2025-08-31T18:15:39,504 Created temporary directory: /tmp/pip-build-tracker-3qazz0sq 2025-08-31T18:15:39,505 Initialized build tracking at /tmp/pip-build-tracker-3qazz0sq 2025-08-31T18:15:39,505 Created build tracker: /tmp/pip-build-tracker-3qazz0sq 2025-08-31T18:15:39,506 Entered build tracker: /tmp/pip-build-tracker-3qazz0sq 2025-08-31T18:15:39,507 Created temporary directory: /tmp/pip-wheel-f4waq17j 2025-08-31T18:15:39,511 Created temporary directory: /tmp/pip-ephem-wheel-cache-sjk4s0o9 2025-08-31T18:15:39,566 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-08-31T18:15:39,568 2 location(s) to search for versions of clasv: 2025-08-31T18:15:39,568 * https://pypi.org/simple/clasv/ 2025-08-31T18:15:39,568 * https://www.piwheels.org/simple/clasv/ 2025-08-31T18:15:39,569 Fetching project page and analyzing links: https://pypi.org/simple/clasv/ 2025-08-31T18:15:39,570 Getting page https://pypi.org/simple/clasv/ 2025-08-31T18:15:39,571 Found index url https://pypi.org/simple/ 2025-08-31T18:15:39,802 Fetched page https://pypi.org/simple/clasv/ as application/vnd.pypi.simple.v1+json 2025-08-31T18:15:39,809 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) 2025-08-31T18:15:39,811 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 2025-08-31T18:15:39,812 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) 2025-08-31T18:15:39,813 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 2025-08-31T18:15:39,815 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) 2025-08-31T18:15:39,816 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 2025-08-31T18:15:39,817 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) 2025-08-31T18:15:39,818 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 2025-08-31T18:15:39,819 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) 2025-08-31T18:15:39,820 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 2025-08-31T18:15:39,820 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) 2025-08-31T18:15:39,821 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 2025-08-31T18:15:39,822 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) 2025-08-31T18:15:39,824 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 2025-08-31T18:15:39,824 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) 2025-08-31T18:15:39,825 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 2025-08-31T18:15:39,825 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) 2025-08-31T18:15:39,826 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 2025-08-31T18:15:39,827 Fetching project page and analyzing links: https://www.piwheels.org/simple/clasv/ 2025-08-31T18:15:39,828 Getting page https://www.piwheels.org/simple/clasv/ 2025-08-31T18:15:39,829 Found index url https://www.piwheels.org/simple/ 2025-08-31T18:15:40,002 Fetched page https://www.piwheels.org/simple/clasv/ as text/html 2025-08-31T18:15:40,004 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) 2025-08-31T18:15:40,005 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) 2025-08-31T18:15:40,006 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) 2025-08-31T18:15:40,006 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) 2025-08-31T18:15:40,007 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) 2025-08-31T18:15:40,008 Skipping link: not a file: https://www.piwheels.org/simple/clasv/ 2025-08-31T18:15:40,008 Skipping link: not a file: https://pypi.org/simple/clasv/ 2025-08-31T18:15:40,029 Given no hashes to check 1 links for project 'clasv': discarding no candidates 2025-08-31T18:15:40,031 Collecting clasv==1.0.4 2025-08-31T18:15:40,034 Created temporary directory: /tmp/pip-unpack-8h52c84w 2025-08-31T18:15:40,263 Downloading clasv-1.0.4.tar.gz (2.0 MB) 2025-08-31T18:15:41,078 Added clasv==1.0.4 from https://files.pythonhosted.org/packages/d4/f4/4a24334f0238c96ad88300acf9f8f037ae20e612ee75d4c6efd241c10a2c/clasv-1.0.4.tar.gz to build tracker '/tmp/pip-build-tracker-3qazz0sq' 2025-08-31T18:15:41,081 Running setup.py (path:/tmp/pip-wheel-f4waq17j/clasv_5a603ad86d1b4c099b8d15945d15668e/setup.py) egg_info for package clasv 2025-08-31T18:15:41,082 Created temporary directory: /tmp/pip-pip-egg-info-vhwkn7ab 2025-08-31T18:15:41,083 Preparing metadata (setup.py): started 2025-08-31T18:15:41,084 Running command python setup.py egg_info 2025-08-31T18:15:41,999 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-08-31T18:15:41,999 !! 2025-08-31T18:15:42,000 ******************************************************************************** 2025-08-31T18:15:42,000 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-08-31T18:15:42,001 License :: OSI Approved :: MIT License 2025-08-31T18:15:42,002 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-08-31T18:15:42,003 ******************************************************************************** 2025-08-31T18:15:42,004 !! 