Bug#1073450: marked as done (ncbi-acc-download: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.12 3.11" returned exit code 13)

Debian Bug Tracking System Thu, 01 Aug 2024 16:39:19 -0700

Your message dated Thu, 01 Aug 2024 23:35:18 +0000
with message-id <e1szfki-001d4e...@fasolo.debian.org>
and subject line Bug#1073450: fixed in ncbi-acc-download 0.2.8-3
has caused the Debian Bug report #1073450,
regarding ncbi-acc-download: FTBFS: dh_auto_test: error: pybuild --test 
--test-pytest -i python{version} -p "3.12 3.11" returned exit code 13
to be marked as done.


This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)


-- 
1073450: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1073450
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems

--- Begin Message ---

Source: ncbi-acc-download
Version: 0.2.8-2
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: lu...@debian.org
Usertags: ftbfs-20240615 ftbfs-trixie

Hi,

During a rebuild of all packages in sid, your package failed to build
on amd64.


Relevant part (hopefully):
>  debian/rules binary
> dh binary --with python3 --buildsystem=pybuild
>    dh_update_autotools_config -O--buildsystem=pybuild
>    dh_autoreconf -O--buildsystem=pybuild
>    dh_auto_configure -O--buildsystem=pybuild
> I: pybuild base:311: python3.12 setup.py config 
> /usr/lib/python3/dist-packages/setuptools/dist.py:744: 
> SetuptoolsDeprecationWarning: Invalid dash-separated options
> !!
> 
>         
> ********************************************************************************
>         Usage of dash-separated 'requires-dist' will not be supported in 
> future
>         versions. Please use the underscore name 'requires_dist' instead.
> 
>         This deprecation is overdue, please update your project and remove 
> deprecated
>         calls to avoid build errors in the future.
> 
>         See 
> https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for 
> details.
>         
> ********************************************************************************
> 
> !!
>   opt = self.warn_dash_deprecation(opt, section)
> running config
> I: pybuild base:311: python3.11 setup.py config 
> /usr/lib/python3/dist-packages/setuptools/dist.py:744: 
> SetuptoolsDeprecationWarning: Invalid dash-separated options
> !!
> 
>         
> ********************************************************************************
>         Usage of dash-separated 'requires-dist' will not be supported in 
> future
>         versions. Please use the underscore name 'requires_dist' instead.
> 
>         This deprecation is overdue, please update your project and remove 
> deprecated
>         calls to avoid build errors in the future.
> 
>         See 
> https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for 
> details.
>         
> ********************************************************************************
> 
> !!
>   opt = self.warn_dash_deprecation(opt, section)
> running config
>    dh_auto_build -O--buildsystem=pybuild
> I: pybuild base:311: /usr/bin/python3.12 setup.py build 
> /usr/lib/python3/dist-packages/setuptools/dist.py:744: 
> SetuptoolsDeprecationWarning: Invalid dash-separated options
> !!
> 
>         
> ********************************************************************************
>         Usage of dash-separated 'requires-dist' will not be supported in 
> future
>         versions. Please use the underscore name 'requires_dist' instead.
> 
>         This deprecation is overdue, please update your project and remove 
> deprecated
>         calls to avoid build errors in the future.
> 
>         See 
> https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for 
> details.
>         
> ********************************************************************************
> 
> !!
>   opt = self.warn_dash_deprecation(opt, section)
> running build
> running build_py
> creating 
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ncbi-acc-download/build/ncbi_acc_download
> copying ncbi_acc_download/__init__.py -> 
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ncbi-acc-download/build/ncbi_acc_download
> copying ncbi_acc_download/validate.py -> 
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ncbi-acc-download/build/ncbi_acc_download
> copying ncbi_acc_download/__main__.py -> 
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ncbi-acc-download/build/ncbi_acc_download
> copying ncbi_acc_download/wgs.py -> 
