2025-08-31T18:17:54,170 Created temporary directory: /tmp/pip-build-tracker-zsh35a9j 2025-08-31T18:17:54,171 Initialized build tracking at /tmp/pip-build-tracker-zsh35a9j 2025-08-31T18:17:54,172 Created build tracker: /tmp/pip-build-tracker-zsh35a9j 2025-08-31T18:17:54,172 Entered build tracker: /tmp/pip-build-tracker-zsh35a9j 2025-08-31T18:17:54,173 Created temporary directory: /tmp/pip-wheel-h0zxpwl6 2025-08-31T18:17:54,177 Created temporary directory: /tmp/pip-ephem-wheel-cache-2f0xkxkh 2025-08-31T18:17:54,232 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-08-31T18:17:54,234 2 location(s) to search for versions of clasv: 2025-08-31T18:17:54,234 * https://pypi.org/simple/clasv/ 2025-08-31T18:17:54,234 * https://www.piwheels.org/simple/clasv/ 2025-08-31T18:17:54,235 Fetching project page and analyzing links: https://pypi.org/simple/clasv/ 2025-08-31T18:17:54,236 Getting page https://pypi.org/simple/clasv/ 2025-08-31T18:17:54,238 Found index url https://pypi.org/simple/ 2025-08-31T18:17:54,391 Fetched page https://pypi.org/simple/clasv/ as application/vnd.pypi.simple.v1+json 2025-08-31T18:17:54,395 Skipping link: No binaries permitted for clasv: https://files.pythonhosted.org/packages/1a/16/db344cddef30afa227564b37850859df2be84ad92983a4e623cc6d22e358/CLASV-0.1.14-py3-none-any.whl (from https://pypi.org/simple/clasv/) (requires-python:>=3.6) 2025-08-31T18:17:54,397 Found link https://files.pythonhosted.org/packages/1f/ea/a546746ef065df29e7d448b541720187f00fb3d6313c131edfce2458dcfb/clasv-0.1.14.tar.gz (from https://pypi.org/simple/clasv/) (requires-python:>=3.6), version: 0.1.14 2025-08-31T18:17:54,397 Skipping link: No binaries permitted for clasv: https://files.pythonhosted.org/packages/01/a7/fb8fe230851b0d19d0c9df27bb7b096c9c7b0d25d999999213f7fb663bea/CLASV-0.1.15-py3-none-any.whl (from https://pypi.org/simple/clasv/) (requires-python:>=3.6) 2025-08-31T18:17:54,398 Found link https://files.pythonhosted.org/packages/04/88/bb8ba072c5ce1e54697cb4049212cf1520972dadbdb0af3e65bd0caf6307/clasv-0.1.15.tar.gz (from https://pypi.org/simple/clasv/) (requires-python:>=3.6), version: 0.1.15 2025-08-31T18:17:54,399 Skipping link: No binaries permitted for clasv: https://files.pythonhosted.org/packages/2f/01/e66257efeac8ad400c86e8f5041ff0b77719174c6cbbb2910eb7e3f04a7e/CLASV-0.1.16-py3-none-any.whl (from https://pypi.org/simple/clasv/) (requires-python:>=3.6) 2025-08-31T18:17:54,399 Found link https://files.pythonhosted.org/packages/f3/ee/d74f763c762dc4eb56f3f4ac5e6fbde566c9d391e6156bfaabce4cc769ed/clasv-0.1.16.tar.gz (from https://pypi.org/simple/clasv/) (requires-python:>=3.6), version: 0.1.16 2025-08-31T18:17:54,400 Skipping link: No binaries permitted for clasv: https://files.pythonhosted.org/packages/d5/e2/e4c26b7e5bdb7b5cf384a243b22a93158d9636b0f9c13e7bf47121d889cf/clasv-1.0.0-py3-none-any.whl (from https://pypi.org/simple/clasv/) (requires-python:>=3.6) 2025-08-31T18:17:54,401 Found link https://files.pythonhosted.org/packages/25/01/75fa1aecd6564f60afab17af9d5847f73575d1c15c7ada4f4619a1b6c14c/clasv-1.0.0.tar.gz (from https://pypi.org/simple/clasv/) (requires-python:>=3.6), version: 1.0.0 2025-08-31T18:17:54,402 Skipping link: No binaries permitted for clasv: https://files.pythonhosted.org/packages/6f/01/71b5679f21f1605748c639f9e46ed4a65deac4073500ac0600e8371e44c3/clasv-1.0.1-py3-none-any.whl (from https://pypi.org/simple/clasv/) (requires-python:>=3.6) 2025-08-31T18:17:54,402 Found link https://files.pythonhosted.org/packages/8b/8a/0c047f0e3d0ddd5747387676aaa40d63c12b3bb76faddaf031d70ed7060d/clasv-1.0.1.tar.gz (from https://pypi.org/simple/clasv/) (requires-python:>=3.6), version: 1.0.1 2025-08-31T18:17:54,403 Skipping link: No binaries permitted for clasv: https://files.pythonhosted.org/packages/ae/db/d58479423cbcd8bfc12fd34b84f8e98911e6e5585b5be6e7ad9139295b29/clasv-1.0.2-py3-none-any.whl (from https://pypi.org/simple/clasv/) (requires-python:>=3.6) 2025-08-31T18:17:54,404 Found link https://files.pythonhosted.org/packages/d8/8b/fa027f178c8e86e464814497c55bb250f9e751d5281ae8d0f8b628c53c21/clasv-1.0.2.tar.gz (from https://pypi.org/simple/clasv/) (requires-python:>=3.6), version: 1.0.2 2025-08-31T18:17:54,405 Skipping link: No binaries permitted for clasv: https://files.pythonhosted.org/packages/eb/a5/b50674274289535cc79168e5ad0afb33d639d23381a8bc5d6e5e6d17a977/clasv-1.0.4-py3-none-any.whl (from https://pypi.org/simple/clasv/) (requires-python:<3.14,>=3.7) 2025-08-31T18:17:54,406 Found link https://files.pythonhosted.org/packages/d4/f4/4a24334f0238c96ad88300acf9f8f037ae20e612ee75d4c6efd241c10a2c/clasv-1.0.4.tar.gz (from https://pypi.org/simple/clasv/) (requires-python:<3.14,>=3.7), version: 1.0.4 2025-08-31T18:17:54,407 Skipping link: No binaries permitted for clasv: https://files.pythonhosted.org/packages/b4/ac/a546b70abb941263c6a1429ab67608fb4de2e84df444ef2c1c1ff430b98a/clasv-1.0.5-py3-none-any.whl (from https://pypi.org/simple/clasv/) (requires-python:<3.14,>=3.7) 2025-08-31T18:17:54,408 Found link https://files.pythonhosted.org/packages/de/b0/ce608a6857fc6753be849706d938c7252569ac46235997cb33b83cdcff18/clasv-1.0.5.tar.gz (from https://pypi.org/simple/clasv/) (requires-python:<3.14,>=3.7), version: 1.0.5 2025-08-31T18:17:54,408 Skipping link: No binaries permitted for clasv: https://files.pythonhosted.org/packages/a2/4b/20f591f8c5794b8aa5e7cb969237227e4d5f8a0fd3317eb24ec8d9846a25/clasv-1.0.6-py3-none-any.whl (from https://pypi.org/simple/clasv/) (requires-python:<3.14,>=3.7) 2025-08-31T18:17:54,409 Found link