2025-08-31T18:15:42,005 self._finalize_license_expression() 2025-08-31T18:15:42,031 Running setup... 2025-08-31T18:15:42,032 running egg_info 2025-08-31T18:15:42,060 creating /tmp/pip-pip-egg-info-vhwkn7ab/CLASV.egg-info 2025-08-31T18:15:42,061 writing /tmp/pip-pip-egg-info-vhwkn7ab/CLASV.egg-info/PKG-INFO 2025-08-31T18:15:42,066 writing dependency_links to /tmp/pip-pip-egg-info-vhwkn7ab/CLASV.egg-info/dependency_links.txt 2025-08-31T18:15:42,067 writing entry points to /tmp/pip-pip-egg-info-vhwkn7ab/CLASV.egg-info/entry_points.txt 2025-08-31T18:15:42,087 writing requirements to /tmp/pip-pip-egg-info-vhwkn7ab/CLASV.egg-info/requires.txt 2025-08-31T18:15:42,089 writing top-level names to /tmp/pip-pip-egg-info-vhwkn7ab/CLASV.egg-info/top_level.txt 2025-08-31T18:15:42,090 writing manifest file '/tmp/pip-pip-egg-info-vhwkn7ab/CLASV.egg-info/SOURCES.txt' 2025-08-31T18:15:42,186 reading manifest file '/tmp/pip-pip-egg-info-vhwkn7ab/CLASV.egg-info/SOURCES.txt' 2025-08-31T18:15:42,188 reading manifest template 'MANIFEST.in' 2025-08-31T18:15:42,261 warning: no files found matching '*.png' under directory 'CLASV' 2025-08-31T18:15:42,276 warning: no files found matching 'config' under directory 'CLASV' 2025-08-31T18:15:42,318 warning: no files found matching 'predictions' under directory 'CLASV' 2025-08-31T18:15:42,359 warning: no files found matching 'raw_data' under directory 'CLASV' 2025-08-31T18:15:42,400 warning: no files found matching 'results' under directory 'CLASV' 2025-08-31T18:15:42,441 warning: no files found matching 'visuals' under directory 'CLASV' 2025-08-31T18:15:42,467 adding license file 'LICENSE' 2025-08-31T18:15:42,477 writing manifest file '/tmp/pip-pip-egg-info-vhwkn7ab/CLASV.egg-info/SOURCES.txt' 2025-08-31T18:15:42,586 Preparing metadata (setup.py): finished with status 'done' 2025-08-31T18:15:42,591 Source in /tmp/pip-wheel-f4waq17j/clasv_5a603ad86d1b4c099b8d15945d15668e has version 1.0.4, which satisfies requirement clasv==1.0.4 from https://files.pythonhosted.org/packages/d4/f4/4a24334f0238c96ad88300acf9f8f037ae20e612ee75d4c6efd241c10a2c/clasv-1.0.4.tar.gz 2025-08-31T18:15:42,592 Removed clasv==1.0.4 from https://files.pythonhosted.org/packages/d4/f4/4a24334f0238c96ad88300acf9f8f037ae20e612ee75d4c6efd241c10a2c/clasv-1.0.4.tar.gz from build tracker '/tmp/pip-build-tracker-3qazz0sq' 2025-08-31T18:15:42,624 Created temporary directory: /tmp/pip-unpack-bwq3o8hd 2025-08-31T18:15:42,625 Created temporary directory: /tmp/pip-unpack-tevhpio4 2025-08-31T18:15:42,626 Building wheels for collected packages: clasv 2025-08-31T18:15:42,630 Created temporary directory: /tmp/pip-wheel-e17pc_g4 2025-08-31T18:15:42,631 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 2025-08-31T18:15:42,632 Building wheel for clasv (setup.py): started 2025-08-31T18:15:42,633 Destination directory: /tmp/pip-wheel-e17pc_g4 2025-08-31T18:15:42,634 Running command python setup.py bdist_wheel 2025-08-31T18:15:43,113 Running setup... 2025-08-31T18:15:43,505 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-08-31T18:15:43,506 !! 2025-08-31T18:15:43,507 ******************************************************************************** 2025-08-31T18:15:43,507 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-08-31T18:15:43,508 License :: OSI Approved :: MIT License 2025-08-31T18:15:43,510 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-08-31T18:15:43,510 ******************************************************************************** 2025-08-31T18:15:43,511 !! 2025-08-31T18:15:43,512 self._finalize_license_expression() 2025-08-31T18:15:43,512 running bdist_wheel 2025-08-31T18:15:43,645 running build 2025-08-31T18:15:43,645 running build_py 2025-08-31T18:15:43,677 creating build/lib/CLASV 2025-08-31T18:15:43,679 copying CLASV/__init__.py -> build/lib/CLASV 2025-08-31T18:15:43,681 copying CLASV/cli.py -> build/lib/CLASV 2025-08-31T18:15:43,683 copying CLASV/core.py -> build/lib/CLASV 2025-08-31T18:15:43,686 copying CLASV/install_seqkit.py -> build/lib/CLASV 2025-08-31T18:15:43,689 copying CLASV/setup.py -> build/lib/CLASV 2025-08-31T18:15:43,691 copying CLASV/pipeline.py -> build/lib/CLASV 2025-08-31T18:15:43,693 copying CLASV/install_nextclade.py -> build/lib/CLASV 2025-08-31T18:15:43,696 copying CLASV/benchmark_clasv.py -> build/lib/CLASV 2025-08-31T18:15:43,698 creating build/lib/CLASV/tools 2025-08-31T18:15:43,700 copying CLASV/tools/__init__.py -> build/lib/CLASV/tools 2025-08-31T18:15:43,702 copying CLASV/tools/benchmark_clasv.py -> build/lib/CLASV/tools 2025-08-31T18:15:43,704 running egg_info 2025-08-31T18:15:43,736 