2023-11-24T07:02:28,162 Created temporary directory: /tmp/pip-build-tracker-7l4xeeal 2023-11-24T07:02:28,163 Initialized build tracking at /tmp/pip-build-tracker-7l4xeeal 2023-11-24T07:02:28,164 Created build tracker: /tmp/pip-build-tracker-7l4xeeal 2023-11-24T07:02:28,164 Entered build tracker: /tmp/pip-build-tracker-7l4xeeal 2023-11-24T07:02:28,165 Created temporary directory: /tmp/pip-wheel-emuxkoun 2023-11-24T07:02:28,169 Created temporary directory: /tmp/pip-ephem-wheel-cache-4wg6_gl9 2023-11-24T07:02:28,191 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-11-24T07:02:28,195 2 location(s) to search for versions of witch-msa: 2023-11-24T07:02:28,195 * https://pypi.org/simple/witch-msa/ 2023-11-24T07:02:28,195 * https://www.piwheels.org/simple/witch-msa/ 2023-11-24T07:02:28,196 Fetching project page and analyzing links: https://pypi.org/simple/witch-msa/ 2023-11-24T07:02:28,197 Getting page https://pypi.org/simple/witch-msa/ 2023-11-24T07:02:28,198 Found index url https://pypi.org/simple/ 2023-11-24T07:02:28,341 Fetched page https://pypi.org/simple/witch-msa/ as application/vnd.pypi.simple.v1+json 2023-11-24T07:02:28,344 Found link https://files.pythonhosted.org/packages/9f/57/80dd0c29162c6b84cd017182095b5cb2aa4dc11260bbae056f3ef0351943/witch-msa-1.0.0rc1.tar.gz (from https://pypi.org/simple/witch-msa/) (requires-python:>=3.7), version: 1.0.0rc1 2023-11-24T07:02:28,344 Skipping link: No binaries permitted for witch-msa: https://files.pythonhosted.org/packages/43/78/272d4d835763bc77476391081248647987723a7b0226719cd93618a44b8a/witch_msa-1.0.0rc1-py3-none-any.whl (from https://pypi.org/simple/witch-msa/) (requires-python:>=3.7) 2023-11-24T07:02:28,345 Found link https://files.pythonhosted.org/packages/04/42/abe66ef86387d93b5b0bc9f23ec71b3660310d62820b56cb6315b13db266/witch-msa-1.0.0rc3.tar.gz (from https://pypi.org/simple/witch-msa/) (requires-python:>=3.7), version: 1.0.0rc3 2023-11-24T07:02:28,346 Skipping link: No binaries permitted for witch-msa: https://files.pythonhosted.org/packages/d5/e8/f939cdd95425dcd48632cc7a2fdaa939beabfed6d2004dff600c8afc0be1/witch_msa-1.0.0rc3-py3-none-any.whl (from https://pypi.org/simple/witch-msa/) (requires-python:>=3.7) 2023-11-24T07:02:28,347 Found link https://files.pythonhosted.org/packages/18/10/e568ef8fa1a5a231130cc83c420b1bed9bf69ceaf17911f5b45f67496b39/witch-msa-1.0.0rc4.tar.gz (from https://pypi.org/simple/witch-msa/) (requires-python:>=3.7), version: 1.0.0rc4 2023-11-24T07:02:28,347 Skipping link: No binaries permitted for witch-msa: https://files.pythonhosted.org/packages/de/20/c1d8c0f03fe35ea092495a73a29d3bca6a94ea55ea917d04b73cc7582215/witch_msa-1.0.0rc4-py3-none-any.whl (from https://pypi.org/simple/witch-msa/) (requires-python:>=3.7) 2023-11-24T07:02:28,348 Found link https://files.pythonhosted.org/packages/19/e6/150568e28ab0565dd78080eba70d4d2254038ef55327b82919e5915c6101/witch-msa-1.0.1.tar.gz (from https://pypi.org/simple/witch-msa/) (requires-python:>=3.7), version: 1.0.1 2023-11-24T07:02:28,349 Skipping link: No binaries permitted for witch-msa: https://files.pythonhosted.org/packages/6a/bf/e791b97aa9ff2e5592b40328ac11461a5dae4ecd40e175d1349be75cf37a/witch_msa-1.0.1-py3-none-any.whl (from https://pypi.org/simple/witch-msa/) (requires-python:>=3.7) 2023-11-24T07:02:28,350 Fetching project page and analyzing links: https://www.piwheels.org/simple/witch-msa/ 2023-11-24T07:02:28,351 Getting page https://www.piwheels.org/simple/witch-msa/ 2023-11-24T07:02:28,352 Found index url https://www.piwheels.org/simple/ 2023-11-24T07:02:28,516 Fetched page https://www.piwheels.org/simple/witch-msa/ as text/html 2023-11-24T07:02:28,518 Skipping link: No binaries permitted for witch-msa: https://www.piwheels.org/simple/witch-msa/witch_msa-1.0.0rc3-py3-none-any.whl#sha256=c99577c2a6e9a75c03f497d93f5f54ee9a04036357ca0b4cfb53f08df1f8023f (from https://www.piwheels.org/simple/witch-msa/) (requires-python:>=3.7) 2023-11-24T07:02:28,518 Skipping link: No binaries permitted for witch-msa: https://www.piwheels.org/simple/witch-msa/witch_msa-1.0.0rc1-py3-none-any.whl#sha256=7639b8df3d4a6b6fc2a4e2654e2da8d9636881239740deb58f44b604e93074d6 (from https://www.piwheels.org/simple/witch-msa/) (requires-python:>=3.7) 2023-11-24T07:02:28,519 Skipping link: not a file: https://www.piwheels.org/simple/witch-msa/ 2023-11-24T07:02:28,520 Skipping link: not a file: https://pypi.org/simple/witch-msa/ 2023-11-24T07:02:28,540 Given no hashes to check 1 links for project 'witch-msa': discarding no candidates 2023-11-24T07:02:28,559 Collecting witch-msa==1.0.0rc4 2023-11-24T07:02:28,561 Created temporary directory: /tmp/pip-unpack-bhu8e1m9 2023-11-24T07:02:28,972 Downloading witch-msa-1.0.0rc4.tar.gz (29.0 MB) 2023-11-24T07:02:38,960 Added witch-msa==1.0.0rc4 from https://files.pythonhosted.org/packages/18/10/e568ef8fa1a5a231130cc83c420b1bed9bf69ceaf17911f5b45f67496b39/witch-msa-1.0.0rc4.tar.gz to build tracker '/tmp/pip-build-tracker-7l4xeeal' 2023-11-24T07:02:38,965 Created temporary directory: /tmp/pip-build-env-ln3jvknf 2023-11-24T07:02:38,969 Installing build dependencies: started 2023-11-24T07:02:38,970 Running command pip subprocess to install build dependencies 2023-11-24T07:02:40,113 Using pip 23.3.1 from /home/piwheels/.local/lib/python3.11/site-packages/pip (python 3.11) 2023-11-24T07:02:40,637 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-11-24T07:02:42,081 Collecting setuptools 2023-11-24T07:02:42,082 Obtaining dependency information for setuptools from https://files.pythonhosted.org/packages/bb/e1/ed2dd0850446b8697ad28d118df885ad04140c64ace06c4bd559f7c8a94f/setuptools-69.0.2-py3-none-any.whl.metadata 2023-11-24T07:02:42,088 Using cached setuptools-69.0.2-py3-none-any.whl.metadata (6.3 kB) 2023-11-24T07:02:42,245 Using cached setuptools-69.0.2-py3-none-any.whl (819 kB) 2023-11-24T07:02:44,825 Installing collected packages: setuptools 2023-11-24T07:02:47,141 Successfully installed setuptools-69.0.2 2023-11-24T07:02:47,629 Installing build dependencies: finished with status 'done' 2023-11-24T07:02:47,633 Getting requirements to build wheel: started 2023-11-24T07:02:47,634 Running command Getting requirements to build wheel 2023-11-24T07:02:48,392 running egg_info 2023-11-24T07:02:48,396 writing witch_msa.egg-info/PKG-INFO 2023-11-24T07:02:48,401 writing dependency_links to witch_msa.egg-info/dependency_links.txt 2023-11-24T07:02:48,404 writing requirements to witch_msa.egg-info/requires.txt 2023-11-24T07:02:48,405 writing top-level names to witch_msa.egg-info/top_level.txt 2023-11-24T07:02:48,425 reading manifest file 'witch_msa.egg-info/SOURCES.txt' 2023-11-24T07:02:48,446 reading manifest template 'MANIFEST.in' 2023-11-24T07:02:48,465 no previously-included directories found matching '*/__pycache__' 2023-11-24T07:02:48,466 warning: no previously-included files matching '*.py[cod]' found anywhere in distribution 2023-11-24T07:02:48,467 adding license file 'LICENSE' 2023-11-24T07:02:48,475 writing manifest file 'witch_msa.egg-info/SOURCES.txt' 2023-11-24T07:02:48,587 Getting requirements to build wheel: finished with status 'done' 2023-11-24T07:02:48,595 Installing backend dependencies: started 2023-11-24T07:02:48,597 Running command pip subprocess to install backend dependencies 2023-11-24T07:02:49,783 Using pip 23.3.1 from /home/piwheels/.local/lib/python3.11/site-packages/pip (python 3.11) 2023-11-24T07:02:50,319 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-11-24T07:02:50,830 Collecting wheel 2023-11-24T07:02:50,845 Using cached https://www.piwheels.org/simple/wheel/wheel-0.41.3-py3-none-any.whl (65 kB) 2023-11-24T07:02:53,229 Installing collected packages: wheel 2023-11-24T07:02:53,466 Creating /tmp/pip-build-env-ln3jvknf/normal/local/bin 2023-11-24T07:02:53,469 changing mode of /tmp/pip-build-env-ln3jvknf/normal/local/bin/wheel to 755 2023-11-24T07:02:53,486 Successfully installed wheel-0.41.3 2023-11-24T07:02:53,940 Installing backend dependencies: finished with status 'done' 2023-11-24T07:02:53,942 Created temporary directory: /tmp/pip-modern-metadata-wkqia_8m 2023-11-24T07:02:53,945 Preparing metadata (pyproject.toml): started 2023-11-24T07:02:53,946 Running command Preparing metadata (pyproject.toml) 2023-11-24T07:02:54,747 running dist_info 2023-11-24T07:02:54,752 creating /tmp/pip-modern-metadata-wkqia_8m/witch_msa.egg-info 2023-11-24T07:02:54,755 writing /tmp/pip-modern-metadata-wkqia_8m/witch_msa.egg-info/PKG-INFO 2023-11-24T07:02:54,761 writing dependency_links to /tmp/pip-modern-metadata-wkqia_8m/witch_msa.egg-info/dependency_links.txt 2023-11-24T07:02:54,763 writing requirements to /tmp/pip-modern-metadata-wkqia_8m/witch_msa.egg-info/requires.txt 2023-11-24T07:02:54,764 writing top-level names to /tmp/pip-modern-metadata-wkqia_8m/witch_msa.egg-info/top_level.txt 2023-11-24T07:02:54,765 writing manifest file '/tmp/pip-modern-metadata-wkqia_8m/witch_msa.egg-info/SOURCES.txt' 2023-11-24T07:02:54,787 reading manifest file '/tmp/pip-modern-metadata-wkqia_8m/witch_msa.egg-info/SOURCES.txt' 2023-11-24T07:02:54,789 reading manifest template 'MANIFEST.in' 2023-11-24T07:02:54,816 no previously-included directories found matching '*/__pycache__' 2023-11-24T07:02:54,817 warning: no previously-included files matching '*.py[cod]' found anywhere in distribution 2023-11-24T07:02:54,818 adding license file 'LICENSE' 2023-11-24T07:02:54,824 writing manifest file '/tmp/pip-modern-metadata-wkqia_8m/witch_msa.egg-info/SOURCES.txt' 2023-11-24T07:02:54,825 creating '/tmp/pip-modern-metadata-wkqia_8m/witch_msa-1.0.0rc4.dist-info' 2023-11-24T07:02:54,980 Preparing metadata (pyproject.toml): finished with status 'done' 2023-11-24T07:02:54,992 Source in /tmp/pip-wheel-emuxkoun/witch-msa_0b05e50c49604edd934ef78fe9b867a5 has version 1.0.0rc4, which satisfies requirement witch-msa==1.0.0rc4 from https://files.pythonhosted.org/packages/18/10/e568ef8fa1a5a231130cc83c420b1bed9bf69ceaf17911f5b45f67496b39/witch-msa-1.0.0rc4.tar.gz 2023-11-24T07:02:54,993 Removed witch-msa==1.0.0rc4 from https://files.pythonhosted.org/packages/18/10/e568ef8fa1a5a231130cc83c420b1bed9bf69ceaf17911f5b45f67496b39/witch-msa-1.0.0rc4.tar.gz from build tracker '/tmp/pip-build-tracker-7l4xeeal' 2023-11-24T07:02:55,013 Created temporary directory: /tmp/pip-unpack-wisulfuy 2023-11-24T07:02:55,014 Created temporary directory: /tmp/pip-unpack-u_1_z9me 2023-11-24T07:02:55,040 Building wheels for collected packages: witch-msa 2023-11-24T07:02:55,044 Created temporary directory: /tmp/pip-wheel-b6rc96eb 2023-11-24T07:02:55,045 Destination directory: /tmp/pip-wheel-b6rc96eb 2023-11-24T07:02:55,047 Building wheel for witch-msa (pyproject.toml): started 2023-11-24T07:02:55,048 Running command Building wheel for witch-msa (pyproject.toml) 2023-11-24T07:02:55,802 running bdist_wheel 2023-11-24T07:02:55,819 running build 2023-11-24T07:02:55,820 running build_py 2023-11-24T07:02:55,824 creating build 2023-11-24T07:02:55,825 creating build/lib 2023-11-24T07:02:55,826 creating build/lib/witch_msa 2023-11-24T07:02:55,827 copying witch_msa/init_configs.py -> build/lib/witch_msa 2023-11-24T07:02:55,829 copying witch_msa/configs.py -> build/lib/witch_msa 2023-11-24T07:02:55,832 copying witch_msa/__init__.py -> build/lib/witch_msa 2023-11-24T07:02:55,835 creating build/lib/witch_msa/gcmm 2023-11-24T07:02:55,836 copying witch_msa/gcmm/weighting.py -> build/lib/witch_msa/gcmm 2023-11-24T07:02:55,838 copying witch_msa/gcmm/callback.py -> build/lib/witch_msa/gcmm 2023-11-24T07:02:55,840 copying witch_msa/gcmm/algorithm.py -> build/lib/witch_msa/gcmm 2023-11-24T07:02:55,843 copying witch_msa/gcmm/loader.py -> build/lib/witch_msa/gcmm 2023-11-24T07:02:55,845 copying witch_msa/gcmm/decompose_tree.py -> build/lib/witch_msa/gcmm 2023-11-24T07:02:55,847 copying witch_msa/gcmm/aligner.py -> build/lib/witch_msa/gcmm 2023-11-24T07:02:55,850 copying witch_msa/gcmm/tree.py -> build/lib/witch_msa/gcmm 2023-11-24T07:02:55,853 copying witch_msa/gcmm/backbone.py -> build/lib/witch_msa/gcmm 2023-11-24T07:02:55,856 copying witch_msa/gcmm/results_handler.py -> build/lib/witch_msa/gcmm 2023-11-24T07:02:55,858 copying witch_msa/gcmm/task.py -> build/lib/witch_msa/gcmm 2023-11-24T07:02:55,861 copying witch_msa/gcmm/__init__.py -> build/lib/witch_msa/gcmm 2023-11-24T07:02:55,862 copying witch_msa/gcmm/gcmm.py -> build/lib/witch_msa/gcmm 2023-11-24T07:02:55,865 copying witch_msa/gcmm/merger.py -> build/lib/witch_msa/gcmm 2023-11-24T07:02:55,867 creating build/lib/witch_msa/helpers 2023-11-24T07:02:55,868 copying witch_msa/helpers/pyhmmer_tools.py -> build/lib/witch_msa/helpers 2023-11-24T07:02:55,870 copying witch_msa/helpers/alignment_tools.py -> build/lib/witch_msa/helpers 2023-11-24T07:02:55,873 copying witch_msa/helpers/general_tools.py -> build/lib/witch_msa/helpers 2023-11-24T07:02:55,876 copying witch_msa/helpers/math_utils.py -> build/lib/witch_msa/helpers 2023-11-24T07:02:55,878 copying witch_msa/helpers/__init__.py -> build/lib/witch_msa/helpers 2023-11-24T07:02:55,880 running egg_info 2023-11-24T07:02:55,883 writing witch_msa.egg-info/PKG-INFO 2023-11-24T07:02:55,888 writing dependency_links to witch_msa.egg-info/dependency_links.txt 2023-11-24T07:02:55,890 writing requirements to witch_msa.egg-info/requires.txt 2023-11-24T07:02:55,891 writing top-level names to witch_msa.egg-info/top_level.txt 2023-11-24T07:02:55,901 reading manifest file 'witch_msa.egg-info/SOURCES.txt' 2023-11-24T07:02:55,906 reading manifest template 'MANIFEST.in' 2023-11-24T07:02:55,919 no previously-included directories found matching '*/__pycache__' 2023-11-24T07:02:55,920 warning: no previously-included files matching '*.py[cod]' found anywhere in distribution 2023-11-24T07:02:55,921 adding license file 'LICENSE' 2023-11-24T07:02:55,929 writing manifest file 'witch_msa.egg-info/SOURCES.txt' 2023-11-24T07:02:55,932 /tmp/pip-build-env-ln3jvknf/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'witch_msa.tools.macOS' is absent from the `packages` configuration. 2023-11-24T07:02:55,932 !! 