2025-06-11T13:13:48,277 Created temporary directory: /tmp/pip-build-tracker-2_43kbyu 2025-06-11T13:13:48,278 Initialized build tracking at /tmp/pip-build-tracker-2_43kbyu 2025-06-11T13:13:48,279 Created build tracker: /tmp/pip-build-tracker-2_43kbyu 2025-06-11T13:13:48,279 Entered build tracker: /tmp/pip-build-tracker-2_43kbyu 2025-06-11T13:13:48,280 Created temporary directory: /tmp/pip-wheel-idhuj1ev 2025-06-11T13:13:48,284 Created temporary directory: /tmp/pip-ephem-wheel-cache-1m689b1_ 2025-06-11T13:13:48,336 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-06-11T13:13:48,339 2 location(s) to search for versions of taxtastic: 2025-06-11T13:13:48,339 * https://pypi.org/simple/taxtastic/ 2025-06-11T13:13:48,339 * https://www.piwheels.org/simple/taxtastic/ 2025-06-11T13:13:48,340 Fetching project page and analyzing links: https://pypi.org/simple/taxtastic/ 2025-06-11T13:13:48,340 Getting page https://pypi.org/simple/taxtastic/ 2025-06-11T13:13:48,342 Found index url https://pypi.org/simple/ 2025-06-11T13:13:48,569 Fetched page https://pypi.org/simple/taxtastic/ as application/vnd.pypi.simple.v1+json 2025-06-11T13:13:48,574 Found link https://files.pythonhosted.org/packages/ca/43/50f961a308692ec4a28cad342bd608b7efb5ca6626f6cb697b233a61d880/taxtastic-0.3.2.tar.gz (from https://pypi.org/simple/taxtastic/), version: 0.3.2 2025-06-11T13:13:48,574 Found link https://files.pythonhosted.org/packages/c9/43/e095da8cfc87c21c2ccbec770f86beb4f36eb80f63eb911ba7d4562fa96f/taxtastic-0.4.0.tar.gz (from https://pypi.org/simple/taxtastic/), version: 0.4.0 2025-06-11T13:13:48,575 Found link https://files.pythonhosted.org/packages/cf/aa/5eba8333044ae88e206dd3eba41cee25913e3b71c2d32f27e8ee2aca1476/taxtastic-0.5.0.tar.gz (from https://pypi.org/simple/taxtastic/), version: 0.5.0 2025-06-11T13:13:48,576 Found link https://files.pythonhosted.org/packages/b2/81/c9ed50ac10c7030da23bc8161bc06cd31ceea70e62fa046d11fe800bc01c/taxtastic-0.5.1.tar.gz (from https://pypi.org/simple/taxtastic/), version: 0.5.1 2025-06-11T13:13:48,577 Found link https://files.pythonhosted.org/packages/bb/10/ee4831097b5f421dfdcddc8cd7b9b7057acd87c9163cce860d9d8984a02d/taxtastic-0.5.2.tar.gz (from https://pypi.org/simple/taxtastic/), version: 0.5.2 2025-06-11T13:13:48,577 Skipping link: No binaries permitted for taxtastic: https://files.pythonhosted.org/packages/7f/48/c397e01cb14e52fa63a5456034d644a918fe983f02f81c6bccd28970d2d2/taxtastic-0.5.3-py2-none-any.whl (from https://pypi.org/simple/taxtastic/) 2025-06-11T13:13:48,578 Found link https://files.pythonhosted.org/packages/d0/c3/6b258c510dba140091f28e17f169a6f1d5c38aee23c28bb7d6d31f62c3fe/taxtastic-0.5.3.tar.gz (from https://pypi.org/simple/taxtastic/), version: 0.5.3 2025-06-11T13:13:48,579 Skipping link: No binaries permitted for taxtastic: https://files.pythonhosted.org/packages/98/27/f07ddd2e1497af6963c4c1afd99f559e877bb200c565f6b8468185ceee84/taxtastic-0.5.4-py2-none-any.whl (from https://pypi.org/simple/taxtastic/) 2025-06-11T13:13:48,580 Found link https://files.pythonhosted.org/packages/de/e5/6a27a42e42e25d3d1d4ca9aa7fa6a20a32dd1669e7750823a4e2f5f4712b/taxtastic-0.5.4.tar.gz (from https://pypi.org/simple/taxtastic/), version: 0.5.4 2025-06-11T13:13:48,581 Found link https://files.pythonhosted.org/packages/3a/ab/d4d047439bcc971dcaf229c15b1689b82b8a15a3a93a4e93667132100be3/taxtastic-0.8.1.tar.gz (from https://pypi.org/simple/taxtastic/), version: 0.8.1 2025-06-11T13:13:48,581 Skipping link: No binaries permitted for taxtastic: https://files.pythonhosted.org/packages/60/2a/7e968f2153f3c61e70bd061225d0d783e31f9ac727399e130bc344c30fbe/taxtastic-0.8.2-py2-none-any.whl (from https://pypi.org/simple/taxtastic/) 2025-06-11T13:13:48,582 Found link https://files.pythonhosted.org/packages/a8/8f/a691dd64801f5aee8b6bd20cdb8e8c3564acd7700eb2b34c8ac88ab0b52a/taxtastic-0.8.2.tar.gz (from https://pypi.org/simple/taxtastic/), version: 0.8.2 2025-06-11T13:13:48,583 Skipping link: No binaries permitted for taxtastic: https://files.pythonhosted.org/packages/8e/96/cae8442db164ddc3a3ee174dff6b2651c0537ceb7e792c61f029262b134a/taxtastic-0.8.3-py2-none-any.whl (from https://pypi.org/simple/taxtastic/) 2025-06-11T13:13:48,584 Found link https://files.pythonhosted.org/packages/a3/38/58a40c13ea4e2e563b3c29d1c85d30998adbdd59840d41c3b91de57d7732/taxtastic-0.8.3.tar.gz (from https://pypi.org/simple/taxtastic/), version: 0.8.3 2025-06-11T13:13:48,585 Found link https://files.pythonhosted.org/packages/d4/ca/2f00085edbcade9cd2f6a16fe2373788d21e6ed903908a025b326d71b709/taxtastic-0.8.4.tar.gz (from https://pypi.org/simple/taxtastic/), version: 0.8.4 2025-06-11T13:13:48,585 Found link https://files.pythonhosted.org/packages/fd/82/bfc0b0b2d407567d36e37d014e2a32c4041ed0c0c932f3d2f50c8501f6f4/taxtastic-0.8.5.tar.gz (from https://pypi.org/simple/taxtastic/), version: 0.8.5 2025-06-11T13:13:48,586 Found link https://files.pythonhosted.org/packages/2a/0e/c7cd58bbe3a28c28065de373094b3382d8e04340f342688965cfb4fbb85f/taxtastic-0.8.9.tar.gz (from https://pypi.org/simple/taxtastic/), version: 0.8.9 2025-06-11T13:13:48,586 Found link https://files.pythonhosted.org/packages/7c/74/feea0e2ce4e0898e6c7371d8299de959ad496380074346d8d18a16920e97/taxtastic-0.8.11.tar.gz (from https://pypi.org/simple/taxtastic/), version: 0.8.11 2025-06-11T13:13:48,587 Skipping link: No binaries permitted for taxtastic: https://files.pythonhosted.org/packages/60/2e/bfe1943043e48c672c66bb7514521846f5b1ce9389628a72c1dab22928aa/taxtastic-0.9.0-py3-none-any.whl (from https://pypi.org/simple/taxtastic/) (requires-python:>=3.4) 2025-06-11T13:13:48,588 Found link https://files.pythonhosted.org/packages/4c/6a/c5b4bd7376718c9443aa283fa8f134fab570ed3770d6d89f5ed7dbf14854/taxtastic-0.9.0.tar.gz (from https://pypi.org/simple/taxtastic/) (requires-python:>=3.4), version: 0.9.0 2025-06-11T13:13:48,589 Skipping link: No binaries permitted for taxtastic: https://files.pythonhosted.org/packages/40/c3/1a1ea56fed23d73916e7e6823c3412ff24eb1d277a8003865b7596940676/taxtastic-0.9.1-py3-none-any.whl (from https://pypi.org/simple/taxtastic/) (requires-python:>=3.4) 2025-06-11T13:13:48,589 Found link https://files.pythonhosted.org/packages/7b/6c/c418efa114c934a0fad64049fee871ee2d7add2ac7423e03fca76089e17f/taxtastic-0.9.1.tar.gz (from https://pypi.org/simple/taxtastic/) (requires-python:>=3.4), version: 0.9.1 2025-06-11T13:13:48,590 Found link https://files.pythonhosted.org/packages/4f/2e/d6317cf64bd1b70b95e2ee9a0d7e54cbe1201cf8e4d792a29c3fd1e4a21a/taxtastic-0.9.2.tar.gz (from https://pypi.org/simple/taxtastic/) (requires-python:>=3.4), version: 0.9.2 2025-06-11T13:13:48,591 Skipping link: No binaries permitted for taxtastic: https://files.pythonhosted.org/packages/be/2f/ab9cf616974b54c657395a7c75e1c0260844a940c78b371e7b8db317d634/taxtastic-0.9.3-py3-none-any.whl (from https://pypi.org/simple/taxtastic/) (requires-python:>=3.4) 2025-06-11T13:13:48,591 Found link https://files.pythonhosted.org/packages/a1/ca/7ed1bab3ca1665245efa8a864737b3e88290ad2dee736f8e0b6d0860c888/taxtastic-0.9.3.tar.gz (from https://pypi.org/simple/taxtastic/) (requires-python:>=3.4), version: 0.9.3 2025-06-11T13:13:48,592 Skipping link: No binaries permitted for taxtastic: https://files.pythonhosted.org/packages/c2/58/7887a54b76a4049739d65251b06c3fc653d882e099ec5142485421181e9f/taxtastic-0.10.0-py3-none-any.whl (from https://pypi.org/simple/taxtastic/) (requires-python:>=3.8) 2025-06-11T13:13:48,593 Found link https://files.pythonhosted.org/packages/7f/8a/49c16e64bc69a043d393c648336985a06c4b5dc1ac18598c32f0c8a35553/taxtastic-0.10.0.tar.gz (from https://pypi.org/simple/taxtastic/) (requires-python:>=3.8), version: 0.10.0 2025-06-11T13:13:48,594 Skipping link: No binaries permitted for taxtastic: https://files.pythonhosted.org/packages/df/8b/6e7f7748e680bb154a5dc76327dcabfcc213c790e5354d9712f572fb7023/taxtastic-0.11.0-py3-none-any.whl (from https://pypi.org/simple/taxtastic/) (requires-python:>=3.8) 2025-06-11T13:13:48,595 Found link https://files.pythonhosted.org/packages/06/62/54b2639d38332cd675ea272b6acdbb071e8932f989f50a54e6d043da9c0d/taxtastic-0.11.0.tar.gz (from https://pypi.org/simple/taxtastic/) (requires-python:>=3.8), version: 0.11.0 2025-06-11T13:13:48,596 Skipping link: No binaries permitted for taxtastic: https://files.pythonhosted.org/packages/99/60/af5f69c946880c33dd06fb24db648c67a08f50e869e0d10fb0c17dbd8cb8/taxtastic-0.11.1-py3-none-any.whl (from https://pypi.org/simple/taxtastic/) (requires-python:>=3.8) 2025-06-11T13:13:48,596 Skipping link: No binaries permitted for taxtastic: https://files.pythonhosted.org/packages/1c/ae/5549f6e429dff9d2d18d73ed7a4c91d24ee85a92d1f52fe17f4a17a5dde5/taxtastic-0.12.0-py3-none-any.whl (from https://pypi.org/simple/taxtastic/) (requires-python:>=3.8) 2025-06-11T13:13:48,597 Found link https://files.pythonhosted.org/packages/4b/22/53415481e5c201aae6af78cf4bfcdca39aa794a2d54dd8ab63c5657a5629/taxtastic-0.12.0.tar.gz (from https://pypi.org/simple/taxtastic/) (requires-python:>=3.8), version: 0.12.0 2025-06-11T13:13:48,598 Fetching project page and analyzing links: https://www.piwheels.org/simple/taxtastic/ 