https://files.pythonhosted.org/packages/26/da/92a0b688197a1d762ced46693a7ec80d8de0d4406f04a083bac4176b452b/clasv-1.0.6.tar.gz (from https://pypi.org/simple/clasv/) (requires-python:<3.14,>=3.7), version: 1.0.6 2025-08-31T18:17:54,410 Fetching project page and analyzing links: https://www.piwheels.org/simple/clasv/ 2025-08-31T18:17:54,411 Getting page https://www.piwheels.org/simple/clasv/ 2025-08-31T18:17:54,412 Found index url https://www.piwheels.org/simple/ 2025-08-31T18:17:54,584 Fetched page https://www.piwheels.org/simple/clasv/ as text/html 2025-08-31T18:17:54,588 Skipping link: No binaries permitted for clasv: https://www.piwheels.org/simple/clasv/clasv-1.0.4-py3-none-any.whl#sha256=03db5788c67d9f72aae0d57f4608cf4481b337adf8087a0d69e8de2449863da6 (from https://www.piwheels.org/simple/clasv/) (requires-python:>=3.7,<3.14) 2025-08-31T18:17:54,588 Skipping link: No binaries permitted for clasv: https://archive1.piwheels.org/simple/clasv/clasv-1.0.1-py3-none-any.whl#sha256=e9390e4b39429a31e3b2ee578bb0e1342144a82b447a3601b3e16b3e7bf89380 (from https://www.piwheels.org/simple/clasv/) (requires-python:>=3.6) 2025-08-31T18:17:54,589 Skipping link: No binaries permitted for clasv: https://archive1.piwheels.org/simple/clasv/clasv-1.0.0-py3-none-any.whl#sha256=57259d69e3ed26589c32ec59cad8baf578af19cc69c1743475c5814f0cc3164e (from https://www.piwheels.org/simple/clasv/) (requires-python:>=3.6) 2025-08-31T18:17:54,590 Skipping link: No binaries permitted for clasv: https://archive1.piwheels.org/simple/clasv/CLASV-0.1.16-py3-none-any.whl#sha256=da2929fcce2e7f68ca008ca3afe547bb1bca0da33b6d3b5f31dc93559d323c2f (from https://www.piwheels.org/simple/clasv/) (requires-python:>=3.6) 2025-08-31T18:17:54,590 Skipping link: No binaries permitted for clasv: https://archive1.piwheels.org/simple/clasv/CLASV-0.1.15-py3-none-any.whl#sha256=e0e432f07cc0268e603ea2fc23ee116450d1514e6a74a467526a515fd1ed177d (from https://www.piwheels.org/simple/clasv/) (requires-python:>=3.6) 2025-08-31T18:17:54,591 Skipping link: No binaries permitted for clasv: https://archive1.piwheels.org/simple/clasv/CLASV-0.1.14-py3-none-any.whl#sha256=df7ac2bc8947ae60805237e722746c632985fb9714d7ad952d4b300baed27f86 (from https://www.piwheels.org/simple/clasv/) (requires-python:>=3.6) 2025-08-31T18:17:54,592 Skipping link: not a file: https://www.piwheels.org/simple/clasv/ 2025-08-31T18:17:54,592 Skipping link: not a file: https://pypi.org/simple/clasv/ 2025-08-31T18:17:54,613 Given no hashes to check 1 links for project 'clasv': discarding no candidates 2025-08-31T18:17:54,615 Collecting clasv==1.0.6 2025-08-31T18:17:54,618 Created temporary directory: /tmp/pip-unpack-g_h9vi_j 2025-08-31T18:17:54,858 Downloading clasv-1.0.6.tar.gz (2.3 MB) 2025-08-31T18:17:55,772 Added clasv==1.0.6 from https://files.pythonhosted.org/packages/26/da/92a0b688197a1d762ced46693a7ec80d8de0d4406f04a083bac4176b452b/clasv-1.0.6.tar.gz to build tracker '/tmp/pip-build-tracker-zsh35a9j' 2025-08-31T18:17:55,775 Running setup.py (path:/tmp/pip-wheel-h0zxpwl6/clasv_2e65e58447b94845a8e6431565743677/setup.py) egg_info for package clasv 2025-08-31T18:17:55,776 Created temporary directory: /tmp/pip-pip-egg-info-k99dzb11 2025-08-31T18:17:55,776 Preparing metadata (setup.py): started 2025-08-31T18:17:55,778 Running command python setup.py egg_info 2025-08-31T18:17:56,686 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-08-31T18:17:56,686 !! 2025-08-31T18:17:56,687 ******************************************************************************** 2025-08-31T18:17:56,688 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-08-31T18:17:56,688 License :: OSI Approved :: MIT License 2025-08-31T18:17:56,690 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-08-31T18:17:56,690 ******************************************************************************** 2025-08-31T18:17:56,691 !! 2025-08-31T18:17:56,692 self._finalize_license_expression() 2025-08-31T18:17:56,716 Running setup... 2025-08-31T18:17:56,717 running egg_info 2025-08-31T18:17:56,743 creating /tmp/pip-pip-egg-info-k99dzb11/CLASV.egg-info 2025-08-31T18:17:56,744 writing /tmp/pip-pip-egg-info-k99dzb11/CLASV.egg-info/PKG-INFO 2025-08-31T18:17:56,750 writing dependency_links to /tmp/pip-pip-egg-info-k99dzb11/CLASV.egg-info/dependency_links.txt 2025-08-31T18:17:56,751 writing entry points to /tmp/pip-pip-egg-info-k99dzb11/CLASV.egg-info/entry_points.txt 2025-08-31T18:17:56,769 writing requirements to /tmp/pip-pip-egg-info-k99dzb11/CLASV.egg-info/requires.txt 2025-08-31T18:17:56,771 writing top-level names to /tmp/pip-pip-egg-info-k99dzb11/CLASV.egg-info/top_level.txt 2025-08-31T18:17:56,772 writing manifest file '/tmp/pip-pip-egg-info-k99dzb11/CLASV.egg-info/SOURCES.txt' 2025-08-31T18:17:56,867 reading manifest file '/tmp/pip-pip-egg-info-k99dzb11/CLASV.egg-info/SOURCES.txt' 2025-08-31T18:17:56,869 reading manifest template 'MANIFEST.in' 2025-08-31T18:17:56,982 warning: no files found matching 'config' under directory 'CLASV' 2025-08-31T18:17:57,054 warning: no files found matching 'predictions' under directory 'CLASV' 2025-08-31T18:17:57,120 warning: no files found matching 'raw_data' under directory 'CLASV' 2025-08-31T18:17:57,162 warning: no files found matching 'results' under directory 'CLASV' 2025-08-31T18:17:57,206 warning: no files found matching 'visuals' under directory 'CLASV' 2025-08-31T18:17:57,233 adding license file 'LICENSE' 2025-08-31T18:17:57,244 writing manifest file '/tmp/pip-pip-egg-info-k99dzb11/CLASV.egg-info/SOURCES.txt' 2025-08-31T18:17:57,353 