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ncbi-acc-download/build/ncbi_acc_download
> copying ncbi_acc_download/errors.py -> 
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ncbi-acc-download/build/ncbi_acc_download
> copying ncbi_acc_download/download.py -> 
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ncbi-acc-download/build/ncbi_acc_download
> copying ncbi_acc_download/core.py -> 
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ncbi-acc-download/build/ncbi_acc_download
> I: pybuild base:311: /usr/bin/python3 setup.py build 
> /usr/lib/python3/dist-packages/setuptools/dist.py:744: 
> SetuptoolsDeprecationWarning: Invalid dash-separated options
> !!
> 
>         
> ********************************************************************************
>         Usage of dash-separated 'requires-dist' will not be supported in 
> future
>         versions. Please use the underscore name 'requires_dist' instead.
> 
>         This deprecation is overdue, please update your project and remove 
> deprecated
>         calls to avoid build errors in the future.
> 
>         See 
> https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for 
> details.
>         
> ********************************************************************************
> 
> !!
>   opt = self.warn_dash_deprecation(opt, section)
> running build
> running build_py
> creating 
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ncbi-acc-download/build/ncbi_acc_download
> copying ncbi_acc_download/__init__.py -> 
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ncbi-acc-download/build/ncbi_acc_download
> copying ncbi_acc_download/validate.py -> 
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ncbi-acc-download/build/ncbi_acc_download
> copying ncbi_acc_download/__main__.py -> 
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ncbi-acc-download/build/ncbi_acc_download
> copying ncbi_acc_download/wgs.py -> 
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ncbi-acc-download/build/ncbi_acc_download
> copying ncbi_acc_download/errors.py -> 
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ncbi-acc-download/build/ncbi_acc_download
> copying ncbi_acc_download/download.py -> 
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ncbi-acc-download/build/ncbi_acc_download
> copying ncbi_acc_download/core.py -> 
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ncbi-acc-download/build/ncbi_acc_download
>    dh_auto_test -O--buildsystem=pybuild
> I: pybuild base:311: cd 
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ncbi-acc-download/build; python3.12 
> -m pytest tests
> ============================= test session starts 
> ==============================
> platform linux -- Python 3.12.4, pytest-8.2.2, pluggy-1.5.0
> rootdir: /<<PKGBUILDDIR>>
> plugins: cov-5.0.0, requests-mock-1.11.0, mock-3.12.0
> collected 32 items
> 
> tests/test_core.py ................                                      [ 
> 50%]
> tests/test_correct.py .                                                  [ 
> 53%]
> tests/test_download.py .                                                 [ 
> 56%]
> tests/test_validate.py ...                                               [ 
> 65%]
> tests/test_wgs.py ....FF.FF.x                                            
> [100%]
> 
> =================================== FAILURES 
> ===================================
> _________________________ test_download_wgs_parts_wgs 
> __________________________
> 
> req = <requests_mock.mocker.Mocker object at 0x7f5355e58c50>
> 
>     def test_download_wgs_parts_wgs(req):
>         cfg = Config(format="genbank")
>         wgs_contig = open(full_path('wgs.gbk'), 'rt')
>         req.get(ENTREZ_URL, body=open(full_path('wgs_full.gbk'), 'rt'))
>     
> >       outhandle = wgs.download_wgs_parts(wgs_contig, cfg)
> 
> tests/test_wgs.py:89: 
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
> _ 
> ncbi_acc_download/wgs.py:114: in download_wgs_parts
>     updated_records.extend(download_wgs_for_record(record, config))
> ncbi_acc_download/wgs.py:164: in download_wgs_for_record
>     write_stream(r, handle, dl_id, config)
> ncbi_acc_download/download.py:118: in write_stream
>     for chunk in request.iter_content(4096, decode_unicode=True):
> /usr/lib/python3/dist-packages/requests/utils.py:568: in 
> stream_decode_response_unicode
>     yield from iterator
> /usr/lib/python3/dist-packages/requests/models.py:820: in generate
>     yield from self.raw.stream(chunk_size, decode_content=True)