writing CLASV.egg-info/PKG-INFO 2025-08-31T18:15:43,742 writing dependency_links to CLASV.egg-info/dependency_links.txt 2025-08-31T18:15:43,743 writing entry points to CLASV.egg-info/entry_points.txt 2025-08-31T18:15:43,762 writing requirements to CLASV.egg-info/requires.txt 2025-08-31T18:15:43,763 writing top-level names to CLASV.egg-info/top_level.txt 2025-08-31T18:15:43,799 reading manifest file 'CLASV.egg-info/SOURCES.txt' 2025-08-31T18:15:43,805 reading manifest template 'MANIFEST.in' 2025-08-31T18:15:43,880 warning: no files found matching '*.png' under directory 'CLASV' 2025-08-31T18:15:43,896 warning: no files found matching 'config' under directory 'CLASV' 2025-08-31T18:15:43,938 warning: no files found matching 'predictions' under directory 'CLASV' 2025-08-31T18:15:43,978 warning: no files found matching 'raw_data' under directory 'CLASV' 2025-08-31T18:15:44,021 warning: no files found matching 'results' under directory 'CLASV' 2025-08-31T18:15:44,065 warning: no files found matching 'visuals' under directory 'CLASV' 2025-08-31T18:15:44,091 adding license file 'LICENSE' 2025-08-31T18:15:44,103 writing manifest file 'CLASV.egg-info/SOURCES.txt' 2025-08-31T18:15:44,106 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'CLASV.__pycache__' is absent from the `packages` configuration. 2025-08-31T18:15:44,107 !! 2025-08-31T18:15:44,109 ******************************************************************************** 2025-08-31T18:15:44,109 ############################ 2025-08-31T18:15:44,110 # Package would be ignored # 2025-08-31T18:15:44,111 ############################ 2025-08-31T18:15:44,112 Python recognizes 'CLASV.__pycache__' as an importable package[^1], 2025-08-31T18:15:44,112 but it is absent from setuptools' `packages` configuration. 2025-08-31T18:15:44,113 This leads to an ambiguous overall configuration. If you want to distribute this 2025-08-31T18:15:44,113 package, please make sure that 'CLASV.__pycache__' is explicitly added 2025-08-31T18:15:44,114 to the `packages` configuration field. 2025-08-31T18:15:44,115 Alternatively, you can also rely on setuptools' discovery methods 2025-08-31T18:15:44,115 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-08-31T18:15:44,115 instead of `find_packages(...)`/`find:`). 2025-08-31T18:15:44,116 You can read more about "package discovery" on setuptools documentation page: 2025-08-31T18:15:44,117 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-08-31T18:15:44,118 If you don't want 'CLASV.__pycache__' to be distributed and are 2025-08-31T18:15:44,119 already explicitly excluding 'CLASV.__pycache__' via 2025-08-31T18:15:44,119 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-08-31T18:15:44,120 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-08-31T18:15:44,120 combination with a more fine grained `package-data` configuration. 2025-08-31T18:15:44,121 You can read more about "package data files" on setuptools documentation page: 2025-08-31T18:15:44,123 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-08-31T18:15:44,124 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-08-31T18:15:44,125 even if it does not contain any `.py` files. 2025-08-31T18:15:44,125 On the other hand, currently there is no concept of package data 2025-08-31T18:15:44,126 directory, all directories are treated like packages. 2025-08-31T18:15:44,126 ******************************************************************************** 2025-08-31T18:15:44,127 !! 2025-08-31T18:15:44,128 check.warn(importable) 2025-08-31T18:15:44,129 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'CLASV.config' is absent from the `packages` configuration. 2025-08-31T18:15:44,129 !! 2025-08-31T18:15:44,130 ******************************************************************************** 2025-08-31T18:15:44,131 ############################ 2025-08-31T18:15:44,131 # Package would be ignored # 2025-08-31T18:15:44,132 ############################ 2025-08-31T18:15:44,132 Python recognizes 'CLASV.config' as an importable package[^1], 2025-08-31T18:15:44,133 but it is absent from setuptools' `packages` configuration. 2025-08-31T18:15:44,134 This leads to an ambiguous overall configuration. If you want to distribute this 2025-08-31T18:15:44,135 package, please make sure that 'CLASV.config' is explicitly added 2025-08-31T18:15:44,135 to the `packages` configuration field. 2025-08-31T18:15:44,136 Alternatively, you can also rely on setuptools' discovery methods 2025-08-31T18:15:44,137 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-08-31T18:15:44,137 instead of `find_packages(...)`/`find:`). 