Preparing metadata (setup.py): finished with status 'done' 2025-08-31T18:17:57,359 Source in /tmp/pip-wheel-h0zxpwl6/clasv_2e65e58447b94845a8e6431565743677 has version 1.0.6, which satisfies requirement clasv==1.0.6 from https://files.pythonhosted.org/packages/26/da/92a0b688197a1d762ced46693a7ec80d8de0d4406f04a083bac4176b452b/clasv-1.0.6.tar.gz 2025-08-31T18:17:57,359 Removed clasv==1.0.6 from https://files.pythonhosted.org/packages/26/da/92a0b688197a1d762ced46693a7ec80d8de0d4406f04a083bac4176b452b/clasv-1.0.6.tar.gz from build tracker '/tmp/pip-build-tracker-zsh35a9j' 2025-08-31T18:17:57,392 Created temporary directory: /tmp/pip-unpack-nt2cbbne 2025-08-31T18:17:57,394 Created temporary directory: /tmp/pip-unpack-fgftm117 2025-08-31T18:17:57,394 Building wheels for collected packages: clasv 2025-08-31T18:17:57,398 Created temporary directory: /tmp/pip-wheel-9zt5ytuj 2025-08-31T18:17:57,399 DEPRECATION: Building 'clasv' 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 'clasv'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2025-08-31T18:17:57,400 Building wheel for clasv (setup.py): started 2025-08-31T18:17:57,401 Destination directory: /tmp/pip-wheel-9zt5ytuj 2025-08-31T18:17:57,402 Running command python setup.py bdist_wheel 2025-08-31T18:17:57,883 Running setup... 2025-08-31T18:17:58,311 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-08-31T18:17:58,311 !! 2025-08-31T18:17:58,312 ******************************************************************************** 2025-08-31T18:17:58,313 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-08-31T18:17:58,314 License :: OSI Approved :: MIT License 2025-08-31T18:17:58,315 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-08-31T18:17:58,316 ******************************************************************************** 2025-08-31T18:17:58,317 !! 2025-08-31T18:17:58,317 self._finalize_license_expression() 2025-08-31T18:17:58,318 running bdist_wheel 2025-08-31T18:17:58,451 running build 2025-08-31T18:17:58,452 running build_py 2025-08-31T18:17:58,484 creating build/lib/CLASV 2025-08-31T18:17:58,486 copying CLASV/install_nextclade.py -> build/lib/CLASV 2025-08-31T18:17:58,488 copying CLASV/__init__.py -> build/lib/CLASV 2025-08-31T18:17:58,490 copying CLASV/pipeline.py -> build/lib/CLASV 2025-08-31T18:17:58,493 copying CLASV/install_seqkit.py -> build/lib/CLASV 2025-08-31T18:17:58,495 copying CLASV/cli.py -> build/lib/CLASV 2025-08-31T18:17:58,497 copying CLASV/benchmark_clasv.py -> build/lib/CLASV 2025-08-31T18:17:58,499 copying CLASV/setup.py -> build/lib/CLASV 2025-08-31T18:17:58,502 copying CLASV/core.py -> build/lib/CLASV 2025-08-31T18:17:58,505 creating build/lib/CLASV/tools 2025-08-31T18:17:58,506 copying CLASV/tools/__init__.py -> build/lib/CLASV/tools 2025-08-31T18:17:58,508 copying CLASV/tools/benchmark_clasv.py -> build/lib/CLASV/tools 2025-08-31T18:17:58,510 running egg_info 2025-08-31T18:17:58,542 writing CLASV.egg-info/PKG-INFO 2025-08-31T18:17:58,547 writing dependency_links to CLASV.egg-info/dependency_links.txt 2025-08-31T18:17:58,548 writing entry points to CLASV.egg-info/entry_points.txt 2025-08-31T18:17:58,567 writing requirements to CLASV.egg-info/requires.txt 2025-08-31T18:17:58,569 writing top-level names to CLASV.egg-info/top_level.txt 2025-08-31T18:17:58,608 reading manifest file 'CLASV.egg-info/SOURCES.txt' 2025-08-31T18:17:58,615 reading manifest template 'MANIFEST.in' 2025-08-31T18:17:58,708 warning: no files found matching 'config' under directory 'CLASV' 2025-08-31T18:17:58,753 warning: no files found matching 'predictions' under directory 'CLASV' 2025-08-31T18:17:58,797 warning: no files found matching 'raw_data' under directory 'CLASV' 2025-08-31T18:17:58,843 warning: no files found matching 'results' under directory 'CLASV' 2025-08-31T18:17:58,887 warning: no files found matching 'visuals' under directory 'CLASV' 2025-08-31T18:17:58,914 adding license file 'LICENSE' 2025-08-31T18:17:58,926 writing manifest file 'CLASV.egg-info/SOURCES.txt' 2025-08-31T18:17:58,929 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'CLASV.__pycache__' is absent from the `packages` configuration. 2025-08-31T18:17:58,930 !! 2025-08-31T18:17:58,931 ******************************************************************************** 2025-08-31T18:17:58,932 ############################ 2025-08-31T18:17:58,932 # Package would be ignored # 2025-08-31T18:17:58,933 ############################ 2025-08-31T18:17:58,934 Python recognizes 'CLASV.__pycache__' as an importable package[^1], 2025-08-31T18:17:58,934 but it is absent from setuptools' `packages` configuration. 2025-08-31T18:17:58,935 This leads to an ambiguous overall configuration. If you want to distribute this 2025-08-31T18:17:58,935 package, please make sure that 'CLASV.__pycache__' is explicitly added 2025-08-31T18:17:58,936 to the `packages` configuration field. 2025-08-31T18:17:58,936 Alternatively, you can also rely on setuptools' discovery methods 2025-08-31T18:17:58,937 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-08-31T18:17:58,937 instead of `find_packages(...)`/`find:`). 2025-08-31T18:17:58,938 You can read more about "package discovery" on setuptools documentation page: 2025-08-31T18:17:58,939 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-08-31T18:17:58,940 If you don't want 'CLASV.__pycache__' to be distributed and are 2025-08-31T18:17:58,940 already explicitly excluding 'CLASV.