> /usr/lib/python3/dist-packages/urllib3/response.py:936: in stream
>     data = self.read(amt=amt, decode_content=decode_content)
> /usr/lib/python3/dist-packages/urllib3/response.py:910: in read
>     data = self._decoded_buffer.get(amt)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
> _ 
> 
> self = <urllib3.response.BytesQueueBuffer object at 0x7f5355e59670>, n = 4096
> 
>     def get(self, n: int) -> bytes:
>         if n == 0:
>             return b""
>         elif not self.buffer:
>             raise RuntimeError("buffer is empty")
>         elif n < 0:
>             raise ValueError("n should be > 0")
>     
>         fetched = 0
>         ret = io.BytesIO()
>         while fetched < n:
>             remaining = n - fetched
>             chunk = self.buffer.popleft()
>             chunk_length = len(chunk)
>             if remaining < chunk_length:
>                 left_chunk, right_chunk = chunk[:remaining], chunk[remaining:]
>                 ret.write(left_chunk)
>                 self.buffer.appendleft(right_chunk)
>                 self._size -= remaining
>                 break
>             else:
> >               ret.write(chunk)
> E               TypeError: a bytes-like object is required, not 'str'
> 
> /usr/lib/python3/dist-packages/urllib3/response.py:272: TypeError
> ______________________ test_download_wgs_parts_wgs_retry 
> _______________________
> 
> req = <requests_mock.mocker.Mocker object at 0x7f5355e27c80>
> 
>     def test_download_wgs_parts_wgs_retry(req):
>         cfg = Config(format="genbank")
>         wgs_contig = open(full_path('wgs.gbk'), 'rt')
>         req.get(ENTREZ_URL, response_list=[
>             {"text": u'Whoa, slow down', "status_code": 429, "headers": 
> {"Retry-After": "0"}},
>             {"body": open(full_path('wgs_full.gbk'), 'rt')},
>         ])
>     
> >       outhandle = wgs.download_wgs_parts(wgs_contig, cfg)
> 
> tests/test_wgs.py:104: 
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
> _ 
> ncbi_acc_download/wgs.py:114: in download_wgs_parts
>     updated_records.extend(download_wgs_for_record(record, config))
> ncbi_acc_download/wgs.py:164: in download_wgs_for_record
>     write_stream(r, handle, dl_id, config)
> ncbi_acc_download/download.py:118: in write_stream
>     for chunk in request.iter_content(4096, decode_unicode=True):
> /usr/lib/python3/dist-packages/requests/utils.py:568: in 
> stream_decode_response_unicode
>     yield from iterator
> /usr/lib/python3/dist-packages/requests/models.py:820: in generate
>     yield from self.raw.stream(chunk_size, decode_content=True)
> /usr/lib/python3/dist-packages/urllib3/response.py:936: in stream
>     data = self.read(amt=amt, decode_content=decode_content)
> /usr/lib/python3/dist-packages/urllib3/response.py:910: in read
>     data = self._decoded_buffer.get(amt)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
> _ 
> 
> self = <urllib3.response.BytesQueueBuffer object at 0x7f5355deba70>, n = 4096
> 
>     def get(self, n: int) -> bytes:
>         if n == 0:
>             return b""
>         elif not self.buffer:
>             raise RuntimeError("buffer is empty")
>         elif n < 0:
>             raise ValueError("n should be > 0")
>     
>         fetched = 0
>         ret = io.BytesIO()
>         while fetched < n:
>             remaining = n - fetched
>             chunk = self.buffer.popleft()
>             chunk_length = len(chunk)
>             if remaining < chunk_length:
>                 left_chunk, right_chunk = chunk[:remaining], chunk[remaining:]
>                 ret.write(left_chunk)
>                 self.buffer.appendleft(right_chunk)
>                 self._size -= remaining
>                 break
>             else:
> >               ret.write(chunk)
> E               TypeError: a bytes-like object is required, not 'str'
> 
> /usr/lib/python3/dist-packages/urllib3/response.py:272: TypeError
> ----------------------------- Captured stdout call 
> -----------------------------
> Too many requests, please consider using --api-key parameter (see 
> https://www.ncbi.nlm.nih.gov/books/NBK25497/).
> _____________________ test_download_wgs_parts_supercontig 
> ______________________
> 
> req = <requests_mock.mocker.Mocker object at 0x7f5355e27ef0>
> 
>     def test_download_wgs_parts_supercontig(req):
>         cfg = Config(format="genbank")
>         supercontig = open(full_path('supercontig.gbk'), 'rt')