2023-11-24T07:02:55,933 ******************************************************************************** 2023-11-24T07:02:55,934 ############################ 2023-11-24T07:02:55,935 # Package would be ignored # 2023-11-24T07:02:55,935 ############################ 2023-11-24T07:02:55,936 Python recognizes 'witch_msa.tools.macOS' as an importable package[^1], 2023-11-24T07:02:55,937 but it is absent from setuptools' `packages` configuration. 2023-11-24T07:02:55,938 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-24T07:02:55,939 package, please make sure that 'witch_msa.tools.macOS' is explicitly added 2023-11-24T07:02:55,939 to the `packages` configuration field. 2023-11-24T07:02:55,940 Alternatively, you can also rely on setuptools' discovery methods 2023-11-24T07:02:55,941 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-24T07:02:55,942 instead of `find_packages(...)`/`find:`). 2023-11-24T07:02:55,943 You can read more about "package discovery" on setuptools documentation page: 2023-11-24T07:02:55,944 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-24T07:02:55,945 If you don't want 'witch_msa.tools.macOS' to be distributed and are 2023-11-24T07:02:55,946 already explicitly excluding 'witch_msa.tools.macOS' via 2023-11-24T07:02:55,946 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-24T07:02:55,947 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-24T07:02:55,947 combination with a more fine grained `package-data` configuration. 2023-11-24T07:02:55,949 You can read more about "package data files" on setuptools documentation page: 2023-11-24T07:02:55,950 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-24T07:02:55,952 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-24T07:02:55,952 even if it does not contain any `.py` files. 2023-11-24T07:02:55,953 On the other hand, currently there is no concept of package data 2023-11-24T07:02:55,953 directory, all directories are treated like packages. 2023-11-24T07:02:55,954 ******************************************************************************** 2023-11-24T07:02:55,954 !! 2023-11-24T07:02:55,955 check.warn(importable) 2023-11-24T07:02:55,955 /tmp/pip-build-env-ln3jvknf/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'witch_msa.tools.magus' is absent from the `packages` configuration. 2023-11-24T07:02:55,956 !! 2023-11-24T07:02:55,956 ******************************************************************************** 2023-11-24T07:02:55,957 ############################ 2023-11-24T07:02:55,957 # Package would be ignored # 2023-11-24T07:02:55,958 ############################ 2023-11-24T07:02:55,958 Python recognizes 'witch_msa.tools.magus' as an importable package[^1], 2023-11-24T07:02:55,958 but it is absent from setuptools' `packages` configuration. 2023-11-24T07:02:55,959 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-24T07:02:55,960 package, please make sure that 'witch_msa.tools.magus' is explicitly added 2023-11-24T07:02:55,960 to the `packages` configuration field. 2023-11-24T07:02:55,961 Alternatively, you can also rely on setuptools' discovery methods 2023-11-24T07:02:55,962 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-24T07:02:55,962 instead of `find_packages(...)`/`find:`). 2023-11-24T07:02:55,963 You can read more about "package discovery" on setuptools documentation page: 2023-11-24T07:02:55,964 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-24T07:02:55,966 If you don't want 'witch_msa.tools.magus' to be distributed and are 2023-11-24T07:02:55,966 already explicitly excluding 'witch_msa.tools.magus' via 2023-11-24T07:02:55,967 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-24T07:02:55,967 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-24T07:02:55,968 combination with a more fine grained `package-data` configuration. 2023-11-24T07:02:55,969 You can read more about "package data files" on setuptools documentation page: 2023-11-24T07:02:55,970 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-24T07:02:55,972 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-24T07:02:55,972 even if it does not contain any `.py` files. 2023-11-24T07:02:55,973 On the other hand, currently there is no concept of package data 2023-11-24T07:02:55,973 directory, all directories are treated like packages. 2023-11-24T07:02:55,974 ******************************************************************************** 2023-11-24T07:02:55,975 !! 2023-11-24T07:02:55,976 check.warn(importable) 2023-11-24T07:02:55,976 /tmp/pip-build-env-ln3jvknf/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'witch_msa.tools.magus.align' is absent from the `packages` configuration. 2023-11-24T07:02:55,977 !! 2023-11-24T07:02:55,978 ******************************************************************************** 2023-11-24T07:02:55,978 ############################ 2023-11-24T07:02:55,981 # Package would be ignored # 2023-11-24T07:02:55,982 ############################ 2023-11-24T07:02:55,983 Python recognizes 'witch_msa.tools.magus.align' as an importable package[^1], 2023-11-24T07:02:55,983 but it is absent from setuptools' `packages` configuration. 2023-11-24T07:02:55,984 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-24T07:02:55,985 package, please make sure that 'witch_msa.tools.magus.align' is explicitly added 2023-11-24T07:02:55,985 to the `packages` configuration field. 2023-11-24T07:02:55,986 Alternatively, you can also rely on setuptools' discovery methods 2023-11-24T07:02:55,986 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-24T07:02:55,987 instead of `find_packages(...)`/`find:`). 2023-11-24T07:02:55,988 You can read more about "package discovery" on setuptools documentation page: 2023-11-24T07:02:55,994 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-24T07:02:55,997 If you don't want 'witch_msa.tools.magus.align' to be distributed and are 2023-11-24T07:02:55,998 already explicitly excluding 'witch_msa.tools.magus.align' via 2023-11-24T07:02:55,999 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-24T07:02:56,002 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-24T07:02:56,002 combination with a more fine grained `package-data` configuration. 2023-11-24T07:02:56,003 You can read more about "package data files" on setuptools documentation page: 2023-11-24T07:02:56,004 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-24T07:02:56,006 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-24T07:02:56,006 even if it does not contain any `.py` files. 2023-11-24T07:02:56,007 On the other hand, currently there is no concept of package data 2023-11-24T07:02:56,007 directory, all directories are treated like packages. 2023-11-24T07:02:56,008 ******************************************************************************** 2023-11-24T07:02:56,009 !! 2023-11-24T07:02:56,009 check.warn(importable) 2023-11-24T07:02:56,010 /tmp/pip-build-env-ln3jvknf/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'witch_msa.tools.magus.align.decompose' is absent from the `packages` configuration. 2023-11-24T07:02:56,010 !! 2023-11-24T07:02:56,012 ******************************************************************************** 2023-11-24T07:02:56,013 ############################ 2023-11-24T07:02:56,013 # Package would be ignored # 2023-11-24T07:02:56,014 ############################ 2023-11-24T07:02:56,014 Python recognizes 'witch_msa.tools.magus.align.decompose' as an importable package[^1], 2023-11-24T07:02:56,015 but it is absent from setuptools' `packages` configuration. 2023-11-24T07:02:56,016 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-24T07:02:56,017 package, please make sure that 'witch_msa.tools.magus.align.decompose' is explicitly added 2023-11-24T07:02:56,018 to the `packages` configuration field. 2023-11-24T07:02:56,019 Alternatively, you can also rely on setuptools' discovery methods 2023-11-24T07:02:56,019 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-24T07:02:56,020 instead of `find_packages(...)`/`find:`). 2023-11-24T07:02:56,022 You can read more about "package discovery" on setuptools documentation page: 2023-11-24T07:02:56,024 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-24T07:02:56,029 If you don't want 'witch_msa.tools.magus.align.decompose' to be distributed and are 2023-11-24T07:02:56,030 already explicitly excluding 'witch_msa.tools.magus.align.decompose' via 2023-11-24T07:02:56,031 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-24T07:02:56,032 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-24T07:02:56,033 combination with a more fine grained `package-data` configuration. 2023-11-24T07:02:56,034 You can read more about "package data files" on setuptools documentation page: 2023-11-24T07:02:56,035 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-24T07:02:56,037 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-24T07:02:56,038 even if it does not contain any `.py` files. 2023-11-24T07:02:56,038 On the other hand, currently there is no concept of package data 2023-11-24T07:02:56,039 directory, all directories are treated like packages. 2023-11-24T07:02:56,039 ******************************************************************************** 2023-11-24T07:02:56,041 !! 2023-11-24T07:02:56,041 check.warn(importable) 2023-11-24T07:02:56,043 /tmp/pip-build-env-ln3jvknf/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'witch_msa.tools.magus.align.merge' is absent from the `packages` configuration. 2023-11-24T07:02:56,047 !! 2023-11-24T07:02:56,048 ******************************************************************************** 2023-11-24T07:02:56,049 ############################ 2023-11-24T07:02:56,049 # Package would be ignored # 2023-11-24T07:02:56,049 ############################ 2023-11-24T07:02:56,050 Python recognizes 'witch_msa.tools.magus.align.merge' as an importable package[^1], 2023-11-24T07:02:56,050 but it is absent from setuptools' `packages` configuration. 2023-11-24T07:02:56,052 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-24T07:02:56,053 package, please make sure that 'witch_msa.tools.magus.align.merge' is explicitly added 2023-11-24T07:02:56,053 to the `packages` configuration field. 2023-11-24T07:02:56,054 Alternatively, you can also rely on setuptools' discovery methods 2023-11-24T07:02:56,055 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-24T07:02:56,055 instead of `find_packages(...)`/`find:`). 2023-11-24T07:02:56,056 You can read more about "package discovery" on setuptools documentation page: 2023-11-24T07:02:56,060 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-24T07:02:56,062 If you don't want 'witch_msa.tools.magus.align.merge' to be distributed and are 2023-11-24T07:02:56,062 already explicitly excluding 'witch_msa.tools.magus.align.merge' via 2023-11-24T07:02:56,063 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-24T07:02:56,063 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-24T07:02:56,064 combination with a more fine grained `package-data` configuration. 2023-11-24T07:02:56,065 You can read more about "package data files" on setuptools documentation page: 2023-11-24T07:02:56,066 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-24T07:02:56,067 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-24T07:02:56,068 even if it does not contain any `.py` files. 2023-11-24T07:02:56,068 On the other hand, currently there is no concept of package data 2023-11-24T07:02:56,069 directory, all directories are treated like packages. 2023-11-24T07:02:56,070 ******************************************************************************** 2023-11-24T07:02:56,071 !! 2023-11-24T07:02:56,071 check.warn(importable) 2023-11-24T07:02:56,072 /tmp/pip-build-env-ln3jvknf/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'witch_msa.tools.magus.align.merge.graph_build' is absent from the `packages` configuration. 2023-11-24T07:02:56,073 !! 2023-11-24T07:02:56,074 ******************************************************************************** 2023-11-24T07:02:56,074 ############################ 2023-11-24T07:02:56,075 # Package would be ignored # 2023-11-24T07:02:56,075 ############################ 2023-11-24T07:02:56,076 Python recognizes 'witch_msa.tools.magus.align.merge.graph_build' as an importable package[^1], 2023-11-24T07:02:56,076 but it is absent from setuptools' `packages` configuration. 2023-11-24T07:02:56,077 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-24T07:02:56,077 package, please make sure that 'witch_msa.tools.magus.align.merge.graph_build' is explicitly added 2023-11-24T07:02:56,078 to the `packages` configuration field. 2023-11-24T07:02:56,079 Alternatively, you can also rely on setuptools' discovery methods 2023-11-24T07:02:56,079 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-24T07:02:56,080 instead of `find_packages(...)`/`find:`). 2023-11-24T07:02:56,081 You can read more about "package discovery" on setuptools documentation page: 2023-11-24T07:02:56,081 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-24T07:02:56,082 If you don't want 'witch_msa.tools.magus.align.merge.graph_build' to be distributed and are 2023-11-24T07:02:56,083 already explicitly excluding 'witch_msa.tools.magus.align.merge.graph_build' via 2023-11-24T07:02:56,083 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-24T07:02:56,084 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-24T07:02:56,084 combination with a more fine grained `package-data` configuration. 2023-11-24T07:02:56,086 You can read more about "package data files" on setuptools documentation page: 2023-11-24T07:02:56,086 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-24T07:02:56,088 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-24T07:02:56,088 even if it does not contain any `.py` files. 2023-11-24T07:02:56,089 On the other hand, currently there is no concept of package data 2023-11-24T07:02:56,089 directory, all directories are treated like packages. 