__pycache__' via 2025-08-31T18:17:58,941 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-08-31T18:17:58,941 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-08-31T18:17:58,942 combination with a more fine grained `package-data` configuration. 2025-08-31T18:17:58,943 You can read more about "package data files" on setuptools documentation page: 2025-08-31T18:17:58,944 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-08-31T18:17:58,945 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-08-31T18:17:58,946 even if it does not contain any `.py` files. 2025-08-31T18:17:58,946 On the other hand, currently there is no concept of package data 2025-08-31T18:17:58,947 directory, all directories are treated like packages. 2025-08-31T18:17:58,948 ******************************************************************************** 2025-08-31T18:17:58,949 !! 2025-08-31T18:17:58,949 check.warn(importable) 2025-08-31T18:17:58,950 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'CLASV.config' is absent from the `packages` configuration. 2025-08-31T18:17:58,950 !! 2025-08-31T18:17:58,951 ******************************************************************************** 2025-08-31T18:17:58,952 ############################ 2025-08-31T18:17:58,952 # Package would be ignored # 2025-08-31T18:17:58,953 ############################ 2025-08-31T18:17:58,953 Python recognizes 'CLASV.config' as an importable package[^1], 2025-08-31T18:17:58,954 but it is absent from setuptools' `packages` configuration. 2025-08-31T18:17:58,955 This leads to an ambiguous overall configuration. If you want to distribute this 2025-08-31T18:17:58,956 package, please make sure that 'CLASV.config' is explicitly added 2025-08-31T18:17:58,956 to the `packages` configuration field. 2025-08-31T18:17:58,957 Alternatively, you can also rely on setuptools' discovery methods 2025-08-31T18:17:58,958 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-08-31T18:17:58,959 instead of `find_packages(...)`/`find:`). 2025-08-31T18:17:58,963 You can read more about "package discovery" on setuptools documentation page: 2025-08-31T18:17:58,964 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-08-31T18:17:58,965 If you don't want 'CLASV.config' to be distributed and are 2025-08-31T18:17:58,966 already explicitly excluding 'CLASV.config' via 2025-08-31T18:17:58,967 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-08-31T18:17:58,967 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-08-31T18:17:58,968 combination with a more fine grained `package-data` configuration. 2025-08-31T18:17:58,970 You can read more about "package data files" on setuptools documentation page: 2025-08-31T18:17:58,971 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-08-31T18:17:58,973 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-08-31T18:17:58,974 even if it does not contain any `.py` files. 2025-08-31T18:17:58,975 On the other hand, currently there is no concept of package data 2025-08-31T18:17:58,976 directory, all directories are treated like packages. 2025-08-31T18:17:58,976 ******************************************************************************** 2025-08-31T18:17:58,977 !! 2025-08-31T18:17:58,978 check.warn(importable) 2025-08-31T18:17:58,978 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'CLASV.raw_data' is absent from the `packages` configuration. 2025-08-31T18:17:58,979 !! 2025-08-31T18:17:58,980 ******************************************************************************** 2025-08-31T18:17:58,981 ############################ 2025-08-31T18:17:58,981 # Package would be ignored # 2025-08-31T18:17:58,982 ############################ 2025-08-31T18:17:58,983 Python recognizes 'CLASV.raw_data' as an importable package[^1], 2025-08-31T18:17:58,983 but it is absent from setuptools' `packages` configuration. 2025-08-31T18:17:58,984 This leads to an ambiguous overall configuration. If you want to distribute this 2025-08-31T18:17:58,985 package, please make sure that 'CLASV.raw_data' is explicitly added 2025-08-31T18:17:58,985 to the `packages` configuration field. 2025-08-31T18:17:58,987 Alternatively, you can also rely on setuptools' discovery methods 2025-08-31T18:17:58,987 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-08-31T18:17:58,988 instead of `find_packages(...)`/`find:`). 2025-08-31T18:17:58,989 You can read more about "package discovery" on setuptools documentation page: 2025-08-31T18:17:58,990 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-08-31T18:17:58,991 If you don't want 'CLASV.raw_data' to be distributed and are 2025-08-31T18:17:58,992 already explicitly excluding 'CLASV.raw_data' via 2025-08-31T18:17:58,992 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-08-31T18:17:58,993 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-08-31T18:17:58,993 combination with a more fine grained `package-data` configuration. 2025-08-31T18:17:58,994 You can read more about "package data files" on setuptools documentation page: 2025-08-31T18:17:58,995 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-08-31T18:17:58,997 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-08-31T18:17:58,997 even if it does not contain any `.py` files. 2025-08-31T18:17:58,998 On the other hand, currently there is no concept of package data 2025-08-31T18:17:58,998 directory, all directories are treated like packages. 2025-08-31T18:17:58,999 ******************************************************************************** 2025-08-31T18:17:59,000 !! 