2025-08-31T18:15:44,139 You can read more about "package discovery" on setuptools documentation page: 2025-08-31T18:15:44,140 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-08-31T18:15:44,141 If you don't want 'CLASV.config' to be distributed and are 2025-08-31T18:15:44,141 already explicitly excluding 'CLASV.config' via 2025-08-31T18:15:44,142 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-08-31T18:15:44,143 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-08-31T18:15:44,143 combination with a more fine grained `package-data` configuration. 2025-08-31T18:15:44,144 You can read more about "package data files" on setuptools documentation page: 2025-08-31T18:15:44,145 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-08-31T18:15:44,147 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-08-31T18:15:44,148 even if it does not contain any `.py` files. 2025-08-31T18:15:44,148 On the other hand, currently there is no concept of package data 2025-08-31T18:15:44,148 directory, all directories are treated like packages. 2025-08-31T18:15:44,149 ******************************************************************************** 2025-08-31T18:15:44,150 !! 2025-08-31T18:15:44,151 check.warn(importable) 2025-08-31T18:15:44,151 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'CLASV.raw_data' is absent from the `packages` configuration. 2025-08-31T18:15:44,152 !! 2025-08-31T18:15:44,153 ******************************************************************************** 2025-08-31T18:15:44,153 ############################ 2025-08-31T18:15:44,154 # Package would be ignored # 2025-08-31T18:15:44,155 ############################ 2025-08-31T18:15:44,155 Python recognizes 'CLASV.raw_data' as an importable package[^1], 2025-08-31T18:15:44,156 but it is absent from setuptools' `packages` configuration. 2025-08-31T18:15:44,157 This leads to an ambiguous overall configuration. If you want to distribute this 2025-08-31T18:15:44,158 package, please make sure that 'CLASV.raw_data' is explicitly added 2025-08-31T18:15:44,158 to the `packages` configuration field. 2025-08-31T18:15:44,160 Alternatively, you can also rely on setuptools' discovery methods 2025-08-31T18:15:44,160 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-08-31T18:15:44,161 instead of `find_packages(...)`/`find:`). 2025-08-31T18:15:44,162 You can read more about "package discovery" on setuptools documentation page: 2025-08-31T18:15:44,163 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-08-31T18:15:44,164 If you don't want 'CLASV.raw_data' to be distributed and are 2025-08-31T18:15:44,165 already explicitly excluding 'CLASV.raw_data' via 2025-08-31T18:15:44,166 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-08-31T18:15:44,166 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-08-31T18:15:44,167 combination with a more fine grained `package-data` configuration. 2025-08-31T18:15:44,168 You can read more about "package data files" on setuptools documentation page: 2025-08-31T18:15:44,170 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-08-31T18:15:44,172 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-08-31T18:15:44,172 even if it does not contain any `.py` files. 2025-08-31T18:15:44,173 On the other hand, currently there is no concept of package data 2025-08-31T18:15:44,173 directory, all directories are treated like packages. 2025-08-31T18:15:44,174 ******************************************************************************** 2025-08-31T18:15:44,175 !! 2025-08-31T18:15:44,175 check.warn(importable) 2025-08-31T18:15:44,176 copying CLASV/MANIFEST.in -> build/lib/CLASV 2025-08-31T18:15:44,176 copying CLASV/README.md -> build/lib/CLASV 2025-08-31T18:15:44,177 copying CLASV/VERSION -> build/lib/CLASV 2025-08-31T18:15:44,177 copying CLASV/predict_lineage.smk -> build/lib/CLASV 2025-08-31T18:15:44,178 copying CLASV/requirements.txt -> build/lib/CLASV 2025-08-31T18:15:44,179 creating build/lib/CLASV/__pycache__ 2025-08-31T18:15:44,179 copying CLASV/__pycache__/__init__.cpython-310.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:15:44,180 copying CLASV/__pycache__/__init__.cpython-311.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:15:44,180 copying CLASV/__pycache__/__init__.cpython-312.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:15:44,180 copying CLASV/__pycache__/__init__.cpython-313.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:15:44,181 copying CLASV/__pycache__/__init__.cpython-38.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:15:44,181 copying CLASV/__pycache__/__init__.cpython-39.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:15:44,182 copying CLASV/__pycache__/cli.cpython-310.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:15:44,182 copying CLASV/__pycache__/cli.cpython-311.