2023-11-24T07:02:56,090 ******************************************************************************** 2023-11-24T07:02:56,091 !! 2023-11-24T07:02:56,091 check.warn(importable) 2023-11-24T07:02:56,092 /tmp/pip-build-env-ln3jvknf/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'witch_msa.tools.magus.align.merge.graph_cluster' is absent from the `packages` configuration. 2023-11-24T07:02:56,092 !! 2023-11-24T07:02:56,093 ******************************************************************************** 2023-11-24T07:02:56,094 ############################ 2023-11-24T07:02:56,094 # Package would be ignored # 2023-11-24T07:02:56,095 ############################ 2023-11-24T07:02:56,095 Python recognizes 'witch_msa.tools.magus.align.merge.graph_cluster' as an importable package[^1], 2023-11-24T07:02:56,096 but it is absent from setuptools' `packages` configuration. 2023-11-24T07:02:56,097 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-24T07:02:56,097 package, please make sure that 'witch_msa.tools.magus.align.merge.graph_cluster' is explicitly added 2023-11-24T07:02:56,098 to the `packages` configuration field. 2023-11-24T07:02:56,099 Alternatively, you can also rely on setuptools' discovery methods 2023-11-24T07:02:56,099 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-24T07:02:56,100 instead of `find_packages(...)`/`find:`). 2023-11-24T07:02:56,101 You can read more about "package discovery" on setuptools documentation page: 2023-11-24T07:02:56,102 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-24T07:02:56,103 If you don't want 'witch_msa.tools.magus.align.merge.graph_cluster' to be distributed and are 2023-11-24T07:02:56,103 already explicitly excluding 'witch_msa.tools.magus.align.merge.graph_cluster' via 2023-11-24T07:02:56,104 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-24T07:02:56,104 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-24T07:02:56,105 combination with a more fine grained `package-data` configuration. 2023-11-24T07:02:56,106 You can read more about "package data files" on setuptools documentation page: 2023-11-24T07:02:56,107 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-24T07:02:56,109 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-24T07:02:56,109 even if it does not contain any `.py` files. 2023-11-24T07:02:56,110 On the other hand, currently there is no concept of package data 2023-11-24T07:02:56,110 directory, all directories are treated like packages. 2023-11-24T07:02:56,111 ******************************************************************************** 2023-11-24T07:02:56,112 !! 2023-11-24T07:02:56,112 check.warn(importable) 2023-11-24T07:02:56,113 /tmp/pip-build-env-ln3jvknf/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'witch_msa.tools.magus.align.merge.graph_trace' is absent from the `packages` configuration. 2023-11-24T07:02:56,113 !! 2023-11-24T07:02:56,114 ******************************************************************************** 2023-11-24T07:02:56,115 ############################ 2023-11-24T07:02:56,115 # Package would be ignored # 2023-11-24T07:02:56,115 ############################ 2023-11-24T07:02:56,116 Python recognizes 'witch_msa.tools.magus.align.merge.graph_trace' as an importable package[^1], 2023-11-24T07:02:56,116 but it is absent from setuptools' `packages` configuration. 2023-11-24T07:02:56,117 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-24T07:02:56,118 package, please make sure that 'witch_msa.tools.magus.align.merge.graph_trace' is explicitly added 2023-11-24T07:02:56,118 to the `packages` configuration field. 2023-11-24T07:02:56,119 Alternatively, you can also rely on setuptools' discovery methods 2023-11-24T07:02:56,120 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-24T07:02:56,120 instead of `find_packages(...)`/`find:`). 2023-11-24T07:02:56,121 You can read more about "package discovery" on setuptools documentation page: 2023-11-24T07:02:56,122 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-24T07:02:56,123 If you don't want 'witch_msa.tools.magus.align.merge.graph_trace' to be distributed and are 2023-11-24T07:02:56,124 already explicitly excluding 'witch_msa.tools.magus.align.merge.graph_trace' via 2023-11-24T07:02:56,124 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-24T07:02:56,125 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-24T07:02:56,125 combination with a more fine grained `package-data` configuration. 2023-11-24T07:02:56,126 You can read more about "package data files" on setuptools documentation page: 2023-11-24T07:02:56,128 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-24T07:02:56,129 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-24T07:02:56,130 even if it does not contain any `.py` files. 2023-11-24T07:02:56,130 On the other hand, currently there is no concept of package data 2023-11-24T07:02:56,130 directory, all directories are treated like packages. 2023-11-24T07:02:56,131 ******************************************************************************** 2023-11-24T07:02:56,132 !! 2023-11-24T07:02:56,132 check.warn(importable) 2023-11-24T07:02:56,133 /tmp/pip-build-env-ln3jvknf/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'witch_msa.tools.magus.helpers' is absent from the `packages` configuration. 2023-11-24T07:02:56,133 !! 2023-11-24T07:02:56,134 ******************************************************************************** 2023-11-24T07:02:56,134 ############################ 2023-11-24T07:02:56,135 # Package would be ignored # 2023-11-24T07:02:56,135 ############################ 2023-11-24T07:02:56,136 Python recognizes 'witch_msa.tools.magus.helpers' as an importable package[^1], 2023-11-24T07:02:56,136 but it is absent from setuptools' `packages` configuration. 2023-11-24T07:02:56,137 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-24T07:02:56,138 package, please make sure that 'witch_msa.tools.magus.helpers' is explicitly added 2023-11-24T07:02:56,138 to the `packages` configuration field. 2023-11-24T07:02:56,139 Alternatively, you can also rely on setuptools' discovery methods 2023-11-24T07:02:56,139 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-24T07:02:56,140 instead of `find_packages(...)`/`find:`). 2023-11-24T07:02:56,141 You can read more about "package discovery" on setuptools documentation page: 2023-11-24T07:02:56,142 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-24T07:02:56,143 If you don't want 'witch_msa.tools.magus.helpers' to be distributed and are 2023-11-24T07:02:56,143 already explicitly excluding 'witch_msa.tools.magus.helpers' via 2023-11-24T07:02:56,144 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-24T07:02:56,144 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-24T07:02:56,145 combination with a more fine grained `package-data` configuration. 2023-11-24T07:02:56,145 You can read more about "package data files" on setuptools documentation page: 2023-11-24T07:02:56,146 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-24T07:02:56,148 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-24T07:02:56,148 even if it does not contain any `.py` files. 2023-11-24T07:02:56,149 On the other hand, currently there is no concept of package data 2023-11-24T07:02:56,149 directory, all directories are treated like packages. 2023-11-24T07:02:56,150 ******************************************************************************** 2023-11-24T07:02:56,151 !! 2023-11-24T07:02:56,151 check.warn(importable) 2023-11-24T07:02:56,152 /tmp/pip-build-env-ln3jvknf/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'witch_msa.tools.magus.tasks' is absent from the `packages` configuration. 2023-11-24T07:02:56,152 !! 2023-11-24T07:02:56,153 ******************************************************************************** 2023-11-24T07:02:56,154 ############################ 2023-11-24T07:02:56,154 # Package would be ignored # 2023-11-24T07:02:56,155 ############################ 2023-11-24T07:02:56,155 Python recognizes 'witch_msa.tools.magus.tasks' as an importable package[^1], 2023-11-24T07:02:56,156 but it is absent from setuptools' `packages` configuration. 2023-11-24T07:02:56,157 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-24T07:02:56,157 package, please make sure that 'witch_msa.tools.magus.tasks' is explicitly added 2023-11-24T07:02:56,158 to the `packages` configuration field. 2023-11-24T07:02:56,158 Alternatively, you can also rely on setuptools' discovery methods 2023-11-24T07:02:56,159 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-24T07:02:56,159 instead of `find_packages(...)`/`find:`). 2023-11-24T07:02:56,160 You can read more about "package discovery" on setuptools documentation page: 2023-11-24T07:02:56,161 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-24T07:02:56,162 If you don't want 'witch_msa.tools.magus.tasks' to be distributed and are 2023-11-24T07:02:56,162 already explicitly excluding 'witch_msa.tools.magus.tasks' via 2023-11-24T07:02:56,163 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-24T07:02:56,163 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-24T07:02:56,163 combination with a more fine grained `package-data` configuration. 2023-11-24T07:02:56,164 You can read more about "package data files" on setuptools documentation page: 2023-11-24T07:02:56,165 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-24T07:02:56,166 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-24T07:02:56,167 even if it does not contain any `.py` files. 2023-11-24T07:02:56,167 On the other hand, currently there is no concept of package data 2023-11-24T07:02:56,168 directory, all directories are treated like packages. 2023-11-24T07:02:56,168 ******************************************************************************** 2023-11-24T07:02:56,169 !! 2023-11-24T07:02:56,170 check.warn(importable) 2023-11-24T07:02:56,170 /tmp/pip-build-env-ln3jvknf/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'witch_msa.tools.magus.tools' is absent from the `packages` configuration. 2023-11-24T07:02:56,171 !! 2023-11-24T07:02:56,172 ******************************************************************************** 2023-11-24T07:02:56,172 ############################ 2023-11-24T07:02:56,173 # Package would be ignored # 2023-11-24T07:02:56,173 ############################ 2023-11-24T07:02:56,174 Python recognizes 'witch_msa.tools.magus.tools' as an importable package[^1], 2023-11-24T07:02:56,174 but it is absent from setuptools' `packages` configuration. 2023-11-24T07:02:56,175 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-24T07:02:56,176 package, please make sure that 'witch_msa.tools.magus.tools' is explicitly added 2023-11-24T07:02:56,176 to the `packages` configuration field. 2023-11-24T07:02:56,177 Alternatively, you can also rely on setuptools' discovery methods 2023-11-24T07:02:56,178 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-24T07:02:56,178 instead of `find_packages(...)`/`find:`). 2023-11-24T07:02:56,179 You can read more about "package discovery" on setuptools documentation page: 2023-11-24T07:02:56,180 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-24T07:02:56,181 If you don't want 'witch_msa.tools.magus.tools' to be distributed and are 2023-11-24T07:02:56,182 already explicitly excluding 'witch_msa.tools.magus.tools' via 2023-11-24T07:02:56,182 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-24T07:02:56,183 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-24T07:02:56,183 combination with a more fine grained `package-data` configuration. 2023-11-24T07:02:56,184 You can read more about "package data files" on setuptools documentation page: 2023-11-24T07:02:56,185 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-24T07:02:56,186 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-24T07:02:56,187 even if it does not contain any `.py` files. 2023-11-24T07:02:56,187 On the other hand, currently there is no concept of package data 2023-11-24T07:02:56,188 directory, all directories are treated like packages. 2023-11-24T07:02:56,188 ******************************************************************************** 2023-11-24T07:02:56,189 !! 2023-11-24T07:02:56,189 check.warn(importable) 2023-11-24T07:02:56,190 /tmp/pip-build-env-ln3jvknf/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'witch_msa.tools.magus.tools.clustal' is absent from the `packages` configuration. 2023-11-24T07:02:56,190 !! 2023-11-24T07:02:56,191 ******************************************************************************** 2023-11-24T07:02:56,192 ############################ 2023-11-24T07:02:56,192 # Package would be ignored # 2023-11-24T07:02:56,193 ############################ 2023-11-24T07:02:56,193 Python recognizes 'witch_msa.tools.magus.tools.clustal' as an importable package[^1], 2023-11-24T07:02:56,194 but it is absent from setuptools' `packages` configuration. 2023-11-24T07:02:56,195 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-24T07:02:56,195 package, please make sure that 'witch_msa.tools.magus.tools.clustal' is explicitly added 2023-11-24T07:02:56,196 to the `packages` configuration field. 2023-11-24T07:02:56,197 Alternatively, you can also rely on setuptools' discovery methods 2023-11-24T07:02:56,197 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-24T07:02:56,198 instead of `find_packages(...)`/`find:`). 2023-11-24T07:02:56,199 You can read more about "package discovery" on setuptools documentation page: 2023-11-24T07:02:56,200 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-24T07:02:56,201 If you don't want 'witch_msa.tools.magus.tools.clustal' to be distributed and are 2023-11-24T07:02:56,201 already explicitly excluding 'witch_msa.tools.magus.tools.clustal' via 2023-11-24T07:02:56,202 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-24T07:02:56,202 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-24T07:02:56,212 combination with a more fine grained `package-data` configuration. 