2025-08-31T18:17:59,000 check.warn(importable) 2025-08-31T18:17:59,001 copying CLASV/MANIFEST.in -> build/lib/CLASV 2025-08-31T18:17:59,001 copying CLASV/README.md -> build/lib/CLASV 2025-08-31T18:17:59,002 copying CLASV/VERSION -> build/lib/CLASV 2025-08-31T18:17:59,003 copying CLASV/predflow_updated.png -> build/lib/CLASV 2025-08-31T18:17:59,003 copying CLASV/predict_lineage.smk -> build/lib/CLASV 2025-08-31T18:17:59,004 copying CLASV/requirements.txt -> build/lib/CLASV 2025-08-31T18:17:59,004 creating build/lib/CLASV/CLASV.egg-info 2025-08-31T18:17:59,004 copying CLASV/CLASV.egg-info/PKG-INFO -> build/lib/CLASV/CLASV.egg-info 2025-08-31T18:17:59,005 copying CLASV/CLASV.egg-info/SOURCES.txt -> build/lib/CLASV/CLASV.egg-info 2025-08-31T18:17:59,005 copying CLASV/CLASV.egg-info/dependency_links.txt -> build/lib/CLASV/CLASV.egg-info 2025-08-31T18:17:59,006 copying CLASV/CLASV.egg-info/entry_points.txt -> build/lib/CLASV/CLASV.egg-info 2025-08-31T18:17:59,006 copying CLASV/CLASV.egg-info/requires.txt -> build/lib/CLASV/CLASV.egg-info 2025-08-31T18:17:59,006 copying CLASV/CLASV.egg-info/top_level.txt -> build/lib/CLASV/CLASV.egg-info 2025-08-31T18:17:59,007 creating build/lib/CLASV/__pycache__ 2025-08-31T18:17:59,007 copying CLASV/__pycache__/__init__.cpython-310.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:59,008 copying CLASV/__pycache__/__init__.cpython-311.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:59,008 copying CLASV/__pycache__/__init__.cpython-312.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:59,009 copying CLASV/__pycache__/__init__.cpython-313.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:59,009 copying CLASV/__pycache__/__init__.cpython-38.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:59,010 copying CLASV/__pycache__/__init__.cpython-39.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:59,012 copying CLASV/__pycache__/cli.cpython-310.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:59,015 copying CLASV/__pycache__/cli.cpython-311.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:59,018 copying CLASV/__pycache__/cli.cpython-312.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:59,020 copying CLASV/__pycache__/cli.cpython-313.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:59,023 copying CLASV/__pycache__/cli.cpython-38.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:59,026 copying CLASV/__pycache__/cli.cpython-39.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:59,028 copying CLASV/__pycache__/core.cpython-310.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:59,032 copying CLASV/__pycache__/core.cpython-311.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:59,035 copying CLASV/__pycache__/core.cpython-312.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:59,038 copying CLASV/__pycache__/core.cpython-313.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:59,041 copying CLASV/__pycache__/core.cpython-38.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:59,044 copying CLASV/__pycache__/core.cpython-39.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:59,047 copying CLASV/__pycache__/install_nextclade.cpython-310.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:59,049 copying CLASV/__pycache__/install_nextclade.cpython-311.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:59,053 copying CLASV/__pycache__/install_nextclade.cpython-312.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:59,056 copying CLASV/__pycache__/install_nextclade.cpython-313.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:59,059 copying CLASV/__pycache__/install_nextclade.cpython-38.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:59,062 copying CLASV/__pycache__/install_nextclade.cpython-39.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:59,065 copying CLASV/__pycache__/install_seqkit.cpython-310.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:59,068 copying CLASV/__pycache__/install_seqkit.cpython-311.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:59,071 copying CLASV/__pycache__/install_seqkit.cpython-312.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:59,074 copying CLASV/__pycache__/install_seqkit.cpython-313.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:59,077 copying CLASV/__pycache__/install_seqkit.cpython-38.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:59,080 copying CLASV/__pycache__/install_seqkit.cpython-39.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:59,082 copying CLASV/__pycache__/pipeline.cpython-310.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:59,085 copying CLASV/__pycache__/pipeline.cpython-311.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:59,088 copying CLASV/__pycache__/pipeline.cpython-312.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:59,090 copying CLASV/__pycache__/pipeline.cpython-313.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:59,093 copying CLASV/__pycache__/pipeline.cpython-38.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:59,096 copying CLASV/__pycache__/pipeline.cpython-39.