2025-06-11T13:13:48,598 Getting page https://www.piwheels.org/simple/taxtastic/ 2025-06-11T13:13:48,599 Found index url https://www.piwheels.org/simple/ 2025-06-11T13:13:48,763 WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/taxtastic/ 2025-06-11T13:13:49,424 WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/taxtastic/ 2025-06-11T13:13:50,582 WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/taxtastic/ 2025-06-11T13:13:52,736 WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/taxtastic/ 2025-06-11T13:13:56,895 WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/taxtastic/ 2025-06-11T13:13:57,055 Could not fetch URL https://www.piwheels.org/simple/taxtastic/: There was a problem confirming the ssl certificate: HTTPSConnectionPool(host='www.piwheels.org', port=443): Max retries exceeded with url: /simple/taxtastic/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))) - skipping 2025-06-11T13:13:57,056 Skipping link: not a file: https://www.piwheels.org/simple/taxtastic/ 2025-06-11T13:13:57,057 Skipping link: not a file: https://pypi.org/simple/taxtastic/ 2025-06-11T13:13:57,077 Given no hashes to check 1 links for project 'taxtastic': discarding no candidates 2025-06-11T13:13:57,079 Collecting taxtastic==0.12.0 2025-06-11T13:13:57,082 Created temporary directory: /tmp/pip-unpack-4b_skjt7 2025-06-11T13:13:57,316 Downloading taxtastic-0.12.0.tar.gz (827 kB) 2025-06-11T13:13:57,872 Added taxtastic==0.12.0 from https://files.pythonhosted.org/packages/4b/22/53415481e5c201aae6af78cf4bfcdca39aa794a2d54dd8ab63c5657a5629/taxtastic-0.12.0.tar.gz to build tracker '/tmp/pip-build-tracker-2_43kbyu' 2025-06-11T13:13:57,874 Running setup.py (path:/tmp/pip-wheel-idhuj1ev/taxtastic_c8cc76cff49540e48e59b9983941871a/setup.py) egg_info for package taxtastic 2025-06-11T13:13:57,875 Created temporary directory: /tmp/pip-pip-egg-info-jkdg2cyd 2025-06-11T13:13:57,876 Preparing metadata (setup.py): started 2025-06-11T13:13:57,877 Running command python setup.py egg_info 2025-06-11T13:13:58,470 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-06-11T13:13:58,470 warnings.warn(msg) 2025-06-11T13:13:58,777 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-06-11T13:13:58,778 !! 2025-06-11T13:13:58,779 ******************************************************************************** 2025-06-11T13:13:58,779 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-06-11T13:13:58,780 License :: OSI Approved :: GNU General Public License (GPL) 2025-06-11T13:13:58,781 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-06-11T13:13:58,782 ******************************************************************************** 2025-06-11T13:13:58,783 !! 2025-06-11T13:13:58,784 self._finalize_license_expression() 2025-06-11T13:13:58,808 running egg_info 2025-06-11T13:13:58,836 creating /tmp/pip-pip-egg-info-jkdg2cyd/taxtastic.egg-info 2025-06-11T13:13:58,837 writing /tmp/pip-pip-egg-info-jkdg2cyd/taxtastic.egg-info/PKG-INFO 2025-06-11T13:13:58,841 writing dependency_links to /tmp/pip-pip-egg-info-jkdg2cyd/taxtastic.egg-info/dependency_links.txt 2025-06-11T13:13:58,843 writing entry points to /tmp/pip-pip-egg-info-jkdg2cyd/taxtastic.egg-info/entry_points.txt 2025-06-11T13:13:58,844 writing requirements to /tmp/pip-pip-egg-info-jkdg2cyd/taxtastic.egg-info/requires.txt 2025-06-11T13:13:58,846 writing top-level names to /tmp/pip-pip-egg-info-jkdg2cyd/taxtastic.egg-info/top_level.txt 2025-06-11T13:13:58,847 writing manifest file '/tmp/pip-pip-egg-info-jkdg2cyd/taxtastic.egg-info/SOURCES.txt' 2025-06-11T13:13:58,942 reading manifest file '/tmp/pip-pip-egg-info-jkdg2cyd/taxtastic.egg-info/SOURCES.txt' 2025-06-11T13:13:58,944 reading manifest template 'MANIFEST.in' 2025-06-11T13:13:58,959 warning: manifest_maker: MANIFEST.in, line 6: 'recursive-exclude' expects ... 2025-06-11T13:13:58,961 warning: no previously-included files matching '*/__pycache__/*' found anywhere in distribution 2025-06-11T13:13:58,961 warning: no previously-included files found matching 'Dockerfile' 2025-06-11T13:13:58,962 warning: no previously-included files found matching 'tests' 2025-06-11T13:13:58,963 warning: manifest_maker: MANIFEST.in, line 11: 'recursive-exclude' expects ... 