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:15:44,183 copying CLASV/__pycache__/cli.cpython-312.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:15:44,183 copying CLASV/__pycache__/cli.cpython-313.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:15:44,184 copying CLASV/__pycache__/cli.cpython-38.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:15:44,184 copying CLASV/__pycache__/cli.cpython-39.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:15:44,185 copying CLASV/__pycache__/core.cpython-310.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:15:44,185 copying CLASV/__pycache__/core.cpython-311.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:15:44,186 copying CLASV/__pycache__/core.cpython-312.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:15:44,186 copying CLASV/__pycache__/core.cpython-313.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:15:44,187 copying CLASV/__pycache__/core.cpython-38.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:15:44,187 copying CLASV/__pycache__/core.cpython-39.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:15:44,188 copying CLASV/__pycache__/install_nextclade.cpython-310.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:15:44,188 copying CLASV/__pycache__/install_nextclade.cpython-311.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:15:44,191 copying CLASV/__pycache__/install_nextclade.cpython-312.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:15:44,194 copying CLASV/__pycache__/install_nextclade.cpython-313.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:15:44,197 copying CLASV/__pycache__/install_nextclade.cpython-38.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:15:44,199 copying CLASV/__pycache__/install_nextclade.cpython-39.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:15:44,202 copying CLASV/__pycache__/install_seqkit.cpython-310.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:15:44,205 copying CLASV/__pycache__/install_seqkit.cpython-311.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:15:44,208 copying CLASV/__pycache__/install_seqkit.cpython-312.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:15:44,211 copying CLASV/__pycache__/install_seqkit.cpython-313.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:15:44,214 copying CLASV/__pycache__/install_seqkit.cpython-38.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:15:44,217 copying CLASV/__pycache__/install_seqkit.cpython-39.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:15:44,221 copying CLASV/__pycache__/pipeline.cpython-310.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:15:44,223 copying CLASV/__pycache__/pipeline.cpython-311.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:15:44,226 copying CLASV/__pycache__/pipeline.cpython-312.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:15:44,230 copying CLASV/__pycache__/pipeline.cpython-313.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:15:44,233 copying CLASV/__pycache__/pipeline.cpython-38.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:15:44,236 copying CLASV/__pycache__/pipeline.cpython-39.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:15:44,239 creating build/lib/CLASV/config 2025-08-31T18:15:44,240 copying CLASV/config/NC_004296.fasta -> build/lib/CLASV/config 2025-08-31T18:15:44,242 copying CLASV/config/RF_LASV_lineage_n100_aa.joblib -> build/lib/CLASV/config 2025-08-31T18:15:44,261 copying CLASV/config/config.yaml -> build/lib/CLASV/config 2025-08-31T18:15:44,264 creating build/lib/CLASV/raw_data 2025-08-31T18:15:44,265 copying CLASV/raw_data/Adesina_et_al_2023_EMI.csv -> build/lib/CLASV/raw_data 2025-08-31T18:15:44,269 copying CLASV/raw_data/Adesina_et_al_2023_EMI.fasta -> build/lib/CLASV/raw_data 2025-08-31T18:15:44,276 copying CLASV/raw_data/All_LASV_06_07_24.csv -> build/lib/CLASV/raw_data 2025-08-31T18:15:44,302 copying CLASV/raw_data/All_LASV_06_07_24.fasta -> build/lib/CLASV/raw_data 2025-08-31T18:15:44,446 copying CLASV/raw_data/Bangura_et_al_2024_EMI.csv -> build/lib/CLASV/raw_data 2025-08-31T18:15:44,449 copying CLASV/raw_data/Bangura_et_al_2024_EMI.fasta -> build/lib/CLASV/raw_data 2025-08-31T18:15:44,455 copying CLASV/tools/README-benchmark.md -> build/lib/CLASV/tools 2025-08-31T18:15:44,459 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-08-31T18:15:44,460 !! 2025-08-31T18:15:44,460 ******************************************************************************** 2025-08-31T18:15:44,461 Please avoid running ``setup.py`` directly. 2025-08-31T18:15:44,462 Instead, use pypa/build, pypa/installer or other 2025-08-31T18:15:44,462 standards-based tools. 2025-08-31T18:15:44,463 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-08-31T18:15:44,464 or your builds will no longer be supported. 