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:59,098 creating build/lib/CLASV/config 2025-08-31T18:17:59,099 copying CLASV/config/NC_004296.fasta -> build/lib/CLASV/config 2025-08-31T18:17:59,101 copying CLASV/config/RF_LASV_lineage_n100_aa.joblib -> build/lib/CLASV/config 2025-08-31T18:17:59,121 copying CLASV/config/config.yaml -> build/lib/CLASV/config 2025-08-31T18:17:59,123 creating build/lib/CLASV/raw_data 2025-08-31T18:17:59,124 copying CLASV/raw_data/Adesina_et_al_2023_EMI.csv -> build/lib/CLASV/raw_data 2025-08-31T18:17:59,128 copying CLASV/raw_data/Adesina_et_al_2023_EMI.fasta -> build/lib/CLASV/raw_data 2025-08-31T18:17:59,133 copying CLASV/raw_data/All_LASV_06_07_24.csv -> build/lib/CLASV/raw_data 2025-08-31T18:17:59,157 copying CLASV/raw_data/All_LASV_06_07_24.fasta -> build/lib/CLASV/raw_data 2025-08-31T18:17:59,440 copying CLASV/raw_data/Bangura_et_al_2024_EMI.csv -> build/lib/CLASV/raw_data 2025-08-31T18:17:59,443 copying CLASV/raw_data/Bangura_et_al_2024_EMI.fasta -> build/lib/CLASV/raw_data 2025-08-31T18:17:59,453 copying CLASV/tools/README-benchmark.md -> build/lib/CLASV/tools 2025-08-31T18:17:59,457 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-08-31T18:17:59,458 !! 2025-08-31T18:17:59,459 ******************************************************************************** 2025-08-31T18:17:59,459 Please avoid running ``setup.py`` directly. 2025-08-31T18:17:59,460 Instead, use pypa/build, pypa/installer or other 2025-08-31T18:17:59,460 standards-based tools. 2025-08-31T18:17:59,461 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-08-31T18:17:59,462 or your builds will no longer be supported. 2025-08-31T18:17:59,463 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-08-31T18:17:59,464 ******************************************************************************** 2025-08-31T18:17:59,465 !! 2025-08-31T18:17:59,466 self.initialize_options() 2025-08-31T18:17:59,488 installing to build/bdist.linux-armv7l/wheel 2025-08-31T18:17:59,489 running install 2025-08-31T18:17:59,514 running install_lib 2025-08-31T18:17:59,545 creating build/bdist.linux-armv7l/wheel 2025-08-31T18:17:59,548 creating build/bdist.linux-armv7l/wheel/CLASV 2025-08-31T18:17:59,550 creating build/bdist.linux-armv7l/wheel/CLASV/config 2025-08-31T18:17:59,551 copying build/lib/CLASV/config/config.yaml -> build/bdist.linux-armv7l/wheel/./CLASV/config 2025-08-31T18:17:59,554 copying build/lib/CLASV/config/NC_004296.fasta -> build/bdist.linux-armv7l/wheel/./CLASV/config 2025-08-31T18:17:59,556 copying build/lib/CLASV/config/RF_LASV_lineage_n100_aa.joblib -> build/bdist.linux-armv7l/wheel/./CLASV/config 2025-08-31T18:17:59,577 copying build/lib/CLASV/install_nextclade.py -> build/bdist.linux-armv7l/wheel/./CLASV 2025-08-31T18:17:59,581 copying build/lib/CLASV/__init__.py -> build/bdist.linux-armv7l/wheel/./CLASV 2025-08-31T18:17:59,583 copying build/lib/CLASV/MANIFEST.in -> build/bdist.linux-armv7l/wheel/./CLASV 2025-08-31T18:17:59,586 copying build/lib/CLASV/predflow_updated.png -> build/bdist.linux-armv7l/wheel/./CLASV 2025-08-31T18:17:59,599 creating build/bdist.linux-armv7l/wheel/CLASV/tools 2025-08-31T18:17:59,600 copying build/lib/CLASV/tools/__init__.py -> build/bdist.linux-armv7l/wheel/./CLASV/tools 2025-08-31T18:17:59,603 copying build/lib/CLASV/tools/benchmark_clasv.py -> build/bdist.linux-armv7l/wheel/./CLASV/tools 2025-08-31T18:17:59,607 copying build/lib/CLASV/tools/README-benchmark.md -> build/bdist.linux-armv7l/wheel/./CLASV/tools 2025-08-31T18:17:59,610 copying build/lib/CLASV/pipeline.py -> build/bdist.linux-armv7l/wheel/./CLASV 2025-08-31T18:17:59,613 copying build/lib/CLASV/install_seqkit.py -> build/bdist.linux-armv7l/wheel/./CLASV 2025-08-31T18:17:59,616 copying build/lib/CLASV/cli.py -> build/bdist.linux-armv7l/wheel/./CLASV 2025-08-31T18:17:59,619 copying build/lib/CLASV/benchmark_clasv.py -> build/bdist.linux-armv7l/wheel/./CLASV 2025-08-31T18:17:59,622 copying build/lib/CLASV/predict_lineage.smk -> build/bdist.linux-armv7l/wheel/./CLASV 2025-08-31T18:17:59,625 copying build/lib/CLASV/VERSION -> build/bdist.linux-armv7l/wheel/./CLASV 2025-08-31T18:17:59,629 creating build/bdist.linux-armv7l/wheel/CLASV/raw_data 2025-08-31T18:17:59,630 copying build/lib/CLASV/raw_data/Bangura_et_al_2024_EMI.fasta -> build/bdist.linux-armv7l/wheel/./CLASV/raw_data 2025-08-31T18:17:59,684 copying build/lib/CLASV/raw_data/All_LASV_06_07_24.fasta -> build/bdist.linux-armv7l/wheel/./CLASV/raw_data 2025-08-31T18:17:59,826 copying build/lib/CLASV/raw_data/All_LASV_06_07_24.csv -> build/bdist.linux-armv7l/wheel/./CLASV/raw_data 2025-08-31T18:17:59,853 copying build/lib/CLASV/raw_data/Adesina_et_al_2023_EMI.fasta -> build/bdist.linux-armv7l/wheel/./CLASV/raw_data 2025-08-31T18:17:59,859 copying build/lib/CLASV/raw_data/Adesina_et_al_2023_EMI.csv -> build/bdist.linux-armv7l/wheel/./CLASV/raw_data 2025-08-31T18:17:59,863 copying build/lib/CLASV/raw_data/Bangura_et_al_2024_EMI.csv -> build/bdist.linux-armv7l/wheel/./CLASV/raw_data 2025-08-31T18:17:59,866 copying build/lib/CLASV/README.md -> build/bdist.linux-armv7l/wheel/./CLASV 2025-08-31T18:17:59,869 creating build/bdist.linux-armv7l/wheel/CLASV/__pycache__ 2025-08-31T18:17:59,870 copying build/lib/CLASV/__pycache__/cli.cpython-39.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:59,872 copying build/lib/CLASV/__pycache__/core.cpython-310.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:59,875 copying build/lib/CLASV/__pycache__/cli.cpython-310.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:59,877 copying build/lib/CLASV/__pycache__/core.cpython-311.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:59,880 copying build/lib/CLASV/__pycache__/install_seqkit.cpython-311.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:59,883 copying build/lib/CLASV/__pycache__/install_nextclade.cpython-38.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:59,885 copying build/lib/CLASV/__pycache__/install_nextclade.cpython-313.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:59,888 copying build/lib/CLASV/__pycache__/core.cpython-38.