2025-06-11T13:13:58,964 adding license file 'LICENSE' 2025-06-11T13:13:58,966 writing manifest file '/tmp/pip-pip-egg-info-jkdg2cyd/taxtastic.egg-info/SOURCES.txt' 2025-06-11T13:13:59,080 Preparing metadata (setup.py): finished with status 'done' 2025-06-11T13:13:59,085 Source in /tmp/pip-wheel-idhuj1ev/taxtastic_c8cc76cff49540e48e59b9983941871a has version 0.12.0, which satisfies requirement taxtastic==0.12.0 from https://files.pythonhosted.org/packages/4b/22/53415481e5c201aae6af78cf4bfcdca39aa794a2d54dd8ab63c5657a5629/taxtastic-0.12.0.tar.gz 2025-06-11T13:13:59,086 Removed taxtastic==0.12.0 from https://files.pythonhosted.org/packages/4b/22/53415481e5c201aae6af78cf4bfcdca39aa794a2d54dd8ab63c5657a5629/taxtastic-0.12.0.tar.gz from build tracker '/tmp/pip-build-tracker-2_43kbyu' 2025-06-11T13:13:59,095 Created temporary directory: /tmp/pip-unpack-v1jub097 2025-06-11T13:13:59,096 Created temporary directory: /tmp/pip-unpack-8_oa1fp7 2025-06-11T13:13:59,097 Building wheels for collected packages: taxtastic 2025-06-11T13:13:59,102 Created temporary directory: /tmp/pip-wheel-_rub37no 2025-06-11T13:13:59,103 DEPRECATION: Building 'taxtastic' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'taxtastic'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2025-06-11T13:13:59,104 Building wheel for taxtastic (setup.py): started 2025-06-11T13:13:59,106 Destination directory: /tmp/pip-wheel-_rub37no 2025-06-11T13:13:59,106 Running command python setup.py bdist_wheel 2025-06-11T13:13:59,685 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-06-11T13:13:59,685 warnings.warn(msg) 2025-06-11T13:13:59,986 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-06-11T13:13:59,986 !! 2025-06-11T13:13:59,987 ******************************************************************************** 2025-06-11T13:13:59,988 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-06-11T13:13:59,989 License :: OSI Approved :: GNU General Public License (GPL) 2025-06-11T13:13:59,990 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-06-11T13:13:59,991 ******************************************************************************** 2025-06-11T13:13:59,992 !! 2025-06-11T13:13:59,992 self._finalize_license_expression() 2025-06-11T13:13:59,993 running bdist_wheel 2025-06-11T13:14:00,125 running build 2025-06-11T13:14:00,126 running build_py 2025-06-11T13:14:00,157 creating build/lib/taxtastic 2025-06-11T13:14:00,159 copying taxtastic/lonely.py -> build/lib/taxtastic 2025-06-11T13:14:00,162 copying taxtastic/taxtable.py -> build/lib/taxtastic 2025-06-11T13:14:00,164 copying taxtastic/ncbi.py -> build/lib/taxtastic 2025-06-11T13:14:00,167 copying taxtastic/taxonomy.py -> build/lib/taxtastic 2025-06-11T13:14:00,170 copying taxtastic/taxdb.py -> build/lib/taxtastic 2025-06-11T13:14:00,173 copying taxtastic/utils.py -> build/lib/taxtastic 2025-06-11T13:14:00,175 copying taxtastic/__init__.py -> build/lib/taxtastic 2025-06-11T13:14:00,177 copying taxtastic/refpkg.py -> build/lib/taxtastic 2025-06-11T13:14:00,181 creating build/lib/taxtastic/subcommands 2025-06-11T13:14:00,183 copying taxtastic/subcommands/lineage_table.py -> build/lib/taxtastic/subcommands 2025-06-11T13:14:00,185 copying taxtastic/subcommands/taxtable.py -> build/lib/taxtastic/subcommands 2025-06-11T13:14:00,187 copying taxtastic/subcommands/rollback.py -> build/lib/taxtastic/subcommands 2025-06-11T13:14:00,189 copying taxtastic/subcommands/extract_nodes.py -> build/lib/taxtastic/subcommands 2025-06-11T13:14:00,192 copying taxtastic/subcommands/findcompany.py -> build/lib/taxtastic/subcommands 2025-06-11T13:14:00,194 copying taxtastic/subcommands/strip.py -> build/lib/taxtastic/subcommands 2025-06-11T13:14:00,196 copying taxtastic/subcommands/update.py -> build/lib/taxtastic/subcommands 2025-06-11T13:14:00,198 copying taxtastic/subcommands/namelookup.py -> build/lib/taxtastic/subcommands 2025-06-11T13:14:00,200 copying taxtastic/subcommands/refpkg_intersection.py -> build/lib/taxtastic/subcommands 2025-06-11T13:14:00,202 copying taxtastic/subcommands/check.py -> build/lib/taxtastic/subcommands 2025-06-11T13:14:00,204 copying taxtastic/subcommands/add_nodes.py -> build/lib/taxtastic/subcommands 2025-06-11T13:14:00,207 copying taxtastic/subcommands/composition.py -> build/lib/taxtastic/subcommands 2025-06-11T13:14:00,209 copying taxtastic/subcommands/lonelynodes.py -> build/lib/taxtastic/subcommands 2025-06-11T13:14:00,211 copying taxtastic/subcommands/named.py -> build/lib/taxtastic/subcommands 2025-06-11T13:14:00,213 copying taxtastic/subcommands/new_database.py -> build/lib/taxtastic/subcommands 2025-06-11T13:14:00,215 copying taxtastic/subcommands/add_to_taxtable.py -> build/lib/taxtastic/subcommands 2025-06-11T13:14:00,217 copying taxtastic/subcommands/rp.py -> build/lib/taxtastic/subcommands 2025-06-11T13:14:00,219 copying taxtastic/subcommands/__init__.py -> build/lib/taxtastic/subcommands 2025-06-11T13:14:00,221 copying taxtastic/subcommands/update_taxids.py -> build/lib/taxtastic/subcommands 2025-06-11T13:14:00,224 copying taxtastic/subcommands/taxids.py -> build/lib/taxtastic/subcommands 2025-06-11T13:14:00,226 copying taxtastic/subcommands/info.py -> build/lib/taxtastic/subcommands 2025-06-11T13:14:00,228 copying taxtastic/subcommands/create.py -> build/lib/taxtastic/subcommands 2025-06-11T13:14:00,230 copying taxtastic/subcommands/reroot.py -> build/lib/taxtastic/subcommands 2025-06-11T13:14:00,232 copying taxtastic/subcommands/get_descendants.py -> build/lib/taxtastic/subcommands 2025-06-11T13:14:00,234 copying taxtastic/subcommands/get_lineage.py -> build/lib/taxtastic/subcommands 2025-06-11T13:14:00,236 copying taxtastic/subcommands/rollforward.py -> build/lib/taxtastic/subcommands 2025-06-11T13:14:00,238 creating build/lib/taxtastic/scripts 2025-06-11T13:14:00,239 copying taxtastic/scripts/__init__.py -> build/lib/taxtastic/scripts 2025-06-11T13:14:00,241 copying taxtastic/scripts/taxit.py -> build/lib/taxtastic/scripts 2025-06-11T13:14:00,243 running egg_info 2025-06-11T13:14:00,271 writing taxtastic.egg-info/PKG-INFO 2025-06-11T13:14:00,275 writing dependency_links to taxtastic.egg-info/dependency_links.txt 2025-06-11T13:14:00,276 writing entry points to taxtastic.egg-info/entry_points.txt 2025-06-11T13:14:00,278 writing requirements to taxtastic.egg-info/requires.txt 2025-06-11T13:14:00,279 writing top-level names to taxtastic.egg-info/top_level.txt 2025-06-11T13:14:00,313 reading manifest file 'taxtastic.egg-info/SOURCES.txt' 2025-06-11T13:14:00,323 reading manifest template 'MANIFEST.in' 2025-06-11T13:14:00,338 warning: manifest_maker: MANIFEST.in, line 6: 'recursive-exclude' expects ... 2025-06-11T13:14:00,340 warning: no previously-included files matching '*/__pycache__/*' found anywhere in distribution 2025-06-11T13:14:00,340 warning: no previously-included files found matching 'Dockerfile' 2025-06-11T13:14:00,341 warning: no previously-included files found matching 'tests' 2025-06-11T13:14:00,342 warning: manifest_maker: MANIFEST.in, line 11: 'recursive-exclude' expects ... 2025-06-11T13:14:00,343 adding license file 'LICENSE' 2025-06-11T13:14:00,349 writing manifest file 'taxtastic.egg-info/SOURCES.txt' 2025-06-11T13:14:00,352 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'taxtastic.data' is absent from the `packages` configuration. 2025-06-11T13:14:00,352 !! 2025-06-11T13:14:00,354 ******************************************************************************** 2025-06-11T13:14:00,354 ############################ 2025-06-11T13:14:00,355 # Package would be ignored # 2025-06-11T13:14:00,356 ############################ 2025-06-11T13:14:00,356 Python recognizes 'taxtastic.data' as an importable package[^1], 2025-06-11T13:14:00,357 but it is absent from setuptools' `packages` configuration. 2025-06-11T13:14:00,358 This leads to an ambiguous overall configuration. If you want to distribute this 2025-06-11T13:14:00,359 package, please make sure that 'taxtastic.data' is explicitly added 2025-06-11T13:14:00,359 to the `packages` configuration field. 2025-06-11T13:14:00,360 Alternatively, you can also rely on setuptools' discovery methods 2025-06-11T13:14:00,361 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-06-11T13:14:00,362 instead of `find_packages(...)`/`find:`). 2025-06-11T13:14:00,363 You can read more about "package discovery" on setuptools documentation page: 2025-06-11T13:14:00,364 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-06-11T13:14:00,365 If you don't want 'taxtastic.data' to be distributed and are 2025-06-11T13:14:00,366 already explicitly excluding 'taxtastic.data' via 2025-06-11T13:14:00,367 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-06-11T13:14:00,367 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-06-11T13:14:00,368 combination with a more fine grained `package-data` configuration. 2025-06-11T13:14:00,369 You can read more about "package data files" on setuptools documentation page: 2025-06-11T13:14:00,370 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-06-11T13:14:00,371 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-06-11T13:14:00,372 even if it does not contain any `.py` files. 2025-06-11T13:14:00,372 On the other hand, currently there is no concept of package data 2025-06-11T13:14:00,373 directory, all directories are treated like packages. 2025-06-11T13:14:00,373 ******************************************************************************** 2025-06-11T13:14:00,374 !! 