2025-08-31T18:15:44,465 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-08-31T18:15:44,465 ******************************************************************************** 2025-08-31T18:15:44,467 !! 2025-08-31T18:15:44,467 self.initialize_options() 2025-08-31T18:15:44,491 installing to build/bdist.linux-armv7l/wheel 2025-08-31T18:15:44,492 running install 2025-08-31T18:15:44,517 running install_lib 2025-08-31T18:15:44,544 creating build/bdist.linux-armv7l/wheel 2025-08-31T18:15:44,547 creating build/bdist.linux-armv7l/wheel/CLASV 2025-08-31T18:15:44,548 copying build/lib/CLASV/predict_lineage.smk -> build/bdist.linux-armv7l/wheel/./CLASV 2025-08-31T18:15:44,551 creating build/bdist.linux-armv7l/wheel/CLASV/config 2025-08-31T18:15:44,552 copying build/lib/CLASV/config/NC_004296.fasta -> build/bdist.linux-armv7l/wheel/./CLASV/config 2025-08-31T18:15:44,554 copying build/lib/CLASV/config/RF_LASV_lineage_n100_aa.joblib -> build/bdist.linux-armv7l/wheel/./CLASV/config 2025-08-31T18:15:44,570 copying build/lib/CLASV/config/config.yaml -> build/bdist.linux-armv7l/wheel/./CLASV/config 2025-08-31T18:15:44,573 copying build/lib/CLASV/__init__.py -> build/bdist.linux-armv7l/wheel/./CLASV 2025-08-31T18:15:44,575 copying build/lib/CLASV/cli.py -> build/bdist.linux-armv7l/wheel/./CLASV 2025-08-31T18:15:44,577 copying build/lib/CLASV/core.py -> build/bdist.linux-armv7l/wheel/./CLASV 2025-08-31T18:15:44,580 copying build/lib/CLASV/install_seqkit.py -> build/bdist.linux-armv7l/wheel/./CLASV 2025-08-31T18:15:44,582 copying build/lib/CLASV/VERSION -> build/bdist.linux-armv7l/wheel/./CLASV 2025-08-31T18:15:44,585 copying build/lib/CLASV/README.md -> build/bdist.linux-armv7l/wheel/./CLASV 2025-08-31T18:15:44,587 copying build/lib/CLASV/setup.py -> build/bdist.linux-armv7l/wheel/./CLASV 2025-08-31T18:15:44,590 copying build/lib/CLASV/pipeline.py -> build/bdist.linux-armv7l/wheel/./CLASV 2025-08-31T18:15:44,593 creating build/bdist.linux-armv7l/wheel/CLASV/tools 2025-08-31T18:15:44,594 copying build/lib/CLASV/tools/__init__.py -> build/bdist.linux-armv7l/wheel/./CLASV/tools 2025-08-31T18:15:44,597 copying build/lib/CLASV/tools/README-benchmark.md -> build/bdist.linux-armv7l/wheel/./CLASV/tools 2025-08-31T18:15:44,600 copying build/lib/CLASV/tools/benchmark_clasv.py -> build/bdist.linux-armv7l/wheel/./CLASV/tools 2025-08-31T18:15:44,604 creating build/bdist.linux-armv7l/wheel/CLASV/__pycache__ 2025-08-31T18:15:44,605 copying build/lib/CLASV/__pycache__/pipeline.cpython-311.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:15:44,608 copying build/lib/CLASV/__pycache__/install_nextclade.cpython-311.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:15:44,611 copying build/lib/CLASV/__pycache__/install_nextclade.cpython-38.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:15:44,614 copying build/lib/CLASV/__pycache__/install_seqkit.cpython-312.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:15:44,617 copying build/lib/CLASV/__pycache__/pipeline.cpython-38.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:15:44,619 copying build/lib/CLASV/__pycache__/install_nextclade.cpython-312.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:15:44,622 copying build/lib/CLASV/__pycache__/core.cpython-39.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:15:44,625 copying build/lib/CLASV/__pycache__/core.cpython-313.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:15:44,628 copying build/lib/CLASV/__pycache__/cli.cpython-311.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:15:44,631 copying build/lib/CLASV/__pycache__/pipeline.cpython-39.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:15:44,633 copying build/lib/CLASV/__pycache__/__init__.cpython-313.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:15:44,636 copying build/lib/CLASV/__pycache__/install_seqkit.cpython-39.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:15:44,639 copying build/lib/CLASV/__pycache__/__init__.cpython-38.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:15:44,641 copying build/lib/CLASV/__pycache__/core.cpython-310.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:15:44,644 copying build/lib/CLASV/__pycache__/install_nextclade.cpython-39.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:15:44,647 copying build/lib/CLASV/__pycache__/cli.cpython-310.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:15:44,650 copying build/lib/CLASV/__pycache__/install_seqkit.cpython-313.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:15:44,652 copying build/lib/CLASV/__pycache__/__init__.cpython-312.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:15:44,655 copying build/lib/CLASV/__pycache__/cli.cpython-313.