>         req.get(ENTREZ_URL, body=open(full_path('supercontig_full.gbk'), 
> 'rt'))
>     
> >       outhandle = wgs.download_wgs_parts(supercontig, cfg)
> 
> tests/test_wgs.py:128: 
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
> _ 
> ncbi_acc_download/wgs.py:116: in download_wgs_parts
>     updated_records.extend(fix_supercontigs(record, config))
> ncbi_acc_download/wgs.py:191: in fix_supercontigs
>     write_stream(r, handle, dl_id, config)
> ncbi_acc_download/download.py:118: in write_stream
>     for chunk in request.iter_content(4096, decode_unicode=True):
> /usr/lib/python3/dist-packages/requests/utils.py:568: in 
> stream_decode_response_unicode
>     yield from iterator
> /usr/lib/python3/dist-packages/requests/models.py:820: in generate
>     yield from self.raw.stream(chunk_size, decode_content=True)
> /usr/lib/python3/dist-packages/urllib3/response.py:936: in stream
>     data = self.read(amt=amt, decode_content=decode_content)
> /usr/lib/python3/dist-packages/urllib3/response.py:910: in read
>     data = self._decoded_buffer.get(amt)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
> _ 
> 
> self = <urllib3.response.BytesQueueBuffer object at 0x7f5355e57e00>, n = 4096
> 
>     def get(self, n: int) -> bytes:
>         if n == 0:
>             return b""
>         elif not self.buffer:
>             raise RuntimeError("buffer is empty")
>         elif n < 0:
>             raise ValueError("n should be > 0")
>     
>         fetched = 0
>         ret = io.BytesIO()
>         while fetched < n:
>             remaining = n - fetched
>             chunk = self.buffer.popleft()
>             chunk_length = len(chunk)
>             if remaining < chunk_length:
>                 left_chunk, right_chunk = chunk[:remaining], chunk[remaining:]
>                 ret.write(left_chunk)
>                 self.buffer.appendleft(right_chunk)
>                 self._size -= remaining
>                 break
>             else:
> >               ret.write(chunk)
> E               TypeError: a bytes-like object is required, not 'str'
> 
> /usr/lib/python3/dist-packages/urllib3/response.py:272: TypeError
> __________________ test_download_wgs_parts_supercontig_retry 
> ___________________
> 
> req = <requests_mock.mocker.Mocker object at 0x7f5355e27a10>
> 
>     def test_download_wgs_parts_supercontig_retry(req):
>         cfg = Config(format="genbank")
>         supercontig = open(full_path('supercontig.gbk'), 'rt')
>         req.get(ENTREZ_URL, response_list=[
>             {"text": u'Whoa, slow down', "status_code": 429, "headers": 
> {"Retry-After": "0"}},
>             {"body": open(full_path('supercontig_full.gbk'), 'rt')}
>         ])
>     
> >       outhandle = wgs.download_wgs_parts(supercontig, cfg)
> 
> tests/test_wgs.py:143: 
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
> _ 
> ncbi_acc_download/wgs.py:116: in download_wgs_parts
>     updated_records.extend(fix_supercontigs(record, config))
> ncbi_acc_download/wgs.py:191: in fix_supercontigs
>     write_stream(r, handle, dl_id, config)
> ncbi_acc_download/download.py:118: in write_stream
>     for chunk in request.iter_content(4096, decode_unicode=True):
> /usr/lib/python3/dist-packages/requests/utils.py:568: in 
> stream_decode_response_unicode
>     yield from iterator
> /usr/lib/python3/dist-packages/requests/models.py:820: in generate
>     yield from self.raw.stream(chunk_size, decode_content=True)
> /usr/lib/python3/dist-packages/urllib3/response.py:936: in stream
>     data = self.read(amt=amt, decode_content=decode_content)
> /usr/lib/python3/dist-packages/urllib3/response.py:910: in read
>     data = self._decoded_buffer.get(amt)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
> _ 
> 
> self = <urllib3.response.BytesQueueBuffer object at 0x7f5355d2efc0>, n = 4096
> 
>     def get(self, n: int) -> bytes:
>         if n == 0:
>             return b""
>         elif not self.buffer:
>             raise RuntimeError("buffer is empty")
>         elif n < 0:
>             raise ValueError("n should be > 0")
>     
>         fetched = 0
>         ret = io.BytesIO()
>         while fetched < n:
>             remaining = n - fetched
>             chunk = self.buffer.popleft()
>             chunk_length = len(chunk)
>             if remaining < chunk_length:
>                 left_chunk, right_chunk = chunk[:remaining], chunk[remaining:]
>                 ret.write(left_chunk)
>                 self.buffer.appendleft(right_chunk)