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:59,890 copying build/lib/CLASV/__pycache__/core.cpython-312.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:59,893 copying build/lib/CLASV/__pycache__/pipeline.cpython-311.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:59,895 copying build/lib/CLASV/__pycache__/pipeline.cpython-39.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:59,898 copying build/lib/CLASV/__pycache__/install_seqkit.cpython-39.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:59,900 copying build/lib/CLASV/__pycache__/install_nextclade.cpython-311.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:59,903 copying build/lib/CLASV/__pycache__/install_seqkit.cpython-313.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:59,906 copying build/lib/CLASV/__pycache__/__init__.cpython-313.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:59,908 copying build/lib/CLASV/__pycache__/install_nextclade.cpython-312.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:59,910 copying build/lib/CLASV/__pycache__/install_seqkit.cpython-38.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:59,912 copying build/lib/CLASV/__pycache__/__init__.cpython-310.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:59,914 copying build/lib/CLASV/__pycache__/install_seqkit.cpython-312.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:59,917 copying build/lib/CLASV/__pycache__/__init__.cpython-38.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:59,919 copying build/lib/CLASV/__pycache__/__init__.cpython-312.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:59,921 copying build/lib/CLASV/__pycache__/pipeline.cpython-312.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:59,923 copying build/lib/CLASV/__pycache__/cli.cpython-313.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:59,925 copying build/lib/CLASV/__pycache__/cli.cpython-311.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:59,927 copying build/lib/CLASV/__pycache__/__init__.cpython-39.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:59,929 copying build/lib/CLASV/__pycache__/core.cpython-313.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:59,932 copying build/lib/CLASV/__pycache__/core.cpython-39.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:59,934 copying build/lib/CLASV/__pycache__/install_seqkit.cpython-310.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:59,937 copying build/lib/CLASV/__pycache__/pipeline.cpython-313.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:59,939 copying build/lib/CLASV/__pycache__/pipeline.cpython-310.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:59,941 copying build/lib/CLASV/__pycache__/cli.cpython-38.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:59,943 copying build/lib/CLASV/__pycache__/install_nextclade.cpython-39.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:59,946 copying build/lib/CLASV/__pycache__/cli.cpython-312.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:59,948 copying build/lib/CLASV/__pycache__/__init__.cpython-311.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:59,950 copying build/lib/CLASV/__pycache__/install_nextclade.cpython-310.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:59,953 copying build/lib/CLASV/__pycache__/pipeline.cpython-38.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:59,955 copying build/lib/CLASV/setup.py -> build/bdist.linux-armv7l/wheel/./CLASV 2025-08-31T18:17:59,957 copying build/lib/CLASV/requirements.txt -> build/bdist.linux-armv7l/wheel/./CLASV 2025-08-31T18:17:59,960 creating build/bdist.linux-armv7l/wheel/CLASV/CLASV.egg-info 2025-08-31T18:17:59,961 copying build/lib/CLASV/CLASV.egg-info/PKG-INFO -> build/bdist.linux-armv7l/wheel/./CLASV/CLASV.egg-info 2025-08-31T18:17:59,964 copying build/lib/CLASV/CLASV.egg-info/top_level.txt -> build/bdist.linux-armv7l/wheel/./CLASV/CLASV.egg-info 2025-08-31T18:17:59,966 copying build/lib/CLASV/CLASV.egg-info/entry_points.txt -> build/bdist.linux-armv7l/wheel/./CLASV/CLASV.egg-info 2025-08-31T18:17:59,968 copying build/lib/CLASV/CLASV.egg-info/dependency_links.txt -> build/bdist.linux-armv7l/wheel/./CLASV/CLASV.egg-info 2025-08-31T18:17:59,971 copying build/lib/CLASV/CLASV.egg-info/requires.txt -> build/bdist.linux-armv7l/wheel/./CLASV/CLASV.egg-info 2025-08-31T18:17:59,973 copying build/lib/CLASV/CLASV.egg-info/SOURCES.txt -> build/bdist.linux-armv7l/wheel/./CLASV/CLASV.egg-info 2025-08-31T18:17:59,974 copying build/lib/CLASV/core.py -> build/bdist.linux-armv7l/wheel/./CLASV 2025-08-31T18:17:59,977 running install_egg_info 2025-08-31T18:18:00,016 Copying CLASV.egg-info to build/bdist.linux-armv7l/wheel/./CLASV-1.0.6-py3.11.egg-info 2025-08-31T18:18:00,028 running install_scripts 2025-08-31T18:18:00,028 Installing Nextclade... 2025-08-31T18:18:00,030 Failed to install Nextclade: [Errno 2] No such file or directory: 'python' 2025-08-31T18:18:00,030 Installing Seqkit... 