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:15:44,658 copying build/lib/CLASV/__pycache__/core.cpython-38.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:15:44,661 copying build/lib/CLASV/__pycache__/install_nextclade.cpython-313.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:15:44,664 copying build/lib/CLASV/__pycache__/core.cpython-311.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:15:44,667 copying build/lib/CLASV/__pycache__/__init__.cpython-311.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:15:44,669 copying build/lib/CLASV/__pycache__/pipeline.cpython-313.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:15:44,672 copying build/lib/CLASV/__pycache__/install_seqkit.cpython-311.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:15:44,675 copying build/lib/CLASV/__pycache__/install_nextclade.cpython-310.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:15:44,678 copying build/lib/CLASV/__pycache__/__init__.cpython-39.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:15:44,680 copying build/lib/CLASV/__pycache__/cli.cpython-312.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:15:44,683 copying build/lib/CLASV/__pycache__/cli.cpython-39.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:15:44,685 copying build/lib/CLASV/__pycache__/core.cpython-312.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:15:44,688 copying build/lib/CLASV/__pycache__/install_seqkit.cpython-310.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:15:44,691 copying build/lib/CLASV/__pycache__/install_seqkit.cpython-38.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:15:44,694 copying build/lib/CLASV/__pycache__/pipeline.cpython-312.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:15:44,696 copying build/lib/CLASV/__pycache__/pipeline.cpython-310.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:15:44,699 copying build/lib/CLASV/__pycache__/__init__.cpython-310.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:15:44,701 copying build/lib/CLASV/__pycache__/cli.cpython-38.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:15:44,703 copying build/lib/CLASV/install_nextclade.py -> build/bdist.linux-armv7l/wheel/./CLASV 2025-08-31T18:15:44,706 copying build/lib/CLASV/requirements.txt -> build/bdist.linux-armv7l/wheel/./CLASV 2025-08-31T18:15:44,708 copying build/lib/CLASV/benchmark_clasv.py -> build/bdist.linux-armv7l/wheel/./CLASV 2025-08-31T18:15:44,711 copying build/lib/CLASV/MANIFEST.in -> build/bdist.linux-armv7l/wheel/./CLASV 2025-08-31T18:15:44,713 creating build/bdist.linux-armv7l/wheel/CLASV/raw_data 2025-08-31T18:15:44,715 copying build/lib/CLASV/raw_data/Bangura_et_al_2024_EMI.fasta -> build/bdist.linux-armv7l/wheel/./CLASV/raw_data 2025-08-31T18:15:44,722 copying build/lib/CLASV/raw_data/Bangura_et_al_2024_EMI.csv -> build/bdist.linux-armv7l/wheel/./CLASV/raw_data 2025-08-31T18:15:44,725 copying build/lib/CLASV/raw_data/All_LASV_06_07_24.fasta -> build/bdist.linux-armv7l/wheel/./CLASV/raw_data 2025-08-31T18:15:44,901 copying build/lib/CLASV/raw_data/Adesina_et_al_2023_EMI.fasta -> build/bdist.linux-armv7l/wheel/./CLASV/raw_data 2025-08-31T18:15:44,908 copying build/lib/CLASV/raw_data/All_LASV_06_07_24.csv -> build/bdist.linux-armv7l/wheel/./CLASV/raw_data 2025-08-31T18:15:44,940 copying build/lib/CLASV/raw_data/Adesina_et_al_2023_EMI.csv -> build/bdist.linux-armv7l/wheel/./CLASV/raw_data 2025-08-31T18:15:44,947 running install_egg_info 2025-08-31T18:15:44,989 Copying CLASV.egg-info to build/bdist.linux-armv7l/wheel/./CLASV-1.0.4-py3.11.egg-info 2025-08-31T18:15:45,002 running install_scripts 2025-08-31T18:15:45,003 Installing Nextclade... 2025-08-31T18:15:45,004 Failed to install Nextclade: [Errno 2] No such file or directory: 'python' 2025-08-31T18:15:45,005 Installing Seqkit... 2025-08-31T18:15:45,006 Failed to install Seqkit: [Errno 2] No such file or directory: 'python' 2025-08-31T18:15:45,020 creating build/bdist.linux-armv7l/wheel/clasv-1.0.4.dist-info/WHEEL 2025-08-31T18:15:45,023 creating '/tmp/pip-wheel-e17pc_g4/clasv-1.0.4-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-08-31T18:15:45,025 adding 'CLASV/MANIFEST.in' 2025-08-31T18:15:45,028 adding 'CLASV/README.md' 2025-08-31T18:15:45,029 adding 'CLASV/VERSION' 2025-08-31T18:15:45,031 adding 'CLASV/__init__.py' 2025-08-31T18:15:45,033 adding 'CLASV/benchmark_clasv.py' 2025-08-31T18:15:45,035 adding 'CLASV/cli.py' 2025-08-31T18:15:45,038 adding 'CLASV/core.py' 2025-08-31T18:15:45,040 adding 'CLASV/install_nextclade.py' 2025-08-31T18:15:45,042 adding 'CLASV/install_seqkit.py' 2025-08-31T18:15:45,044 adding 'CLASV/pipeline.py' 2025-08-31T18:15:45,046 adding 