>                 self._size -= remaining
>                 break
>             else:
> >               ret.write(chunk)
> E               TypeError: a bytes-like object is required, not 'str'
> 
> /usr/lib/python3/dist-packages/urllib3/response.py:272: TypeError
> ----------------------------- Captured stdout call 
> -----------------------------
> Too many requests, please consider using --api-key parameter (see 
> https://www.ncbi.nlm.nih.gov/books/NBK25497/).
> =========================== short test summary info 
> ============================
> FAILED tests/test_wgs.py::test_download_wgs_parts_wgs - TypeError: a 
> bytes-li...
> FAILED tests/test_wgs.py::test_download_wgs_parts_wgs_retry - TypeError: a 
> by...
> FAILED tests/test_wgs.py::test_download_wgs_parts_supercontig - TypeError: a 
> ...
> FAILED tests/test_wgs.py::test_download_wgs_parts_supercontig_retry - 
> TypeErr...
> =================== 4 failed, 27 passed, 1 xfailed in 0.72s 
> ====================
> E: pybuild pybuild:389: test: plugin distutils failed with: exit code=1: cd 
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ncbi-acc-download/build; python3.12 
> -m pytest tests
> I: pybuild base:311: cd 
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ncbi-acc-download/build; python3.11 
> -m pytest tests
> ============================= test session starts 
> ==============================
> platform linux -- Python 3.11.9, pytest-8.2.2, pluggy-1.5.0
> rootdir: /<<PKGBUILDDIR>>
> plugins: cov-5.0.0, requests-mock-1.11.0, mock-3.12.0
> collected 32 items
> 
> tests/test_core.py ................                                      [ 
> 50%]
> tests/test_correct.py .                                                  [ 
> 53%]
> tests/test_download.py .                                                 [ 
> 56%]
> tests/test_validate.py ...                                               [ 
> 65%]
> tests/test_wgs.py ....FF.FF.x                                            
> [100%]
> 
> =================================== FAILURES 
> ===================================
> _________________________ test_download_wgs_parts_wgs 
> __________________________
> 
> req = <requests_mock.mocker.Mocker object at 0x7fe159522b10>
> 
>     def test_download_wgs_parts_wgs(req):
>         cfg = Config(format="genbank")
>         wgs_contig = open(full_path('wgs.gbk'), 'rt')
>         req.get(ENTREZ_URL, body=open(full_path('wgs_full.gbk'), 'rt'))
>     
> >       outhandle = wgs.download_wgs_parts(wgs_contig, cfg)
> 
> tests/test_wgs.py:89: 
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
> _ 
> ncbi_acc_download/wgs.py:114: in download_wgs_parts
>     updated_records.extend(download_wgs_for_record(record, config))
> ncbi_acc_download/wgs.py:164: in download_wgs_for_record
>     write_stream(r, handle, dl_id, config)
> ncbi_acc_download/download.py:118: in write_stream
>     for chunk in request.iter_content(4096, decode_unicode=True):
> /usr/lib/python3/dist-packages/requests/utils.py:568: in 
> stream_decode_response_unicode
>     yield from iterator
> /usr/lib/python3/dist-packages/requests/models.py:820: in generate
>     yield from self.raw.stream(chunk_size, decode_content=True)
> /usr/lib/python3/dist-packages/urllib3/response.py:936: in stream
>     data = self.read(amt=amt, decode_content=decode_content)
> /usr/lib/python3/dist-packages/urllib3/response.py:910: in read
>     data = self._decoded_buffer.get(amt)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
> _ 
> 
> self = <urllib3.response.BytesQueueBuffer object at 0x7fe159520650>, n = 4096
> 
>     def get(self, n: int) -> bytes:
>         if n == 0:
>             return b""
>         elif not self.buffer:
>             raise RuntimeError("buffer is empty")
>         elif n < 0:
>             raise ValueError("n should be > 0")
>     
>         fetched = 0
>         ret = io.BytesIO()
>         while fetched < n:
>             remaining = n - fetched
>             chunk = self.buffer.popleft()
>             chunk_length = len(chunk)
>             if remaining < chunk_length:
>                 left_chunk, right_chunk = chunk[:remaining], chunk[remaining:]
>                 ret.write(left_chunk)
>                 self.buffer.appendleft(right_chunk)
>                 self._size -= remaining
>                 break
>             else:
> >               ret.write(chunk)
> E               TypeError: a bytes-like object is required, not 'str'
> 