2023-11-24T07:02:56,219 You can read more about "package data files" on setuptools documentation page: 2023-11-24T07:02:56,256 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-24T07:02:56,257 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-24T07:02:56,258 even if it does not contain any `.py` files. 2023-11-24T07:02:56,258 On the other hand, currently there is no concept of package data 2023-11-24T07:02:56,259 directory, all directories are treated like packages. 2023-11-24T07:02:56,260 ******************************************************************************** 2023-11-24T07:02:56,261 !! 2023-11-24T07:02:56,261 check.warn(importable) 2023-11-24T07:02:56,262 /tmp/pip-build-env-ln3jvknf/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'witch_msa.tools.magus.tools.fasttree' is absent from the `packages` configuration. 2023-11-24T07:02:56,262 !! 2023-11-24T07:02:56,263 ******************************************************************************** 2023-11-24T07:02:56,264 ############################ 2023-11-24T07:02:56,265 # Package would be ignored # 2023-11-24T07:02:56,267 ############################ 2023-11-24T07:02:56,268 Python recognizes 'witch_msa.tools.magus.tools.fasttree' as an importable package[^1], 2023-11-24T07:02:56,268 but it is absent from setuptools' `packages` configuration. 2023-11-24T07:02:56,269 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-24T07:02:56,269 package, please make sure that 'witch_msa.tools.magus.tools.fasttree' is explicitly added 2023-11-24T07:02:56,270 to the `packages` configuration field. 2023-11-24T07:02:56,271 Alternatively, you can also rely on setuptools' discovery methods 2023-11-24T07:02:56,271 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-24T07:02:56,272 instead of `find_packages(...)`/`find:`). 2023-11-24T07:02:56,276 You can read more about "package discovery" on setuptools documentation page: 2023-11-24T07:02:56,277 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-24T07:02:56,279 If you don't want 'witch_msa.tools.magus.tools.fasttree' to be distributed and are 2023-11-24T07:02:56,279 already explicitly excluding 'witch_msa.tools.magus.tools.fasttree' via 2023-11-24T07:02:56,280 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-24T07:02:56,281 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-24T07:02:56,291 combination with a more fine grained `package-data` configuration. 2023-11-24T07:02:56,300 You can read more about "package data files" on setuptools documentation page: 2023-11-24T07:02:56,303 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-24T07:02:56,304 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-24T07:02:56,305 even if it does not contain any `.py` files. 2023-11-24T07:02:56,311 On the other hand, currently there is no concept of package data 2023-11-24T07:02:56,316 directory, all directories are treated like packages. 2023-11-24T07:02:56,318 ******************************************************************************** 2023-11-24T07:02:56,321 !! 2023-11-24T07:02:56,326 check.warn(importable) 2023-11-24T07:02:56,327 /tmp/pip-build-env-ln3jvknf/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'witch_msa.tools.magus.tools.hmmer' is absent from the `packages` configuration. 2023-11-24T07:02:56,327 !! 2023-11-24T07:02:56,332 ******************************************************************************** 2023-11-24T07:02:56,332 ############################ 2023-11-24T07:02:56,333 # Package would be ignored # 2023-11-24T07:02:56,333 ############################ 2023-11-24T07:02:56,334 Python recognizes 'witch_msa.tools.magus.tools.hmmer' as an importable package[^1], 2023-11-24T07:02:56,335 but it is absent from setuptools' `packages` configuration. 2023-11-24T07:02:56,340 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-24T07:02:56,345 package, please make sure that 'witch_msa.tools.magus.tools.hmmer' is explicitly added 2023-11-24T07:02:56,351 to the `packages` configuration field. 2023-11-24T07:02:56,352 Alternatively, you can also rely on setuptools' discovery methods 2023-11-24T07:02:56,352 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-24T07:02:56,353 instead of `find_packages(...)`/`find:`). 2023-11-24T07:02:56,354 You can read more about "package discovery" on setuptools documentation page: 2023-11-24T07:02:56,355 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-24T07:02:56,356 If you don't want 'witch_msa.tools.magus.tools.hmmer' to be distributed and are 2023-11-24T07:02:56,356 already explicitly excluding 'witch_msa.tools.magus.tools.hmmer' via 2023-11-24T07:02:56,357 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-24T07:02:56,357 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-24T07:02:56,358 combination with a more fine grained `package-data` configuration. 2023-11-24T07:02:56,360 You can read more about "package data files" on setuptools documentation page: 2023-11-24T07:02:56,361 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-24T07:02:56,362 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-24T07:02:56,363 even if it does not contain any `.py` files. 2023-11-24T07:02:56,363 On the other hand, currently there is no concept of package data 2023-11-24T07:02:56,372 directory, all directories are treated like packages. 2023-11-24T07:02:56,375 ******************************************************************************** 2023-11-24T07:02:56,384 !! 2023-11-24T07:02:56,385 check.warn(importable) 2023-11-24T07:02:56,385 /tmp/pip-build-env-ln3jvknf/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'witch_msa.tools.magus.tools.mafft' is absent from the `packages` configuration. 2023-11-24T07:02:56,386 !! 2023-11-24T07:02:56,387 ******************************************************************************** 2023-11-24T07:02:56,387 ############################ 2023-11-24T07:02:56,388 # Package would be ignored # 2023-11-24T07:02:56,388 ############################ 2023-11-24T07:02:56,389 Python recognizes 'witch_msa.tools.magus.tools.mafft' as an importable package[^1], 2023-11-24T07:02:56,390 but it is absent from setuptools' `packages` configuration. 2023-11-24T07:02:56,391 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-24T07:02:56,392 package, please make sure that 'witch_msa.tools.magus.tools.mafft' is explicitly added 2023-11-24T07:02:56,394 to the `packages` configuration field. 2023-11-24T07:02:56,397 Alternatively, you can also rely on setuptools' discovery methods 2023-11-24T07:02:56,400 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-24T07:02:56,402 instead of `find_packages(...)`/`find:`). 2023-11-24T07:02:56,403 You can read more about "package discovery" on setuptools documentation page: 2023-11-24T07:02:56,404 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-24T07:02:56,405 If you don't want 'witch_msa.tools.magus.tools.mafft' to be distributed and are 2023-11-24T07:02:56,405 already explicitly excluding 'witch_msa.tools.magus.tools.mafft' via 2023-11-24T07:02:56,406 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-24T07:02:56,407 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-24T07:02:56,409 combination with a more fine grained `package-data` configuration. 2023-11-24T07:02:56,414 You can read more about "package data files" on setuptools documentation page: 2023-11-24T07:02:56,416 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-24T07:02:56,417 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-24T07:02:56,417 even if it does not contain any `.py` files. 2023-11-24T07:02:56,418 On the other hand, currently there is no concept of package data 2023-11-24T07:02:56,418 directory, all directories are treated like packages. 2023-11-24T07:02:56,419 ******************************************************************************** 2023-11-24T07:02:56,420 !! 2023-11-24T07:02:56,420 check.warn(importable) 2023-11-24T07:02:56,421 /tmp/pip-build-env-ln3jvknf/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'witch_msa.tools.magus.tools.mafft.mafftdir.bin' is absent from the `packages` configuration. 2023-11-24T07:02:56,421 !! 2023-11-24T07:02:56,422 ******************************************************************************** 2023-11-24T07:02:56,423 ############################ 2023-11-24T07:02:56,423 # Package would be ignored # 2023-11-24T07:02:56,424 ############################ 2023-11-24T07:02:56,424 Python recognizes 'witch_msa.tools.magus.tools.mafft.mafftdir.bin' as an importable package[^1], 2023-11-24T07:02:56,425 but it is absent from setuptools' `packages` configuration. 2023-11-24T07:02:56,426 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-24T07:02:56,426 package, please make sure that 'witch_msa.tools.magus.tools.mafft.mafftdir.bin' is explicitly added 2023-11-24T07:02:56,427 to the `packages` configuration field. 2023-11-24T07:02:56,428 Alternatively, you can also rely on setuptools' discovery methods 2023-11-24T07:02:56,428 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-24T07:02:56,429 instead of `find_packages(...)`/`find:`). 2023-11-24T07:02:56,430 You can read more about "package discovery" on setuptools documentation page: 2023-11-24T07:02:56,432 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-24T07:02:56,433 If you don't want 'witch_msa.tools.magus.tools.mafft.mafftdir.bin' to be distributed and are 2023-11-24T07:02:56,434 already explicitly excluding 'witch_msa.tools.magus.tools.mafft.mafftdir.bin' via 2023-11-24T07:02:56,435 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-24T07:02:56,435 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-24T07:02:56,436 combination with a more fine grained `package-data` configuration. 2023-11-24T07:02:56,439 You can read more about "package data files" on setuptools documentation page: 2023-11-24T07:02:56,445 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-24T07:02:56,475 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-24T07:02:56,476 even if it does not contain any `.py` files. 2023-11-24T07:02:56,478 On the other hand, currently there is no concept of package data 2023-11-24T07:02:56,478 directory, all directories are treated like packages. 2023-11-24T07:02:56,479 ******************************************************************************** 2023-11-24T07:02:56,480 !! 2023-11-24T07:02:56,481 check.warn(importable) 2023-11-24T07:02:56,482 /tmp/pip-build-env-ln3jvknf/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'witch_msa.tools.magus.tools.mafft.mafftdir.libexec' is absent from the `packages` configuration. 2023-11-24T07:02:56,483 !! 2023-11-24T07:02:56,484 ******************************************************************************** 2023-11-24T07:02:56,485 ############################ 2023-11-24T07:02:56,486 # Package would be ignored # 2023-11-24T07:02:56,492 ############################ 2023-11-24T07:02:56,493 Python recognizes 'witch_msa.tools.magus.tools.mafft.mafftdir.libexec' as an importable package[^1], 2023-11-24T07:02:56,494 but it is absent from setuptools' `packages` configuration. 2023-11-24T07:02:56,501 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-24T07:02:56,502 package, please make sure that 'witch_msa.tools.magus.tools.mafft.mafftdir.libexec' is explicitly added 2023-11-24T07:02:56,502 to the `packages` configuration field. 2023-11-24T07:02:56,503 Alternatively, you can also rely on setuptools' discovery methods 2023-11-24T07:02:56,504 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-24T07:02:56,504 instead of `find_packages(...)`/`find:`). 2023-11-24T07:02:56,505 You can read more about "package discovery" on setuptools documentation page: 2023-11-24T07:02:56,506 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-24T07:02:56,507 If you don't want 'witch_msa.tools.magus.tools.mafft.mafftdir.libexec' to be distributed and are 2023-11-24T07:02:56,507 already explicitly excluding 'witch_msa.tools.magus.tools.mafft.mafftdir.libexec' via 2023-11-24T07:02:56,508 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-24T07:02:56,508 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-24T07:02:56,508 combination with a more fine grained `package-data` configuration. 2023-11-24T07:02:56,511 You can read more about "package data files" on setuptools documentation page: 2023-11-24T07:02:56,519 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-24T07:02:56,520 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-24T07:02:56,521 even if it does not contain any `.py` files. 2023-11-24T07:02:56,521 On the other hand, currently there is no concept of package data 2023-11-24T07:02:56,522 directory, all directories are treated like packages. 2023-11-24T07:02:56,522 ******************************************************************************** 2023-11-24T07:02:56,523 !! 2023-11-24T07:02:56,524 check.warn(importable) 2023-11-24T07:02:56,525 /tmp/pip-build-env-ln3jvknf/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'witch_msa.tools.magus.tools.mcl.bin' is absent from the `packages` configuration. 2023-11-24T07:02:56,525 !! 2023-11-24T07:02:56,529 ******************************************************************************** 2023-11-24T07:02:56,533 ############################ 2023-11-24T07:02:56,533 # Package would be ignored # 2023-11-24T07:02:56,536 ############################ 2023-11-24T07:02:56,537 Python recognizes 'witch_msa.tools.magus.tools.mcl.bin' as an importable package[^1], 2023-11-24T07:02:56,538 but it is absent from setuptools' `packages` configuration. 2023-11-24T07:02:56,539 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-24T07:02:56,540 package, please make sure that 'witch_msa.tools.magus.tools.mcl.bin' is explicitly added 2023-11-24T07:02:56,541 to the `packages` configuration field. 2023-11-24T07:02:56,542 Alternatively, you can also rely on setuptools' discovery methods 2023-11-24T07:02:56,542 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-24T07:02:56,543 instead of `find_packages(...)`/`find:`). 