367
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/evol/model.py:367: SyntaxWarning: invalid escape sequence '\.'
if sub('\..*', '', model) in AVAIL:
ete3/evol/model.py:368
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/evol/model.py:368: SyntaxWarning: invalid escape sequence '\.'
return model, AVAIL [sub('\..*', '', model)]
ete3/webplugin/webapp.py:44
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/webplugin/webapp.py:44: DeprecationWarning: 'cgi' is deprecated and slated for removal in Python 3.13
import cgi
ete3/phylomedb/phylomeDB3.py:75
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/phylomedb/phylomeDB3.py:75: SyntaxWarning: invalid escape sequence '\w'
ID_PATTERN = re.compile("^[Pp][Hh][Yy]\w{7}(_\w{2,7})?$")
ete3/phylomedb/phylomeDB3.py:153
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/phylomedb/phylomeDB3.py:153: SyntaxWarning: invalid escape sequence '\w'
m = re.search("Phy(\w{7})_[\w\d]+", name)
ete3/phylomedb/phylomeDB3.py:500
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/phylomedb/phylomeDB3.py:500: SyntaxWarning: invalid escape sequence '\w'
QUERY_OLD_REGEXP_FILTER = "^\w{3}\d{1,}$"
ete3/phylomedb/phylomeDB3.py:756
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/phylomedb/phylomeDB3.py:756: SyntaxWarning: invalid escape sequence '\w'
QUERY_GEN_REGEXP_FILTER = "^[\w\d\-_,;:.|#@\/\\\()'<>!]+$"
ete3/phylomedb/phylomeDB3.py:757
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/phylomedb/phylomeDB3.py:757: SyntaxWarning: invalid escape sequence '\w'
QUERY_OLD_REGEXP_FILTER = "^\w{3}\d{1,}$"
ete3/phylomedb/phylomeDB3.py:758
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/phylomedb/phylomeDB3.py:758: SyntaxWarning: invalid escape sequence '\w'
QUERY_INT_REGEXP_FILTER = "^[Pp][Hh][Yy]\w{7}(_\w{2,7})?$"
.pybuild/cpython3_3.12_ete3/build/ete3/test/test_api.py::TestEvolEvolTree::test_call_histface
.pybuild/cpython3_3.12_ete3/build/ete3/test/test_api.py::TestEvolEvolTree::test_pickling
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/evol/parser/codemlparser.py:304: UserWarning: WARNING: labelling does not correspond (bad tree?)!!
Getting them from /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/test/ete_evol_data//protamine/PRM1/paml/M2/M2.out
warn('WARNING: labelling does not correspond (bad tree?)!!\n' + \
.pybuild/cpython3_3.12_ete3/build/ete3/test/test_api.py::TestEvolEvolTree::test_deep_copy
.pybuild/cpython3_3.12_ete3/build/ete3/test/test_api.py::TestEvolEvolTree::test_labelling_tree
.pybuild/cpython3_3.12_ete3/build/ete3/test/test_api.py::TestEvolEvolTree::test_load_model
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/evol/parser/codemlparser.py:304: UserWarning: WARNING: labelling does not correspond (bad tree?)!!
Getting them from /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/test/ete_evol_data//protamine/PRM1/paml/fb/fb.out
warn('WARNING: labelling does not correspond (bad tree?)!!\n' + \
.pybuild/cpython3_3.12_ete3/build/ete3/test/test_api.py::TestEvolEvolTree::test_get_most_likely
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/evol/parser/codemlparser.py:304: UserWarning: WARNING: labelling does not correspond (bad tree?)!!
Getting them from /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/test/ete_evol_data//protamine/PRM1/paml/M1/M1.out
warn('WARNING: labelling does not correspond (bad tree?)!!\n' + \
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
================ 46 passed, 7 deselected, 49 warnings in 3.12s =================
If required, the full build log is available here (for the next 30 days):
https://debusine.debian.net/artifact/783332/
This bug has been filed at "normal" severity, as we haven't started the
transition to add 3.13 as a supported version, yet. This will be raised to RC
as soon as that happens, hopefully well before trixie.
Thanks,
Stefano
More information about the Debian-med-packaging
mailing list