2025-06-11T13:14:00,375 check.warn(importable) 2025-06-11T13:14:00,375 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'taxtastic.templates' is absent from the `packages` configuration. 2025-06-11T13:14:00,376 !! 2025-06-11T13:14:00,377 ******************************************************************************** 2025-06-11T13:14:00,378 ############################ 2025-06-11T13:14:00,378 # Package would be ignored # 2025-06-11T13:14:00,379 ############################ 2025-06-11T13:14:00,380 Python recognizes 'taxtastic.templates' as an importable package[^1], 2025-06-11T13:14:00,380 but it is absent from setuptools' `packages` configuration. 2025-06-11T13:14:00,382 This leads to an ambiguous overall configuration. If you want to distribute this 2025-06-11T13:14:00,382 package, please make sure that 'taxtastic.templates' is explicitly added 2025-06-11T13:14:00,383 to the `packages` configuration field. 2025-06-11T13:14:00,384 Alternatively, you can also rely on setuptools' discovery methods 2025-06-11T13:14:00,385 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-06-11T13:14:00,385 instead of `find_packages(...)`/`find:`). 2025-06-11T13:14:00,387 You can read more about "package discovery" on setuptools documentation page: 2025-06-11T13:14:00,388 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-06-11T13:14:00,389 If you don't want 'taxtastic.templates' to be distributed and are 2025-06-11T13:14:00,390 already explicitly excluding 'taxtastic.templates' via 2025-06-11T13:14:00,391 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-06-11T13:14:00,391 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-06-11T13:14:00,392 combination with a more fine grained `package-data` configuration. 2025-06-11T13:14:00,393 You can read more about "package data files" on setuptools documentation page: 2025-06-11T13:14:00,395 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-06-11T13:14:00,397 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-06-11T13:14:00,397 even if it does not contain any `.py` files. 2025-06-11T13:14:00,398 On the other hand, currently there is no concept of package data 2025-06-11T13:14:00,399 directory, all directories are treated like packages. 2025-06-11T13:14:00,399 ******************************************************************************** 2025-06-11T13:14:00,401 !! 2025-06-11T13:14:00,401 check.warn(importable) 2025-06-11T13:14:00,402 creating build/lib/taxtastic/data 2025-06-11T13:14:00,403 copying taxtastic/data/ver -> build/lib/taxtastic/data 2025-06-11T13:14:00,404 creating build/lib/taxtastic/templates 2025-06-11T13:14:00,404 copying taxtastic/templates/add_pg_constraints.sql -> build/lib/taxtastic/templates 2025-06-11T13:14:00,405 copying taxtastic/templates/add_pg_indexes.sql -> build/lib/taxtastic/templates 2025-06-11T13:14:00,405 copying taxtastic/templates/drop_pg_constraints.sql -> build/lib/taxtastic/templates 2025-06-11T13:14:00,406 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-06-11T13:14:00,407 !! 2025-06-11T13:14:00,408 ******************************************************************************** 2025-06-11T13:14:00,408 Please avoid running ``setup.py`` directly. 2025-06-11T13:14:00,409 Instead, use pypa/build, pypa/installer or other 2025-06-11T13:14:00,409 standards-based tools. 2025-06-11T13:14:00,410 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-06-11T13:14:00,411 or your builds will no longer be supported. 2025-06-11T13:14:00,412 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-06-11T13:14:00,413 ******************************************************************************** 2025-06-11T13:14:00,414 !! 2025-06-11T13:14:00,414 self.initialize_options() 2025-06-11T13:14:00,434 installing to build/bdist.linux-armv7l/wheel 2025-06-11T13:14:00,435 running install 2025-06-11T13:14:00,458 running install_lib 2025-06-11T13:14:00,486 creating build/bdist.linux-armv7l/wheel 2025-06-11T13:14:00,488 creating build/bdist.linux-armv7l/wheel/taxtastic 2025-06-11T13:14:00,490 copying build/lib/taxtastic/lonely.py -> build/bdist.linux-armv7l/wheel/./taxtastic 2025-06-11T13:14:00,492 creating build/bdist.linux-armv7l/wheel/taxtastic/data 2025-06-11T13:14:00,494 copying build/lib/taxtastic/data/ver -> build/bdist.linux-armv7l/wheel/./taxtastic/data 2025-06-11T13:14:00,496 copying build/lib/taxtastic/taxtable.py -> build/bdist.linux-armv7l/wheel/./taxtastic 2025-06-11T13:14:00,498 copying build/lib/taxtastic/ncbi.py -> build/bdist.linux-armv7l/wheel/./taxtastic 2025-06-11T13:14:00,501 copying build/lib/taxtastic/taxonomy.py -> build/bdist.linux-armv7l/wheel/./taxtastic 2025-06-11T13:14:00,504 creating build/bdist.linux-armv7l/wheel/taxtastic/subcommands 2025-06-11T13:14:00,506 copying build/lib/taxtastic/subcommands/lineage_table.py -> build/bdist.linux-armv7l/wheel/./taxtastic/subcommands 2025-06-11T13:14:00,508 copying build/lib/taxtastic/subcommands/taxtable.py -> build/bdist.linux-armv7l/wheel/./taxtastic/subcommands 2025-06-11T13:14:00,510 copying build/lib/taxtastic/subcommands/rollback.py -> build/bdist.linux-armv7l/wheel/./taxtastic/subcommands 2025-06-11T13:14:00,513 copying build/lib/taxtastic/subcommands/extract_nodes.py -> build/bdist.linux-armv7l/wheel/./taxtastic/subcommands 2025-06-11T13:14:00,515 copying build/lib/taxtastic/subcommands/findcompany.py -> build/bdist.linux-armv7l/wheel/./taxtastic/subcommands 2025-06-11T13:14:00,517 copying build/lib/taxtastic/subcommands/strip.py -> build/bdist.linux-armv7l/wheel/./taxtastic/subcommands 2025-06-11T13:14:00,519 copying build/lib/taxtastic/subcommands/update.py -> build/bdist.linux-armv7l/wheel/./taxtastic/subcommands 2025-06-11T13:14:00,522 copying build/lib/taxtastic/subcommands/namelookup.py -> build/bdist.linux-armv7l/wheel/./taxtastic/subcommands 2025-06-11T13:14:00,524 copying build/lib/taxtastic/subcommands/refpkg_intersection.py -> build/bdist.linux-armv7l/wheel/./taxtastic/subcommands 2025-06-11T13:14:00,526 copying build/lib/taxtastic/subcommands/check.py -> build/bdist.linux-armv7l/wheel/./taxtastic/subcommands 2025-06-11T13:14:00,528 copying build/lib/taxtastic/subcommands/add_nodes.py -> build/bdist.linux-armv7l/wheel/./taxtastic/subcommands 2025-06-11T13:14:00,530 copying build/lib/taxtastic/subcommands/composition.py -> build/bdist.linux-armv7l/wheel/./taxtastic/subcommands 2025-06-11T13:14:00,532 copying build/lib/taxtastic/subcommands/lonelynodes.py -> build/bdist.linux-armv7l/wheel/./taxtastic/subcommands 2025-06-11T13:14:00,534 copying build/lib/taxtastic/subcommands/named.py -> build/bdist.linux-armv7l/wheel/./taxtastic/subcommands 2025-06-11T13:14:00,536 copying build/lib/taxtastic/subcommands/new_database.py -> build/bdist.linux-armv7l/wheel/./taxtastic/subcommands 2025-06-11T13:14:00,538 copying build/lib/taxtastic/subcommands/add_to_taxtable.py -> build/bdist.linux-armv7l/wheel/./taxtastic/subcommands 2025-06-11T13:14:00,541 copying build/lib/taxtastic/subcommands/rp.py -> build/bdist.linux-armv7l/wheel/./taxtastic/subcommands 2025-06-11T13:14:00,543 copying build/lib/taxtastic/subcommands/__init__.py -> build/bdist.linux-armv7l/wheel/./taxtastic/subcommands 2025-06-11T13:14:00,545 copying build/lib/taxtastic/subcommands/update_taxids.py -> build/bdist.linux-armv7l/wheel/./taxtastic/subcommands 2025-06-11T13:14:00,547 copying build/lib/taxtastic/subcommands/taxids.py -> build/bdist.linux-armv7l/wheel/./taxtastic/subcommands 2025-06-11T13:14:00,549 copying build/lib/taxtastic/subcommands/info.py -> build/bdist.linux-armv7l/wheel/./taxtastic/subcommands 2025-06-11T13:14:00,551 copying build/lib/taxtastic/subcommands/create.py -> build/bdist.linux-armv7l/wheel/./taxtastic/subcommands 2025-06-11T13:14:00,554 copying build/lib/taxtastic/subcommands/reroot.py -> build/bdist.linux-armv7l/wheel/./taxtastic/subcommands 2025-06-11T13:14:00,556 copying build/lib/taxtastic/subcommands/get_descendants.py -> build/bdist.linux-armv7l/wheel/./taxtastic/subcommands 2025-06-11T13:14:00,557 copying build/lib/taxtastic/subcommands/get_lineage.py -> build/bdist.linux-armv7l/wheel/./taxtastic/subcommands 2025-06-11T13:14:00,559 copying build/lib/taxtastic/subcommands/rollforward.py -> build/bdist.linux-armv7l/wheel/./taxtastic/subcommands 2025-06-11T13:14:00,562 creating build/bdist.linux-armv7l/wheel/taxtastic/scripts 2025-06-11T13:14:00,563 copying build/lib/taxtastic/scripts/__init__.py -> build/bdist.linux-armv7l/wheel/./taxtastic/scripts 2025-06-11T13:14:00,564 copying build/lib/taxtastic/scripts/taxit.py -> build/bdist.linux-armv7l/wheel/./taxtastic/scripts 2025-06-11T13:14:00,567 copying build/lib/taxtastic/taxdb.py -> build/bdist.linux-armv7l/wheel/./taxtastic 2025-06-11T13:14:00,569 copying build/lib/taxtastic/utils.py -> build/bdist.linux-armv7l/wheel/./taxtastic 2025-06-11T13:14:00,571 copying build/lib/taxtastic/__init__.py -> build/bdist.linux-armv7l/wheel/./taxtastic 2025-06-11T13:14:00,574 creating build/bdist.linux-armv7l/wheel/taxtastic/templates 2025-06-11T13:14:00,575 copying build/lib/taxtastic/templates/add_pg_indexes.sql -> build/bdist.linux-armv7l/wheel/./taxtastic/templates 2025-06-11T13:14:00,577 copying build/lib/taxtastic/templates/add_pg_constraints.sql -> build/bdist.linux-armv7l/wheel/./taxtastic/templates 2025-06-11T13:14:00,578 copying build/lib/taxtastic/templates/drop_pg_constraints.sql -> build/bdist.linux-armv7l/wheel/./taxtastic/templates 2025-06-11T13:14:00,580 copying build/lib/taxtastic/refpkg.py -> build/bdist.linux-armv7l/wheel/./taxtastic 2025-06-11T13:14:00,583 running install_egg_info 2025-06-11T13:14:00,618 Copying taxtastic.egg-info to build/bdist.linux-armv7l/wheel/./taxtastic-0.12.0-py3.11.egg-info 2025-06-11T13:14:00,632 running install_scripts 2025-06-11T13:14:00,647 creating build/bdist.linux-armv7l/wheel/taxtastic-0.12.0.dist-info/WHEEL 2025-06-11T13:14:00,649 creating '/tmp/pip-wheel-_rub37no/taxtastic-0.12.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-06-11T13:14:00,652 adding 'taxtastic/__init__.py' 2025-06-11T13:14:00,653 adding 'taxtastic/lonely.py' 2025-06-11T13:14:00,656 adding 'taxtastic/ncbi.py' 2025-06-11T13:14:00,661 adding 'taxtastic/refpkg.py' 2025-06-11T13:14:00,663 adding 'taxtastic/taxdb.py' 2025-06-11T13:14:00,667 adding 'taxtastic/taxonomy.py' 2025-06-11T13:14:00,669 adding 'taxtastic/taxtable.py' 2025-06-11T13:14:00,671 adding 'taxtastic/utils.py' 2025-06-11T13:14:00,673 adding 'taxtastic/data/ver' 2025-06-11T13:14:00,675 adding 'taxtastic/scripts/__init__.py' 2025-06-11T13:14:00,676 adding 'taxtastic/scripts/taxit.py' 2025-06-11T13:14:00,678 adding 'taxtastic/subcommands/__init__.py' 2025-06-11T13:14:00,680 adding 'taxtastic/subcommands/add_nodes.py' 2025-06-11T13:14:00,681 adding 'taxtastic/subcommands/add_to_taxtable.py' 2025-06-11T13:14:00,682 adding 'taxtastic/subcommands/check.py' 2025-06-11T13:14:00,684 adding 'taxtastic/subcommands/composition.py' 2025-06-11T13:14:00,685 adding 'taxtastic/subcommands/create.py' 2025-06-11T13:14:00,686 adding 'taxtastic/subcommands/extract_nodes.py' 2025-06-11T13:14:00,688 adding 'taxtastic/subcommands/findcompany.py' 2025-06-11T13:14:00,689 adding 'taxtastic/subcommands/get_descendants.py' 2025-06-11T13:14:00,690 adding 'taxtastic/subcommands/get_lineage.py' 2025-06-11T13:14:00,692 adding 'taxtastic/subcommands/info.py' 2025-06-11T13:14:00,693 adding 'taxtastic/subcommands/lineage_table.py' 2025-06-11T13:14:00,695 adding 'taxtastic/subcommands/lonelynodes.py' 2025-06-11T13:14:00,696 adding 'taxtastic/subcommands/named.py' 2025-06-11T13:14:00,698 adding 'taxtastic/subcommands/namelookup.py' 2025-06-11T13:14:00,699 adding 'taxtastic/subcommands/new_database.py' 2025-06-11T13:14:00,701 adding 'taxtastic/subcommands/refpkg_intersection.py' 2025-06-11T13:14:00,702 adding 'taxtastic/subcommands/reroot.py' 2025-06-11T13:14:00,703 adding 'taxtastic/subcommands/rollback.py' 2025-06-11T13:14:00,705 adding 'taxtastic/subcommands/rollforward.py' 2025-06-11T13:14:00,706 adding 'taxtastic/subcommands/rp.py' 2025-06-11T13:14:00,707 adding 'taxtastic/subcommands/strip.py' 2025-06-11T13:14:00,709 adding 'taxtastic/subcommands/taxids.py' 2025-06-11T13:14:00,710 adding 'taxtastic/subcommands/taxtable.py' 2025-06-11T13:14:00,712 adding 'taxtastic/subcommands/update.py' 2025-06-11T13:14:00,713 adding 'taxtastic/subcommands/update_taxids.py' 2025-06-11T13:14:00,715 adding 'taxtastic/templates/add_pg_constraints.sql' 2025-06-11T13:14:00,716 adding 'taxtastic/templates/add_pg_indexes.sql' 2025-06-11T13:14:00,718 adding 'taxtastic/templates/drop_pg_constraints.sql' 2025-06-11T13:14:00,725 adding 'taxtastic-0.12.0.dist-info/licenses/LICENSE' 2025-06-11T13:14:00,727 adding 'taxtastic-0.12.0.dist-info/METADATA' 2025-06-11T13:14:00,728 adding 'taxtastic-0.12.0.dist-info/WHEEL' 2025-06-11T13:14:00,729 adding 'taxtastic-0.12.0.dist-info/entry_points.txt' 2025-06-11T13:14:00,730 adding 'taxtastic-0.12.0.dist-info/top_level.txt' 2025-06-11T13:14:00,731 adding 'taxtastic-0.12.0.dist-info/RECORD' 2025-06-11T13:14:00,734 removing build/bdist.linux-armv7l/wheel 2025-06-11T13:14:00,864 Building wheel for taxtastic (setup.py): finished with status 'done' 2025-06-11T13:14:00,867 Created wheel for taxtastic: filename=taxtastic-0.12.0-py3-none-any.whl size=94304 sha256=25bcf561d27cd5388842a80c62b626f997f3fffa44325ce5fa30c3b2089d8583 2025-06-11T13:14:00,869 Stored in directory: /tmp/pip-ephem-wheel-cache-1m689b1_/wheels/45/5c/96/def5ff10755ccc6714f02c5f8a1759cd31fb0d2954f83052c8 2025-06-11T13:14:00,884 Successfully built taxtastic 2025-06-11T13:14:00,890 Removed build tracker: '/tmp/pip-build-tracker-2_43kbyu'