> /usr/lib/python3/dist-packages/urllib3/response.py:272: TypeError
> ______________________ test_download_wgs_parts_wgs_retry 
> _______________________
> 
> req = <requests_mock.mocker.Mocker object at 0x7fe159432790>
> 
>     def test_download_wgs_parts_wgs_retry(req):
>         cfg = Config(format="genbank")
>         wgs_contig = open(full_path('wgs.gbk'), 'rt')
>         req.get(ENTREZ_URL, response_list=[
>             {"text": u'Whoa, slow down', "status_code": 429, "headers": 
> {"Retry-After": "0"}},
>             {"body": open(full_path('wgs_full.gbk'), 'rt')},
>         ])
>     
> >       outhandle = wgs.download_wgs_parts(wgs_contig, cfg)
> 
> tests/test_wgs.py:104: 
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
> _ 
> ncbi_acc_download/wgs.py:114: in download_wgs_parts
>     updated_records.extend(download_wgs_for_record(record, config))
> ncbi_acc_download/wgs.py:164: in download_wgs_for_record
>     write_stream(r, handle, dl_id, config)
> ncbi_acc_download/download.py:118: in write_stream
>     for chunk in request.iter_content(4096, decode_unicode=True):
> /usr/lib/python3/dist-packages/requests/utils.py:568: in 
> stream_decode_response_unicode
>     yield from iterator
> /usr/lib/python3/dist-packages/requests/models.py:820: in generate
>     yield from self.raw.stream(chunk_size, decode_content=True)
> /usr/lib/python3/dist-packages/urllib3/response.py:936: in stream
>     data = self.read(amt=amt, decode_content=decode_content)
> /usr/lib/python3/dist-packages/urllib3/response.py:910: in read
>     data = self._decoded_buffer.get(amt)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
> _ 
> 
> self = <urllib3.response.BytesQueueBuffer object at 0x7fe159409710>, n = 4096
> 
>     def get(self, n: int) -> bytes:
>         if n == 0:
>             return b""
>         elif not self.buffer:
>             raise RuntimeError("buffer is empty")
>         elif n < 0:
>             raise ValueError("n should be > 0")
>     
>         fetched = 0
>         ret = io.BytesIO()
>         while fetched < n:
>             remaining = n - fetched
>             chunk = self.buffer.popleft()
>             chunk_length = len(chunk)
>             if remaining < chunk_length:
>                 left_chunk, right_chunk = chunk[:remaining], chunk[remaining:]
>                 ret.write(left_chunk)
>                 self.buffer.appendleft(right_chunk)
>                 self._size -= remaining
>                 break
>             else:
> >               ret.write(chunk)
> E               TypeError: a bytes-like object is required, not 'str'
> 
> /usr/lib/python3/dist-packages/urllib3/response.py:272: TypeError
> ----------------------------- Captured stdout call 
> -----------------------------
> Too many requests, please consider using --api-key parameter (see 
> https://www.ncbi.nlm.nih.gov/books/NBK25497/).
> _____________________ test_download_wgs_parts_supercontig 
> ______________________
> 
> req = <requests_mock.mocker.Mocker object at 0x7fe1594b3290>
> 
>     def test_download_wgs_parts_supercontig(req):
>         cfg = Config(format="genbank")
>         supercontig = open(full_path('supercontig.gbk'), 'rt')
>         req.get(ENTREZ_URL, body=open(full_path('supercontig_full.gbk'), 
> 'rt'))
>     
> >       outhandle = wgs.download_wgs_parts(supercontig, cfg)
> 
> tests/test_wgs.py:128: 
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
> _ 
> ncbi_acc_download/wgs.py:116: in download_wgs_parts
>     updated_records.extend(fix_supercontigs(record, config))
> ncbi_acc_download/wgs.py:191: in fix_supercontigs
>     write_stream(r, handle, dl_id, config)
> ncbi_acc_download/download.py:118: in write_stream
>     for chunk in request.iter_content(4096, decode_unicode=True):
> /usr/lib/python3/dist-packages/requests/utils.py:568: in 
> stream_decode_response_unicode
>     yield from iterator
> /usr/lib/python3/dist-packages/requests/models.py:820: in generate
>     yield from self.raw.stream(chunk_size, decode_content=True)
> /usr/lib/python3/dist-packages/urllib3/response.py:936: in stream
>     data = self.read(amt=amt, decode_content=decode_content)
> /usr/lib/python3/dist-packages/urllib3/response.py:910: in read
>     data = self._decoded_buffer.get(amt)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
> _ 
> 
> self = <urllib3.response.BytesQueueBuffer object at 0x7fe1594dd250>, n = 4096
> 
>     def get(self, n: int) -> bytes:
>         if n == 0:
>             return b""
