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.