2023-11-24T07:02:56,544 You can read more about "package discovery" on setuptools documentation page: 2023-11-24T07:02:56,555 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-24T07:02:56,556 If you don't want 'witch_msa.tools.magus.tools.mcl.bin' to be distributed and are 2023-11-24T07:02:56,557 already explicitly excluding 'witch_msa.tools.magus.tools.mcl.bin' via 2023-11-24T07:02:56,557 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-24T07:02:56,558 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-24T07:02:56,558 combination with a more fine grained `package-data` configuration. 2023-11-24T07:02:56,559 You can read more about "package data files" on setuptools documentation page: 2023-11-24T07:02:56,560 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-24T07:02:56,561 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-24T07:02:56,562 even if it does not contain any `.py` files. 2023-11-24T07:02:56,562 On the other hand, currently there is no concept of package data 2023-11-24T07:02:56,563 directory, all directories are treated like packages. 2023-11-24T07:02:56,563 ******************************************************************************** 2023-11-24T07:02:56,565 !! 2023-11-24T07:02:56,565 check.warn(importable) 2023-11-24T07:02:56,572 /tmp/pip-build-env-ln3jvknf/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'witch_msa.tools.magus.tools.mlrmcl' is absent from the `packages` configuration. 2023-11-24T07:02:56,577 !! 2023-11-24T07:02:56,578 ******************************************************************************** 2023-11-24T07:02:56,578 ############################ 2023-11-24T07:02:56,579 # Package would be ignored # 2023-11-24T07:02:56,579 ############################ 2023-11-24T07:02:56,580 Python recognizes 'witch_msa.tools.magus.tools.mlrmcl' as an importable package[^1], 2023-11-24T07:02:56,580 but it is absent from setuptools' `packages` configuration. 2023-11-24T07:02:56,581 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-24T07:02:56,582 package, please make sure that 'witch_msa.tools.magus.tools.mlrmcl' is explicitly added 2023-11-24T07:02:56,583 to the `packages` configuration field. 2023-11-24T07:02:56,586 Alternatively, you can also rely on setuptools' discovery methods 2023-11-24T07:02:56,587 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-24T07:02:56,591 instead of `find_packages(...)`/`find:`). 2023-11-24T07:02:56,592 You can read more about "package discovery" on setuptools documentation page: 2023-11-24T07:02:56,593 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-24T07:02:56,594 If you don't want 'witch_msa.tools.magus.tools.mlrmcl' to be distributed and are 2023-11-24T07:02:56,595 already explicitly excluding 'witch_msa.tools.magus.tools.mlrmcl' via 2023-11-24T07:02:56,596 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-24T07:02:56,596 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-24T07:02:56,597 combination with a more fine grained `package-data` configuration. 2023-11-24T07:02:56,598 You can read more about "package data files" on setuptools documentation page: 2023-11-24T07:02:56,599 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-24T07:02:56,607 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-24T07:02:56,609 even if it does not contain any `.py` files. 2023-11-24T07:02:56,612 On the other hand, currently there is no concept of package data 2023-11-24T07:02:56,613 directory, all directories are treated like packages. 2023-11-24T07:02:56,614 ******************************************************************************** 2023-11-24T07:02:56,615 !! 2023-11-24T07:02:56,615 check.warn(importable) 2023-11-24T07:02:56,616 /tmp/pip-build-env-ln3jvknf/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'witch_msa.tools.magus.tools.raxmlng' is absent from the `packages` configuration. 2023-11-24T07:02:56,616 !! 2023-11-24T07:02:56,617 ******************************************************************************** 2023-11-24T07:02:56,620 ############################ 2023-11-24T07:02:56,622 # Package would be ignored # 2023-11-24T07:02:56,623 ############################ 2023-11-24T07:02:56,624 Python recognizes 'witch_msa.tools.magus.tools.raxmlng' as an importable package[^1], 2023-11-24T07:02:56,624 but it is absent from setuptools' `packages` configuration. 2023-11-24T07:02:56,625 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-24T07:02:56,626 package, please make sure that 'witch_msa.tools.magus.tools.raxmlng' is explicitly added 2023-11-24T07:02:56,626 to the `packages` configuration field. 2023-11-24T07:02:56,627 Alternatively, you can also rely on setuptools' discovery methods 2023-11-24T07:02:56,628 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-24T07:02:56,628 instead of `find_packages(...)`/`find:`). 2023-11-24T07:02:56,629 You can read more about "package discovery" on setuptools documentation page: 2023-11-24T07:02:56,631 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-24T07:02:56,633 If you don't want 'witch_msa.tools.magus.tools.raxmlng' to be distributed and are 2023-11-24T07:02:56,634 already explicitly excluding 'witch_msa.tools.magus.tools.raxmlng' via 2023-11-24T07:02:56,635 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-24T07:02:56,635 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-24T07:02:56,636 combination with a more fine grained `package-data` configuration. 2023-11-24T07:02:56,638 You can read more about "package data files" on setuptools documentation page: 2023-11-24T07:02:56,639 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-24T07:02:56,641 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-24T07:02:56,642 even if it does not contain any `.py` files. 2023-11-24T07:02:56,643 On the other hand, currently there is no concept of package data 2023-11-24T07:02:56,644 directory, all directories are treated like packages. 2023-11-24T07:02:56,645 ******************************************************************************** 2023-11-24T07:02:56,646 !! 2023-11-24T07:02:56,647 check.warn(importable) 2023-11-24T07:02:56,648 copying witch_msa/default.config -> build/lib/witch_msa 2023-11-24T07:02:56,649 creating build/lib/witch_msa/tools 2023-11-24T07:02:56,649 creating build/lib/witch_msa/tools/macOS 2023-11-24T07:02:56,650 copying witch_msa/tools/macOS/FastTreeMP -> build/lib/witch_msa/tools/macOS 2023-11-24T07:02:56,650 copying witch_msa/tools/macOS/hmmalign -> build/lib/witch_msa/tools/macOS 2023-11-24T07:02:56,651 copying witch_msa/tools/macOS/hmmbuild -> build/lib/witch_msa/tools/macOS 2023-11-24T07:02:56,651 copying witch_msa/tools/macOS/hmmsearch -> build/lib/witch_msa/tools/macOS 2023-11-24T07:02:56,652 copying witch_msa/tools/macOS/mafft -> build/lib/witch_msa/tools/macOS 2023-11-24T07:02:56,653 copying witch_msa/tools/macOS/mcl -> build/lib/witch_msa/tools/macOS 2023-11-24T07:02:56,653 creating build/lib/witch_msa/tools/magus 2023-11-24T07:02:56,654 copying witch_msa/tools/magus/README.md -> build/lib/witch_msa/tools/magus 2023-11-24T07:02:56,654 copying witch_msa/tools/magus/configuration.py -> build/lib/witch_msa/tools/magus 2023-11-24T07:02:56,655 copying witch_msa/tools/magus/magus.py -> build/lib/witch_msa/tools/magus 2023-11-24T07:02:56,655 creating build/lib/witch_msa/tools/magus/align 2023-11-24T07:02:56,656 copying witch_msa/tools/magus/align/__init__.py -> build/lib/witch_msa/tools/magus/align 2023-11-24T07:02:56,656 copying witch_msa/tools/magus/align/aligner.py -> build/lib/witch_msa/tools/magus/align 2023-11-24T07:02:56,657 copying witch_msa/tools/magus/align/alignment_context.py -> build/lib/witch_msa/tools/magus/align 2023-11-24T07:02:56,657 creating build/lib/witch_msa/tools/magus/align/decompose 2023-11-24T07:02:56,658 copying witch_msa/tools/magus/align/decompose/__init__.py -> build/lib/witch_msa/tools/magus/align/decompose 2023-11-24T07:02:56,658 copying witch_msa/tools/magus/align/decompose/decomposer.py -> build/lib/witch_msa/tools/magus/align/decompose 2023-11-24T07:02:56,659 copying witch_msa/tools/magus/align/decompose/initial_tree.py -> build/lib/witch_msa/tools/magus/align/decompose 2023-11-24T07:02:56,659 copying witch_msa/tools/magus/align/decompose/kmh.py -> build/lib/witch_msa/tools/magus/align/decompose 2023-11-24T07:02:56,660 creating build/lib/witch_msa/tools/magus/align/merge 2023-11-24T07:02:56,661 copying witch_msa/tools/magus/align/merge/__init__.py -> build/lib/witch_msa/tools/magus/align/merge 2023-11-24T07:02:56,664 copying witch_msa/tools/magus/align/merge/alignment_graph.py -> build/lib/witch_msa/tools/magus/align/merge 2023-11-24T07:02:56,672 copying witch_msa/tools/magus/align/merge/alignment_writer.py -> build/lib/witch_msa/tools/magus/align/merge 2023-11-24T07:02:56,675 copying witch_msa/tools/magus/align/merge/merger.py -> build/lib/witch_msa/tools/magus/align/merge 2023-11-24T07:02:56,676 copying witch_msa/tools/magus/align/merge/optimizer.py -> build/lib/witch_msa/tools/magus/align/merge 2023-11-24T07:02:56,676 creating build/lib/witch_msa/tools/magus/align/merge/graph_build 2023-11-24T07:02:56,677 copying witch_msa/tools/magus/align/merge/graph_build/__init__.py -> build/lib/witch_msa/tools/magus/align/merge/graph_build 2023-11-24T07:02:56,677 copying witch_msa/tools/magus/align/merge/graph_build/graph_builder.py -> build/lib/witch_msa/tools/magus/align/merge/graph_build 2023-11-24T07:02:56,678 creating build/lib/witch_msa/tools/magus/align/merge/graph_cluster 2023-11-24T07:02:56,678 copying witch_msa/tools/magus/align/merge/graph_cluster/__init__.py -> build/lib/witch_msa/tools/magus/align/merge/graph_cluster 2023-11-24T07:02:56,679 copying witch_msa/tools/magus/align/merge/graph_cluster/clean_clusters.py -> build/lib/witch_msa/tools/magus/align/merge/graph_cluster 2023-11-24T07:02:56,679 copying witch_msa/tools/magus/align/merge/graph_cluster/clusterer.py -> build/lib/witch_msa/tools/magus/align/merge/graph_cluster 2023-11-24T07:02:56,680 copying witch_msa/tools/magus/align/merge/graph_cluster/mcl.py -> build/lib/witch_msa/tools/magus/align/merge/graph_cluster 2023-11-24T07:02:56,680 copying witch_msa/tools/magus/align/merge/graph_cluster/mlr_mcl.py -> build/lib/witch_msa/tools/magus/align/merge/graph_cluster 2023-11-24T07:02:56,681 copying witch_msa/tools/magus/align/merge/graph_cluster/rg.py -> build/lib/witch_msa/tools/magus/align/merge/graph_cluster 2023-11-24T07:02:56,681 creating build/lib/witch_msa/tools/magus/align/merge/graph_trace 2023-11-24T07:02:56,682 copying witch_msa/tools/magus/align/merge/graph_trace/__init__.py -> build/lib/witch_msa/tools/magus/align/merge/graph_trace 2023-11-24T07:02:56,683 copying witch_msa/tools/magus/align/merge/graph_trace/fm.py -> build/lib/witch_msa/tools/magus/align/merge/graph_trace 2023-11-24T07:02:56,683 copying witch_msa/tools/magus/align/merge/graph_trace/min_clusters.py -> build/lib/witch_msa/tools/magus/align/merge/graph_trace 2023-11-24T07:02:56,684 copying witch_msa/tools/magus/align/merge/graph_trace/mwt_search.py -> build/lib/witch_msa/tools/magus/align/merge/graph_trace 2023-11-24T07:02:56,688 copying witch_msa/tools/magus/align/merge/graph_trace/naive.py -> build/lib/witch_msa/tools/magus/align/merge/graph_trace 2023-11-24T07:02:56,689 copying witch_msa/tools/magus/align/merge/graph_trace/rg_fast_search.py -> build/lib/witch_msa/tools/magus/align/merge/graph_trace 2023-11-24T07:02:56,691 copying witch_msa/tools/magus/align/merge/graph_trace/rg_search.py -> build/lib/witch_msa/tools/magus/align/merge/graph_trace 2023-11-24T07:02:56,693 copying witch_msa/tools/magus/align/merge/graph_trace/tracer.py -> build/lib/witch_msa/tools/magus/align/merge/graph_trace 2023-11-24T07:02:56,694 creating build/lib/witch_msa/tools/magus/helpers 2023-11-24T07:02:56,695 copying witch_msa/tools/magus/helpers/__init__.py -> build/lib/witch_msa/tools/magus/helpers 2023-11-24T07:02:56,695 copying witch_msa/tools/magus/helpers/hmmutils.py -> build/lib/witch_msa/tools/magus/helpers 2023-11-24T07:02:56,696 copying witch_msa/tools/magus/helpers/sequenceutils.py -> build/lib/witch_msa/tools/magus/helpers 2023-11-24T07:02:56,696 copying witch_msa/tools/magus/helpers/treeutils.py -> build/lib/witch_msa/tools/magus/helpers 2023-11-24T07:02:56,697 creating build/lib/witch_msa/tools/magus/tasks 2023-11-24T07:02:56,697 copying witch_msa/tools/magus/tasks/__init__.py -> build/lib/witch_msa/tools/magus/tasks 2023-11-24T07:02:56,698 copying witch_msa/tools/magus/tasks/controller.py -> build/lib/witch_msa/tools/magus/tasks 2023-11-24T07:02:56,698 copying witch_msa/tools/magus/tasks/files.py -> build/lib/witch_msa/tools/magus/tasks 2023-11-24T07:02:56,699 copying witch_msa/tools/magus/tasks/manager.py -> build/lib/witch_msa/tools/magus/tasks 2023-11-24T07:02:56,699 copying witch_msa/tools/magus/tasks/task.py -> build/lib/witch_msa/tools/magus/tasks 2023-11-24T07:02:56,700 creating build/lib/witch_msa/tools/magus/tools 2023-11-24T07:02:56,700 copying witch_msa/tools/magus/tools/__init__.py -> build/lib/witch_msa/tools/magus/tools 2023-11-24T07:02:56,701 copying witch_msa/tools/magus/tools/external_tools.py -> build/lib/witch_msa/tools/magus/tools 2023-11-24T07:02:56,701 creating build/lib/witch_msa/tools/magus/tools/clustal 2023-11-24T07:02:56,702 copying witch_msa/tools/magus/tools/clustal/clustalo -> build/lib/witch_msa/tools/magus/tools/clustal 2023-11-24T07:02:56,703 creating build/lib/witch_msa/tools/magus/tools/fasttree 2023-11-24T07:02:56,703 copying witch_msa/tools/magus/tools/fasttree/FastTree -> build/lib/witch_msa/tools/magus/tools/fasttree 2023-11-24T07:02:56,705 copying witch_msa/tools/magus/tools/fasttree/FastTreeMP -> build/lib/witch_msa/tools/magus/tools/fasttree 2023-11-24T07:02:56,709 creating build/lib/witch_msa/tools/magus/tools/hmmer 2023-11-24T07:02:56,711 copying witch_msa/tools/magus/tools/hmmer/hmmalign -> build/lib/witch_msa/tools/magus/tools/hmmer 2023-11-24T07:02:56,712 copying witch_msa/tools/magus/tools/hmmer/hmmbuild -> build/lib/witch_msa/tools/magus/tools/hmmer 2023-11-24T07:02:56,713 copying witch_msa/tools/magus/tools/hmmer/hmmsearch -> build/lib/witch_msa/tools/magus/tools/hmmer 2023-11-24T07:02:56,716 creating build/lib/witch_msa/tools/magus/tools/mafft 2023-11-24T07:02:56,717 copying witch_msa/tools/magus/tools/mafft/mafft -> build/lib/witch_msa/tools/magus/tools/mafft 2023-11-24T07:02:56,718 creating build/lib/witch_msa/tools/magus/tools/mafft/mafftdir 2023-11-24T07:02:56,718 creating build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/bin 2023-11-24T07:02:56,719 copying witch_msa/tools/magus/tools/mafft/mafftdir/bin/mafft -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/bin 2023-11-24T07:02:56,719 creating build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:56,720 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/addsingle -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:56,720 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/contrafoldwrap -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:56,721 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/countlen -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:56,721 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dash_client -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:56,722 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/disttbfast -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:56,722 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dndblast -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:56,723 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dndfast7 -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:56,723 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dndpre -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:56,724 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dvtditr -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:56,724 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/f2cl -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:56,725 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/getlag -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:56,725 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/hex2maffttext -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:56,726 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafft-distance -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:56,727 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafft-homologs.1 -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:56,729 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafft-profile -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:56,730 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafft.1 -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:56,731 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafftash_premafft.pl -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:56,734 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/maffttext2hex -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:56,736 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/makedirectionlist -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:56,737 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mccaskillwrap -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:56,739 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/multi2hat3s -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:56,755 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/nodepair -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:56,777 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/pairash -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:56,798 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/pairlocalalign -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:56,818 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/regtable2seq -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:56,836 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/replaceu -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:56,852 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/restoreu -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:56,869 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/score -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:56,886 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/seekquencer_premafft.pl -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:56,889 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/seq2regtable -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:56,901 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/setcore -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:56,923 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/setdirection -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:56,938 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/sextet5 -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:56,956 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/splittbfast -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:56,977 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/tbfast -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:56,999 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/version -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:57,009 creating build/lib/witch_msa/tools/magus/tools/mcl 2023-11-24T07:02:57,010 creating build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:02:57,011 copying witch_msa/tools/magus/tools/mcl/bin/clm -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:02:57,035 copying witch_msa/tools/magus/tools/mcl/bin/clmformat -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:02:57,056 copying witch_msa/tools/magus/tools/mcl/bin/clxdo -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:02:57,058 copying witch_msa/tools/magus/tools/mcl/bin/mcl -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:02:57,077 copying witch_msa/tools/magus/tools/mcl/bin/mclblastline -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:02:57,080 copying witch_msa/tools/magus/tools/mcl/bin/mclcm -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:02:57,101 copying witch_msa/tools/magus/tools/mcl/bin/mclpipeline -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:02:57,104 copying witch_msa/tools/magus/tools/mcl/bin/mcx -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:02:57,128 copying witch_msa/tools/magus/tools/mcl/bin/mcxarray -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:02:57,152 copying witch_msa/tools/magus/tools/mcl/bin/mcxassemble -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:02:57,173 copying witch_msa/tools/magus/tools/mcl/bin/mcxdeblast -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:02:57,176 copying witch_msa/tools/magus/tools/mcl/bin/mcxdump -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:02:57,197 copying witch_msa/tools/magus/tools/mcl/bin/mcxi -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:02:57,217 copying witch_msa/tools/magus/tools/mcl/bin/mcxload -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:02:57,239 copying witch_msa/tools/magus/tools/mcl/bin/mcxmap -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:02:57,252 copying witch_msa/tools/magus/tools/mcl/bin/mcxrand -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:02:57,265 copying witch_msa/tools/magus/tools/mcl/bin/mcxsubs -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:02:57,286 creating build/lib/witch_msa/tools/magus/tools/mlrmcl 2023-11-24T07:02:57,287 copying witch_msa/tools/magus/tools/mlrmcl/README -> build/lib/witch_msa/tools/magus/tools/mlrmcl 2023-11-24T07:02:57,290 copying witch_msa/tools/magus/tools/mlrmcl/mlrmcl -> build/lib/witch_msa/tools/magus/tools/mlrmcl 2023-11-24T07:02:57,294 copying witch_msa/tools/magus/tools/mlrmcl/ncut -> build/lib/witch_msa/tools/magus/tools/mlrmcl 2023-11-24T07:02:57,298 creating build/lib/witch_msa/tools/magus/tools/raxmlng 2023-11-24T07:02:57,299 copying witch_msa/tools/magus/tools/raxmlng/raxml-ng -> build/lib/witch_msa/tools/magus/tools/raxmlng 2023-11-24T07:02:57,416 running build_scripts 2023-11-24T07:02:57,416 creating build/scripts-3.11 2023-11-24T07:02:57,417 copying and adjusting bin/witch-msa -> build/scripts-3.11 2023-11-24T07:02:57,419 copying and adjusting witch.py -> build/scripts-3.11 2023-11-24T07:02:57,420 changing mode of build/scripts-3.11/witch-msa from 644 to 755 2023-11-24T07:02:57,420 changing mode of build/scripts-3.11/witch.py from 644 to 755 2023-11-24T07:02:57,427 installing to build/bdist.linux-armv7l/wheel 2023-11-24T07:02:57,428 running install 2023-11-24T07:02:57,452 running install_lib 2023-11-24T07:02:57,456 creating build/bdist.linux-armv7l 2023-11-24T07:02:57,457 creating build/bdist.linux-armv7l/wheel 2023-11-24T07:02:57,458 creating build/bdist.linux-armv7l/wheel/witch_msa 2023-11-24T07:02:57,459 copying build/lib/witch_msa/init_configs.py -> build/bdist.linux-armv7l/wheel/witch_msa 2023-11-24T07:02:57,462 copying build/lib/witch_msa/default.config -> build/bdist.linux-armv7l/wheel/witch_msa 2023-11-24T07:02:57,464 creating build/bdist.linux-armv7l/wheel/witch_msa/tools 2023-11-24T07:02:57,465 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/macOS 2023-11-24T07:02:57,466 copying build/lib/witch_msa/tools/macOS/hmmalign -> build/bdist.linux-armv7l/wheel/witch_msa/tools/macOS 2023-11-24T07:02:57,481 copying build/lib/witch_msa/tools/macOS/hmmsearch -> build/bdist.linux-armv7l/wheel/witch_msa/tools/macOS 2023-11-24T07:02:57,498 copying build/lib/witch_msa/tools/macOS/hmmbuild -> build/bdist.linux-armv7l/wheel/witch_msa/tools/macOS 2023-11-24T07:02:57,513 copying build/lib/witch_msa/tools/macOS/mcl -> build/bdist.linux-armv7l/wheel/witch_msa/tools/macOS 2023-11-24T07:02:57,520 copying build/lib/witch_msa/tools/macOS/mafft -> build/bdist.linux-armv7l/wheel/witch_msa/tools/macOS 2023-11-24T07:02:57,524 copying build/lib/witch_msa/tools/macOS/FastTreeMP -> build/bdist.linux-armv7l/wheel/witch_msa/tools/macOS 2023-11-24T07:02:57,532 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus 2023-11-24T07:02:57,534 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tasks 2023-11-24T07:02:57,535 copying build/lib/witch_msa/tools/magus/tasks/manager.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tasks 2023-11-24T07:02:57,538 copying build/lib/witch_msa/tools/magus/tasks/task.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tasks 2023-11-24T07:02:57,540 copying build/lib/witch_msa/tools/magus/tasks/__init__.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tasks 2023-11-24T07:02:57,542 copying build/lib/witch_msa/tools/magus/tasks/files.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tasks 2023-11-24T07:02:57,545 copying build/lib/witch_msa/tools/magus/tasks/controller.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tasks 2023-11-24T07:02:57,547 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align 2023-11-24T07:02:57,548 copying build/lib/witch_msa/tools/magus/align/alignment_context.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align 2023-11-24T07:02:57,552 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/decompose 2023-11-24T07:02:57,553 copying build/lib/witch_msa/tools/magus/align/decompose/decomposer.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/decompose 2023-11-24T07:02:57,556 copying build/lib/witch_msa/tools/magus/align/decompose/__init__.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/decompose 2023-11-24T07:02:57,558 copying build/lib/witch_msa/tools/magus/align/decompose/kmh.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/decompose 2023-11-24T07:02:57,560 copying build/lib/witch_msa/tools/magus/align/decompose/initial_tree.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/decompose 2023-11-24T07:02:57,564 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge 2023-11-24T07:02:57,565 copying build/lib/witch_msa/tools/magus/align/merge/alignment_graph.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge 2023-11-24T07:02:57,568 copying build/lib/witch_msa/tools/magus/align/merge/alignment_writer.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge 2023-11-24T07:02:57,571 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge/graph_build 2023-11-24T07:02:57,572 copying build/lib/witch_msa/tools/magus/align/merge/graph_build/__init__.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge/graph_build 2023-11-24T07:02:57,574 copying build/lib/witch_msa/tools/magus/align/merge/graph_build/graph_builder.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge/graph_build 2023-11-24T07:02:57,577 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge/graph_trace 2023-11-24T07:02:57,579 copying build/lib/witch_msa/tools/magus/align/merge/graph_trace/min_clusters.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge/graph_trace 2023-11-24T07:02:57,582 copying build/lib/witch_msa/tools/magus/align/merge/graph_trace/rg_fast_search.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge/graph_trace 2023-11-24T07:02:57,584 copying build/lib/witch_msa/tools/magus/align/merge/graph_trace/fm.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge/graph_trace 2023-11-24T07:02:57,587 copying build/lib/witch_msa/tools/magus/align/merge/graph_trace/rg_search.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge/graph_trace 2023-11-24T07:02:57,590 copying build/lib/witch_msa/tools/magus/align/merge/graph_trace/__init__.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge/graph_trace 2023-11-24T07:02:57,591 copying build/lib/witch_msa/tools/magus/align/merge/graph_trace/mwt_search.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge/graph_trace 2023-11-24T07:02:57,594 copying build/lib/witch_msa/tools/magus/align/merge/graph_trace/tracer.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge/graph_trace 2023-11-24T07:02:57,597 copying build/lib/witch_msa/tools/magus/align/merge/graph_trace/naive.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge/graph_trace 2023-11-24T07:02:57,599 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge/graph_cluster 2023-11-24T07:02:57,600 copying build/lib/witch_msa/tools/magus/align/merge/graph_cluster/clean_clusters.