>         elif not self.buffer:
>             raise RuntimeError("buffer is empty")
>         elif n < 0:
>             raise ValueError("n should be > 0")
>     
>         fetched = 0
>         ret = io.BytesIO()
>         while fetched < n:
>             remaining = n - fetched
>             chunk = self.buffer.popleft()
>             chunk_length = len(chunk)
>             if remaining < chunk_length:
>                 left_chunk, right_chunk = chunk[:remaining], chunk[remaining:]
>                 ret.write(left_chunk)
>                 self.buffer.appendleft(right_chunk)
>                 self._size -= remaining
>                 break
>             else:
> >               ret.write(chunk)
> E               TypeError: a bytes-like object is required, not 'str'
> 
> /usr/lib/python3/dist-packages/urllib3/response.py:272: TypeError
> __________________ test_download_wgs_parts_supercontig_retry 
> ___________________
> 
> req = <requests_mock.mocker.Mocker object at 0x7fe15aedcdd0>
> 
>     def test_download_wgs_parts_supercontig_retry(req):
>         cfg = Config(format="genbank")
>         supercontig = open(full_path('supercontig.gbk'), 'rt')
>         req.get(ENTREZ_URL, response_list=[
>             {"text": u'Whoa, slow down', "status_code": 429, "headers": 
> {"Retry-After": "0"}},
>             {"body": open(full_path('supercontig_full.gbk'), 'rt')}
>         ])
>     
> >       outhandle = wgs.download_wgs_parts(supercontig, cfg)
> 
> tests/test_wgs.py:143: 
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
> _ 
> ncbi_acc_download/wgs.py:116: in download_wgs_parts
>     updated_records.extend(fix_supercontigs(record, config))
> ncbi_acc_download/wgs.py:191: in fix_supercontigs
>     write_stream(r, handle, dl_id, config)
> ncbi_acc_download/download.py:118: in write_stream
>     for chunk in request.iter_content(4096, decode_unicode=True):
> /usr/lib/python3/dist-packages/requests/utils.py:568: in 
> stream_decode_response_unicode
>     yield from iterator
> /usr/lib/python3/dist-packages/requests/models.py:820: in generate
>     yield from self.raw.stream(chunk_size, decode_content=True)
> /usr/lib/python3/dist-packages/urllib3/response.py:936: in stream
>     data = self.read(amt=amt, decode_content=decode_content)
> /usr/lib/python3/dist-packages/urllib3/response.py:910: in read
>     data = self._decoded_buffer.get(amt)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
> _ 
> 
> self = <urllib3.response.BytesQueueBuffer object at 0x7fe15930b650>, n = 4096
> 
>     def get(self, n: int) -> bytes:
>         if n == 0:
>             return b""
>         elif not self.buffer:
>             raise RuntimeError("buffer is empty")
>         elif n < 0:
>             raise ValueError("n should be > 0")
>     
>         fetched = 0
>         ret = io.BytesIO()
>         while fetched < n:
>             remaining = n - fetched
>             chunk = self.buffer.popleft()
>             chunk_length = len(chunk)
>             if remaining < chunk_length:
>                 left_chunk, right_chunk = chunk[:remaining], chunk[remaining:]
>                 ret.write(left_chunk)
>                 self.buffer.appendleft(right_chunk)
>                 self._size -= remaining
>                 break
>             else:
> >               ret.write(chunk)
> E               TypeError: a bytes-like object is required, not 'str'
> 
> /usr/lib/python3/dist-packages/urllib3/response.py:272: TypeError
> ----------------------------- Captured stdout call 
> -----------------------------
> Too many requests, please consider using --api-key parameter (see 
> https://www.ncbi.nlm.nih.gov/books/NBK25497/).
> =========================== short test summary info 
> ============================
> FAILED tests/test_wgs.py::test_download_wgs_parts_wgs - TypeError: a 
> bytes-li...
> FAILED tests/test_wgs.py::test_download_wgs_parts_wgs_retry - TypeError: a 
> by...
> FAILED tests/test_wgs.py::test_download_wgs_parts_supercontig - TypeError: a 
> ...
> FAILED tests/test_wgs.py::test_download_wgs_parts_supercontig_retry - 
> TypeErr...
> =================== 4 failed, 27 passed, 1 xfailed in 0.85s 
> ====================
> E: pybuild pybuild:389: test: plugin distutils failed with: exit code=1: cd 
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ncbi-acc-download/build; python3.11 
> -m pytest tests
> dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.12 
> 3.11" returned exit code 13