2025-08-31T18:18:00,031 Failed to install Seqkit: [Errno 2] No such file or directory: 'python' 2025-08-31T18:18:00,044 creating build/bdist.linux-armv7l/wheel/clasv-1.0.6.dist-info/WHEEL 2025-08-31T18:18:00,047 creating '/tmp/pip-wheel-9zt5ytuj/clasv-1.0.6-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-08-31T18:18:00,050 adding 'CLASV/MANIFEST.in' 2025-08-31T18:18:00,052 adding 'CLASV/README.md' 2025-08-31T18:18:00,054 adding 'CLASV/VERSION' 2025-08-31T18:18:00,055 adding 'CLASV/__init__.py' 2025-08-31T18:18:00,057 adding 'CLASV/benchmark_clasv.py' 2025-08-31T18:18:00,058 adding 'CLASV/cli.py' 2025-08-31T18:18:00,061 adding 'CLASV/core.py' 2025-08-31T18:18:00,063 adding 'CLASV/install_nextclade.py' 2025-08-31T18:18:00,064 adding 'CLASV/install_seqkit.py' 2025-08-31T18:18:00,067 adding 'CLASV/pipeline.py' 2025-08-31T18:18:00,116 adding 'CLASV/predflow_updated.png' 2025-08-31T18:18:00,120 adding 'CLASV/predict_lineage.smk' 2025-08-31T18:18:00,121 adding 'CLASV/requirements.txt' 2025-08-31T18:18:00,123 adding 'CLASV/setup.py' 2025-08-31T18:18:00,125 adding 'CLASV/CLASV.egg-info/PKG-INFO' 2025-08-31T18:18:00,126 adding 'CLASV/CLASV.egg-info/SOURCES.txt' 2025-08-31T18:18:00,128 adding 'CLASV/CLASV.egg-info/dependency_links.txt' 2025-08-31T18:18:00,129 adding 'CLASV/CLASV.egg-info/entry_points.txt' 2025-08-31T18:18:00,130 adding 'CLASV/CLASV.egg-info/requires.txt' 2025-08-31T18:18:00,131 adding 'CLASV/CLASV.egg-info/top_level.txt' 2025-08-31T18:18:00,133 adding 'CLASV/__pycache__/__init__.cpython-310.pyc' 2025-08-31T18:18:00,135 adding 'CLASV/__pycache__/__init__.cpython-311.pyc' 2025-08-31T18:18:00,136 adding 'CLASV/__pycache__/__init__.cpython-312.pyc' 2025-08-31T18:18:00,137 adding 'CLASV/__pycache__/__init__.cpython-313.pyc' 2025-08-31T18:18:00,138 adding 'CLASV/__pycache__/__init__.cpython-38.pyc' 2025-08-31T18:18:00,140 adding 'CLASV/__pycache__/__init__.cpython-39.pyc' 2025-08-31T18:18:00,141 adding 'CLASV/__pycache__/cli.cpython-310.pyc' 2025-08-31T18:18:00,143 adding 'CLASV/__pycache__/cli.cpython-311.pyc' 2025-08-31T18:18:00,144 adding 'CLASV/__pycache__/cli.cpython-312.pyc' 2025-08-31T18:18:00,146 adding 'CLASV/__pycache__/cli.cpython-313.pyc' 2025-08-31T18:18:00,148 adding 'CLASV/__pycache__/cli.cpython-38.pyc' 2025-08-31T18:18:00,149 adding 'CLASV/__pycache__/cli.cpython-39.pyc' 2025-08-31T18:18:00,152 adding 'CLASV/__pycache__/core.cpython-310.pyc' 2025-08-31T18:18:00,155 adding 'CLASV/__pycache__/core.cpython-311.pyc' 2025-08-31T18:18:00,158 adding 'CLASV/__pycache__/core.cpython-312.pyc' 2025-08-31T18:18:00,161 adding 'CLASV/__pycache__/core.cpython-313.pyc' 2025-08-31T18:18:00,163 adding 'CLASV/__pycache__/core.cpython-38.pyc' 2025-08-31T18:18:00,165 adding 'CLASV/__pycache__/core.cpython-39.pyc' 2025-08-31T18:18:00,167 adding 'CLASV/__pycache__/install_nextclade.cpython-310.pyc' 2025-08-31T18:18:00,169 adding 'CLASV/__pycache__/install_nextclade.cpython-311.pyc' 2025-08-31T18:18:00,171 adding 'CLASV/__pycache__/install_nextclade.cpython-312.pyc' 2025-08-31T18:18:00,173 adding 'CLASV/__pycache__/install_nextclade.cpython-313.pyc' 2025-08-31T18:18:00,174 adding 'CLASV/__pycache__/install_nextclade.cpython-38.pyc' 2025-08-31T18:18:00,176 adding 'CLASV/__pycache__/install_nextclade.cpython-39.pyc' 2025-08-31T18:18:00,178 adding 'CLASV/__pycache__/install_seqkit.cpython-310.pyc' 2025-08-31T18:18:00,180 adding 'CLASV/__pycache__/install_seqkit.cpython-311.pyc' 2025-08-31T18:18:00,182 adding 'CLASV/__pycache__/install_seqkit.cpython-312.pyc' 2025-08-31T18:18:00,184 adding 'CLASV/__pycache__/install_seqkit.cpython-313.pyc' 2025-08-31T18:18:00,185 adding 'CLASV/__pycache__/install_seqkit.cpython-38.pyc' 2025-08-31T18:18:00,187 adding 'CLASV/__pycache__/install_seqkit.cpython-39.pyc' 2025-08-31T18:18:00,188 adding 'CLASV/__pycache__/pipeline.cpython-310.pyc' 2025-08-31T18:18:00,190 adding 'CLASV/__pycache__/pipeline.cpython-311.pyc' 2025-08-31T18:18:00,192 adding 'CLASV/__pycache__/pipeline.cpython-312.pyc' 2025-08-31T18:18:00,193 adding 'CLASV/__pycache__/pipeline.cpython-313.pyc' 2025-08-31T18:18:00,195 adding 'CLASV/__pycache__/pipeline.cpython-38.pyc' 2025-08-31T18:18:00,196 adding 'CLASV/__pycache__/pipeline.cpython-39.pyc' 2025-08-31T18:18:00,198 adding 'CLASV/config/NC_004296.fasta' 2025-08-31T18:18:00,257 adding 'CLASV/config/RF_LASV_lineage_n100_aa.joblib' 2025-08-31T18:18:00,264 adding 'CLASV/config/config.yaml' 2025-08-31T18:18:00,267 adding 'CLASV/raw_data/Adesina_et_al_2023_EMI.csv' 2025-08-31T18:18:00,277 adding 'CLASV/raw_data/Adesina_et_al_2023_EMI.fasta' 2025-08-31T18:18:00,323 adding 'CLASV/raw_data/All_LASV_06_07_24.csv' 2025-08-31T18:18:03,730 adding 'CLASV/raw_data/All_LASV_06_07_24.fasta' 2025-08-31T18:18:03,790 adding 'CLASV/raw_data/Bangura_et_al_2024_EMI.csv' 2025-08-31T18:18:03,847 adding 'CLASV/raw_data/Bangura_et_al_2024_EMI.fasta' 2025-08-31T18:18:03,850 adding 'CLASV/tools/README-benchmark.md' 2025-08-31T18:18:03,851 adding 'CLASV/tools/__init__.py' 2025-08-31T18:18:03,854 adding 'CLASV/tools/benchmark_clasv.py' 2025-08-31T18:18:03,857 adding 'clasv-1.0.6.dist-info/licenses/LICENSE' 2025-08-31T18:18:03,859 adding 'clasv-1.0.6.dist-info/METADATA' 2025-08-31T18:18:03,860 adding 'clasv-1.0.6.dist-info/WHEEL' 2025-08-31T18:18:03,861 adding 'clasv-1.0.6.dist-info/entry_points.txt' 2025-08-31T18:18:03,862 adding 'clasv-1.0.6.dist-info/top_level.txt' 2025-08-31T18:18:03,863 adding 'clasv-1.0.6.dist-info/RECORD' 2025-08-31T18:18:03,897 removing build/bdist.linux-armv7l/wheel 2025-08-31T18:18:04,036 Building wheel for clasv (setup.py): finished with status 'done' 2025-08-31T18:18:04,066 Created wheel for clasv: filename=clasv-1.0.6-py3-none-any.whl size=2819059 sha256=817d3c98a65caa8b3b398477cdcf0209bfdad7d1f5ce738ab69f846c1b04d66a 2025-08-31T18:18:04,067 Stored in directory: /tmp/pip-ephem-wheel-cache-2f0xkxkh/wheels/38/a7/d4/3a8db5de928c9224c2d5b59eb48aa9b77056c23e56b1d59d77 2025-08-31T18:18:04,084 Successfully built clasv 2025-08-31T18:18:04,166 Removed build tracker: '/tmp/pip-build-tracker-zsh35a9j'