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge/graph_cluster 2023-11-24T07:02:57,603 copying build/lib/witch_msa/tools/magus/align/merge/graph_cluster/mcl.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge/graph_cluster 2023-11-24T07:02:57,605 copying build/lib/witch_msa/tools/magus/align/merge/graph_cluster/rg.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge/graph_cluster 2023-11-24T07:02:57,607 copying build/lib/witch_msa/tools/magus/align/merge/graph_cluster/mlr_mcl.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge/graph_cluster 2023-11-24T07:02:57,610 copying build/lib/witch_msa/tools/magus/align/merge/graph_cluster/clusterer.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge/graph_cluster 2023-11-24T07:02:57,612 copying build/lib/witch_msa/tools/magus/align/merge/graph_cluster/__init__.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge/graph_cluster 2023-11-24T07:02:57,615 copying build/lib/witch_msa/tools/magus/align/merge/__init__.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge 2023-11-24T07:02:57,617 copying build/lib/witch_msa/tools/magus/align/merge/optimizer.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge 2023-11-24T07:02:57,620 copying build/lib/witch_msa/tools/magus/align/merge/merger.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge 2023-11-24T07:02:57,622 copying build/lib/witch_msa/tools/magus/align/aligner.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align 2023-11-24T07:02:57,625 copying build/lib/witch_msa/tools/magus/align/__init__.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align 2023-11-24T07:02:57,628 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools 2023-11-24T07:02:57,630 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/fasttree 2023-11-24T07:02:57,631 copying build/lib/witch_msa/tools/magus/tools/fasttree/FastTree -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/fasttree 2023-11-24T07:02:57,642 copying build/lib/witch_msa/tools/magus/tools/fasttree/FastTreeMP -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/fasttree 2023-11-24T07:02:57,654 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mlrmcl 2023-11-24T07:02:57,654 copying build/lib/witch_msa/tools/magus/tools/mlrmcl/mlrmcl -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mlrmcl 2023-11-24T07:02:57,659 copying build/lib/witch_msa/tools/magus/tools/mlrmcl/README -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mlrmcl 2023-11-24T07:02:57,661 copying build/lib/witch_msa/tools/magus/tools/mlrmcl/ncut -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mlrmcl 2023-11-24T07:02:57,666 copying build/lib/witch_msa/tools/magus/tools/external_tools.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools 2023-11-24T07:02:57,668 copying build/lib/witch_msa/tools/magus/tools/__init__.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools 2023-11-24T07:02:57,671 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/hmmer 2023-11-24T07:02:57,672 copying build/lib/witch_msa/tools/magus/tools/hmmer/hmmalign -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/hmmer 2023-11-24T07:02:57,695 copying build/lib/witch_msa/tools/magus/tools/hmmer/hmmsearch -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/hmmer 2023-11-24T07:02:57,719 copying build/lib/witch_msa/tools/magus/tools/hmmer/hmmbuild -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/hmmer 2023-11-24T07:02:57,742 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/raxmlng 2023-11-24T07:02:57,743 copying build/lib/witch_msa/tools/magus/tools/raxmlng/raxml-ng -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/raxmlng 2023-11-24T07:02:57,843 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl 2023-11-24T07:02:57,844 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:02:57,846 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/clxdo -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:02:57,849 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mcxdeblast -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:02:57,851 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mclpipeline -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:02:57,854 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mcxassemble -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:02:57,873 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mcx -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:02:57,897 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mclcm -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:02:57,917 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mclblastline -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:02:57,919 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mcxsubs -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:02:57,940 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mcxi -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:02:57,961 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/clmformat -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:02:57,984 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mcxload -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:02:58,005 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mcxarray -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:02:58,025 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mcxdump -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:02:58,047 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mcl -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:02:58,069 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mcxrand -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:02:58,085 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/clm -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:02:58,109 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mcxmap -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:02:58,122 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft 2023-11-24T07:02:58,123 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir 2023-11-24T07:02:58,125 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/bin 2023-11-24T07:02:58,126 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/bin/mafft -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/bin 2023-11-24T07:02:58,131 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:58,132 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/addsingle -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:58,153 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/seekquencer_premafft.pl -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:58,156 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafftash_premafft.pl -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:58,158 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/nodepair -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:58,179 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/pairash -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:58,200 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/splittbfast -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:58,221 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafft-distance -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:58,236 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/multi2hat3s -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:58,254 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/makedirectionlist -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:58,281 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dndfast7 -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:58,297 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/pairlocalalign -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:58,320 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dash_client -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:58,394 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mccaskillwrap -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:58,409 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/sextet5 -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:58,423 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/getlag -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:58,442 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/setdirection -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:58,456 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dndblast -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:58,473 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/regtable2seq -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:58,489 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/seq2regtable -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:58,501 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dndpre -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:58,519 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/restoreu -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:58,537 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafft.1 -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:58,539 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/tbfast -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:58,562 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/version -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:58,572 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/hex2maffttext -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:58,583 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/maffttext2hex -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:58,595 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/score -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:58,610 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/f2cl -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:58,625 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/setcore -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:58,650 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafft-profile -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:58,673 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/disttbfast -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:58,698 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/countlen -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:58,710 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dvtditr -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:58,733 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/contrafoldwrap -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:58,749 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/replaceu -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:58,763 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafft-homologs.1 -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:02:58,766 copying build/lib/witch_msa/tools/magus/tools/mafft/mafft -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft 2023-11-24T07:02:58,768 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/clustal 2023-11-24T07:02:58,769 copying build/lib/witch_msa/tools/magus/tools/clustal/clustalo -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/clustal 2023-11-24T07:02:58,849 copying build/lib/witch_msa/tools/magus/configuration.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus 2023-11-24T07:02:58,852 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/helpers 2023-11-24T07:02:58,853 copying build/lib/witch_msa/tools/magus/helpers/treeutils.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/helpers 2023-11-24T07:02:58,856 copying build/lib/witch_msa/tools/magus/helpers/sequenceutils.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/helpers 2023-11-24T07:02:58,858 copying build/lib/witch_msa/tools/magus/helpers/hmmutils.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/helpers 2023-11-24T07:02:58,860 copying build/lib/witch_msa/tools/magus/helpers/__init__.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/helpers 2023-11-24T07:02:58,861 copying build/lib/witch_msa/tools/magus/README.md -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus 2023-11-24T07:02:58,864 copying build/lib/witch_msa/tools/magus/magus.