The full build log is available from:
http://qa-logs.debian.net/2024/06/15/ncbi-acc-download_0.2.8-2_unstable.log

All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20240615;users=lu...@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20240615&fusertaguser=lu...@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results

A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!

If you reassign this bug to another package, please mark it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects

If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.

--- End Message ---

--- Begin Message ---

Source: ncbi-acc-download
Source-Version: 0.2.8-3
Done: Andreas Tille <ti...@debian.org>

We believe that the bug you reported is fixed in the latest version of
ncbi-acc-download, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 1073...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Andreas Tille <ti...@debian.org> (supplier of updated ncbi-acc-download package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256

Format: 1.8
Date: Fri, 02 Aug 2024 00:02:28 +0200
Source: ncbi-acc-download
Architecture: source
Version: 0.2.8-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Closes: 1073450
Changes:
 ncbi-acc-download (0.2.8-3) unstable; urgency=medium
 .
   * Team upload.
 .
   [ Benjamin Drung ]
   * Fix test
     Closes: #1073450
 .
   [ Andreas Tille ]
   * Standards-Version: 4.7.0 (routine-update)
   * Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update)
   * Rename test script to run-unit-test
   * Test all supported Python3 versions
Checksums-Sha1:
 71dd8815141a36d01ee44431c48787f13b20b912 2434 ncbi-acc-download_0.2.8-3.dsc
 1b225f88a960b13fe8eeef07785ed4a8de43a940 4420 
ncbi-acc-download_0.2.8-3.debian.tar.xz
 1bd898e1c58431c16998fac4640a33e32fc19caa 8976 
ncbi-acc-download_0.2.8-3_amd64.buildinfo
Checksums-Sha256:
 7ad1e1f0126a1286fb4399e2205c734e82bc1b31f87945e44dfafddfd7306ad3 2434 
ncbi-acc-download_0.2.8-3.dsc
 7a7eccce3de2b4f5c7f1403cbfbc8891dd13b4acf7ac7629d37ef89022092678 4420 
ncbi-acc-download_0.2.8-3.debian.tar.xz
 b81a788aed2c275f3ca30c26561608acfe7439b3d6e275c0850367fab0c6e982 8976 
ncbi-acc-download_0.2.8-3_amd64.buildinfo
Files:
 84a86b54060769b4ed3c1c66abb3bb42 2434 science optional 
ncbi-acc-download_0.2.8-3.dsc
 12193eac9f46154d8a7ef20239c0e590 4420 science optional 
ncbi-acc-download_0.2.8-3.debian.tar.xz
 aaf035f6e79d10167d96ec3fb0389dd4 8976 science optional 
ncbi-acc-download_0.2.8-3_amd64.buildinfo

-----BEGIN PGP SIGNATURE-----
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=oyvX
-----END PGP SIGNATURE-----

pgppLtIIh9_c4.pgp
Description: PGP signature

--- End Message ---

Bug#1073450: marked as done (ncbi-acc-download: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.12 3.11" returned exit code 13)

Reply via email to