'CLASV/predict_lineage.smk' 2025-08-31T18:15:45,048 adding 'CLASV/requirements.txt' 2025-08-31T18:15:45,050 adding 'CLASV/setup.py' 2025-08-31T18:15:45,053 adding 'CLASV/__pycache__/__init__.cpython-310.pyc' 2025-08-31T18:15:45,054 adding 'CLASV/__pycache__/__init__.cpython-311.pyc' 2025-08-31T18:15:45,056 adding 'CLASV/__pycache__/__init__.cpython-312.pyc' 2025-08-31T18:15:45,057 adding 'CLASV/__pycache__/__init__.cpython-313.pyc' 2025-08-31T18:15:45,058 adding 'CLASV/__pycache__/__init__.cpython-38.pyc' 2025-08-31T18:15:45,059 adding 'CLASV/__pycache__/__init__.cpython-39.pyc' 2025-08-31T18:15:45,060 adding 'CLASV/__pycache__/cli.cpython-310.pyc' 2025-08-31T18:15:45,062 adding 'CLASV/__pycache__/cli.cpython-311.pyc' 2025-08-31T18:15:45,063 adding 'CLASV/__pycache__/cli.cpython-312.pyc' 2025-08-31T18:15:45,065 adding 'CLASV/__pycache__/cli.cpython-313.pyc' 2025-08-31T18:15:45,066 adding 'CLASV/__pycache__/cli.cpython-38.pyc' 2025-08-31T18:15:45,067 adding 'CLASV/__pycache__/cli.cpython-39.pyc' 2025-08-31T18:15:45,069 adding 'CLASV/__pycache__/core.cpython-310.pyc' 2025-08-31T18:15:45,072 adding 'CLASV/__pycache__/core.cpython-311.pyc' 2025-08-31T18:15:45,075 adding 'CLASV/__pycache__/core.cpython-312.pyc' 2025-08-31T18:15:45,078 adding 'CLASV/__pycache__/core.cpython-313.pyc' 2025-08-31T18:15:45,080 adding 'CLASV/__pycache__/core.cpython-38.pyc' 2025-08-31T18:15:45,082 adding 'CLASV/__pycache__/core.cpython-39.pyc' 2025-08-31T18:15:45,084 adding 'CLASV/__pycache__/install_nextclade.cpython-310.pyc' 2025-08-31T18:15:45,086 adding 'CLASV/__pycache__/install_nextclade.cpython-311.pyc' 2025-08-31T18:15:45,088 adding 'CLASV/__pycache__/install_nextclade.cpython-312.pyc' 2025-08-31T18:15:45,090 adding 'CLASV/__pycache__/install_nextclade.cpython-313.pyc' 2025-08-31T18:15:45,091 adding 'CLASV/__pycache__/install_nextclade.cpython-38.pyc' 2025-08-31T18:15:45,093 adding 'CLASV/__pycache__/install_nextclade.cpython-39.pyc' 2025-08-31T18:15:45,095 adding 'CLASV/__pycache__/install_seqkit.cpython-310.pyc' 2025-08-31T18:15:45,097 adding 'CLASV/__pycache__/install_seqkit.cpython-311.pyc' 2025-08-31T18:15:45,099 adding 'CLASV/__pycache__/install_seqkit.cpython-312.pyc' 2025-08-31T18:15:45,101 adding 'CLASV/__pycache__/install_seqkit.cpython-313.pyc' 2025-08-31T18:15:45,103 adding 'CLASV/__pycache__/install_seqkit.cpython-38.pyc' 2025-08-31T18:15:45,104 adding 'CLASV/__pycache__/install_seqkit.cpython-39.pyc' 2025-08-31T18:15:45,106 adding 'CLASV/__pycache__/pipeline.cpython-310.pyc' 2025-08-31T18:15:45,108 adding 'CLASV/__pycache__/pipeline.cpython-311.pyc' 2025-08-31T18:15:45,109 adding 'CLASV/__pycache__/pipeline.cpython-312.pyc' 2025-08-31T18:15:45,111 adding 'CLASV/__pycache__/pipeline.cpython-313.pyc' 2025-08-31T18:15:45,113 adding 'CLASV/__pycache__/pipeline.cpython-38.pyc' 2025-08-31T18:15:45,114 adding 'CLASV/__pycache__/pipeline.cpython-39.pyc' 2025-08-31T18:15:45,116 adding 'CLASV/config/NC_004296.fasta' 2025-08-31T18:15:45,176 adding 'CLASV/config/RF_LASV_lineage_n100_aa.joblib' 2025-08-31T18:15:45,182 adding 'CLASV/config/config.yaml' 2025-08-31T18:15:45,186 adding 'CLASV/raw_data/Adesina_et_al_2023_EMI.csv' 2025-08-31T18:15:45,196 adding 'CLASV/raw_data/Adesina_et_al_2023_EMI.fasta' 2025-08-31T18:15:45,239 adding 'CLASV/raw_data/All_LASV_06_07_24.csv' 2025-08-31T18:15:48,725 adding 'CLASV/raw_data/All_LASV_06_07_24.fasta' 2025-08-31T18:15:48,786 adding 'CLASV/raw_data/Bangura_et_al_2024_EMI.csv' 2025-08-31T18:15:48,844 adding 'CLASV/raw_data/Bangura_et_al_2024_EMI.fasta' 2025-08-31T18:15:48,847 adding 'CLASV/tools/README-benchmark.md' 2025-08-31T18:15:48,848 adding 'CLASV/tools/__init__.py' 2025-08-31T18:15:48,851 adding 'CLASV/tools/benchmark_clasv.py' 2025-08-31T18:15:48,855 adding 'clasv-1.0.4.dist-info/licenses/LICENSE' 2025-08-31T18:15:48,857 adding 'clasv-1.0.4.dist-info/METADATA' 2025-08-31T18:15:48,858 adding 'clasv-1.0.4.dist-info/WHEEL' 2025-08-31T18:15:48,859 adding 'clasv-1.0.4.dist-info/entry_points.txt' 2025-08-31T18:15:48,860 adding 'clasv-1.0.4.dist-info/top_level.txt' 2025-08-31T18:15:48,861 adding 'clasv-1.0.4.dist-info/RECORD' 2025-08-31T18:15:48,892 removing build/bdist.linux-armv7l/wheel 2025-08-31T18:15:49,026 Building wheel for clasv (setup.py): finished with status 'done' 2025-08-31T18:15:49,111 Created wheel for clasv: filename=clasv-1.0.4-py3-none-any.whl size=2537008 sha256=03db5788c67d9f72aae0d57f4608cf4481b337adf8087a0d69e8de2449863da6 2025-08-31T18:15:49,112 Stored in directory: /tmp/pip-ephem-wheel-cache-sjk4s0o9/wheels/77/fb/50/14881f4dd766de0a1a0f8981361cf4b541d4f47558d3e2689f 2025-08-31T18:15:49,137 Successfully built clasv 2025-08-31T18:15:49,211 Removed build tracker: '/tmp/pip-build-tracker-3qazz0sq'