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus 2023-11-24T07:02:58,866 copying build/lib/witch_msa/configs.py -> build/bdist.linux-armv7l/wheel/witch_msa 2023-11-24T07:02:58,868 creating build/bdist.linux-armv7l/wheel/witch_msa/helpers 2023-11-24T07:02:58,869 copying build/lib/witch_msa/helpers/pyhmmer_tools.py -> build/bdist.linux-armv7l/wheel/witch_msa/helpers 2023-11-24T07:02:58,871 copying build/lib/witch_msa/helpers/alignment_tools.py -> build/bdist.linux-armv7l/wheel/witch_msa/helpers 2023-11-24T07:02:58,875 copying build/lib/witch_msa/helpers/general_tools.py -> build/bdist.linux-armv7l/wheel/witch_msa/helpers 2023-11-24T07:02:58,877 copying build/lib/witch_msa/helpers/math_utils.py -> build/bdist.linux-armv7l/wheel/witch_msa/helpers 2023-11-24T07:02:58,879 copying build/lib/witch_msa/helpers/__init__.py -> build/bdist.linux-armv7l/wheel/witch_msa/helpers 2023-11-24T07:02:58,880 copying build/lib/witch_msa/__init__.py -> build/bdist.linux-armv7l/wheel/witch_msa 2023-11-24T07:02:58,883 creating build/bdist.linux-armv7l/wheel/witch_msa/gcmm 2023-11-24T07:02:58,884 copying build/lib/witch_msa/gcmm/weighting.py -> build/bdist.linux-armv7l/wheel/witch_msa/gcmm 2023-11-24T07:02:58,886 copying build/lib/witch_msa/gcmm/callback.py -> build/bdist.linux-armv7l/wheel/witch_msa/gcmm 2023-11-24T07:02:58,888 copying build/lib/witch_msa/gcmm/algorithm.py -> build/bdist.linux-armv7l/wheel/witch_msa/gcmm 2023-11-24T07:02:58,891 copying build/lib/witch_msa/gcmm/loader.py -> build/bdist.linux-armv7l/wheel/witch_msa/gcmm 2023-11-24T07:02:58,894 copying build/lib/witch_msa/gcmm/decompose_tree.py -> build/bdist.linux-armv7l/wheel/witch_msa/gcmm 2023-11-24T07:02:58,896 copying build/lib/witch_msa/gcmm/aligner.py -> build/bdist.linux-armv7l/wheel/witch_msa/gcmm 2023-11-24T07:02:58,898 copying build/lib/witch_msa/gcmm/tree.py -> build/bdist.linux-armv7l/wheel/witch_msa/gcmm 2023-11-24T07:02:58,901 copying build/lib/witch_msa/gcmm/backbone.py -> build/bdist.linux-armv7l/wheel/witch_msa/gcmm 2023-11-24T07:02:58,903 copying build/lib/witch_msa/gcmm/results_handler.py -> build/bdist.linux-armv7l/wheel/witch_msa/gcmm 2023-11-24T07:02:58,905 copying build/lib/witch_msa/gcmm/task.py -> build/bdist.linux-armv7l/wheel/witch_msa/gcmm 2023-11-24T07:02:58,908 copying build/lib/witch_msa/gcmm/__init__.py -> build/bdist.linux-armv7l/wheel/witch_msa/gcmm 2023-11-24T07:02:58,909 copying build/lib/witch_msa/gcmm/gcmm.py -> build/bdist.linux-armv7l/wheel/witch_msa/gcmm 2023-11-24T07:02:58,912 copying build/lib/witch_msa/gcmm/merger.py -> build/bdist.linux-armv7l/wheel/witch_msa/gcmm 2023-11-24T07:02:58,914 running install_egg_info 2023-11-24T07:02:58,917 Copying witch_msa.egg-info to build/bdist.linux-armv7l/wheel/witch_msa-1.0.0rc4-py3.11.egg-info 2023-11-24T07:02:58,929 running install_scripts 2023-11-24T07:02:58,930 creating build/bdist.linux-armv7l/wheel/witch_msa-1.0.0rc4.data 2023-11-24T07:02:58,931 creating build/bdist.linux-armv7l/wheel/witch_msa-1.0.0rc4.data/scripts 2023-11-24T07:02:58,932 copying build/scripts-3.11/witch-msa -> build/bdist.linux-armv7l/wheel/witch_msa-1.0.0rc4.data/scripts 2023-11-24T07:02:58,934 copying build/scripts-3.11/witch.py -> build/bdist.linux-armv7l/wheel/witch_msa-1.0.0rc4.data/scripts 2023-11-24T07:02:58,935 changing mode of build/bdist.linux-armv7l/wheel/witch_msa-1.0.0rc4.data/scripts/witch-msa to 755 2023-11-24T07:02:58,936 changing mode of build/bdist.linux-armv7l/wheel/witch_msa-1.0.0rc4.data/scripts/witch.py to 755 2023-11-24T07:02:58,957 creating build/bdist.linux-armv7l/wheel/witch_msa-1.0.0rc4.dist-info/WHEEL 2023-11-24T07:02:58,960 creating '/tmp/pip-wheel-b6rc96eb/.tmp-bypifzqt/witch_msa-1.0.0rc4-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2023-11-24T07:02:58,963 adding 'witch_msa/__init__.py' 2023-11-24T07:02:58,965 adding 'witch_msa/configs.py' 2023-11-24T07:02:58,966 adding 'witch_msa/default.config' 2023-11-24T07:02:58,968 adding 'witch_msa/init_configs.py' 2023-11-24T07:02:58,970 adding 'witch_msa/gcmm/__init__.py' 2023-11-24T07:02:58,973 adding 'witch_msa/gcmm/algorithm.py' 2023-11-24T07:02:58,976 adding 'witch_msa/gcmm/aligner.py' 2023-11-24T07:02:58,979 adding 'witch_msa/gcmm/backbone.py' 2023-11-24T07:02:58,980 adding 'witch_msa/gcmm/callback.py' 2023-11-24T07:02:58,981 adding 'witch_msa/gcmm/decompose_tree.py' 2023-11-24T07:02:58,983 adding 'witch_msa/gcmm/gcmm.py' 2023-11-24T07:02:58,986 adding 'witch_msa/gcmm/loader.py' 2023-11-24T07:02:58,987 adding 'witch_msa/gcmm/merger.py' 2023-11-24T07:02:58,989 adding 'witch_msa/gcmm/results_handler.py' 2023-11-24T07:02:58,990 adding 'witch_msa/gcmm/task.py' 2023-11-24T07:02:58,993 adding 'witch_msa/gcmm/tree.py' 2023-11-24T07:02:58,995 adding 'witch_msa/gcmm/weighting.py' 2023-11-24T07:02:58,996 adding 'witch_msa/helpers/__init__.py' 2023-11-24T07:02:59,003 adding 'witch_msa/helpers/alignment_tools.py' 2023-11-24T07:02:59,004 adding 'witch_msa/helpers/general_tools.py' 2023-11-24T07:02:59,005 adding 'witch_msa/helpers/math_utils.py' 2023-11-24T07:02:59,007 adding 'witch_msa/helpers/pyhmmer_tools.py' 2023-11-24T07:02:59,063 adding 'witch_msa/tools/macOS/FastTreeMP' 2023-11-24T07:02:59,208 adding 'witch_msa/tools/macOS/hmmalign' 2023-11-24T07:02:59,377 adding 'witch_msa/tools/macOS/hmmbuild' 2023-11-24T07:02:59,554 adding 'witch_msa/tools/macOS/hmmsearch' 2023-11-24T07:02:59,571 adding 'witch_msa/tools/macOS/mafft' 2023-11-24T07:02:59,640 adding 'witch_msa/tools/macOS/mcl' 2023-11-24T07:02:59,646 adding 'witch_msa/tools/magus/README.md' 2023-11-24T07:02:59,647 adding 'witch_msa/tools/magus/configuration.py' 2023-11-24T07:02:59,649 adding 'witch_msa/tools/magus/magus.py' 2023-11-24T07:02:59,650 adding 'witch_msa/tools/magus/align/__init__.py' 2023-11-24T07:02:59,652 adding 'witch_msa/tools/magus/align/aligner.py' 2023-11-24T07:02:59,653 adding 'witch_msa/tools/magus/align/alignment_context.py' 2023-11-24T07:02:59,655 adding 'witch_msa/tools/magus/align/decompose/__init__.py' 2023-11-24T07:02:59,656 adding 'witch_msa/tools/magus/align/decompose/decomposer.py' 2023-11-24T07:02:59,658 adding 'witch_msa/tools/magus/align/decompose/initial_tree.py' 2023-11-24T07:02:59,659 adding 'witch_msa/tools/magus/align/decompose/kmh.py' 2023-11-24T07:02:59,661 adding 'witch_msa/tools/magus/align/merge/__init__.py' 2023-11-24T07:02:59,662 adding 'witch_msa/tools/magus/align/merge/alignment_graph.py' 2023-11-24T07:02:59,664 adding 'witch_msa/tools/magus/align/merge/alignment_writer.py' 2023-11-24T07:02:59,665 adding 'witch_msa/tools/magus/align/merge/merger.py' 2023-11-24T07:02:59,668 adding 'witch_msa/tools/magus/align/merge/optimizer.py' 2023-11-24T07:02:59,670 adding 'witch_msa/tools/magus/align/merge/graph_build/__init__.py' 2023-11-24T07:02:59,671 adding 'witch_msa/tools/magus/align/merge/graph_build/graph_builder.py' 2023-11-24T07:02:59,673 adding 'witch_msa/tools/magus/align/merge/graph_cluster/__init__.py' 2023-11-24T07:02:59,675 adding 'witch_msa/tools/magus/align/merge/graph_cluster/clean_clusters.py' 2023-11-24T07:02:59,676 adding 'witch_msa/tools/magus/align/merge/graph_cluster/clusterer.py' 2023-11-24T07:02:59,677 adding 'witch_msa/tools/magus/align/merge/graph_cluster/mcl.py' 2023-11-24T07:02:59,678 adding 'witch_msa/tools/magus/align/merge/graph_cluster/mlr_mcl.py' 2023-11-24T07:02:59,680 adding 'witch_msa/tools/magus/align/merge/graph_cluster/rg.py' 2023-11-24T07:02:59,681 adding 'witch_msa/tools/magus/align/merge/graph_trace/__init__.py' 2023-11-24T07:02:59,683 adding 'witch_msa/tools/magus/align/merge/graph_trace/fm.py' 2023-11-24T07:02:59,685 adding 'witch_msa/tools/magus/align/merge/graph_trace/min_clusters.py' 2023-11-24T07:02:59,687 adding 'witch_msa/tools/magus/align/merge/graph_trace/mwt_search.py' 2023-11-24T07:02:59,689 adding 'witch_msa/tools/magus/align/merge/graph_trace/naive.py' 2023-11-24T07:02:59,690 adding 'witch_msa/tools/magus/align/merge/graph_trace/rg_fast_search.py' 2023-11-24T07:02:59,692 adding 'witch_msa/tools/magus/align/merge/graph_trace/rg_search.py' 2023-11-24T07:02:59,694 adding 'witch_msa/tools/magus/align/merge/graph_trace/tracer.py' 2023-11-24T07:02:59,695 adding 'witch_msa/tools/magus/helpers/__init__.py' 2023-11-24T07:02:59,697 adding 'witch_msa/tools/magus/helpers/hmmutils.py' 2023-11-24T07:02:59,698 adding 'witch_msa/tools/magus/helpers/sequenceutils.py' 2023-11-24T07:02:59,700 adding 'witch_msa/tools/magus/helpers/treeutils.py' 2023-11-24T07:02:59,702 adding 'witch_msa/tools/magus/tasks/__init__.py' 2023-11-24T07:02:59,703 adding 'witch_msa/tools/magus/tasks/controller.py' 2023-11-24T07:02:59,704 adding 'witch_msa/tools/magus/tasks/files.py' 2023-11-24T07:02:59,706 adding 'witch_msa/tools/magus/tasks/manager.py' 2023-11-24T07:02:59,708 adding 'witch_msa/tools/magus/tasks/task.py' 2023-11-24T07:02:59,709 adding 'witch_msa/tools/magus/tools/__init__.py' 2023-11-24T07:02:59,711 adding 'witch_msa/tools/magus/tools/external_tools.py' 2023-11-24T07:03:00,521 adding 'witch_msa/tools/magus/tools/clustal/clustalo' 2023-11-24T07:03:00,628 adding 'witch_msa/tools/magus/tools/fasttree/FastTree' 2023-11-24T07:03:00,700 adding 'witch_msa/tools/magus/tools/fasttree/FastTreeMP' 2023-11-24T07:03:00,909 adding 'witch_msa/tools/magus/tools/hmmer/hmmalign' 2023-11-24T07:03:01,134 adding 'witch_msa/tools/magus/tools/hmmer/hmmbuild' 2023-11-24T07:03:01,379 adding 'witch_msa/tools/magus/tools/hmmer/hmmsearch' 2023-11-24T07:03:01,393 adding 'witch_msa/tools/magus/tools/mafft/mafft' 2023-11-24T07:03:01,404 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/bin/mafft' 2023-11-24T07:03:01,656 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/addsingle' 2023-11-24T07:03:01,837 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/contrafoldwrap' 2023-11-24T07:03:01,963 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/countlen' 2023-11-24T07:03:02,777 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dash_client' 2023-11-24T07:03:03,065 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/disttbfast' 2023-11-24T07:03:03,248 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dndblast' 2023-11-24T07:03:03,429 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dndfast7' 2023-11-24T07:03:03,607 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dndpre' 2023-11-24T07:03:03,858 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dvtditr' 2023-11-24T07:03:04,002 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/f2cl' 2023-11-24T07:03:04,238 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/getlag' 2023-11-24T07:03:04,351 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/hex2maffttext' 2023-11-24T07:03:04,529 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafft-distance' 2023-11-24T07:03:04,538 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafft-homologs.1' 2023-11-24T07:03:04,768 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafft-profile' 2023-11-24T07:03:04,780 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafft.1' 2023-11-24T07:03:04,782 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafftash_premafft.pl' 2023-11-24T07:03:04,886 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/maffttext2hex' 2023-11-24T07:03:05,123 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/makedirectionlist' 2023-11-24T07:03:05,303 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mccaskillwrap' 2023-11-24T07:03:05,493 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/multi2hat3s' 2023-11-24T07:03:05,741 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/nodepair' 2023-11-24T07:03:05,982 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/pairash' 2023-11-24T07:03:06,226 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/pairlocalalign' 2023-11-24T07:03:06,397 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/regtable2seq' 2023-11-24T07:03:06,565 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/replaceu' 2023-11-24T07:03:06,734 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/restoreu' 2023-11-24T07:03:06,910 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/score' 2023-11-24T07:03:06,920 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/seekquencer_premafft.pl' 2023-11-24T07:03:07,039 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/seq2regtable' 2023-11-24T07:03:07,272 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/setcore' 2023-11-24T07:03:07,443 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/setdirection' 2023-11-24T07:03:07,623 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/sextet5' 2023-11-24T07:03:07,865 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/splittbfast' 2023-11-24T07:03:08,126 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/tbfast' 2023-11-24T07:03:08,240 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/version' 2023-11-24T07:03:08,499 adding 'witch_msa/tools/magus/tools/mcl/bin/clm' 2023-11-24T07:03:08,741 adding 'witch_msa/tools/magus/tools/mcl/bin/clmformat' 2023-11-24T07:03:08,744 adding 'witch_msa/tools/magus/tools/mcl/bin/clxdo' 2023-11-24T07:03:08,951 adding 'witch_msa/tools/magus/tools/mcl/bin/mcl' 2023-11-24T07:03:08,958 adding 'witch_msa/tools/magus/tools/mcl/bin/mclblastline' 2023-11-24T07:03:09,171 adding 'witch_msa/tools/magus/tools/mcl/bin/mclcm' 2023-11-24T07:03:09,183 adding 'witch_msa/tools/magus/tools/mcl/bin/mclpipeline' 2023-11-24T07:03:09,441 adding 'witch_msa/tools/magus/tools/mcl/bin/mcx' 2023-11-24T07:03:09,671 adding 'witch_msa/tools/magus/tools/mcl/bin/mcxarray' 2023-11-24T07:03:09,891 adding 'witch_msa/tools/magus/tools/mcl/bin/mcxassemble' 2023-11-24T07:03:09,894 adding 'witch_msa/tools/magus/tools/mcl/bin/mcxdeblast' 2023-11-24T07:03:10,100 adding 'witch_msa/tools/magus/tools/mcl/bin/mcxdump' 2023-11-24T07:03:10,335 adding 'witch_msa/tools/magus/tools/mcl/bin/mcxi' 2023-11-24T07:03:10,551 adding 'witch_msa/tools/magus/tools/mcl/bin/mcxload' 2023-11-24T07:03:10,683 adding 'witch_msa/tools/magus/tools/mcl/bin/mcxmap' 2023-11-24T07:03:10,816 adding 'witch_msa/tools/magus/tools/mcl/bin/mcxrand' 2023-11-24T07:03:11,044 adding 'witch_msa/tools/magus/tools/mcl/bin/mcxsubs' 2023-11-24T07:03:11,056 adding 'witch_msa/tools/magus/tools/mlrmcl/README' 2023-11-24T07:03:11,077 adding 'witch_msa/tools/magus/tools/mlrmcl/mlrmcl' 2023-11-24T07:03:11,096 adding 'witch_msa/tools/magus/tools/mlrmcl/ncut' 2023-11-24T07:03:12,285 adding 'witch_msa/tools/magus/tools/raxmlng/raxml-ng' 2023-11-24T07:03:12,341 adding 'witch_msa-1.0.0rc4.data/scripts/witch-msa' 2023-11-24T07:03:12,342 adding 'witch_msa-1.0.0rc4.data/scripts/witch.py' 2023-11-24T07:03:12,348 adding 'witch_msa-1.0.0rc4.dist-info/LICENSE' 2023-11-24T07:03:12,356 adding 'witch_msa-1.0.0rc4.dist-info/METADATA' 2023-11-24T07:03:12,358 adding 'witch_msa-1.0.0rc4.dist-info/WHEEL' 2023-11-24T07:03:12,359 adding 'witch_msa-1.0.0rc4.dist-info/top_level.txt' 2023-11-24T07:03:12,361 adding 'witch_msa-1.0.0rc4.dist-info/RECORD' 2023-11-24T07:03:12,673 removing build/bdist.linux-armv7l/wheel 2023-11-24T07:03:12,863 Building wheel for witch-msa (pyproject.toml): finished with status 'done' 2023-11-24T07:03:13,541 Created wheel for witch-msa: filename=witch_msa-1.0.0rc4-py3-none-any.whl size=29115997 sha256=2c2a928f16f5a02983f953a35cc22dfab97abebe5984290e665cfb59e940d4e3 2023-11-24T07:03:13,542 Stored in directory: /tmp/pip-ephem-wheel-cache-4wg6_gl9/wheels/d5/31/b5/c1ba92399c956df4d2df5447757fc414d11220e1b8630c5406 2023-11-24T07:03:13,589 Successfully built witch-msa 2023-11-24T07:03:14,272 Removed build tracker: '/tmp/pip-build-tracker-7l4xeeal'